0:00:00.000027 INFO: Moved old log file ./run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/log.txt to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/log.0.bkp.txt
0:00:00.000166 INFO: Output directory: /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR, cwd: /home/robbe/ProteoBench_diaPASEF.
0:00:00.000200 INFO: User provided config file: config_alphadia112_rs_Astral.yaml.
0:00:00.000226 INFO: User provided config dict: {}.
0:00:00.012754 PROGRESS:           _      _         ___ ___   _   
0:00:00.012815 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.012841 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.012868 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.012896 PROGRESS:            |_|                           
0:00:00.012916 PROGRESS: 
0:00:00.012935 PROGRESS: version: 1.12.1
0:00:00.012964 INFO: hostname: thestral
0:00:00.013026 INFO: date: 2025-10-15 12:33:35
0:00:00.013051 INFO: ================ AlphaX Environment ===============
0:00:00.013073 INFO: alphatims       : 1.0.8
0:00:00.013091 INFO: alpharaw        : 0.4.5
0:00:00.013110 INFO: alphabase       : 1.5.0
0:00:00.013128 INFO: alphapeptdeep   : 1.3.0
0:00:00.013144 INFO: directlfq       : 0.2.19
0:00:00.013164 INFO: ===================================================
0:00:00.013182 INFO: ================= Pip Environment =================
0:00:00.068446 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
0:00:00.068569 INFO: ===================================================
0:00:00.068607 INFO: Running step 'library'
0:00:00.068667 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.079604 INFO: loading additional config provided via CLI
0:00:00.079668 INFO: loading additional config provided via CLI parameters
0:00:00.080052 INFO: Updating config with 'user defined'
0:00:00.080194 INFO: Updating config with 'user defined (cli)'
0:00:00.080234 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default_ng.yaml
0:00:00.080814 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': 5, 'target_ms2_tolerance': 10, '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/library'}]
0:00:00.081105 INFO: Updating config with 'ng_default'
0:00:00.081145 INFO: Updating config with 'user defined'
0:00:00.081258 INFO: Updating config with 'user defined (cli)'
0:00:00.081281 INFO: Updating config with 'multistep search'
0:00:00.081317 INFO: ├──version: 1
0:00:00.081342 INFO: ├──workflow_name: None
0:00:00.081368 INFO: [32;20m├──output_directory: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library [multistep search, default: None][0m
0:00:00.081390 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
0:00:00.081410 INFO: ├──raw_paths:
0:00:00.081429 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:00:00.081452 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:00:00.081471 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:00:00.081493 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:00:00.081511 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:00:00.081531 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:00:00.081552 INFO: ├──fasta_paths:
0:00:00.081571 INFO: │   [32;20m- ./ProteoBenchFASTA_DDAQuantification.fasta [user defined (cli), default: None][0m
0:00:00.081591 INFO: ├──quant_directory: None
0:00:00.081610 INFO: ├──general
0:00:00.081630 INFO: │   [32;20m├──thread_count: 80 [user defined, default: 10][0m
0:00:00.081648 INFO: │   ├──transfer_step_enabled: False
0:00:00.081669 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
0:00:00.081689 INFO: │   ├──reuse_calibration: False
0:00:00.081707 INFO: │   ├──reuse_quant: False
0:00:00.081724 INFO: │   ├──astral_ms1: False
0:00:00.081743 INFO: │   ├──log_level: INFO
0:00:00.081763 INFO: │   ├──mmap_detector_events: False
0:00:00.081784 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:00:00.081805 INFO: │   ├──save_figures: True
0:00:00.081823 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.081841 INFO: │   ├──save_flat_library: False
0:00:00.081859 INFO: │   ├──input_library_type: base
0:00:00.081877 INFO: │   ├──save_mbr_library: True
0:00:00.081897 INFO: │   └──random_state: None
0:00:00.081917 INFO: ├──library_loading
0:00:00.081936 INFO: │   └──rt_heuristic: 180
0:00:00.081954 INFO: ├──library_prediction
0:00:00.081973 INFO: │   ├──enabled: False
0:00:00.081990 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.082010 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.082028 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.082048 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.082068 INFO: │   ├──missed_cleavages: 1
0:00:00.082086 INFO: │   ├──precursor_len:
0:00:00.082105 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.082125 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.082143 INFO: │   ├──precursor_charge:
0:00:00.082162 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.082180 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.082198 INFO: │   ├──precursor_mz:
0:00:00.082216 INFO: │   │   - 400
0:00:00.082233 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
0:00:00.082251 INFO: │   ├──fragment_mz:
0:00:00.082270 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
0:00:00.082288 INFO: │   │   - 2000
0:00:00.082307 INFO: │   ├──nce: 25.0
0:00:00.082324 INFO: │   ├──fragment_types:
0:00:00.082343 INFO: │   │   - b
0:00:00.082361 INFO: │   │   - y
0:00:00.082381 INFO: │   ├──max_fragment_charge: 2
0:00:00.082399 INFO: │   [32;20m├──instrument: Astral [user defined, default: Lumos][0m
0:00:00.082422 INFO: │   ├──peptdeep_model_path: None
0:00:00.082440 INFO: │   └──peptdeep_model_type: generic
0:00:00.082458 INFO: ├──custom_modifications:
0:00:00.082476 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.082494 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.082513 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.082531 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.082549 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.082567 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.082585 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.082602 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.082620 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.082639 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.082658 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.082676 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.082696 INFO: │   ├──name: Label:13C(12)@K
0:00:00.082713 INFO: │   └──composition: C(12)
0:00:00.082731 INFO: ├──search
0:00:00.082751 INFO: │   [32;20m├──extraction_backend: ng [user defined, default: classic][0m
0:00:00.082770 INFO: │   ├──target_ms1_tolerance: 5
0:00:00.082788 INFO: │   ├──target_ms2_tolerance: 10
0:00:00.082806 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.082824 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.082843 INFO: │   ├──quant_window: 3
0:00:00.082861 INFO: │   ├──target_num_candidates: 3
0:00:00.082880 INFO: │   ├──channel_filter: 
0:00:00.082897 INFO: │   ├──exclude_shared_ions: True
0:00:00.082915 INFO: │   ├──compete_for_fragments: True
0:00:00.082932 INFO: │   ├──quant_all: True
0:00:00.082951 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.082969 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.082988 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.083006 INFO: │   ├──experimental_xic: True
0:00:00.083027 INFO: │   └──optimized_peak_group_score: False
0:00:00.083047 INFO: ├──calibration
0:00:00.083066 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
0:00:00.083085 INFO: │   ├──optimization_lock_target: 200
0:00:00.083102 INFO: │   ├──max_steps: 20
0:00:00.083122 INFO: │   ├──min_steps: 2
0:00:00.083140 INFO: │   ├──max_skips: 1
0:00:00.083158 INFO: │   ├──max_fragments: 5000
0:00:00.083176 INFO: │   └──min_correlation: 0.7
0:00:00.083195 INFO: ├──search_initial
0:00:00.083214 INFO: │   ├──initial_num_candidates: 1
0:00:00.083231 INFO: │   ├──initial_ms1_tolerance: 30
0:00:00.083251 INFO: │   ├──initial_ms2_tolerance: 30
0:00:00.083268 INFO: │   ├──initial_mobility_tolerance: 0.1
0:00:00.083287 INFO: │   └──initial_rt_tolerance: 0.5
0:00:00.083305 INFO: ├──selection_config
0:00:00.083325 INFO: │   ├──peak_len_rt: 10.0
0:00:00.083344 INFO: │   ├──sigma_scale_rt: 0.5
0:00:00.083363 INFO: │   ├──peak_len_mobility: 0.01
0:00:00.083381 INFO: │   ├──sigma_scale_mobility: 1.0
0:00:00.083399 INFO: │   ├──top_k_precursors: 3
0:00:00.083417 INFO: │   ├──kernel_size: 30
0:00:00.083434 INFO: │   ├──f_mobility: 1.0
0:00:00.083453 INFO: │   ├──f_rt: 0.99
0:00:00.083471 INFO: │   ├──center_fraction: 0.5
0:00:00.083488 INFO: │   ├──min_size_mobility: 8
0:00:00.083507 INFO: │   ├──min_size_rt: 3
0:00:00.083525 INFO: │   ├──max_size_mobility: 20
0:00:00.083542 INFO: │   ├──max_size_rt: 15
0:00:00.083560 INFO: │   ├──group_channels: False
0:00:00.083579 INFO: │   ├──use_weighted_score: True
0:00:00.083597 INFO: │   ├──join_close_candidates: False
0:00:00.083615 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:00:00.083642 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:00:00.083660 INFO: ├──scoring_config
0:00:00.083678 INFO: │   ├──score_grouped: False
0:00:00.083697 INFO: │   ├──top_k_isotopes: 3
0:00:00.083714 INFO: │   ├──reference_channel: -1
0:00:00.083732 INFO: │   ├──precursor_mz_tolerance: 10
0:00:00.083750 INFO: │   └──fragment_mz_tolerance: 15
0:00:00.083767 INFO: ├──library_multiplexing
0:00:00.083786 INFO: │   ├──enabled: False
0:00:00.083805 INFO: │   ├──input_channel: 0
0:00:00.083824 INFO: │   └──multiplex_mapping:
0:00:00.083841 INFO: ├──multiplexing
0:00:00.083858 INFO: │   ├──enabled: False
0:00:00.083877 INFO: │   ├──target_channels: 4,8
0:00:00.083895 INFO: │   ├──decoy_channel: 12
0:00:00.083913 INFO: │   ├──reference_channel: 0
0:00:00.083930 INFO: │   └──competetive_scoring: True
0:00:00.083948 INFO: ├──fdr
0:00:00.083967 INFO: │   ├──fdr: 0.01
0:00:00.083985 INFO: │   ├──group_level: proteins
0:00:00.084002 INFO: │   ├──inference_strategy: heuristic
0:00:00.084020 INFO: │   ├──competetive_scoring: True
0:00:00.084038 INFO: │   ├──keep_decoys: False
0:00:00.084056 INFO: │   ├──channel_wise_fdr: False
0:00:00.084073 INFO: │   ├──enable_two_step_classifier: False
0:00:00.084091 INFO: │   ├──two_step_classifier_max_iterations: 5
0:00:00.084109 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:00:00.084126 INFO: ├──search_output
0:00:00.084145 INFO: │   ├──file_format: tsv
0:00:00.084162 INFO: │   ├──peptide_level_lfq: False
0:00:00.084180 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:00:00.084198 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.084216 INFO: │   ├──min_k_fragments: 12
0:00:00.084234 INFO: │   ├──min_correlation: 0.9
0:00:00.084252 INFO: │   ├──num_samples_quadratic: 50
0:00:00.084270 INFO: │   ├──min_nonnan: 3
0:00:00.084289 INFO: │   └──normalize_lfq: True
0:00:00.084306 INFO: ├──optimization
0:00:00.084324 INFO: │   ├──order_of_optimization: None
0:00:00.084342 INFO: │   ├──ms2_error
0:00:00.084362 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.084381 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.084399 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.084418 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.084436 INFO: │   │   ├──try_narrower_values: True
0:00:00.084455 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.084473 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.084491 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.084509 INFO: │   ├──ms1_error
0:00:00.084528 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.084546 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.084564 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.084584 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.084602 INFO: │   │   ├──try_narrower_values: False
0:00:00.084622 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.084640 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.084659 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.084677 INFO: │   ├──mobility_error
0:00:00.084697 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.084716 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.084734 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.084752 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.084770 INFO: │   │   ├──try_narrower_values: False
0:00:00.084789 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.084807 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.084828 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.084846 INFO: │   └──rt_error
0:00:00.084865 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.084883 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.084902 INFO: │       ├──automatic_update_percentile_range: 0.99
0:00:00.084920 INFO: │       ├──automatic_update_factor: 1.1
0:00:00.084937 INFO: │       ├──try_narrower_values: True
0:00:00.084955 INFO: │       ├──maximal_decrease: 0.2
0:00:00.084973 INFO: │       ├──favour_narrower_optimum: True
0:00:00.084998 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:00:00.085017 INFO: ├──optimization_manager
0:00:00.085035 INFO: │   ├──fwhm_rt: 5
0:00:00.085053 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.085072 INFO: │   └──score_cutoff: 0
0:00:00.085089 INFO: ├──transfer_library
0:00:00.085107 INFO: │   ├──enabled: False
0:00:00.085124 INFO: │   ├──fragment_types:
0:00:00.085142 INFO: │   │   - b
0:00:00.085160 INFO: │   │   - y
0:00:00.085179 INFO: │   ├──max_charge: 2
0:00:00.085197 INFO: │   ├──top_k_samples: 3
0:00:00.085215 INFO: │   ├──norm_delta_max: True
0:00:00.085235 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.085253 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.085271 INFO: └──transfer_learning
0:00:00.085289 INFO:     ├──enabled: False
0:00:00.085307 INFO:     ├──batch_size: 2000
0:00:00.085325 INFO:     ├──max_lr: 0.0001
0:00:00.085344 INFO:     ├──train_fraction: 0.7
0:00:00.085362 INFO:     ├──validation_fraction: 0.2
0:00:00.085380 INFO:     ├──test_fraction: 0.1
0:00:00.085398 INFO:     ├──test_interval: 1
0:00:00.085417 INFO:     ├──lr_patience: 3
0:00:00.085435 INFO:     ├──epochs: 51
0:00:00.085453 INFO:     ├──warmup_epochs: 5
0:00:00.085470 INFO:     ├──nce: 25
0:00:00.085490 INFO:     [32;20m└──instrument: Astral [user defined, default: Lumos][0m
0:00:00.090149 INFO: Moved existing config file run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/frozen_config.yaml to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/frozen_config.0.bkp.yaml
0:00:00.090306 INFO: Registering 7 custom modifications
0:00:00.122564 INFO: Searching 6 files:
0:00:00.122655 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:00:00.122679 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:00:00.122699 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:00:00.122717 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:00:00.122735 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:00:00.122751 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:00:00.122771 INFO: Using 1 fasta files:
0:00:00.122789 INFO:   ./ProteoBenchFASTA_DDAQuantification.fasta
0:00:00.122807 INFO: Using library: /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf
0:00:00.122827 INFO: Saving output to: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library
0:00:00.122854 PROGRESS: Loading spectral library
0:00:00.122880 PROGRESS: Loading library (type: base) from disk..
0:00:00.122912 INFO: Running DynamicLoader
0:00:00.122976 INFO: Loading .hdf library from /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf
0:00:32.006082 INFO: Running PrecursorInitializer
0:00:32.006457 INFO: Running AnnotateFasta
0:00:32.134110 INFO: Dropping decoys from input library before annotation
0:00:54.440996 INFO: Running IsotopeGenerator
0:00:54.441628 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
0:00:54.441689 INFO: Running RTNormalization
0:00:54.441771 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:00:54.441853 INFO: Saving library to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/speclib.hdf
0:01:30.413522 INFO: Running DecoyGenerator
0:03:13.501802 INFO: Running FlattenLibrary
0:03:46.368788 INFO: Running InitFlatColumns
0:03:46.652833 INFO: Running LogFlatLibraryStats
0:03:46.652968 INFO: ============ Library Stats ============
0:03:46.653018 INFO: Number of precursors: 12,218,312
0:03:48.322118 INFO: 	thereof targets:6,124,046
0:03:48.322254 INFO: 	thereof decoys: 6,094,266
0:03:48.407922 INFO: Number of elution groups: 6,124,046
0:03:48.408049 INFO: 	average size: 2.00
0:03:48.689665 INFO: Number of proteins: 117,993
0:03:48.719190 INFO: Number of channels: 1 ([0])
0:03:48.719357 INFO: Isotopes Distribution for 4 isotopes
0:03:48.719386 INFO: =======================================
0:03:48.727796 PROGRESS: Starting Search Workflows
0:03:48.728009 PROGRESS: 
0:03:48.728096 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant
0:03:48.728167 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/figures
0:03:48.728388 INFO: Initializing TimingManager
0:03:48.728939 INFO: Initializing RawFileManager
0:03:59.512407 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.
0:03:59.516428 INFO: Determining DIA cycle
0:04:00.199567 INFO: Found cycle with start 0.00 min and length 300.
0:04:00.359011 INFO: RT (min)            : 0.0 - 26.9
0:04:00.359109 INFO: RT duration (sec)   : 1611.2
0:04:00.359138 INFO: RT duration (min)   : 26.9
0:04:00.359160 INFO: Cycle len (scans)   : 300
0:04:00.359179 INFO: Cycle len (sec)     : 1.65
0:04:00.359200 INFO: Number of cycles    : 977
0:04:00.359218 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:04:00.359244 INFO: Creating DIA data object took: 11.630197763442993
0:04:01.206166 INFO: Creating DIA data NG object took: 0.846792459487915
0:04:02.733955 INFO: Initializing CalibrationManager
0:04:02.734214 INFO: Setting up calibration estimators ..
0:04:02.734273 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:04:02.734347 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
0:04:02.734424 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:04:02.734474 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:04:02.734525 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
0:04:02.734572 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:04:02.734615 INFO: Done setting up calibration estimators.
0:04:02.735328 INFO: Initializing OptimizationManager
0:04:02.735487 INFO: initial parameter: ms1_error = 30
0:04:02.735541 INFO: initial parameter: ms2_error = 30
0:04:02.735585 INFO: initial parameter: rt_error = 805.5992431640625
0:04:02.735629 INFO: initial parameter: mobility_error = 0.1
0:04:02.735670 INFO: initial parameter: num_candidates = 1
0:04:02.735710 INFO: initial parameter: fwhm_rt = 5
0:04:02.735747 INFO: initial parameter: fwhm_mobility = 0.01
0:04:02.735787 INFO: initial parameter: score_cutoff = 0
0:04:02.735826 INFO: initial parameter: classifier_version = -1
0:04:02.735893 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:04:02.736151 INFO: FDRManager: loading saved state not requested, will be initialized.
0:04:02.736186 INFO: Initializing FDRManager
0:04:02.736220 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:04:03.947996 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:04:05.278600 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:04:05.279016 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
0:04:05.279124 PROGRESS: Starting initial search for precursors.
0:04:05.279204 INFO: Starting optimization step 0.
0:04:05.279267 PROGRESS: === Extracting elution groups 0 to 200 ===
0:04:05.279323 INFO: Using ng extraction backend
0:04:05.279386 PROGRESS: Extracting batch of 396 precursors
0:04:05.281860 INFO: === Search parameters used ===
0:04:05.281955 INFO: rt_error       : 805.5992431640625
0:04:05.282018 INFO: mobility_error : 0.1
0:04:05.282065 INFO: num_candidates : 1
0:04:05.282108 INFO: ms1_error      : 30
0:04:05.282148 INFO: ms2_error      : 30
0:04:05.282185 INFO: fwhm_rt        : 5
0:04:05.282225 INFO: quant_window   : 3
0:04:05.282265 INFO: ==============================================
0:04:05.301040 INFO: performing precursor FDR with 40 features
0:04:05.301111 INFO: Decoy channel: -1
0:04:05.301137 INFO: Competetive: True
0:04:05.302091 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:05.304217 INFO: Using random state 397847 for train-test-split
0:04:05.753831 INFO: Test AUC: 0.522
0:04:05.753917 INFO: Train AUC: 0.496
0:04:05.753947 INFO: AUC difference: 5.17%
0:04:05.753971 WARNING: AUC difference > 5%. This may indicate overfitting.
0:04:05.975459 INFO: Resetting torch num_threads to 80
0:04:05.976776 PROGRESS: === Extracted 394 precursors and 1879 fragments ===
0:04:05.977118 INFO: === FDR correction performed with classifier version -1 ===
0:04:05.977547 PROGRESS: ============================= Precursor FDR =============================
0:04:05.977628 PROGRESS: Total precursors accumulated: 0
0:04:05.977688 PROGRESS: Target precursors: 0 (0.00%)
0:04:05.977740 PROGRESS: Decoy precursors: 0 (0.00%)
0:04:05.977787 PROGRESS: 
0:04:05.977833 PROGRESS: Precursor Summary:
0:04:05.977939 PROGRESS: 
0:04:05.977999 PROGRESS: Protein Summary:
0:04:05.978073 PROGRESS: =========================================================================
0:04:05.978233 INFO: Target number of precursors not reached yet.
0:04:06.042903 INFO: Starting optimization step 1.
0:04:06.043112 PROGRESS: === Extracting elution groups 200 to 600 ===
0:04:06.043197 INFO: Using ng extraction backend
0:04:06.043265 PROGRESS: Extracting batch of 786 precursors
0:04:06.045888 INFO: === Search parameters used ===
0:04:06.045981 INFO: rt_error       : 805.5992431640625
0:04:06.046030 INFO: mobility_error : 0.1
0:04:06.046074 INFO: num_candidates : 1
0:04:06.046116 INFO: ms1_error      : 30
0:04:06.046157 INFO: ms2_error      : 30
0:04:06.046196 INFO: fwhm_rt        : 5
0:04:06.046236 INFO: quant_window   : 3
0:04:06.046274 INFO: ==============================================
0:04:06.069161 INFO: performing precursor FDR with 40 features
0:04:06.069228 INFO: Decoy channel: -1
0:04:06.069255 INFO: Competetive: True
0:04:06.071944 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:06.073437 INFO: Using random state 896947 for train-test-split
0:04:06.081585 INFO: Test AUC: 0.476
0:04:06.081645 INFO: Train AUC: 0.515
0:04:06.081676 INFO: AUC difference: 7.57%
0:04:06.081702 WARNING: AUC difference > 5%. This may indicate overfitting.
0:04:06.293363 INFO: Resetting torch num_threads to 80
0:04:06.295342 PROGRESS: === Extracted 1169 precursors and 5549 fragments ===
0:04:06.295681 INFO: === FDR correction performed with classifier version -1 ===
0:04:06.296124 PROGRESS: ============================= Precursor FDR =============================
0:04:06.296209 PROGRESS: Total precursors accumulated: 2
0:04:06.296266 PROGRESS: Target precursors: 2 (100.00%)
0:04:06.296316 PROGRESS: Decoy precursors: 0 (0.00%)
0:04:06.296360 PROGRESS: 
0:04:06.296404 PROGRESS: Precursor Summary:
0:04:06.297334 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:04:06.297421 PROGRESS: 
0:04:06.297481 PROGRESS: Protein Summary:
0:04:06.298504 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:04:06.298593 PROGRESS: =========================================================================
0:04:06.298765 INFO: Target number of precursors not reached yet.
0:04:06.365461 INFO: Starting optimization step 2.
0:04:06.365659 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:04:06.365741 INFO: Using ng extraction backend
0:04:06.365803 PROGRESS: Extracting batch of 1592 precursors
0:04:06.369882 INFO: === Search parameters used ===
0:04:06.369987 INFO: rt_error       : 805.5992431640625
0:04:06.370036 INFO: mobility_error : 0.1
0:04:06.370079 INFO: num_candidates : 1
0:04:06.370122 INFO: ms1_error      : 30
0:04:06.370163 INFO: ms2_error      : 30
0:04:06.370201 INFO: fwhm_rt        : 5
0:04:06.370240 INFO: quant_window   : 3
0:04:06.370278 INFO: ==============================================
0:04:06.400608 INFO: performing precursor FDR with 40 features
0:04:06.400680 INFO: Decoy channel: -1
0:04:06.400707 INFO: Competetive: True
0:04:06.404181 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:06.406138 INFO: Using random state 332037 for train-test-split
0:04:06.419078 INFO: Test AUC: 0.488
0:04:06.419143 INFO: Train AUC: 0.510
0:04:06.419172 INFO: AUC difference: 4.24%
0:04:06.873501 INFO: Resetting torch num_threads to 80
0:04:06.875910 PROGRESS: === Extracted 2751 precursors and 13122 fragments ===
0:04:06.876242 INFO: === FDR correction performed with classifier version -1 ===
0:04:06.876687 PROGRESS: ============================= Precursor FDR =============================
0:04:06.876773 PROGRESS: Total precursors accumulated: 2
0:04:06.876837 PROGRESS: Target precursors: 2 (100.00%)
0:04:06.876890 PROGRESS: Decoy precursors: 0 (0.00%)
0:04:06.876936 PROGRESS: 
0:04:06.876978 PROGRESS: Precursor Summary:
0:04:06.877894 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:04:06.877977 PROGRESS: 
0:04:06.878031 PROGRESS: Protein Summary:
0:04:06.879025 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:04:06.879109 PROGRESS: =========================================================================
0:04:06.879303 INFO: Target number of precursors not reached yet.
0:04:06.948697 INFO: Starting optimization step 3.
0:04:06.948890 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:04:06.948971 INFO: Using ng extraction backend
0:04:06.949044 PROGRESS: Extracting batch of 3177 precursors
0:04:06.956024 INFO: === Search parameters used ===
0:04:06.956131 INFO: rt_error       : 805.5992431640625
0:04:06.956182 INFO: mobility_error : 0.1
0:04:06.956229 INFO: num_candidates : 1
0:04:06.956271 INFO: ms1_error      : 30
0:04:06.956310 INFO: ms2_error      : 30
0:04:06.956349 INFO: fwhm_rt        : 5
0:04:06.956387 INFO: quant_window   : 3
0:04:06.956436 INFO: ==============================================
0:04:06.999007 INFO: performing precursor FDR with 40 features
0:04:06.999093 INFO: Decoy channel: -1
0:04:06.999121 INFO: Competetive: True
0:04:07.003849 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:07.006444 INFO: Using random state 956348 for train-test-split
0:04:07.027954 INFO: Test AUC: 0.466
0:04:07.028025 INFO: Train AUC: 0.515
0:04:07.028054 INFO: AUC difference: 9.46%
0:04:07.028076 WARNING: AUC difference > 5%. This may indicate overfitting.
0:04:07.237658 INFO: Resetting torch num_threads to 80
0:04:07.240683 PROGRESS: === Extracted 5904 precursors and 28052 fragments ===
0:04:07.241026 INFO: === FDR correction performed with classifier version -1 ===
0:04:07.241459 PROGRESS: ============================= Precursor FDR =============================
0:04:07.241543 PROGRESS: Total precursors accumulated: 0
0:04:07.241600 PROGRESS: Target precursors: 0 (0.00%)
0:04:07.241651 PROGRESS: Decoy precursors: 0 (0.00%)
0:04:07.241696 PROGRESS: 
0:04:07.241739 PROGRESS: Precursor Summary:
0:04:07.241843 PROGRESS: 
0:04:07.241907 PROGRESS: Protein Summary:
0:04:07.241979 PROGRESS: =========================================================================
0:04:07.242198 INFO: Target number of precursors not reached yet.
0:04:07.315447 INFO: Starting optimization step 4.
0:04:07.315654 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:04:07.315735 INFO: Using ng extraction backend
0:04:07.315797 PROGRESS: Extracting batch of 6340 precursors
0:04:07.328081 INFO: === Search parameters used ===
0:04:07.328205 INFO: rt_error       : 805.5992431640625
0:04:07.328255 INFO: mobility_error : 0.1
0:04:07.328298 INFO: num_candidates : 1
0:04:07.328339 INFO: ms1_error      : 30
0:04:07.329063 INFO: ms2_error      : 30
0:04:07.329122 INFO: fwhm_rt        : 5
0:04:07.329162 INFO: quant_window   : 3
0:04:07.329201 INFO: ==============================================
0:04:07.397696 INFO: performing precursor FDR with 40 features
0:04:07.397798 INFO: Decoy channel: -1
0:04:07.397823 INFO: Competetive: True
0:04:07.404211 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:07.411129 INFO: Using random state 354222 for train-test-split
0:04:07.461449 INFO: Test AUC: 0.512
0:04:07.461540 INFO: Train AUC: 0.504
0:04:07.461571 INFO: AUC difference: 1.61%
0:04:07.677438 INFO: Resetting torch num_threads to 80
0:04:07.681508 PROGRESS: === Extracted 12173 precursors and 57356 fragments ===
0:04:07.681863 INFO: === FDR correction performed with classifier version -1 ===
0:04:07.682292 PROGRESS: ============================= Precursor FDR =============================
0:04:07.682379 PROGRESS: Total precursors accumulated: 0
0:04:07.682436 PROGRESS: Target precursors: 0 (0.00%)
0:04:07.682486 PROGRESS: Decoy precursors: 0 (0.00%)
0:04:07.682530 PROGRESS: 
0:04:07.682574 PROGRESS: Precursor Summary:
0:04:07.682679 PROGRESS: 
0:04:07.682740 PROGRESS: Protein Summary:
0:04:07.682810 PROGRESS: =========================================================================
0:04:07.683072 INFO: Target number of precursors not reached yet.
0:04:07.764956 INFO: Starting optimization step 5.
0:04:07.765194 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:04:07.765275 INFO: Using ng extraction backend
0:04:07.765341 PROGRESS: Extracting batch of 12663 precursors
0:04:07.788373 INFO: === Search parameters used ===
0:04:07.788525 INFO: rt_error       : 805.5992431640625
0:04:07.788586 INFO: mobility_error : 0.1
0:04:07.788632 INFO: num_candidates : 1
0:04:07.788673 INFO: ms1_error      : 30
0:04:07.788713 INFO: ms2_error      : 30
0:04:07.788751 INFO: fwhm_rt        : 5
0:04:07.788790 INFO: quant_window   : 3
0:04:07.788829 INFO: ==============================================
0:04:07.910233 INFO: performing precursor FDR with 40 features
0:04:07.910345 INFO: Decoy channel: -1
0:04:07.910373 INFO: Competetive: True
0:04:07.922775 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:07.930386 INFO: Using random state 845748 for train-test-split
0:04:08.202609 INFO: Test AUC: 0.524
0:04:08.202723 INFO: Train AUC: 0.532
0:04:08.202753 INFO: AUC difference: 1.35%
0:04:08.419641 INFO: Resetting torch num_threads to 80
0:04:08.426036 PROGRESS: === Extracted 24702 precursors and 116046 fragments ===
0:04:08.426462 INFO: === FDR correction performed with classifier version -1 ===
0:04:08.426955 PROGRESS: ============================= Precursor FDR =============================
0:04:08.427042 PROGRESS: Total precursors accumulated: 1
0:04:08.427101 PROGRESS: Target precursors: 1 (100.00%)
0:04:08.427152 PROGRESS: Decoy precursors: 0 (0.00%)
0:04:08.427197 PROGRESS: 
0:04:08.427242 PROGRESS: Precursor Summary:
0:04:08.428169 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:04:08.428255 PROGRESS: 
0:04:08.428311 PROGRESS: Protein Summary:
0:04:08.429327 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:04:08.429414 PROGRESS: =========================================================================
0:04:08.429821 INFO: Target number of precursors not reached yet.
0:04:08.528071 INFO: Starting optimization step 6.
0:04:08.528303 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:04:08.528398 INFO: Using ng extraction backend
0:04:08.528464 PROGRESS: Extracting batch of 25339 precursors
0:04:08.572534 INFO: === Search parameters used ===
0:04:08.572720 INFO: rt_error       : 805.5992431640625
0:04:08.572770 INFO: mobility_error : 0.1
0:04:08.572816 INFO: num_candidates : 1
0:04:08.572857 INFO: ms1_error      : 30
0:04:08.572899 INFO: ms2_error      : 30
0:04:08.572938 INFO: fwhm_rt        : 5
0:04:08.572978 INFO: quant_window   : 3
0:04:08.573028 INFO: ==============================================
0:04:08.785781 INFO: performing precursor FDR with 40 features
0:04:08.785898 INFO: Decoy channel: -1
0:04:08.785925 INFO: Competetive: True
0:04:08.810699 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:08.823051 INFO: Using random state 927625 for train-test-split
0:04:09.435704 INFO: Test AUC: 0.555
0:04:09.435817 INFO: Train AUC: 0.576
0:04:09.435848 INFO: AUC difference: 3.71%
0:04:09.664815 INFO: Resetting torch num_threads to 80
0:04:09.674441 PROGRESS: === Extracted 49766 precursors and 233332 fragments ===
0:04:09.674967 INFO: === FDR correction performed with classifier version -1 ===
0:04:09.675533 PROGRESS: ============================= Precursor FDR =============================
0:04:09.675621 PROGRESS: Total precursors accumulated: 29
0:04:09.675680 PROGRESS: Target precursors: 29 (100.00%)
0:04:09.675730 PROGRESS: Decoy precursors: 0 (0.00%)
0:04:09.675776 PROGRESS: 
0:04:09.675818 PROGRESS: Precursor Summary:
0:04:09.676766 PROGRESS: Channel   0:	 0.050 FDR:    29; 0.010 FDR:    29; 0.001 FDR:    29
0:04:09.676864 PROGRESS: 
0:04:09.676921 PROGRESS: Protein Summary:
0:04:09.677983 PROGRESS: Channel   0:	 0.050 FDR:    28; 0.010 FDR:    28; 0.001 FDR:    28
0:04:09.678071 PROGRESS: =========================================================================
0:04:09.678822 INFO: Target number of precursors not reached yet.
0:04:09.811689 INFO: Starting optimization step 7.
0:04:09.811930 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:04:09.812013 INFO: Using ng extraction backend
0:04:09.812082 PROGRESS: Extracting batch of 50691 precursors
0:04:09.899789 INFO: === Search parameters used ===
0:04:09.900023 INFO: rt_error       : 805.5992431640625
0:04:09.900073 INFO: mobility_error : 0.1
0:04:09.900117 INFO: num_candidates : 1
0:04:09.900159 INFO: ms1_error      : 30
0:04:09.900198 INFO: ms2_error      : 30
0:04:09.900239 INFO: fwhm_rt        : 5
0:04:09.900280 INFO: quant_window   : 3
0:04:09.900324 INFO: ==============================================
0:04:10.260743 INFO: performing precursor FDR with 40 features
0:04:10.260852 INFO: Decoy channel: -1
0:04:10.260879 INFO: Competetive: True
0:04:10.298895 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:10.324597 INFO: Using random state 274674 for train-test-split
0:04:11.696854 INFO: Test AUC: 0.579
0:04:11.696970 INFO: Train AUC: 0.597
0:04:11.697008 INFO: AUC difference: 3.10%
0:04:11.942932 INFO: Resetting torch num_threads to 80
0:04:11.961379 PROGRESS: === Extracted 99917 precursors and 469358 fragments ===
0:04:11.961934 INFO: === FDR correction performed with classifier version -1 ===
0:04:11.962527 PROGRESS: ============================= Precursor FDR =============================
0:04:11.962635 PROGRESS: Total precursors accumulated: 254
0:04:11.962695 PROGRESS: Target precursors: 252 (99.21%)
0:04:11.962748 PROGRESS: Decoy precursors: 2 (0.79%)
0:04:11.962797 PROGRESS: 
0:04:11.962843 PROGRESS: Precursor Summary:
0:04:11.963782 PROGRESS: Channel   0:	 0.050 FDR:   252; 0.010 FDR:   252; 0.001 FDR:   192
0:04:11.963873 PROGRESS: 
0:04:11.963927 PROGRESS: Protein Summary:
0:04:11.965013 PROGRESS: Channel   0:	 0.050 FDR:   242; 0.010 FDR:   242; 0.001 FDR:   184
0:04:11.965106 PROGRESS: =========================================================================
0:04:11.966604 INFO: Target number of precursors reached.
0:04:12.002429 INFO: fragments_df: keeping 2174 of 469358 [sum(precursor_idx_mask)=2677 sum(mass_error_mask)=469358 stop_rank=2174
0:04:12.207052 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:04:12.301659 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:04:12.542821 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:04:12.543236 INFO: Using score_cutoff 13.567808945846558 (fac=0.99, q=1)
0:04:12.543592 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:04:12.543674 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:04:12.543731 INFO: Updating optimization_manager: score_cutoff        : 0 -> 13.567808945846558
0:04:12.543788 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:04:12.607629 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:04:12.761724 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:04:12.761978 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:04:12.762080 INFO: Starting optimization step 8.
0:04:12.762149 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:04:12.762224 INFO: Using ng extraction backend
0:04:12.762294 PROGRESS: Extracting batch of 100984 precursors
0:04:12.939065 INFO: === Search parameters used ===
0:04:12.939308 INFO: rt_error       : 805.5992431640625
0:04:12.939368 INFO: mobility_error : 0.1
0:04:12.939416 INFO: num_candidates : 3
0:04:12.939459 INFO: ms1_error      : 30
0:04:12.939501 INFO: ms2_error      : 30
0:04:12.939540 INFO: fwhm_rt        : 3.0
0:04:12.939580 INFO: quant_window   : 3
0:04:12.939619 INFO: ==============================================
0:04:14.157051 INFO: performing precursor FDR with 40 features
0:04:14.157313 INFO: Decoy channel: -1
0:04:14.157341 INFO: Competetive: True
0:04:14.227886 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:14.327334 INFO: Using random state 142258 for train-test-split
0:04:18.232040 INFO: Test AUC: 0.591
0:04:18.232157 INFO: Train AUC: 0.605
0:04:18.232188 INFO: AUC difference: 2.24%
0:04:18.543448 INFO: Resetting torch num_threads to 80
0:04:18.553619 PROGRESS: === Extracted 299716 precursors and 1378036 fragments ===
0:04:18.553988 INFO: === FDR correction performed with classifier version 7 ===
0:04:18.554428 PROGRESS: ============================= Precursor FDR =============================
0:04:18.554511 PROGRESS: Total precursors accumulated: 225
0:04:18.554568 PROGRESS: Target precursors: 223 (99.11%)
0:04:18.554624 PROGRESS: Decoy precursors: 2 (0.89%)
0:04:18.554671 PROGRESS: 
0:04:18.554715 PROGRESS: Precursor Summary:
0:04:18.555562 PROGRESS: Channel   0:	 0.050 FDR:   223; 0.010 FDR:   223; 0.001 FDR:    18
0:04:18.555645 PROGRESS: 
0:04:18.555698 PROGRESS: Protein Summary:
0:04:18.556665 PROGRESS: Channel   0:	 0.050 FDR:   212; 0.010 FDR:   212; 0.001 FDR:    18
0:04:18.556752 PROGRESS: =========================================================================
0:04:18.561036 INFO: Target number of precursors reached.
0:04:18.649804 INFO: fragments_df: keeping 2827 of 1378036 [sum(precursor_idx_mask)=5192 sum(mass_error_mask)=1378036 stop_rank=2827
0:04:18.859192 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:04:18.969570 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:04:19.341792 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:04:19.342201 INFO: Using score_cutoff 15.159263195228577 (fac=0.99, q=1)
0:04:19.342485 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:04:19.342563 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:04:19.342615 INFO: Updating optimization_manager: score_cutoff        : 13.567808945846558 -> 15.159263195228577
0:04:19.342672 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:04:19.406498 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:04:19.551131 INFO: === checking if optimization conditions were reached ===
0:04:19.552928 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:04:19.553042 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:04:19.553611 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:04:19.553673 INFO: ==============================================
0:04:19.553738 INFO: Starting optimization step 9.
0:04:19.553794 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:04:19.553854 INFO: Using ng extraction backend
0:04:19.553912 PROGRESS: Extracting batch of 100984 precursors
0:04:19.728413 INFO: === Search parameters used ===
0:04:19.728648 INFO: rt_error       : 805.5992431640625
0:04:19.728700 INFO: mobility_error : 0.1
0:04:19.728746 INFO: num_candidates : 3
0:04:19.728790 INFO: ms1_error      : 30
0:04:19.728831 INFO: ms2_error      : 10.0
0:04:19.728873 INFO: fwhm_rt        : 3.0
0:04:19.728913 INFO: quant_window   : 3
0:04:19.728953 INFO: ==============================================
0:04:20.934755 INFO: performing precursor FDR with 40 features
0:04:20.934870 INFO: Decoy channel: -1
0:04:20.934896 INFO: Competetive: True
0:04:21.007211 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:21.109808 INFO: Using random state 63235 for train-test-split
0:04:25.270896 INFO: Test AUC: 0.593
0:04:25.271012 INFO: Train AUC: 0.607
0:04:25.271043 INFO: AUC difference: 2.36%
0:04:25.578529 INFO: Resetting torch num_threads to 80
0:04:25.589605 PROGRESS: === Extracted 302174 precursors and 1612079 fragments ===
0:04:25.589976 INFO: === FDR correction performed with classifier version 8 ===
0:04:25.590452 PROGRESS: ============================= Precursor FDR =============================
0:04:25.590535 PROGRESS: Total precursors accumulated: 540
0:04:25.590602 PROGRESS: Target precursors: 535 (99.07%)
0:04:25.590656 PROGRESS: Decoy precursors: 5 (0.93%)
0:04:25.590699 PROGRESS: 
0:04:25.590743 PROGRESS: Precursor Summary:
0:04:25.591690 PROGRESS: Channel   0:	 0.050 FDR:   535; 0.010 FDR:   535; 0.001 FDR:   327
0:04:25.591774 PROGRESS: 
0:04:25.591830 PROGRESS: Protein Summary:
0:04:25.592986 PROGRESS: Channel   0:	 0.050 FDR:   504; 0.010 FDR:   504; 0.001 FDR:   304
0:04:25.593085 PROGRESS: =========================================================================
0:04:25.597619 INFO: Target number of precursors reached.
0:04:25.703253 INFO: fragments_df: keeping 5000 of 1612079 [sum(precursor_idx_mask)=12731 sum(mass_error_mask)=1612079 stop_rank=5000
0:04:25.844995 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:04:25.985461 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:04:26.658663 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:04:26.659073 INFO: Using score_cutoff 10.735837893676758 (fac=0.99, q=1)
0:04:26.659361 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:04:26.659436 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:04:26.659490 INFO: Updating optimization_manager: score_cutoff        : 15.159263195228577 -> 10.735837893676758
0:04:26.659549 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:04:26.690710 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:04:26.759451 INFO: === checking if optimization conditions were reached ===
0:04:26.761834 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:04:26.761949 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:04:26.762024 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:04:26.762096 INFO: ==============================================
0:04:26.762173 PROGRESS: Optimization finished for ms2_error.
0:04:26.909214 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:04:26.940654 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:04:27.010028 INFO: Starting optimization step 0.
0:04:27.010278 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:04:27.010368 INFO: Using ng extraction backend
0:04:27.010443 PROGRESS: Extracting batch of 50293 precursors
0:04:27.099875 INFO: === Search parameters used ===
0:04:27.100116 INFO: rt_error       : 805.5992431640625
0:04:27.100176 INFO: mobility_error : 0.1
0:04:27.100220 INFO: num_candidates : 3
0:04:27.100280 INFO: ms1_error      : 30
0:04:27.100322 INFO: ms2_error      : 10.0
0:04:27.100362 INFO: fwhm_rt        : 3.0
0:04:27.100402 INFO: quant_window   : 3
0:04:27.100443 INFO: ==============================================
0:04:27.742259 INFO: performing precursor FDR with 40 features
0:04:27.742374 INFO: Decoy channel: -1
0:04:27.742399 INFO: Competetive: True
0:04:27.780645 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:27.815034 INFO: Using random state 962570 for train-test-split
0:04:29.853728 INFO: Test AUC: 0.599
0:04:29.853846 INFO: Train AUC: 0.616
0:04:29.853878 INFO: AUC difference: 2.65%
0:04:30.415560 INFO: Resetting torch num_threads to 80
0:04:30.421331 PROGRESS: === Extracted 150495 precursors and 803134 fragments ===
0:04:30.421670 INFO: === FDR correction performed with classifier version 9 ===
0:04:30.422101 PROGRESS: ============================= Precursor FDR =============================
0:04:30.422184 PROGRESS: Total precursors accumulated: 210
0:04:30.422239 PROGRESS: Target precursors: 208 (99.05%)
0:04:30.422287 PROGRESS: Decoy precursors: 2 (0.95%)
0:04:30.422330 PROGRESS: 
0:04:30.422370 PROGRESS: Precursor Summary:
0:04:30.423257 PROGRESS: Channel   0:	 0.050 FDR:   208; 0.010 FDR:   208; 0.001 FDR:   165
0:04:30.423344 PROGRESS: 
0:04:30.423397 PROGRESS: Protein Summary:
0:04:30.424401 PROGRESS: Channel   0:	 0.050 FDR:   201; 0.010 FDR:   201; 0.001 FDR:   162
0:04:30.424484 PROGRESS: =========================================================================
0:04:30.426421 INFO: Target number of precursors reached.
0:04:30.478867 INFO: fragments_df: keeping 2475 of 803134 [sum(precursor_idx_mask)=5097 sum(mass_error_mask)=803134 stop_rank=2475
0:04:30.614104 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:04:30.726816 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:04:31.052232 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:04:31.052639 INFO: Using score_cutoff 13.45352257490158 (fac=0.99, q=1)
0:04:31.052930 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:04:31.053025 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:04:31.053080 INFO: Updating optimization_manager: score_cutoff        : 10.735837893676758 -> 13.45352257490158
0:04:31.053135 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:04:31.083999 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:04:31.146506 INFO: === checking if optimization conditions were reached ===
0:04:31.146769 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:04:31.148934 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 100.11249609277094
0:04:31.149060 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 100.1125.
0:04:31.149141 INFO: ==============================================
0:04:31.149220 INFO: Starting optimization step 1.
0:04:31.149286 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:04:31.149357 INFO: Using ng extraction backend
0:04:31.149425 PROGRESS: Extracting batch of 50293 precursors
0:04:31.238779 INFO: === Search parameters used ===
0:04:31.239015 INFO: rt_error       : 100.11249609277094
0:04:31.239071 INFO: mobility_error : 0.1
0:04:31.239118 INFO: num_candidates : 3
0:04:31.239160 INFO: ms1_error      : 30
0:04:31.239202 INFO: ms2_error      : 10.0
0:04:31.239244 INFO: fwhm_rt        : 3.0
0:04:31.239296 INFO: quant_window   : 3
0:04:31.239338 INFO: ==============================================
0:04:31.809119 INFO: performing precursor FDR with 40 features
0:04:31.809237 INFO: Decoy channel: -1
0:04:31.809264 INFO: Competetive: True
0:04:31.846010 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:31.882811 INFO: Using random state 962570 for train-test-split
0:04:33.872089 INFO: Test AUC: 0.593
0:04:33.872218 INFO: Train AUC: 0.608
0:04:33.872249 INFO: AUC difference: 2.57%
0:04:34.132659 INFO: Resetting torch num_threads to 80
0:04:34.138992 PROGRESS: === Extracted 146944 precursors and 593138 fragments ===
0:04:34.139346 INFO: === FDR correction performed with classifier version 9 ===
0:04:34.139799 PROGRESS: ============================= Precursor FDR =============================
0:04:34.139884 PROGRESS: Total precursors accumulated: 295
0:04:34.139942 PROGRESS: Target precursors: 293 (99.32%)
0:04:34.139991 PROGRESS: Decoy precursors: 2 (0.68%)
0:04:34.140035 PROGRESS: 
0:04:34.140079 PROGRESS: Precursor Summary:
0:04:34.140974 PROGRESS: Channel   0:	 0.050 FDR:   293; 0.010 FDR:   293; 0.001 FDR:   274
0:04:34.141066 PROGRESS: 
0:04:34.141119 PROGRESS: Protein Summary:
0:04:34.142189 PROGRESS: Channel   0:	 0.050 FDR:   282; 0.010 FDR:   282; 0.001 FDR:   264
0:04:34.142273 PROGRESS: =========================================================================
0:04:34.144227 INFO: Target number of precursors reached.
0:04:34.184900 INFO: fragments_df: keeping 3089 of 593138 [sum(precursor_idx_mask)=6599 sum(mass_error_mask)=593138 stop_rank=3089
0:04:34.319735 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:04:34.420715 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:04:34.757984 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:04:34.758399 INFO: Using score_cutoff 7.876846341705322 (fac=0.99, q=1)
0:04:34.758679 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:04:34.758754 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:04:34.758806 INFO: Updating optimization_manager: score_cutoff        : 13.45352257490158 -> 7.876846341705322
0:04:34.758860 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:04:34.790189 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:04:34.857682 INFO: === checking if optimization conditions were reached ===
0:04:34.857935 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:04:34.859823 INFO: Updating optimization_manager: rt_error            : 100.11249609277094 -> 82.08462698123512
0:04:34.859930 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 82.0846.
0:04:34.860009 INFO: ==============================================
0:04:34.860096 INFO: Starting optimization step 2.
0:04:34.860165 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:04:34.860242 INFO: Using ng extraction backend
0:04:34.860314 PROGRESS: Extracting batch of 50293 precursors
0:04:34.947143 INFO: === Search parameters used ===
0:04:34.947397 INFO: rt_error       : 82.08462698123512
0:04:34.947464 INFO: mobility_error : 0.1
0:04:34.947529 INFO: num_candidates : 3
0:04:34.947587 INFO: ms1_error      : 30
0:04:34.947661 INFO: ms2_error      : 10.0
0:04:34.947717 INFO: fwhm_rt        : 3.0
0:04:34.947773 INFO: quant_window   : 3
0:04:34.947826 INFO: ==============================================
0:04:35.515047 INFO: performing precursor FDR with 40 features
0:04:35.515162 INFO: Decoy channel: -1
0:04:35.515189 INFO: Competetive: True
0:04:35.550509 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:35.584364 INFO: Using random state 962570 for train-test-split
0:04:37.583561 INFO: Test AUC: 0.593
0:04:37.583683 INFO: Train AUC: 0.608
0:04:37.583714 INFO: AUC difference: 2.49%
0:04:37.843644 INFO: Resetting torch num_threads to 80
0:04:37.849535 PROGRESS: === Extracted 145686 precursors and 566156 fragments ===
0:04:37.849884 INFO: === FDR correction performed with classifier version 9 ===
0:04:37.850314 PROGRESS: ============================= Precursor FDR =============================
0:04:37.850395 PROGRESS: Total precursors accumulated: 248
0:04:37.850450 PROGRESS: Target precursors: 246 (99.19%)
0:04:37.850497 PROGRESS: Decoy precursors: 2 (0.81%)
0:04:37.850539 PROGRESS: 
0:04:37.850580 PROGRESS: Precursor Summary:
0:04:37.851435 PROGRESS: Channel   0:	 0.050 FDR:   246; 0.010 FDR:   246; 0.001 FDR:   195
0:04:37.851520 PROGRESS: 
0:04:37.851572 PROGRESS: Protein Summary:
0:04:37.852900 PROGRESS: Channel   0:	 0.050 FDR:   238; 0.010 FDR:   238; 0.001 FDR:   189
0:04:37.852984 PROGRESS: =========================================================================
0:04:37.854920 INFO: Target number of precursors reached.
0:04:37.892420 INFO: fragments_df: keeping 2749 of 566156 [sum(precursor_idx_mask)=5635 sum(mass_error_mask)=566156 stop_rank=2749
0:04:38.029028 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:04:38.147202 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:04:38.507981 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:04:38.508393 INFO: Using score_cutoff 13.29723849105835 (fac=0.99, q=1)
0:04:38.508683 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:04:38.508759 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:04:38.508813 INFO: Updating optimization_manager: score_cutoff        : 7.876846341705322 -> 13.29723849105835
0:04:38.508870 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:04:38.540265 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:04:38.606734 INFO: === checking if optimization conditions were reached ===
0:04:38.606962 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:04:38.608890 INFO: Updating optimization_manager: rt_error            : 82.08462698123512 -> 62.29999646843583
0:04:38.609001 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 62.3000.
0:04:38.609069 INFO: ==============================================
0:04:38.609137 INFO: Starting optimization step 3.
0:04:38.609194 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:04:38.609253 INFO: Using ng extraction backend
0:04:38.609310 PROGRESS: Extracting batch of 50293 precursors
0:04:38.695935 INFO: === Search parameters used ===
0:04:38.696169 INFO: rt_error       : 62.29999646843583
0:04:38.696219 INFO: mobility_error : 0.1
0:04:38.696870 INFO: num_candidates : 3
0:04:38.696925 INFO: ms1_error      : 30
0:04:38.696966 INFO: ms2_error      : 10.0
0:04:38.697018 INFO: fwhm_rt        : 3.0
0:04:38.697060 INFO: quant_window   : 3
0:04:38.697098 INFO: ==============================================
0:04:39.250964 INFO: performing precursor FDR with 40 features
0:04:39.251079 INFO: Decoy channel: -1
0:04:39.251105 INFO: Competetive: True
0:04:39.284942 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:39.316956 INFO: Using random state 962570 for train-test-split
0:04:41.244254 INFO: Test AUC: 0.597
0:04:41.244370 INFO: Train AUC: 0.608
0:04:41.244402 INFO: AUC difference: 1.71%
0:04:41.501378 INFO: Resetting torch num_threads to 80
0:04:41.507525 PROGRESS: === Extracted 142702 precursors and 528702 fragments ===
0:04:41.507859 INFO: === FDR correction performed with classifier version 9 ===
0:04:41.508306 PROGRESS: ============================= Precursor FDR =============================
0:04:41.508389 PROGRESS: Total precursors accumulated: 310
0:04:41.508447 PROGRESS: Target precursors: 307 (99.03%)
0:04:41.508498 PROGRESS: Decoy precursors: 3 (0.97%)
0:04:41.508544 PROGRESS: 
0:04:41.508590 PROGRESS: Precursor Summary:
0:04:41.509504 PROGRESS: Channel   0:	 0.050 FDR:   307; 0.010 FDR:   307; 0.001 FDR:   221
0:04:41.509590 PROGRESS: 
0:04:41.509645 PROGRESS: Protein Summary:
0:04:41.510704 PROGRESS: Channel   0:	 0.050 FDR:   298; 0.010 FDR:   298; 0.001 FDR:   215
0:04:41.510789 PROGRESS: =========================================================================
0:04:41.512689 INFO: Target number of precursors reached.
0:04:41.547766 INFO: fragments_df: keeping 3082 of 528702 [sum(precursor_idx_mask)=6618 sum(mass_error_mask)=528702 stop_rank=3082
0:04:41.749177 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:04:41.873052 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:04:42.274380 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:04:42.274777 INFO: Using score_cutoff 12.072379586791993 (fac=0.99, q=1)
0:04:42.275060 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:04:42.275137 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:04:42.275192 INFO: Updating optimization_manager: score_cutoff        : 13.29723849105835 -> 12.072379586791993
0:04:42.275247 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:04:42.306734 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:04:42.370158 INFO: === checking if optimization conditions were reached ===
0:04:42.370409 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:04:42.372703 INFO: Updating optimization_manager: rt_error            : 62.29999646843583 -> 49.28838400423219
0:04:42.372822 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 49.2884.
0:04:42.372895 INFO: ==============================================
0:04:42.372973 INFO: Starting optimization step 4.
0:04:42.373053 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:04:42.373130 INFO: Using ng extraction backend
0:04:42.373201 PROGRESS: Extracting batch of 50293 precursors
0:04:42.462832 INFO: === Search parameters used ===
0:04:42.463054 INFO: rt_error       : 49.28838400423219
0:04:42.463110 INFO: mobility_error : 0.1
0:04:42.463157 INFO: num_candidates : 3
0:04:42.463200 INFO: ms1_error      : 30
0:04:42.463240 INFO: ms2_error      : 10.0
0:04:42.463280 INFO: fwhm_rt        : 3.0
0:04:42.463320 INFO: quant_window   : 3
0:04:42.463360 INFO: ==============================================
0:04:42.972233 INFO: performing precursor FDR with 40 features
0:04:42.972353 INFO: Decoy channel: -1
0:04:42.972379 INFO: Competetive: True
0:04:43.006355 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:43.036190 INFO: Using random state 962570 for train-test-split
0:04:44.724551 INFO: Test AUC: 0.590
0:04:44.724665 INFO: Train AUC: 0.608
0:04:44.724696 INFO: AUC difference: 2.89%
0:04:44.978076 INFO: Resetting torch num_threads to 80
0:04:44.983671 PROGRESS: === Extracted 133197 precursors and 477580 fragments ===
0:04:44.984005 INFO: === FDR correction performed with classifier version 9 ===
0:04:44.984433 PROGRESS: ============================= Precursor FDR =============================
0:04:44.984515 PROGRESS: Total precursors accumulated: 249
0:04:44.984571 PROGRESS: Target precursors: 247 (99.20%)
0:04:44.984621 PROGRESS: Decoy precursors: 2 (0.80%)
0:04:44.984665 PROGRESS: 
0:04:44.984707 PROGRESS: Precursor Summary:
0:04:44.985566 PROGRESS: Channel   0:	 0.050 FDR:   247; 0.010 FDR:   247; 0.001 FDR:    64
0:04:44.985655 PROGRESS: 
0:04:44.985706 PROGRESS: Protein Summary:
0:04:44.986691 PROGRESS: Channel   0:	 0.050 FDR:   241; 0.010 FDR:   241; 0.001 FDR:    63
0:04:44.986776 PROGRESS: =========================================================================
0:04:44.988525 INFO: Target number of precursors reached.
0:04:45.021291 INFO: fragments_df: keeping 2467 of 477580 [sum(precursor_idx_mask)=4925 sum(mass_error_mask)=477580 stop_rank=2467
0:04:45.157182 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:04:45.275897 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:04:45.599194 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:04:45.599597 INFO: Using score_cutoff 11.996275583839417 (fac=0.99, q=1)
0:04:45.599874 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:04:45.599947 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:04:45.599998 INFO: Updating optimization_manager: score_cutoff        : 12.072379586791993 -> 11.996275583839417
0:04:45.600049 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:04:45.631886 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:04:45.695774 INFO: === checking if optimization conditions were reached ===
0:04:45.696005 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:04:45.697960 INFO: Updating optimization_manager: rt_error            : 49.28838400423219 -> 34.66476095804995
0:04:45.698062 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 34.6648.
0:04:45.698127 INFO: ==============================================
0:04:45.698192 INFO: Starting optimization step 5.
0:04:45.698247 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:04:45.698309 INFO: Using ng extraction backend
0:04:45.698365 PROGRESS: Extracting batch of 50293 precursors
0:04:45.785074 INFO: === Search parameters used ===
0:04:45.785302 INFO: rt_error       : 34.66476095804995
0:04:45.785353 INFO: mobility_error : 0.1
0:04:45.785398 INFO: num_candidates : 3
0:04:45.785439 INFO: ms1_error      : 30
0:04:45.785477 INFO: ms2_error      : 10.0
0:04:45.785515 INFO: fwhm_rt        : 3.0
0:04:45.785554 INFO: quant_window   : 3
0:04:45.785591 INFO: ==============================================
0:04:46.289846 INFO: performing precursor FDR with 40 features
0:04:46.289958 INFO: Decoy channel: -1
0:04:46.289989 INFO: Competetive: True
0:04:46.324366 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:46.356515 INFO: Using random state 962570 for train-test-split
0:04:48.134705 INFO: Test AUC: 0.595
0:04:48.134825 INFO: Train AUC: 0.609
0:04:48.134855 INFO: AUC difference: 2.30%
0:04:48.395236 INFO: Resetting torch num_threads to 80
0:04:48.401276 PROGRESS: === Extracted 133615 precursors and 481105 fragments ===
0:04:48.401629 INFO: === FDR correction performed with classifier version 9 ===
0:04:48.402064 PROGRESS: ============================= Precursor FDR =============================
0:04:48.402146 PROGRESS: Total precursors accumulated: 324
0:04:48.402201 PROGRESS: Target precursors: 321 (99.07%)
0:04:48.402248 PROGRESS: Decoy precursors: 3 (0.93%)
0:04:48.402291 PROGRESS: 
0:04:48.402332 PROGRESS: Precursor Summary:
0:04:48.403209 PROGRESS: Channel   0:	 0.050 FDR:   321; 0.010 FDR:   321; 0.001 FDR:   212
0:04:48.403292 PROGRESS: 
0:04:48.403344 PROGRESS: Protein Summary:
0:04:48.404393 PROGRESS: Channel   0:	 0.050 FDR:   314; 0.010 FDR:   314; 0.001 FDR:   208
0:04:48.404477 PROGRESS: =========================================================================
0:04:48.406262 INFO: Target number of precursors reached.
0:04:48.438956 INFO: fragments_df: keeping 2928 of 481105 [sum(precursor_idx_mask)=6127 sum(mass_error_mask)=481105 stop_rank=2928
0:04:48.574957 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:04:48.699520 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:04:49.084918 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:04:49.085341 INFO: Using score_cutoff 9.319106328964233 (fac=0.99, q=1)
0:04:49.085617 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:04:49.085692 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:04:49.085743 INFO: Updating optimization_manager: score_cutoff        : 11.996275583839417 -> 9.319106328964233
0:04:49.085795 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:04:49.117116 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:04:49.186161 INFO: === checking if optimization conditions were reached ===
0:04:49.186388 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:04:49.188356 INFO: Updating optimization_manager: rt_error            : 34.66476095804995 -> 33.82004674776908
0:04:49.188453 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 33.8200.
0:04:49.188516 INFO: ==============================================
0:04:49.188582 INFO: Starting optimization step 6.
0:04:49.188639 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:04:49.188712 INFO: Using ng extraction backend
0:04:49.188770 PROGRESS: Extracting batch of 50293 precursors
0:04:49.275440 INFO: === Search parameters used ===
0:04:49.275682 INFO: rt_error       : 33.82004674776908
0:04:49.275741 INFO: mobility_error : 0.1
0:04:49.275798 INFO: num_candidates : 3
0:04:49.275839 INFO: ms1_error      : 30
0:04:49.275878 INFO: ms2_error      : 10.0
0:04:49.275917 INFO: fwhm_rt        : 3.0
0:04:49.275954 INFO: quant_window   : 3
0:04:49.275993 INFO: ==============================================
0:04:49.791318 INFO: performing precursor FDR with 40 features
0:04:49.791432 INFO: Decoy channel: -1
0:04:49.791459 INFO: Competetive: True
0:04:49.825297 INFO: Setting torch num_threads to 2 for FDR classification task
0:04:49.856221 INFO: Using random state 962570 for train-test-split
0:04:51.640155 INFO: Test AUC: 0.597
0:04:51.640273 INFO: Train AUC: 0.609
0:04:51.640305 INFO: AUC difference: 1.85%
0:04:51.902399 INFO: Resetting torch num_threads to 80
0:04:51.908216 PROGRESS: === Extracted 133710 precursors and 483718 fragments ===
0:04:51.908565 INFO: === FDR correction performed with classifier version 9 ===
0:04:51.909013 PROGRESS: ============================= Precursor FDR =============================
0:04:51.909096 PROGRESS: Total precursors accumulated: 281
0:04:51.909153 PROGRESS: Target precursors: 279 (99.29%)
0:04:51.909201 PROGRESS: Decoy precursors: 2 (0.71%)
0:04:51.909246 PROGRESS: 
0:04:51.909290 PROGRESS: Precursor Summary:
0:04:51.910163 PROGRESS: Channel   0:	 0.050 FDR:   279; 0.010 FDR:   279; 0.001 FDR:   157
0:04:51.910246 PROGRESS: 
0:04:51.910300 PROGRESS: Protein Summary:
0:04:51.911625 PROGRESS: Channel   0:	 0.050 FDR:   273; 0.010 FDR:   273; 0.001 FDR:   154
0:04:51.911711 PROGRESS: =========================================================================
0:04:51.913502 INFO: Target number of precursors reached.
0:04:51.946920 INFO: fragments_df: keeping 2649 of 483718 [sum(precursor_idx_mask)=5428 sum(mass_error_mask)=483718 stop_rank=2649
0:04:52.081714 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:04:52.201904 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:04:52.549724 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:04:52.550134 INFO: Using score_cutoff 10.6424284532547 (fac=0.99, q=1)
0:04:52.550413 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:04:52.550488 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:04:52.550541 INFO: Updating optimization_manager: score_cutoff        : 9.319106328964233 -> 10.6424284532547
0:04:52.550595 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:04:52.582683 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:04:52.647576 INFO: === checking if optimization conditions were reached ===
0:04:52.647816 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:04:52.648884 INFO: Updating optimization_manager: rt_error            : 33.82004674776908 -> 34.66476095804995
0:04:52.649020 INFO: Updating optimization_manager: classifier_version  : 9 -> 15
0:04:52.649119 INFO: Updating optimization_manager: score_cutoff        : 10.6424284532547 -> 9.319106328964233
0:04:52.649221 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:04:52.649308 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:04:52.649391 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 34.6648 found after 7 searches.
0:04:52.649454 INFO: ==============================================
0:04:52.649519 PROGRESS: Optimization finished for rt_error.
0:04:52.787571 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:04:52.819952 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:04:52.912089 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:04:52.912286 PROGRESS: ==============================================
0:04:52.912352 PROGRESS: ms2_error      : 10.0000
0:04:52.912404 PROGRESS: rt_error       : 34.6648
0:04:52.912449 PROGRESS: ==============================================
0:04:52.913424 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:05:00.875597 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:05:18.252522 INFO: Using ng extraction backend
0:05:18.253062 PROGRESS: Extracting batch of 12001526 precursors
0:05:34.166028 INFO: === Search parameters used ===
0:05:34.166290 INFO: rt_error       : 34.66476095804995
0:05:34.166354 INFO: mobility_error : 0.1
0:05:34.166401 INFO: num_candidates : 3
0:05:34.166443 INFO: ms1_error      : 30
0:05:34.166496 INFO: ms2_error      : 10.0
0:05:34.166537 INFO: fwhm_rt        : 3.0
0:05:34.166575 INFO: quant_window   : 3
0:05:34.166611 INFO: ==============================================
0:06:12.859162 INFO: Removed 20878631 precursors with score below cutoff 9.319106328964233
0:06:27.152186 INFO: performing precursor FDR with 40 features
0:06:27.152398 INFO: Decoy channel: -1
0:06:27.152429 INFO: Competetive: True
0:06:28.398536 INFO: Setting torch num_threads to 2 for FDR classification task
0:06:33.014877 INFO: Using random state 313186 for train-test-split
0:09:20.142608 INFO: Test AUC: 0.624
0:09:20.143880 INFO: Train AUC: 0.624
0:09:20.143926 INFO: AUC difference: 0.03%
0:09:24.063266 INFO: Resetting torch num_threads to 80
0:09:25.775031 PROGRESS: ============================= Precursor FDR =============================
0:09:25.775306 PROGRESS: Total precursors accumulated: 72,812
0:09:25.775375 PROGRESS: Target precursors: 72,092 (99.01%)
0:09:25.775428 PROGRESS: Decoy precursors: 720 (0.99%)
0:09:25.775478 PROGRESS: 
0:09:25.775524 PROGRESS: Precursor Summary:
0:09:25.795923 PROGRESS: Channel   0:	 0.050 FDR: 72,092; 0.010 FDR: 72,092; 0.001 FDR: 48,520
0:09:25.796151 PROGRESS: 
0:09:25.796212 PROGRESS: Protein Summary:
0:09:25.824433 PROGRESS: Channel   0:	 0.050 FDR: 12,180; 0.010 FDR: 12,180; 0.001 FDR: 9,072
0:09:25.824654 PROGRESS: =========================================================================
0:09:25.894258 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/psm.parquet
0:09:26.043142 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.parquet
0:09:26.254078 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:09:26.823730 PROGRESS: 
0:09:26.823887 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant
0:09:26.823959 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/figures
0:09:26.824130 INFO: Initializing TimingManager
0:09:26.824571 INFO: Initializing RawFileManager
0:09:37.151043 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.
0:09:37.155156 INFO: Determining DIA cycle
0:09:37.171460 INFO: Found cycle with start 0.00 min and length 300.
0:09:37.335258 INFO: RT (min)            : 0.0 - 26.9
0:09:37.335350 INFO: RT duration (sec)   : 1611.2
0:09:37.335378 INFO: RT duration (min)   : 26.9
0:09:37.335403 INFO: Cycle len (scans)   : 300
0:09:37.335423 INFO: Cycle len (sec)     : 1.65
0:09:37.335445 INFO: Number of cycles    : 978
0:09:37.335465 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:09:37.335522 INFO: Creating DIA data object took: 10.510848999023438
0:09:37.967989 INFO: Creating DIA data NG object took: 0.6323409080505371
0:09:39.361378 INFO: Initializing CalibrationManager
0:09:39.361642 INFO: Setting up calibration estimators ..
0:09:39.361705 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:09:39.361804 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'}' ..
0:09:39.361929 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:09:39.361983 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:09:39.362053 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}}' ..
0:09:39.362107 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:09:39.362152 INFO: Done setting up calibration estimators.
0:09:39.362356 INFO: Initializing OptimizationManager
0:09:39.362500 INFO: initial parameter: ms1_error = 30
0:09:39.362554 INFO: initial parameter: ms2_error = 30
0:09:39.362599 INFO: initial parameter: rt_error = 805.6019897460938
0:09:39.362640 INFO: initial parameter: mobility_error = 0.1
0:09:39.362679 INFO: initial parameter: num_candidates = 1
0:09:39.362718 INFO: initial parameter: fwhm_rt = 5
0:09:39.362759 INFO: initial parameter: fwhm_mobility = 0.01
0:09:39.362797 INFO: initial parameter: score_cutoff = 0
0:09:39.362836 INFO: initial parameter: classifier_version = -1
0:09:39.362904 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:09:39.363234 INFO: FDRManager: loading saved state not requested, will be initialized.
0:09:39.363268 INFO: Initializing FDRManager
0:09:39.363311 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:09:40.563614 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:09:41.302359 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:09:41.302770 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
0:09:41.302908 PROGRESS: Starting initial search for precursors.
0:09:41.302995 INFO: Starting optimization step 0.
0:09:41.303056 PROGRESS: === Extracting elution groups 0 to 200 ===
0:09:41.303123 INFO: Using ng extraction backend
0:09:41.303189 PROGRESS: Extracting batch of 396 precursors
0:09:41.306853 INFO: === Search parameters used ===
0:09:41.306959 INFO: rt_error       : 805.6019897460938
0:09:41.307010 INFO: mobility_error : 0.1
0:09:41.307054 INFO: num_candidates : 1
0:09:41.307096 INFO: ms1_error      : 30
0:09:41.307136 INFO: ms2_error      : 30
0:09:41.307174 INFO: fwhm_rt        : 5
0:09:41.307217 INFO: quant_window   : 3
0:09:41.307256 INFO: ==============================================
0:09:41.332240 INFO: performing precursor FDR with 40 features
0:09:41.332337 INFO: Decoy channel: -1
0:09:41.332364 INFO: Competetive: True
0:09:41.333300 INFO: Setting torch num_threads to 2 for FDR classification task
0:09:41.790601 INFO: Using random state 705608 for train-test-split
0:09:41.798258 INFO: Test AUC: 0.598
0:09:41.798328 INFO: Train AUC: 0.463
0:09:41.798358 INFO: AUC difference: 29.19%
0:09:41.798380 WARNING: AUC difference > 5%. This may indicate overfitting.
0:09:42.008017 INFO: Resetting torch num_threads to 80
0:09:42.009306 PROGRESS: === Extracted 391 precursors and 1831 fragments ===
0:09:42.009630 INFO: === FDR correction performed with classifier version -1 ===
0:09:42.010071 PROGRESS: ============================= Precursor FDR =============================
0:09:42.010161 PROGRESS: Total precursors accumulated: 2
0:09:42.010220 PROGRESS: Target precursors: 2 (100.00%)
0:09:42.010270 PROGRESS: Decoy precursors: 0 (0.00%)
0:09:42.010314 PROGRESS: 
0:09:42.010359 PROGRESS: Precursor Summary:
0:09:42.011275 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:09:42.011361 PROGRESS: 
0:09:42.011415 PROGRESS: Protein Summary:
0:09:42.012426 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:09:42.012514 PROGRESS: =========================================================================
0:09:42.013952 INFO: Target number of precursors not reached yet.
0:09:42.078331 INFO: Starting optimization step 1.
0:09:42.078511 PROGRESS: === Extracting elution groups 200 to 600 ===
0:09:42.078588 INFO: Using ng extraction backend
0:09:42.078649 PROGRESS: Extracting batch of 786 precursors
0:09:42.081643 INFO: === Search parameters used ===
0:09:42.081755 INFO: rt_error       : 805.6019897460938
0:09:42.081806 INFO: mobility_error : 0.1
0:09:42.081852 INFO: num_candidates : 1
0:09:42.081893 INFO: ms1_error      : 30
0:09:42.081933 INFO: ms2_error      : 30
0:09:42.081975 INFO: fwhm_rt        : 5
0:09:42.082014 INFO: quant_window   : 3
0:09:42.082053 INFO: ==============================================
0:09:42.154176 INFO: performing precursor FDR with 40 features
0:09:42.154265 INFO: Decoy channel: -1
0:09:42.154291 INFO: Competetive: True
0:09:42.157136 INFO: Setting torch num_threads to 2 for FDR classification task
0:09:42.158670 INFO: Using random state 405267 for train-test-split
0:09:42.166892 INFO: Test AUC: 0.589
0:09:42.166946 INFO: Train AUC: 0.486
0:09:42.166975 INFO: AUC difference: 21.11%
0:09:42.166997 WARNING: AUC difference > 5%. This may indicate overfitting.
0:09:42.372200 INFO: Resetting torch num_threads to 80
0:09:42.374152 PROGRESS: === Extracted 1172 precursors and 5506 fragments ===
0:09:42.374483 INFO: === FDR correction performed with classifier version -1 ===
0:09:42.374907 PROGRESS: ============================= Precursor FDR =============================
0:09:42.374993 PROGRESS: Total precursors accumulated: 0
0:09:42.375051 PROGRESS: Target precursors: 0 (0.00%)
0:09:42.375102 PROGRESS: Decoy precursors: 0 (0.00%)
0:09:42.375145 PROGRESS: 
0:09:42.375190 PROGRESS: Precursor Summary:
0:09:42.375302 PROGRESS: 
0:09:42.375367 PROGRESS: Protein Summary:
0:09:42.375440 PROGRESS: =========================================================================
0:09:42.375619 INFO: Target number of precursors not reached yet.
0:09:42.442286 INFO: Starting optimization step 2.
0:09:42.442481 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:09:42.442559 INFO: Using ng extraction backend
0:09:42.442622 PROGRESS: Extracting batch of 1592 precursors
0:09:42.446821 INFO: === Search parameters used ===
0:09:42.446948 INFO: rt_error       : 805.6019897460938
0:09:42.446998 INFO: mobility_error : 0.1
0:09:42.447045 INFO: num_candidates : 1
0:09:42.447087 INFO: ms1_error      : 30
0:09:42.447127 INFO: ms2_error      : 30
0:09:42.447169 INFO: fwhm_rt        : 5
0:09:42.447208 INFO: quant_window   : 3
0:09:42.447247 INFO: ==============================================
0:09:42.479216 INFO: performing precursor FDR with 40 features
0:09:42.479292 INFO: Decoy channel: -1
0:09:42.479324 INFO: Competetive: True
0:09:42.482520 INFO: Setting torch num_threads to 2 for FDR classification task
0:09:42.484614 INFO: Using random state 985099 for train-test-split
0:09:42.497066 INFO: Test AUC: 0.481
0:09:42.497125 INFO: Train AUC: 0.497
0:09:42.497163 INFO: AUC difference: 3.35%
0:09:42.712060 INFO: Resetting torch num_threads to 80
0:09:42.714456 PROGRESS: === Extracted 2752 precursors and 12933 fragments ===
0:09:42.714801 INFO: === FDR correction performed with classifier version -1 ===
0:09:42.715253 PROGRESS: ============================= Precursor FDR =============================
0:09:42.715350 PROGRESS: Total precursors accumulated: 0
0:09:42.715435 PROGRESS: Target precursors: 0 (0.00%)
0:09:42.715504 PROGRESS: Decoy precursors: 0 (0.00%)
0:09:42.715568 PROGRESS: 
0:09:42.715629 PROGRESS: Precursor Summary:
0:09:42.715752 PROGRESS: 
0:09:42.715829 PROGRESS: Protein Summary:
0:09:42.715923 PROGRESS: =========================================================================
0:09:42.716130 INFO: Target number of precursors not reached yet.
0:09:42.785209 INFO: Starting optimization step 3.
0:09:42.785435 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:09:42.785533 INFO: Using ng extraction backend
0:09:42.785613 PROGRESS: Extracting batch of 3177 precursors
0:09:42.792985 INFO: === Search parameters used ===
0:09:42.793134 INFO: rt_error       : 805.6019897460938
0:09:42.793201 INFO: mobility_error : 0.1
0:09:42.793269 INFO: num_candidates : 1
0:09:42.793319 INFO: ms1_error      : 30
0:09:42.793380 INFO: ms2_error      : 30
0:09:42.793437 INFO: fwhm_rt        : 5
0:09:42.793507 INFO: quant_window   : 3
0:09:42.793564 INFO: ==============================================
0:09:42.836375 INFO: performing precursor FDR with 40 features
0:09:42.836460 INFO: Decoy channel: -1
0:09:42.836492 INFO: Competetive: True
0:09:42.840598 INFO: Setting torch num_threads to 2 for FDR classification task
0:09:42.843384 INFO: Using random state 549710 for train-test-split
0:09:42.862828 INFO: Test AUC: 0.505
0:09:42.862902 INFO: Train AUC: 0.493
0:09:42.862944 INFO: AUC difference: 2.35%
0:09:43.075013 INFO: Resetting torch num_threads to 80
0:09:43.078769 PROGRESS: === Extracted 5885 precursors and 27703 fragments ===
0:09:43.079127 INFO: === FDR correction performed with classifier version -1 ===
0:09:43.079591 PROGRESS: ============================= Precursor FDR =============================
0:09:43.079690 PROGRESS: Total precursors accumulated: 0
0:09:43.079767 PROGRESS: Target precursors: 0 (0.00%)
0:09:43.079834 PROGRESS: Decoy precursors: 0 (0.00%)
0:09:43.079897 PROGRESS: 
0:09:43.079957 PROGRESS: Precursor Summary:
0:09:43.080095 PROGRESS: 
0:09:43.080174 PROGRESS: Protein Summary:
0:09:43.080270 PROGRESS: =========================================================================
0:09:43.080519 INFO: Target number of precursors not reached yet.
0:09:43.153968 INFO: Starting optimization step 4.
0:09:43.154202 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:09:43.154297 INFO: Using ng extraction backend
0:09:43.154379 PROGRESS: Extracting batch of 6340 precursors
0:09:43.167236 INFO: === Search parameters used ===
0:09:43.167381 INFO: rt_error       : 805.6019897460938
0:09:43.167449 INFO: mobility_error : 0.1
0:09:43.167518 INFO: num_candidates : 1
0:09:43.167568 INFO: ms1_error      : 30
0:09:43.167629 INFO: ms2_error      : 30
0:09:43.167686 INFO: fwhm_rt        : 5
0:09:43.167753 INFO: quant_window   : 3
0:09:43.167815 INFO: ==============================================
0:09:43.240797 INFO: performing precursor FDR with 40 features
0:09:43.240902 INFO: Decoy channel: -1
0:09:43.240934 INFO: Competetive: True
0:09:43.246883 INFO: Setting torch num_threads to 2 for FDR classification task
0:09:43.250529 INFO: Using random state 425083 for train-test-split
0:09:43.287001 INFO: Test AUC: 0.493
0:09:43.287105 INFO: Train AUC: 0.491
0:09:43.287142 INFO: AUC difference: 0.42%
0:09:43.504538 INFO: Resetting torch num_threads to 80
0:09:43.508735 PROGRESS: === Extracted 12138 precursors and 56682 fragments ===
0:09:43.509141 INFO: === FDR correction performed with classifier version -1 ===
0:09:43.509644 PROGRESS: ============================= Precursor FDR =============================
0:09:43.509744 PROGRESS: Total precursors accumulated: 2
0:09:43.509821 PROGRESS: Target precursors: 2 (100.00%)
0:09:43.509888 PROGRESS: Decoy precursors: 0 (0.00%)
0:09:43.509951 PROGRESS: 
0:09:43.510013 PROGRESS: Precursor Summary:
0:09:43.510986 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:09:43.511085 PROGRESS: 
0:09:43.511156 PROGRESS: Protein Summary:
0:09:43.512216 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:09:43.512320 PROGRESS: =========================================================================
0:09:43.512641 INFO: Target number of precursors not reached yet.
0:09:43.594255 INFO: Starting optimization step 5.
0:09:43.594498 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:09:43.594606 INFO: Using ng extraction backend
0:09:43.594691 PROGRESS: Extracting batch of 12663 precursors
0:09:43.618034 INFO: === Search parameters used ===
0:09:43.618215 INFO: rt_error       : 805.6019897460938
0:09:43.618287 INFO: mobility_error : 0.1
0:09:43.618361 INFO: num_candidates : 1
0:09:43.618424 INFO: ms1_error      : 30
0:09:43.618486 INFO: ms2_error      : 30
0:09:43.618547 INFO: fwhm_rt        : 5
0:09:43.618607 INFO: quant_window   : 3
0:09:43.618665 INFO: ==============================================
0:09:43.756986 INFO: performing precursor FDR with 40 features
0:09:43.757110 INFO: Decoy channel: -1
0:09:43.757146 INFO: Competetive: True
0:09:43.767838 INFO: Setting torch num_threads to 2 for FDR classification task
0:09:43.773518 INFO: Using random state 234953 for train-test-split
0:09:43.963134 INFO: Test AUC: 0.526
0:09:43.963249 INFO: Train AUC: 0.534
0:09:43.963279 INFO: AUC difference: 1.52%
0:09:44.182528 INFO: Resetting torch num_threads to 80
0:09:44.188614 PROGRESS: === Extracted 24633 precursors and 115281 fragments ===
0:09:44.189042 INFO: === FDR correction performed with classifier version -1 ===
0:09:44.189544 PROGRESS: ============================= Precursor FDR =============================
0:09:44.189628 PROGRESS: Total precursors accumulated: 19
0:09:44.189687 PROGRESS: Target precursors: 19 (100.00%)
0:09:44.189737 PROGRESS: Decoy precursors: 0 (0.00%)
0:09:44.189781 PROGRESS: 
0:09:44.189824 PROGRESS: Precursor Summary:
0:09:44.190760 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
0:09:44.190845 PROGRESS: 
0:09:44.190899 PROGRESS: Protein Summary:
0:09:44.191924 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
0:09:44.192008 PROGRESS: =========================================================================
0:09:44.192444 INFO: Target number of precursors not reached yet.
0:09:44.294568 INFO: Starting optimization step 6.
0:09:44.294805 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:09:44.294890 INFO: Using ng extraction backend
0:09:44.294953 PROGRESS: Extracting batch of 25339 precursors
0:09:44.341693 INFO: === Search parameters used ===
0:09:44.341920 INFO: rt_error       : 805.6019897460938
0:09:44.341974 INFO: mobility_error : 0.1
0:09:44.342019 INFO: num_candidates : 1
0:09:44.342062 INFO: ms1_error      : 30
0:09:44.342103 INFO: ms2_error      : 30
0:09:44.342142 INFO: fwhm_rt        : 5
0:09:44.342181 INFO: quant_window   : 3
0:09:44.342219 INFO: ==============================================
0:09:44.550693 INFO: performing precursor FDR with 40 features
0:09:44.550817 INFO: Decoy channel: -1
0:09:44.550844 INFO: Competetive: True
0:09:44.569713 INFO: Setting torch num_threads to 2 for FDR classification task
0:09:44.581697 INFO: Using random state 604291 for train-test-split
0:09:45.013154 INFO: Test AUC: 0.558
0:09:45.013265 INFO: Train AUC: 0.571
0:09:45.013293 INFO: AUC difference: 2.17%
0:09:45.254865 INFO: Resetting torch num_threads to 80
0:09:45.264385 PROGRESS: === Extracted 49665 precursors and 231545 fragments ===
0:09:45.264856 INFO: === FDR correction performed with classifier version -1 ===
0:09:45.265366 PROGRESS: ============================= Precursor FDR =============================
0:09:45.265461 PROGRESS: Total precursors accumulated: 145
0:09:45.265520 PROGRESS: Target precursors: 144 (99.31%)
0:09:45.265568 PROGRESS: Decoy precursors: 1 (0.69%)
0:09:45.265612 PROGRESS: 
0:09:45.265655 PROGRESS: Precursor Summary:
0:09:45.266544 PROGRESS: Channel   0:	 0.050 FDR:   144; 0.010 FDR:   144; 0.001 FDR:   136
0:09:45.266647 PROGRESS: 
0:09:45.266703 PROGRESS: Protein Summary:
0:09:45.267700 PROGRESS: Channel   0:	 0.050 FDR:   139; 0.010 FDR:   139; 0.001 FDR:   132
0:09:45.267788 PROGRESS: =========================================================================
0:09:45.268444 INFO: Target number of precursors not reached yet.
0:09:45.402131 INFO: Starting optimization step 7.
0:09:45.402359 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:09:45.402441 INFO: Using ng extraction backend
0:09:45.402515 PROGRESS: Extracting batch of 50691 precursors
0:09:45.490084 INFO: === Search parameters used ===
0:09:45.490329 INFO: rt_error       : 805.6019897460938
0:09:45.490386 INFO: mobility_error : 0.1
0:09:45.490434 INFO: num_candidates : 1
0:09:45.490476 INFO: ms1_error      : 30
0:09:45.490519 INFO: ms2_error      : 30
0:09:45.490559 INFO: fwhm_rt        : 5
0:09:45.490601 INFO: quant_window   : 3
0:09:45.490640 INFO: ==============================================
0:09:45.842666 INFO: performing precursor FDR with 40 features
0:09:45.842773 INFO: Decoy channel: -1
0:09:45.842799 INFO: Competetive: True
0:09:45.878515 INFO: Setting torch num_threads to 2 for FDR classification task
0:09:45.902646 INFO: Using random state 400569 for train-test-split
0:09:47.392214 INFO: Test AUC: 0.581
0:09:47.392330 INFO: Train AUC: 0.598
0:09:47.392361 INFO: AUC difference: 2.97%
0:09:47.641626 INFO: Resetting torch num_threads to 80
0:09:47.659188 PROGRESS: === Extracted 99812 precursors and 465578 fragments ===
0:09:47.659754 INFO: === FDR correction performed with classifier version -1 ===
0:09:47.660299 PROGRESS: ============================= Precursor FDR =============================
0:09:47.660400 PROGRESS: Total precursors accumulated: 292
0:09:47.660463 PROGRESS: Target precursors: 290 (99.32%)
0:09:47.660515 PROGRESS: Decoy precursors: 2 (0.68%)
0:09:47.660562 PROGRESS: 
0:09:47.660608 PROGRESS: Precursor Summary:
0:09:47.661601 PROGRESS: Channel   0:	 0.050 FDR:   290; 0.010 FDR:   290; 0.001 FDR:   252
0:09:47.661694 PROGRESS: 
0:09:47.661752 PROGRESS: Protein Summary:
0:09:47.662836 PROGRESS: Channel   0:	 0.050 FDR:   273; 0.010 FDR:   273; 0.001 FDR:   239
0:09:47.662926 PROGRESS: =========================================================================
0:09:47.664427 INFO: Target number of precursors reached.
0:09:47.699743 INFO: fragments_df: keeping 2435 of 465578 [sum(precursor_idx_mask)=3114 sum(mass_error_mask)=465578 stop_rank=2435
0:09:47.903150 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:09:48.007384 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:09:48.278756 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:09:48.279154 INFO: Using score_cutoff 14.007738326454163 (fac=0.99, q=1)
0:09:48.279433 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:09:48.279511 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:09:48.279565 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.007738326454163
0:09:48.279617 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:09:48.340925 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:09:48.476671 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:09:48.476895 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:09:48.477014 INFO: Starting optimization step 8.
0:09:48.477100 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:09:48.477188 INFO: Using ng extraction backend
0:09:48.477268 PROGRESS: Extracting batch of 100984 precursors
0:09:48.649345 INFO: === Search parameters used ===
0:09:48.649630 INFO: rt_error       : 805.6019897460938
0:09:48.649707 INFO: mobility_error : 0.1
0:09:48.649770 INFO: num_candidates : 3
0:09:48.649828 INFO: ms1_error      : 30
0:09:48.649885 INFO: ms2_error      : 30
0:09:48.649941 INFO: fwhm_rt        : 3.0
0:09:48.649995 INFO: quant_window   : 3
0:09:48.650052 INFO: ==============================================
0:09:49.981242 INFO: performing precursor FDR with 40 features
0:09:49.981360 INFO: Decoy channel: -1
0:09:49.981385 INFO: Competetive: True
0:09:50.059318 INFO: Setting torch num_threads to 2 for FDR classification task
0:09:50.167320 INFO: Using random state 615914 for train-test-split
0:09:54.087226 INFO: Test AUC: 0.589
0:09:54.087345 INFO: Train AUC: 0.607
0:09:54.087378 INFO: AUC difference: 2.82%
0:09:54.396639 INFO: Resetting torch num_threads to 80
0:09:54.406769 PROGRESS: === Extracted 299609 precursors and 1368075 fragments ===
0:09:54.407146 INFO: === FDR correction performed with classifier version 7 ===
0:09:54.407597 PROGRESS: ============================= Precursor FDR =============================
0:09:54.407683 PROGRESS: Total precursors accumulated: 213
0:09:54.407742 PROGRESS: Target precursors: 211 (99.06%)
0:09:54.407801 PROGRESS: Decoy precursors: 2 (0.94%)
0:09:54.407852 PROGRESS: 
0:09:54.407896 PROGRESS: Precursor Summary:
0:09:54.408763 PROGRESS: Channel   0:	 0.050 FDR:   211; 0.010 FDR:   211; 0.001 FDR:   138
0:09:54.408849 PROGRESS: 
0:09:54.408902 PROGRESS: Protein Summary:
0:09:54.409917 PROGRESS: Channel   0:	 0.050 FDR:   202; 0.010 FDR:   202; 0.001 FDR:   133
0:09:54.410016 PROGRESS: =========================================================================
0:09:54.414356 INFO: Target number of precursors reached.
0:09:54.504250 INFO: fragments_df: keeping 2670 of 1368075 [sum(precursor_idx_mask)=4902 sum(mass_error_mask)=1368075 stop_rank=2670
0:09:54.711286 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:09:54.825451 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:09:55.161765 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:09:55.162170 INFO: Using score_cutoff 15.115428889274597 (fac=0.99, q=1)
0:09:55.162448 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:09:55.162525 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:09:55.162579 INFO: Updating optimization_manager: score_cutoff        : 14.007738326454163 -> 15.115428889274597
0:09:55.162633 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:09:55.224943 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:09:55.364925 INFO: === checking if optimization conditions were reached ===
0:09:55.366696 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:09:55.366794 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:09:55.366858 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:09:55.366916 INFO: ==============================================
0:09:55.366978 INFO: Starting optimization step 9.
0:09:55.367033 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:09:55.367090 INFO: Using ng extraction backend
0:09:55.367146 PROGRESS: Extracting batch of 100984 precursors
0:09:55.539888 INFO: === Search parameters used ===
0:09:55.540161 INFO: rt_error       : 805.6019897460938
0:09:55.540219 INFO: mobility_error : 0.1
0:09:55.540266 INFO: num_candidates : 3
0:09:55.540309 INFO: ms1_error      : 30
0:09:55.540352 INFO: ms2_error      : 10.0
0:09:55.540394 INFO: fwhm_rt        : 3.0
0:09:55.540435 INFO: quant_window   : 3
0:09:55.540475 INFO: ==============================================
0:09:56.816903 INFO: performing precursor FDR with 40 features
0:09:56.817026 INFO: Decoy channel: -1
0:09:56.817053 INFO: Competetive: True
0:09:56.893327 INFO: Setting torch num_threads to 2 for FDR classification task
0:09:56.995989 INFO: Using random state 168754 for train-test-split
0:10:01.110191 INFO: Test AUC: 0.597
0:10:01.110313 INFO: Train AUC: 0.605
0:10:01.110346 INFO: AUC difference: 1.36%
0:10:01.422112 INFO: Resetting torch num_threads to 80
0:10:01.432971 PROGRESS: === Extracted 302155 precursors and 1604431 fragments ===
0:10:01.433360 INFO: === FDR correction performed with classifier version 8 ===
0:10:01.433851 PROGRESS: ============================= Precursor FDR =============================
0:10:01.433939 PROGRESS: Total precursors accumulated: 558
0:10:01.434005 PROGRESS: Target precursors: 553 (99.10%)
0:10:01.434057 PROGRESS: Decoy precursors: 5 (0.90%)
0:10:01.434101 PROGRESS: 
0:10:01.434144 PROGRESS: Precursor Summary:
0:10:01.435104 PROGRESS: Channel   0:	 0.050 FDR:   553; 0.010 FDR:   553; 0.001 FDR:   381
0:10:01.435190 PROGRESS: 
0:10:01.435244 PROGRESS: Protein Summary:
0:10:01.436407 PROGRESS: Channel   0:	 0.050 FDR:   519; 0.010 FDR:   519; 0.001 FDR:   355
0:10:01.436498 PROGRESS: =========================================================================
0:10:01.441077 INFO: Target number of precursors reached.
0:10:01.546290 INFO: fragments_df: keeping 5000 of 1604431 [sum(precursor_idx_mask)=12950 sum(mass_error_mask)=1604431 stop_rank=5000
0:10:01.735689 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:10:01.856695 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:10:02.501669 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:10:02.502076 INFO: Using score_cutoff 9.150416626739501 (fac=0.99, q=1)
0:10:02.502357 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:10:02.502444 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:10:02.502499 INFO: Updating optimization_manager: score_cutoff        : 15.115428889274597 -> 9.150416626739501
0:10:02.502553 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:10:02.533199 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:10:02.604599 INFO: === checking if optimization conditions were reached ===
0:10:02.606948 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:10:02.607061 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:10:02.607134 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:10:02.607200 INFO: ==============================================
0:10:02.607273 PROGRESS: Optimization finished for ms2_error.
0:10:02.755099 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:10:02.785886 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:10:02.851407 INFO: Starting optimization step 0.
0:10:02.851651 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:10:02.851739 INFO: Using ng extraction backend
0:10:02.851811 PROGRESS: Extracting batch of 50293 precursors
0:10:02.941843 INFO: === Search parameters used ===
0:10:02.942100 INFO: rt_error       : 805.6019897460938
0:10:02.942154 INFO: mobility_error : 0.1
0:10:02.942199 INFO: num_candidates : 3
0:10:02.942240 INFO: ms1_error      : 30
0:10:02.942280 INFO: ms2_error      : 10.0
0:10:02.942320 INFO: fwhm_rt        : 3.0
0:10:02.942360 INFO: quant_window   : 3
0:10:02.942399 INFO: ==============================================
0:10:03.581136 INFO: performing precursor FDR with 40 features
0:10:03.581250 INFO: Decoy channel: -1
0:10:03.581277 INFO: Competetive: True
0:10:03.624380 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:03.676469 INFO: Using random state 158836 for train-test-split
0:10:05.768440 INFO: Test AUC: 0.602
0:10:05.768561 INFO: Train AUC: 0.615
0:10:05.768593 INFO: AUC difference: 2.21%
0:10:06.028421 INFO: Resetting torch num_threads to 80
0:10:06.043626 PROGRESS: === Extracted 150472 precursors and 799120 fragments ===
0:10:06.043978 INFO: === FDR correction performed with classifier version 9 ===
0:10:06.044440 PROGRESS: ============================= Precursor FDR =============================
0:10:06.044524 PROGRESS: Total precursors accumulated: 259
0:10:06.044580 PROGRESS: Target precursors: 257 (99.23%)
0:10:06.044629 PROGRESS: Decoy precursors: 2 (0.77%)
0:10:06.044673 PROGRESS: 
0:10:06.044715 PROGRESS: Precursor Summary:
0:10:06.045595 PROGRESS: Channel   0:	 0.050 FDR:   257; 0.010 FDR:   257; 0.001 FDR:    27
0:10:06.045682 PROGRESS: 
0:10:06.045735 PROGRESS: Protein Summary:
0:10:06.046738 PROGRESS: Channel   0:	 0.050 FDR:   250; 0.010 FDR:   250; 0.001 FDR:    27
0:10:06.046824 PROGRESS: =========================================================================
0:10:06.048940 INFO: Target number of precursors reached.
0:10:06.103782 INFO: fragments_df: keeping 2896 of 799120 [sum(precursor_idx_mask)=6037 sum(mass_error_mask)=799120 stop_rank=2896
0:10:06.240464 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:10:06.331024 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:10:06.645351 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:10:06.645780 INFO: Using score_cutoff 8.096874393081665 (fac=0.99, q=1)
0:10:06.646072 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:10:06.646164 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:10:06.646222 INFO: Updating optimization_manager: score_cutoff        : 9.150416626739501 -> 8.096874393081665
0:10:06.646278 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:10:06.677324 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:10:06.744654 INFO: === checking if optimization conditions were reached ===
0:10:06.744931 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:10:06.746995 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 315.08319067025604
0:10:06.747126 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 315.0832.
0:10:06.747202 INFO: ==============================================
0:10:06.747279 INFO: Starting optimization step 1.
0:10:06.747342 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:10:06.747411 INFO: Using ng extraction backend
0:10:06.747476 PROGRESS: Extracting batch of 50293 precursors
0:10:06.837638 INFO: === Search parameters used ===
0:10:06.837896 INFO: rt_error       : 315.08319067025604
0:10:06.837951 INFO: mobility_error : 0.1
0:10:06.837996 INFO: num_candidates : 3
0:10:06.838039 INFO: ms1_error      : 30
0:10:06.838082 INFO: ms2_error      : 10.0
0:10:06.838123 INFO: fwhm_rt        : 3.0
0:10:06.838174 INFO: quant_window   : 3
0:10:06.838215 INFO: ==============================================
0:10:07.444418 INFO: performing precursor FDR with 40 features
0:10:07.444533 INFO: Decoy channel: -1
0:10:07.444558 INFO: Competetive: True
0:10:07.493511 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:07.532831 INFO: Using random state 158836 for train-test-split
0:10:09.656186 INFO: Test AUC: 0.592
0:10:09.656307 INFO: Train AUC: 0.615
0:10:09.656339 INFO: AUC difference: 3.73%
0:10:10.385245 INFO: Resetting torch num_threads to 80
0:10:10.395907 PROGRESS: === Extracted 150249 precursors and 765893 fragments ===
0:10:10.396255 INFO: === FDR correction performed with classifier version 9 ===
0:10:10.396716 PROGRESS: ============================= Precursor FDR =============================
0:10:10.396798 PROGRESS: Total precursors accumulated: 220
0:10:10.396855 PROGRESS: Target precursors: 218 (99.09%)
0:10:10.396904 PROGRESS: Decoy precursors: 2 (0.91%)
0:10:10.396948 PROGRESS: 
0:10:10.396998 PROGRESS: Precursor Summary:
0:10:10.397885 PROGRESS: Channel   0:	 0.050 FDR:   218; 0.010 FDR:   218; 0.001 FDR:   196
0:10:10.397970 PROGRESS: 
0:10:10.398022 PROGRESS: Protein Summary:
0:10:10.399039 PROGRESS: Channel   0:	 0.050 FDR:   212; 0.010 FDR:   212; 0.001 FDR:   191
0:10:10.399123 PROGRESS: =========================================================================
0:10:10.401092 INFO: Target number of precursors reached.
0:10:10.450944 INFO: fragments_df: keeping 2628 of 765893 [sum(precursor_idx_mask)=5291 sum(mass_error_mask)=765893 stop_rank=2628
0:10:10.622988 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:10:10.718359 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:10:11.031203 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:10:11.031852 INFO: Using score_cutoff 13.602173363113403 (fac=0.99, q=1)
0:10:11.032213 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:10:11.032292 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:10:11.032347 INFO: Updating optimization_manager: score_cutoff        : 8.096874393081665 -> 13.602173363113403
0:10:11.032415 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:10:11.063869 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:10:11.131126 INFO: === checking if optimization conditions were reached ===
0:10:11.131391 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:10:11.133758 INFO: Updating optimization_manager: rt_error            : 315.08319067025604 -> 96.74416793025317
0:10:11.133872 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 96.7442.
0:10:11.133947 INFO: ==============================================
0:10:11.134028 INFO: Starting optimization step 2.
0:10:11.134097 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:10:11.134179 INFO: Using ng extraction backend
0:10:11.134258 PROGRESS: Extracting batch of 50293 precursors
0:10:11.223885 INFO: === Search parameters used ===
0:10:11.224136 INFO: rt_error       : 96.74416793025317
0:10:11.224191 INFO: mobility_error : 0.1
0:10:11.224252 INFO: num_candidates : 3
0:10:11.224295 INFO: ms1_error      : 30
0:10:11.224341 INFO: ms2_error      : 10.0
0:10:11.224382 INFO: fwhm_rt        : 3.0
0:10:11.224422 INFO: quant_window   : 3
0:10:11.224459 INFO: ==============================================
0:10:11.797096 INFO: performing precursor FDR with 40 features
0:10:11.797257 INFO: Decoy channel: -1
0:10:11.797285 INFO: Competetive: True
0:10:11.835329 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:11.885098 INFO: Using random state 158836 for train-test-split
0:10:13.923379 INFO: Test AUC: 0.594
0:10:13.923511 INFO: Train AUC: 0.608
0:10:13.923541 INFO: AUC difference: 2.28%
0:10:14.186328 INFO: Resetting torch num_threads to 80
0:10:14.192952 PROGRESS: === Extracted 146531 precursors and 583433 fragments ===
0:10:14.193346 INFO: === FDR correction performed with classifier version 9 ===
0:10:14.193815 PROGRESS: ============================= Precursor FDR =============================
0:10:14.193900 PROGRESS: Total precursors accumulated: 306
0:10:14.193957 PROGRESS: Target precursors: 303 (99.02%)
0:10:14.194007 PROGRESS: Decoy precursors: 3 (0.98%)
0:10:14.194051 PROGRESS: 
0:10:14.194095 PROGRESS: Precursor Summary:
0:10:14.194988 PROGRESS: Channel   0:	 0.050 FDR:   303; 0.010 FDR:   303; 0.001 FDR:   269
0:10:14.195074 PROGRESS: 
0:10:14.195127 PROGRESS: Protein Summary:
0:10:14.196198 PROGRESS: Channel   0:	 0.050 FDR:   293; 0.010 FDR:   293; 0.001 FDR:   261
0:10:14.196290 PROGRESS: =========================================================================
0:10:14.198281 INFO: Target number of precursors reached.
0:10:14.238725 INFO: fragments_df: keeping 3216 of 583433 [sum(precursor_idx_mask)=6849 sum(mass_error_mask)=583433 stop_rank=3216
0:10:14.376697 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:10:14.494952 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:10:14.914689 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:10:14.915095 INFO: Using score_cutoff 11.502066223526 (fac=0.99, q=1)
0:10:14.915390 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:10:14.915468 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:10:14.915522 INFO: Updating optimization_manager: score_cutoff        : 13.602173363113403 -> 11.502066223526
0:10:14.915576 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:10:14.945612 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:10:15.008034 INFO: === checking if optimization conditions were reached ===
0:10:15.008295 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:10:15.010666 INFO: Updating optimization_manager: rt_error            : 96.74416793025317 -> 80.07326712398644
0:10:15.010780 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 80.0733.
0:10:15.010854 INFO: ==============================================
0:10:15.010931 INFO: Starting optimization step 3.
0:10:15.010998 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:10:15.011073 INFO: Using ng extraction backend
0:10:15.011141 PROGRESS: Extracting batch of 50293 precursors
0:10:15.103244 INFO: === Search parameters used ===
0:10:15.103513 INFO: rt_error       : 80.07326712398644
0:10:15.103573 INFO: mobility_error : 0.1
0:10:15.103636 INFO: num_candidates : 3
0:10:15.103681 INFO: ms1_error      : 30
0:10:15.103722 INFO: ms2_error      : 10.0
0:10:15.103761 INFO: fwhm_rt        : 3.0
0:10:15.103800 INFO: quant_window   : 3
0:10:15.103838 INFO: ==============================================
0:10:15.673905 INFO: performing precursor FDR with 40 features
0:10:15.674018 INFO: Decoy channel: -1
0:10:15.674042 INFO: Competetive: True
0:10:15.710260 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:15.759208 INFO: Using random state 158836 for train-test-split
0:10:17.776015 INFO: Test AUC: 0.589
0:10:17.776132 INFO: Train AUC: 0.610
0:10:17.776164 INFO: AUC difference: 3.52%
0:10:18.036525 INFO: Resetting torch num_threads to 80
0:10:18.042736 PROGRESS: === Extracted 145600 precursors and 565981 fragments ===
0:10:18.043082 INFO: === FDR correction performed with classifier version 9 ===
0:10:18.043539 PROGRESS: ============================= Precursor FDR =============================
0:10:18.043624 PROGRESS: Total precursors accumulated: 321
0:10:18.043683 PROGRESS: Target precursors: 318 (99.07%)
0:10:18.043732 PROGRESS: Decoy precursors: 3 (0.93%)
0:10:18.043779 PROGRESS: 
0:10:18.043822 PROGRESS: Precursor Summary:
0:10:18.044749 PROGRESS: Channel   0:	 0.050 FDR:   318; 0.010 FDR:   318; 0.001 FDR:   286
0:10:18.044836 PROGRESS: 
0:10:18.044889 PROGRESS: Protein Summary:
0:10:18.045983 PROGRESS: Channel   0:	 0.050 FDR:   306; 0.010 FDR:   306; 0.001 FDR:   279
0:10:18.046076 PROGRESS: =========================================================================
0:10:18.048033 INFO: Target number of precursors reached.
0:10:18.086163 INFO: fragments_df: keeping 3256 of 565981 [sum(precursor_idx_mask)=7058 sum(mass_error_mask)=565981 stop_rank=3256
0:10:18.221562 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:10:18.330522 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:10:18.687712 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:10:18.688118 INFO: Using score_cutoff 9.111514665412903 (fac=0.99, q=1)
0:10:18.688397 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:10:18.688474 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:10:18.688528 INFO: Updating optimization_manager: score_cutoff        : 11.502066223526 -> 9.111514665412903
0:10:18.688581 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:10:18.719450 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:10:18.786370 INFO: === checking if optimization conditions were reached ===
0:10:18.786592 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:10:18.788538 INFO: Updating optimization_manager: rt_error            : 80.07326712398644 -> 69.59437761993004
0:10:18.788636 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 69.5944.
0:10:18.788702 INFO: ==============================================
0:10:18.788769 INFO: Starting optimization step 4.
0:10:18.788824 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:10:18.788884 INFO: Using ng extraction backend
0:10:18.788940 PROGRESS: Extracting batch of 50293 precursors
0:10:18.875863 INFO: === Search parameters used ===
0:10:18.876130 INFO: rt_error       : 69.59437761993004
0:10:18.876185 INFO: mobility_error : 0.1
0:10:18.876231 INFO: num_candidates : 3
0:10:18.876274 INFO: ms1_error      : 30
0:10:18.876315 INFO: ms2_error      : 10.0
0:10:18.876356 INFO: fwhm_rt        : 3.0
0:10:18.876395 INFO: quant_window   : 3
0:10:18.876433 INFO: ==============================================
0:10:19.436278 INFO: performing precursor FDR with 40 features
0:10:19.436391 INFO: Decoy channel: -1
0:10:19.436417 INFO: Competetive: True
0:10:19.473539 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:19.522315 INFO: Using random state 158836 for train-test-split
0:10:21.452025 INFO: Test AUC: 0.589
0:10:21.452141 INFO: Train AUC: 0.611
0:10:21.452171 INFO: AUC difference: 3.69%
0:10:21.713958 INFO: Resetting torch num_threads to 80
0:10:21.720210 PROGRESS: === Extracted 144898 precursors and 556932 fragments ===
0:10:21.720551 INFO: === FDR correction performed with classifier version 9 ===
0:10:21.721011 PROGRESS: ============================= Precursor FDR =============================
0:10:21.721098 PROGRESS: Total precursors accumulated: 335
0:10:21.721155 PROGRESS: Target precursors: 332 (99.10%)
0:10:21.721205 PROGRESS: Decoy precursors: 3 (0.90%)
0:10:21.721247 PROGRESS: 
0:10:21.721289 PROGRESS: Precursor Summary:
0:10:21.722171 PROGRESS: Channel   0:	 0.050 FDR:   332; 0.010 FDR:   332; 0.001 FDR:   306
0:10:21.722257 PROGRESS: 
0:10:21.722310 PROGRESS: Protein Summary:
0:10:21.723388 PROGRESS: Channel   0:	 0.050 FDR:   321; 0.010 FDR:   321; 0.001 FDR:   295
0:10:21.723476 PROGRESS: =========================================================================
0:10:21.725378 INFO: Target number of precursors reached.
0:10:21.763913 INFO: fragments_df: keeping 3260 of 556932 [sum(precursor_idx_mask)=7015 sum(mass_error_mask)=556932 stop_rank=3260
0:10:21.903071 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:10:22.005167 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:10:22.365615 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:10:22.366019 INFO: Using score_cutoff 3.5859145329952242 (fac=0.99, q=1)
0:10:22.366297 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:10:22.366374 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:10:22.366427 INFO: Updating optimization_manager: score_cutoff        : 9.111514665412903 -> 3.5859145329952242
0:10:22.366479 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:10:22.397702 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:10:22.466618 INFO: === checking if optimization conditions were reached ===
0:10:22.466846 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:10:22.468804 INFO: Updating optimization_manager: rt_error            : 69.59437761993004 -> 51.14552280869507
0:10:22.468905 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 51.1455.
0:10:22.468970 INFO: ==============================================
0:10:22.469055 INFO: Starting optimization step 5.
0:10:22.469115 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:10:22.469179 INFO: Using ng extraction backend
0:10:22.469234 PROGRESS: Extracting batch of 50293 precursors
0:10:22.556042 INFO: === Search parameters used ===
0:10:22.556285 INFO: rt_error       : 51.14552280869507
0:10:22.556339 INFO: mobility_error : 0.1
0:10:22.556383 INFO: num_candidates : 3
0:10:22.556427 INFO: ms1_error      : 30
0:10:22.556468 INFO: ms2_error      : 10.0
0:10:22.556507 INFO: fwhm_rt        : 3.0
0:10:22.556548 INFO: quant_window   : 3
0:10:22.556586 INFO: ==============================================
0:10:23.090006 INFO: performing precursor FDR with 40 features
0:10:23.090122 INFO: Decoy channel: -1
0:10:23.090149 INFO: Competetive: True
0:10:23.124808 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:23.158032 INFO: Using random state 158836 for train-test-split
0:10:25.046063 INFO: Test AUC: 0.597
0:10:25.046178 INFO: Train AUC: 0.609
0:10:25.046209 INFO: AUC difference: 1.88%
0:10:25.304511 INFO: Resetting torch num_threads to 80
0:10:25.310555 PROGRESS: === Extracted 136639 precursors and 499774 fragments ===
0:10:25.310899 INFO: === FDR correction performed with classifier version 9 ===
0:10:25.311344 PROGRESS: ============================= Precursor FDR =============================
0:10:25.311430 PROGRESS: Total precursors accumulated: 321
0:10:25.311489 PROGRESS: Target precursors: 318 (99.07%)
0:10:25.311540 PROGRESS: Decoy precursors: 3 (0.93%)
0:10:25.311586 PROGRESS: 
0:10:25.311629 PROGRESS: Precursor Summary:
0:10:25.312518 PROGRESS: Channel   0:	 0.050 FDR:   318; 0.010 FDR:   318; 0.001 FDR:   234
0:10:25.312605 PROGRESS: 
0:10:25.312661 PROGRESS: Protein Summary:
0:10:25.313737 PROGRESS: Channel   0:	 0.050 FDR:   308; 0.010 FDR:   308; 0.001 FDR:   228
0:10:25.313834 PROGRESS: =========================================================================
0:10:25.315605 INFO: Target number of precursors reached.
0:10:25.349568 INFO: fragments_df: keeping 3054 of 499774 [sum(precursor_idx_mask)=6424 sum(mass_error_mask)=499774 stop_rank=3054
0:10:25.485531 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:10:25.588038 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:10:25.921257 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:10:25.921661 INFO: Using score_cutoff 11.540280852699281 (fac=0.99, q=1)
0:10:25.921953 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:10:25.922033 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:10:25.922088 INFO: Updating optimization_manager: score_cutoff        : 3.5859145329952242 -> 11.540280852699281
0:10:25.922142 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:10:25.953316 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:10:26.018731 INFO: === checking if optimization conditions were reached ===
0:10:26.018955 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:10:26.020889 INFO: Updating optimization_manager: rt_error            : 51.14552280869507 -> 35.44566579282542
0:10:26.021000 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 35.4457.
0:10:26.021069 INFO: ==============================================
0:10:26.021138 INFO: Starting optimization step 6.
0:10:26.021197 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:10:26.021271 INFO: Using ng extraction backend
0:10:26.021332 PROGRESS: Extracting batch of 50293 precursors
0:10:26.110817 INFO: === Search parameters used ===
0:10:26.111071 INFO: rt_error       : 35.44566579282542
0:10:26.111124 INFO: mobility_error : 0.1
0:10:26.111169 INFO: num_candidates : 3
0:10:26.111213 INFO: ms1_error      : 30
0:10:26.111253 INFO: ms2_error      : 10.0
0:10:26.111295 INFO: fwhm_rt        : 3.0
0:10:26.111334 INFO: quant_window   : 3
0:10:26.111372 INFO: ==============================================
0:10:26.631098 INFO: performing precursor FDR with 40 features
0:10:26.631216 INFO: Decoy channel: -1
0:10:26.631241 INFO: Competetive: True
0:10:26.664528 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:26.709009 INFO: Using random state 158836 for train-test-split
0:10:28.404369 INFO: Test AUC: 0.593
0:10:28.404486 INFO: Train AUC: 0.612
0:10:28.404518 INFO: AUC difference: 3.11%
0:10:28.660180 INFO: Resetting torch num_threads to 80
0:10:28.666150 PROGRESS: === Extracted 134196 precursors and 489262 fragments ===
0:10:28.666489 INFO: === FDR correction performed with classifier version 9 ===
0:10:28.666936 PROGRESS: ============================= Precursor FDR =============================
0:10:28.667021 PROGRESS: Total precursors accumulated: 328
0:10:28.667078 PROGRESS: Target precursors: 325 (99.09%)
0:10:28.667128 PROGRESS: Decoy precursors: 3 (0.91%)
0:10:28.667173 PROGRESS: 
0:10:28.667217 PROGRESS: Precursor Summary:
0:10:28.668100 PROGRESS: Channel   0:	 0.050 FDR:   325; 0.010 FDR:   325; 0.001 FDR:   274
0:10:28.668186 PROGRESS: 
0:10:28.668240 PROGRESS: Protein Summary:
0:10:28.669346 PROGRESS: Channel   0:	 0.050 FDR:   316; 0.010 FDR:   316; 0.001 FDR:   266
0:10:28.669435 PROGRESS: =========================================================================
0:10:28.671152 INFO: Target number of precursors reached.
0:10:28.705254 INFO: fragments_df: keeping 3023 of 489262 [sum(precursor_idx_mask)=6387 sum(mass_error_mask)=489262 stop_rank=3023
0:10:28.840823 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:10:28.944528 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:10:29.277016 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:10:29.277437 INFO: Using score_cutoff 7.810968594932557 (fac=0.99, q=1)
0:10:29.277715 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:10:29.277793 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:10:29.277845 INFO: Updating optimization_manager: score_cutoff        : 11.540280852699281 -> 7.810968594932557
0:10:29.277899 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:10:29.309360 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:10:29.378632 INFO: === checking if optimization conditions were reached ===
0:10:29.378860 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:10:29.380819 INFO: Updating optimization_manager: rt_error            : 35.44566579282542 -> 33.40030908330267
0:10:29.380922 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 33.4003.
0:10:29.380986 INFO: ==============================================
0:10:29.381078 INFO: Starting optimization step 7.
0:10:29.381138 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:10:29.381199 INFO: Using ng extraction backend
0:10:29.381254 PROGRESS: Extracting batch of 50293 precursors
0:10:29.468012 INFO: === Search parameters used ===
0:10:29.468254 INFO: rt_error       : 33.40030908330267
0:10:29.468306 INFO: mobility_error : 0.1
0:10:29.468353 INFO: num_candidates : 3
0:10:29.468397 INFO: ms1_error      : 30
0:10:29.468437 INFO: ms2_error      : 10.0
0:10:29.468477 INFO: fwhm_rt        : 3.0
0:10:29.468518 INFO: quant_window   : 3
0:10:29.468557 INFO: ==============================================
0:10:29.992898 INFO: performing precursor FDR with 40 features
0:10:29.993023 INFO: Decoy channel: -1
0:10:29.993050 INFO: Competetive: True
0:10:30.029953 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:30.072034 INFO: Using random state 158836 for train-test-split
0:10:31.929535 INFO: Test AUC: 0.589
0:10:31.929651 INFO: Train AUC: 0.613
0:10:31.929682 INFO: AUC difference: 3.81%
0:10:32.185647 INFO: Resetting torch num_threads to 80
0:10:32.191683 PROGRESS: === Extracted 134152 precursors and 488943 fragments ===
0:10:32.192029 INFO: === FDR correction performed with classifier version 9 ===
0:10:32.192474 PROGRESS: ============================= Precursor FDR =============================
0:10:32.192558 PROGRESS: Total precursors accumulated: 339
0:10:32.192613 PROGRESS: Target precursors: 336 (99.12%)
0:10:32.192661 PROGRESS: Decoy precursors: 3 (0.88%)
0:10:32.192703 PROGRESS: 
0:10:32.192743 PROGRESS: Precursor Summary:
0:10:32.193651 PROGRESS: Channel   0:	 0.050 FDR:   336; 0.010 FDR:   336; 0.001 FDR:   222
0:10:32.193745 PROGRESS: 
0:10:32.193801 PROGRESS: Protein Summary:
0:10:32.194863 PROGRESS: Channel   0:	 0.050 FDR:   328; 0.010 FDR:   328; 0.001 FDR:   217
0:10:32.194952 PROGRESS: =========================================================================
0:10:32.196731 INFO: Target number of precursors reached.
0:10:32.230915 INFO: fragments_df: keeping 3110 of 488943 [sum(precursor_idx_mask)=6635 sum(mass_error_mask)=488943 stop_rank=3110
0:10:32.367107 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:10:32.471638 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:10:32.813349 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:10:32.813757 INFO: Using score_cutoff 11.290505046844482 (fac=0.99, q=1)
0:10:32.814040 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:10:32.814119 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:10:32.814173 INFO: Updating optimization_manager: score_cutoff        : 7.810968594932557 -> 11.290505046844482
0:10:32.814226 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:10:32.845883 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:10:32.911485 INFO: === checking if optimization conditions were reached ===
0:10:32.911749 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
0:10:32.914086 INFO: Updating optimization_manager: rt_error            : 33.40030908330267 -> 33.540266812404
0:10:32.914201 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 33.5403.
0:10:32.914291 INFO: ==============================================
0:10:32.914370 INFO: Starting optimization step 8.
0:10:32.914435 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:10:32.914502 INFO: Using ng extraction backend
0:10:32.914568 PROGRESS: Extracting batch of 50293 precursors
0:10:33.002226 INFO: === Search parameters used ===
0:10:33.002490 INFO: rt_error       : 33.540266812404
0:10:33.002548 INFO: mobility_error : 0.1
0:10:33.002610 INFO: num_candidates : 3
0:10:33.002653 INFO: ms1_error      : 30
0:10:33.002693 INFO: ms2_error      : 10.0
0:10:33.002731 INFO: fwhm_rt        : 3.0
0:10:33.002769 INFO: quant_window   : 3
0:10:33.002806 INFO: ==============================================
0:10:33.524687 INFO: performing precursor FDR with 40 features
0:10:33.524816 INFO: Decoy channel: -1
0:10:33.524843 INFO: Competetive: True
0:10:33.560742 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:33.605847 INFO: Using random state 158836 for train-test-split
0:10:35.305091 INFO: Test AUC: 0.585
0:10:35.305209 INFO: Train AUC: 0.613
0:10:35.305239 INFO: AUC difference: 4.52%
0:10:35.561713 INFO: Resetting torch num_threads to 80
0:10:35.567703 PROGRESS: === Extracted 134169 precursors and 488942 fragments ===
0:10:35.568047 INFO: === FDR correction performed with classifier version 9 ===
0:10:35.568497 PROGRESS: ============================= Precursor FDR =============================
0:10:35.568583 PROGRESS: Total precursors accumulated: 314
0:10:35.568668 PROGRESS: Target precursors: 311 (99.04%)
0:10:35.568717 PROGRESS: Decoy precursors: 3 (0.96%)
0:10:35.568760 PROGRESS: 
0:10:35.568801 PROGRESS: Precursor Summary:
0:10:35.569717 PROGRESS: Channel   0:	 0.050 FDR:   311; 0.010 FDR:   311; 0.001 FDR:   290
0:10:35.569806 PROGRESS: 
0:10:35.569859 PROGRESS: Protein Summary:
0:10:35.570942 PROGRESS: Channel   0:	 0.050 FDR:   303; 0.010 FDR:   303; 0.001 FDR:   282
0:10:35.571031 PROGRESS: =========================================================================
0:10:35.572858 INFO: Target number of precursors reached.
0:10:35.607041 INFO: fragments_df: keeping 2938 of 488942 [sum(precursor_idx_mask)=6163 sum(mass_error_mask)=488942 stop_rank=2938
0:10:35.767209 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:10:35.875517 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:10:36.195646 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:10:36.196056 INFO: Using score_cutoff 11.046951730728148 (fac=0.99, q=1)
0:10:36.196334 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:10:36.196413 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:10:36.196468 INFO: Updating optimization_manager: score_cutoff        : 11.290505046844482 -> 11.046951730728148
0:10:36.196519 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:10:36.228135 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:10:36.295621 INFO: === checking if optimization conditions were reached ===
0:10:36.295879 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
0:10:36.297187 INFO: Updating optimization_manager: rt_error            : 33.540266812404 -> 33.40030908330267
0:10:36.297348 INFO: Updating optimization_manager: classifier_version  : 9 -> 17
0:10:36.297457 INFO: Updating optimization_manager: score_cutoff        : 11.046951730728148 -> 11.290505046844482
0:10:36.297555 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:10:36.297649 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:10:36.297744 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 33.4003 found after 9 searches.
0:10:36.297816 INFO: ==============================================
0:10:36.297893 PROGRESS: Optimization finished for rt_error.
0:10:36.450304 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:10:36.482239 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:10:36.582559 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:10:36.582786 PROGRESS: ==============================================
0:10:36.582864 PROGRESS: ms2_error      : 10.0000
0:10:36.582926 PROGRESS: rt_error       : 33.4003
0:10:36.582981 PROGRESS: ==============================================
0:10:36.583545 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:10:44.526721 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:11:02.275445 INFO: Using ng extraction backend
0:11:02.275910 PROGRESS: Extracting batch of 12001526 precursors
0:11:18.151801 INFO: === Search parameters used ===
0:11:18.152220 INFO: rt_error       : 33.40030908330267
0:11:18.152289 INFO: mobility_error : 0.1
0:11:18.152340 INFO: num_candidates : 3
0:11:18.152389 INFO: ms1_error      : 30
0:11:18.152431 INFO: ms2_error      : 10.0
0:11:18.152472 INFO: fwhm_rt        : 3.0
0:11:18.152511 INFO: quant_window   : 3
0:11:18.152547 INFO: ==============================================
0:11:38.992407 INFO: Removed 24614947 precursors with score below cutoff 11.290505046844482
0:11:46.608929 INFO: performing precursor FDR with 40 features
0:11:46.609066 INFO: Decoy channel: -1
0:11:46.609095 INFO: Competetive: True
0:11:47.395692 INFO: Setting torch num_threads to 2 for FDR classification task
0:11:50.522736 INFO: Using random state 433065 for train-test-split
0:13:47.756040 INFO: Test AUC: 0.625
0:13:47.756279 INFO: Train AUC: 0.626
0:13:47.756315 INFO: AUC difference: 0.22%
0:13:50.502944 INFO: Resetting torch num_threads to 80
0:13:52.058367 PROGRESS: ============================= Precursor FDR =============================
0:13:52.058650 PROGRESS: Total precursors accumulated: 73,739
0:13:52.058718 PROGRESS: Target precursors: 73,009 (99.01%)
0:13:52.058770 PROGRESS: Decoy precursors: 730 (0.99%)
0:13:52.058819 PROGRESS: 
0:13:52.058863 PROGRESS: Precursor Summary:
0:13:52.079613 PROGRESS: Channel   0:	 0.050 FDR: 73,009; 0.010 FDR: 73,009; 0.001 FDR: 49,177
0:13:52.079845 PROGRESS: 
0:13:52.079906 PROGRESS: Protein Summary:
0:13:52.107927 PROGRESS: Channel   0:	 0.050 FDR: 12,515; 0.010 FDR: 12,515; 0.001 FDR: 9,084
0:13:52.108156 PROGRESS: =========================================================================
0:13:52.163132 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/psm.parquet
0:13:52.344477 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.parquet
0:13:52.624104 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:13:53.455776 PROGRESS: 
0:13:53.455934 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant
0:13:53.456007 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/figures
0:13:53.456179 INFO: Initializing TimingManager
0:13:53.456616 INFO: Initializing RawFileManager
0:14:03.244720 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.
0:14:03.248838 INFO: Determining DIA cycle
0:14:03.263980 INFO: Found cycle with start 0.00 min and length 300.
0:14:03.422568 INFO: RT (min)            : 0.0 - 26.9
0:14:03.422662 INFO: RT duration (sec)   : 1611.2
0:14:03.422690 INFO: RT duration (min)   : 26.9
0:14:03.422714 INFO: Cycle len (scans)   : 300
0:14:03.422733 INFO: Cycle len (sec)     : 1.65
0:14:03.422753 INFO: Number of cycles    : 977
0:14:03.422771 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:14:03.422798 INFO: Creating DIA data object took: 9.966090440750122
0:14:04.052432 INFO: Creating DIA data NG object took: 0.6295323371887207
0:14:05.191321 INFO: Initializing CalibrationManager
0:14:05.191585 INFO: Setting up calibration estimators ..
0:14:05.191642 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:14:05.191719 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'}' ..
0:14:05.191820 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:14:05.191871 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:14:05.191940 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}}' ..
0:14:05.191992 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:14:05.192036 INFO: Done setting up calibration estimators.
0:14:05.192230 INFO: Initializing OptimizationManager
0:14:05.192364 INFO: initial parameter: ms1_error = 30
0:14:05.192416 INFO: initial parameter: ms2_error = 30
0:14:05.192464 INFO: initial parameter: rt_error = 805.6004638671875
0:14:05.192507 INFO: initial parameter: mobility_error = 0.1
0:14:05.192547 INFO: initial parameter: num_candidates = 1
0:14:05.192586 INFO: initial parameter: fwhm_rt = 5
0:14:05.192625 INFO: initial parameter: fwhm_mobility = 0.01
0:14:05.192665 INFO: initial parameter: score_cutoff = 0
0:14:05.192703 INFO: initial parameter: classifier_version = -1
0:14:05.192769 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:14:05.193011 INFO: FDRManager: loading saved state not requested, will be initialized.
0:14:05.193046 INFO: Initializing FDRManager
0:14:05.193081 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:14:06.392086 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:14:07.127688 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:14:07.128524 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
0:14:07.128632 PROGRESS: Starting initial search for precursors.
0:14:07.128727 INFO: Starting optimization step 0.
0:14:07.128789 PROGRESS: === Extracting elution groups 0 to 200 ===
0:14:07.128851 INFO: Using ng extraction backend
0:14:07.128912 PROGRESS: Extracting batch of 396 precursors
0:14:07.130909 INFO: === Search parameters used ===
0:14:07.131002 INFO: rt_error       : 805.6004638671875
0:14:07.131051 INFO: mobility_error : 0.1
0:14:07.131096 INFO: num_candidates : 1
0:14:07.131136 INFO: ms1_error      : 30
0:14:07.131176 INFO: ms2_error      : 30
0:14:07.131213 INFO: fwhm_rt        : 5
0:14:07.131251 INFO: quant_window   : 3
0:14:07.131290 INFO: ==============================================
0:14:07.154955 INFO: performing precursor FDR with 40 features
0:14:07.155058 INFO: Decoy channel: -1
0:14:07.155085 INFO: Competetive: True
0:14:07.155973 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:07.158085 INFO: Using random state 849126 for train-test-split
0:14:07.164539 INFO: Test AUC: 0.490
0:14:07.164593 INFO: Train AUC: 0.499
0:14:07.164623 INFO: AUC difference: 1.83%
0:14:07.374054 INFO: Resetting torch num_threads to 80
0:14:07.375322 PROGRESS: === Extracted 393 precursors and 1883 fragments ===
0:14:07.375652 INFO: === FDR correction performed with classifier version -1 ===
0:14:07.376100 PROGRESS: ============================= Precursor FDR =============================
0:14:07.376187 PROGRESS: Total precursors accumulated: 2
0:14:07.376246 PROGRESS: Target precursors: 2 (100.00%)
0:14:07.376297 PROGRESS: Decoy precursors: 0 (0.00%)
0:14:07.376342 PROGRESS: 
0:14:07.376387 PROGRESS: Precursor Summary:
0:14:07.377319 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:14:07.377408 PROGRESS: 
0:14:07.377466 PROGRESS: Protein Summary:
0:14:07.378464 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:14:07.378552 PROGRESS: =========================================================================
0:14:07.378719 INFO: Target number of precursors not reached yet.
0:14:07.442905 INFO: Starting optimization step 1.
0:14:07.443103 PROGRESS: === Extracting elution groups 200 to 600 ===
0:14:07.443180 INFO: Using ng extraction backend
0:14:07.443243 PROGRESS: Extracting batch of 786 precursors
0:14:07.445937 INFO: === Search parameters used ===
0:14:07.446047 INFO: rt_error       : 805.6004638671875
0:14:07.446099 INFO: mobility_error : 0.1
0:14:07.446144 INFO: num_candidates : 1
0:14:07.446188 INFO: ms1_error      : 30
0:14:07.446228 INFO: ms2_error      : 30
0:14:07.446271 INFO: fwhm_rt        : 5
0:14:07.446313 INFO: quant_window   : 3
0:14:07.446354 INFO: ==============================================
0:14:07.504861 INFO: performing precursor FDR with 40 features
0:14:07.504946 INFO: Decoy channel: -1
0:14:07.504971 INFO: Competetive: True
0:14:07.507761 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:07.509222 INFO: Using random state 687617 for train-test-split
0:14:07.517313 INFO: Test AUC: 0.499
0:14:07.517367 INFO: Train AUC: 0.498
0:14:07.517397 INFO: AUC difference: 0.21%
0:14:07.724573 INFO: Resetting torch num_threads to 80
0:14:07.726564 PROGRESS: === Extracted 1169 precursors and 5518 fragments ===
0:14:07.726892 INFO: === FDR correction performed with classifier version -1 ===
0:14:07.727336 PROGRESS: ============================= Precursor FDR =============================
0:14:07.727426 PROGRESS: Total precursors accumulated: 1
0:14:07.727484 PROGRESS: Target precursors: 1 (100.00%)
0:14:07.727533 PROGRESS: Decoy precursors: 0 (0.00%)
0:14:07.727578 PROGRESS: 
0:14:07.727622 PROGRESS: Precursor Summary:
0:14:07.728537 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:14:07.728625 PROGRESS: 
0:14:07.728682 PROGRESS: Protein Summary:
0:14:07.729700 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:14:07.729789 PROGRESS: =========================================================================
0:14:07.729985 INFO: Target number of precursors not reached yet.
0:14:07.796473 INFO: Starting optimization step 2.
0:14:07.796669 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:14:07.796746 INFO: Using ng extraction backend
0:14:07.796807 PROGRESS: Extracting batch of 1592 precursors
0:14:07.801066 INFO: === Search parameters used ===
0:14:07.801172 INFO: rt_error       : 805.6004638671875
0:14:07.801222 INFO: mobility_error : 0.1
0:14:07.801266 INFO: num_candidates : 1
0:14:07.801309 INFO: ms1_error      : 30
0:14:07.801351 INFO: ms2_error      : 30
0:14:07.801398 INFO: fwhm_rt        : 5
0:14:07.801439 INFO: quant_window   : 3
0:14:07.801477 INFO: ==============================================
0:14:07.840623 INFO: performing precursor FDR with 40 features
0:14:07.840703 INFO: Decoy channel: -1
0:14:07.840730 INFO: Competetive: True
0:14:07.844034 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:07.845707 INFO: Using random state 959090 for train-test-split
0:14:07.857053 INFO: Test AUC: 0.490
0:14:07.857113 INFO: Train AUC: 0.501
0:14:07.857142 INFO: AUC difference: 2.11%
0:14:08.063809 INFO: Resetting torch num_threads to 80
0:14:08.066230 PROGRESS: === Extracted 2751 precursors and 13057 fragments ===
0:14:08.066561 INFO: === FDR correction performed with classifier version -1 ===
0:14:08.067019 PROGRESS: ============================= Precursor FDR =============================
0:14:08.067108 PROGRESS: Total precursors accumulated: 2
0:14:08.067166 PROGRESS: Target precursors: 2 (100.00%)
0:14:08.067216 PROGRESS: Decoy precursors: 0 (0.00%)
0:14:08.067264 PROGRESS: 
0:14:08.067308 PROGRESS: Precursor Summary:
0:14:08.068218 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:14:08.068306 PROGRESS: 
0:14:08.068361 PROGRESS: Protein Summary:
0:14:08.069386 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:14:08.069479 PROGRESS: =========================================================================
0:14:08.069688 INFO: Target number of precursors not reached yet.
0:14:08.138708 INFO: Starting optimization step 3.
0:14:08.138913 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:14:08.138990 INFO: Using ng extraction backend
0:14:08.139050 PROGRESS: Extracting batch of 3177 precursors
0:14:08.146024 INFO: === Search parameters used ===
0:14:08.146140 INFO: rt_error       : 805.6004638671875
0:14:08.146204 INFO: mobility_error : 0.1
0:14:08.146251 INFO: num_candidates : 1
0:14:08.146295 INFO: ms1_error      : 30
0:14:08.146335 INFO: ms2_error      : 30
0:14:08.146381 INFO: fwhm_rt        : 5
0:14:08.146422 INFO: quant_window   : 3
0:14:08.146461 INFO: ==============================================
0:14:08.199862 INFO: performing precursor FDR with 40 features
0:14:08.199955 INFO: Decoy channel: -1
0:14:08.199982 INFO: Competetive: True
0:14:08.203979 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:08.206244 INFO: Using random state 444284 for train-test-split
0:14:08.225136 INFO: Test AUC: 0.519
0:14:08.225206 INFO: Train AUC: 0.491
0:14:08.225236 INFO: AUC difference: 5.56%
0:14:08.225261 WARNING: AUC difference > 5%. This may indicate overfitting.
0:14:09.047178 INFO: Resetting torch num_threads to 80
0:14:09.050430 PROGRESS: === Extracted 5894 precursors and 27935 fragments ===
0:14:09.050771 INFO: === FDR correction performed with classifier version -1 ===
0:14:09.051198 PROGRESS: ============================= Precursor FDR =============================
0:14:09.051285 PROGRESS: Total precursors accumulated: 0
0:14:09.051342 PROGRESS: Target precursors: 0 (0.00%)
0:14:09.051392 PROGRESS: Decoy precursors: 0 (0.00%)
0:14:09.051437 PROGRESS: 
0:14:09.051481 PROGRESS: Precursor Summary:
0:14:09.051584 PROGRESS: 
0:14:09.051646 PROGRESS: Protein Summary:
0:14:09.051718 PROGRESS: =========================================================================
0:14:09.051943 INFO: Target number of precursors not reached yet.
0:14:09.125882 INFO: Starting optimization step 4.
0:14:09.126093 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:14:09.126172 INFO: Using ng extraction backend
0:14:09.126234 PROGRESS: Extracting batch of 6340 precursors
0:14:09.139096 INFO: === Search parameters used ===
0:14:09.139225 INFO: rt_error       : 805.6004638671875
0:14:09.139286 INFO: mobility_error : 0.1
0:14:09.139335 INFO: num_candidates : 1
0:14:09.139376 INFO: ms1_error      : 30
0:14:09.139416 INFO: ms2_error      : 30
0:14:09.139454 INFO: fwhm_rt        : 5
0:14:09.139491 INFO: quant_window   : 3
0:14:09.139528 INFO: ==============================================
0:14:09.211195 INFO: performing precursor FDR with 40 features
0:14:09.211304 INFO: Decoy channel: -1
0:14:09.211330 INFO: Competetive: True
0:14:09.217125 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:09.220421 INFO: Using random state 117040 for train-test-split
0:14:09.256628 INFO: Test AUC: 0.493
0:14:09.256724 INFO: Train AUC: 0.497
0:14:09.256754 INFO: AUC difference: 0.76%
0:14:09.470110 INFO: Resetting torch num_threads to 80
0:14:09.474243 PROGRESS: === Extracted 12164 precursors and 57205 fragments ===
0:14:09.474606 INFO: === FDR correction performed with classifier version -1 ===
0:14:09.475039 PROGRESS: ============================= Precursor FDR =============================
0:14:09.475126 PROGRESS: Total precursors accumulated: 0
0:14:09.475187 PROGRESS: Target precursors: 0 (0.00%)
0:14:09.475237 PROGRESS: Decoy precursors: 0 (0.00%)
0:14:09.475283 PROGRESS: 
0:14:09.475327 PROGRESS: Precursor Summary:
0:14:09.475434 PROGRESS: 
0:14:09.475494 PROGRESS: Protein Summary:
0:14:09.475567 PROGRESS: =========================================================================
0:14:09.475833 INFO: Target number of precursors not reached yet.
0:14:09.557449 INFO: Starting optimization step 5.
0:14:09.557674 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:14:09.557752 INFO: Using ng extraction backend
0:14:09.557826 PROGRESS: Extracting batch of 12663 precursors
0:14:09.581435 INFO: === Search parameters used ===
0:14:09.581598 INFO: rt_error       : 805.6004638671875
0:14:09.581649 INFO: mobility_error : 0.1
0:14:09.581696 INFO: num_candidates : 1
0:14:09.581739 INFO: ms1_error      : 30
0:14:09.581780 INFO: ms2_error      : 30
0:14:09.581822 INFO: fwhm_rt        : 5
0:14:09.581861 INFO: quant_window   : 3
0:14:09.581900 INFO: ==============================================
0:14:09.707124 INFO: performing precursor FDR with 40 features
0:14:09.707241 INFO: Decoy channel: -1
0:14:09.707267 INFO: Competetive: True
0:14:09.716846 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:09.722420 INFO: Using random state 798935 for train-test-split
0:14:09.959219 INFO: Test AUC: 0.537
0:14:09.959330 INFO: Train AUC: 0.550
0:14:09.959359 INFO: AUC difference: 2.42%
0:14:10.182693 INFO: Resetting torch num_threads to 80
0:14:10.188691 PROGRESS: === Extracted 24689 precursors and 116108 fragments ===
0:14:10.189132 INFO: === FDR correction performed with classifier version -1 ===
0:14:10.189649 PROGRESS: ============================= Precursor FDR =============================
0:14:10.189738 PROGRESS: Total precursors accumulated: 26
0:14:10.189797 PROGRESS: Target precursors: 26 (100.00%)
0:14:10.189847 PROGRESS: Decoy precursors: 0 (0.00%)
0:14:10.189892 PROGRESS: 
0:14:10.189937 PROGRESS: Precursor Summary:
0:14:10.190858 PROGRESS: Channel   0:	 0.050 FDR:    26; 0.010 FDR:    26; 0.001 FDR:    26
0:14:10.190947 PROGRESS: 
0:14:10.191016 PROGRESS: Protein Summary:
0:14:10.192046 PROGRESS: Channel   0:	 0.050 FDR:    26; 0.010 FDR:    26; 0.001 FDR:    26
0:14:10.192144 PROGRESS: =========================================================================
0:14:10.192567 INFO: Target number of precursors not reached yet.
0:14:10.290265 INFO: Starting optimization step 6.
0:14:10.290494 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:14:10.290574 INFO: Using ng extraction backend
0:14:10.290636 PROGRESS: Extracting batch of 25339 precursors
0:14:10.335848 INFO: === Search parameters used ===
0:14:10.336038 INFO: rt_error       : 805.6004638671875
0:14:10.336090 INFO: mobility_error : 0.1
0:14:10.336137 INFO: num_candidates : 1
0:14:10.336179 INFO: ms1_error      : 30
0:14:10.336221 INFO: ms2_error      : 30
0:14:10.336262 INFO: fwhm_rt        : 5
0:14:10.336301 INFO: quant_window   : 3
0:14:10.336340 INFO: ==============================================
0:14:10.551545 INFO: performing precursor FDR with 40 features
0:14:10.551657 INFO: Decoy channel: -1
0:14:10.551683 INFO: Competetive: True
0:14:10.569268 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:10.581138 INFO: Using random state 384553 for train-test-split
0:14:11.152075 INFO: Test AUC: 0.569
0:14:11.152189 INFO: Train AUC: 0.587
0:14:11.152218 INFO: AUC difference: 3.01%
0:14:11.387507 INFO: Resetting torch num_threads to 80
0:14:11.396949 PROGRESS: === Extracted 49754 precursors and 233575 fragments ===
0:14:11.397498 INFO: === FDR correction performed with classifier version -1 ===
0:14:11.397998 PROGRESS: ============================= Precursor FDR =============================
0:14:11.398086 PROGRESS: Total precursors accumulated: 112
0:14:11.398143 PROGRESS: Target precursors: 111 (99.11%)
0:14:11.398193 PROGRESS: Decoy precursors: 1 (0.89%)
0:14:11.398250 PROGRESS: 
0:14:11.398293 PROGRESS: Precursor Summary:
0:14:11.399153 PROGRESS: Channel   0:	 0.050 FDR:   111; 0.010 FDR:   111; 0.001 FDR:    20
0:14:11.399240 PROGRESS: 
0:14:11.399294 PROGRESS: Protein Summary:
0:14:11.400268 PROGRESS: Channel   0:	 0.050 FDR:   109; 0.010 FDR:   109; 0.001 FDR:    20
0:14:11.400357 PROGRESS: =========================================================================
0:14:11.401073 INFO: Target number of precursors not reached yet.
0:14:11.532830 INFO: Starting optimization step 7.
0:14:11.533081 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:14:11.533164 INFO: Using ng extraction backend
0:14:11.533228 PROGRESS: Extracting batch of 50691 precursors
0:14:11.620863 INFO: === Search parameters used ===
0:14:11.621108 INFO: rt_error       : 805.6004638671875
0:14:11.621162 INFO: mobility_error : 0.1
0:14:11.621210 INFO: num_candidates : 1
0:14:11.621252 INFO: ms1_error      : 30
0:14:11.621295 INFO: ms2_error      : 30
0:14:11.621337 INFO: fwhm_rt        : 5
0:14:11.621377 INFO: quant_window   : 3
0:14:11.621418 INFO: ==============================================
0:14:11.979962 INFO: performing precursor FDR with 40 features
0:14:11.980089 INFO: Decoy channel: -1
0:14:11.980114 INFO: Competetive: True
0:14:12.017053 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:12.040919 INFO: Using random state 17655 for train-test-split
0:14:13.499459 INFO: Test AUC: 0.577
0:14:13.499600 INFO: Train AUC: 0.604
0:14:13.499642 INFO: AUC difference: 4.36%
0:14:13.796747 INFO: Resetting torch num_threads to 80
0:14:13.822729 PROGRESS: === Extracted 99883 precursors and 469354 fragments ===
0:14:13.823348 INFO: === FDR correction performed with classifier version -1 ===
0:14:13.823980 PROGRESS: ============================= Precursor FDR =============================
0:14:13.824084 PROGRESS: Total precursors accumulated: 325
0:14:13.824143 PROGRESS: Target precursors: 322 (99.08%)
0:14:13.824194 PROGRESS: Decoy precursors: 3 (0.92%)
0:14:13.824239 PROGRESS: 
0:14:13.824283 PROGRESS: Precursor Summary:
0:14:13.825266 PROGRESS: Channel   0:	 0.050 FDR:   322; 0.010 FDR:   322; 0.001 FDR:   120
0:14:13.825360 PROGRESS: 
0:14:13.825414 PROGRESS: Protein Summary:
0:14:13.826513 PROGRESS: Channel   0:	 0.050 FDR:   305; 0.010 FDR:   305; 0.001 FDR:   115
0:14:13.826600 PROGRESS: =========================================================================
0:14:13.828107 INFO: Target number of precursors reached.
0:14:13.872260 INFO: fragments_df: keeping 2667 of 469354 [sum(precursor_idx_mask)=3442 sum(mass_error_mask)=469354 stop_rank=2667
0:14:14.114468 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:14:14.281902 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:14:14.688020 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:14:14.688452 INFO: Using score_cutoff 14.181022088813782 (fac=0.99, q=1)
0:14:14.688760 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:14:14.688850 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:14:14.688927 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.181022088813782
0:14:14.689000 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:14.764826 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:14.925232 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:14:14.925576 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:14:14.925694 INFO: Starting optimization step 8.
0:14:14.925763 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:14:14.925840 INFO: Using ng extraction backend
0:14:14.925910 PROGRESS: Extracting batch of 100984 precursors
0:14:15.142612 INFO: === Search parameters used ===
0:14:15.142888 INFO: rt_error       : 805.6004638671875
0:14:15.142973 INFO: mobility_error : 0.1
0:14:15.143035 INFO: num_candidates : 3
0:14:15.143086 INFO: ms1_error      : 30
0:14:15.143136 INFO: ms2_error      : 30
0:14:15.143183 INFO: fwhm_rt        : 3.0
0:14:15.143228 INFO: quant_window   : 3
0:14:15.143270 INFO: ==============================================
0:14:16.501523 INFO: performing precursor FDR with 40 features
0:14:16.501639 INFO: Decoy channel: -1
0:14:16.501664 INFO: Competetive: True
0:14:16.574428 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:16.678278 INFO: Using random state 922573 for train-test-split
0:14:20.758950 INFO: Test AUC: 0.593
0:14:20.759073 INFO: Train AUC: 0.608
0:14:20.759103 INFO: AUC difference: 2.43%
0:14:21.072379 INFO: Resetting torch num_threads to 80
0:14:21.082955 PROGRESS: === Extracted 299677 precursors and 1374257 fragments ===
0:14:21.083336 INFO: === FDR correction performed with classifier version 7 ===
0:14:21.083785 PROGRESS: ============================= Precursor FDR =============================
0:14:21.083879 PROGRESS: Total precursors accumulated: 257
0:14:21.083939 PROGRESS: Target precursors: 255 (99.22%)
0:14:21.083989 PROGRESS: Decoy precursors: 2 (0.78%)
0:14:21.084033 PROGRESS: 
0:14:21.084075 PROGRESS: Precursor Summary:
0:14:21.084957 PROGRESS: Channel   0:	 0.050 FDR:   255; 0.010 FDR:   255; 0.001 FDR:   178
0:14:21.085061 PROGRESS: 
0:14:21.085117 PROGRESS: Protein Summary:
0:14:21.086159 PROGRESS: Channel   0:	 0.050 FDR:   241; 0.010 FDR:   241; 0.001 FDR:   168
0:14:21.086248 PROGRESS: =========================================================================
0:14:21.090732 INFO: Target number of precursors reached.
0:14:21.180665 INFO: fragments_df: keeping 3204 of 1374257 [sum(precursor_idx_mask)=5883 sum(mass_error_mask)=1374257 stop_rank=3204
0:14:21.387884 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:14:21.490297 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:14:21.863287 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:14:21.863689 INFO: Using score_cutoff 14.170214281654358 (fac=0.99, q=1)
0:14:21.863968 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:14:21.864046 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:14:21.864099 INFO: Updating optimization_manager: score_cutoff        : 14.181022088813782 -> 14.170214281654358
0:14:21.864153 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:21.926618 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:22.071863 INFO: === checking if optimization conditions were reached ===
0:14:22.073709 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:14:22.073810 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:14:22.073876 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:14:22.073935 INFO: ==============================================
0:14:22.073999 INFO: Starting optimization step 9.
0:14:22.074056 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:14:22.074114 INFO: Using ng extraction backend
0:14:22.074169 PROGRESS: Extracting batch of 100984 precursors
0:14:22.246149 INFO: === Search parameters used ===
0:14:22.246392 INFO: rt_error       : 805.6004638671875
0:14:22.246446 INFO: mobility_error : 0.1
0:14:22.246491 INFO: num_candidates : 3
0:14:22.246531 INFO: ms1_error      : 30
0:14:22.246574 INFO: ms2_error      : 10.0
0:14:22.246615 INFO: fwhm_rt        : 3.0
0:14:22.246655 INFO: quant_window   : 3
0:14:22.246696 INFO: ==============================================
0:14:23.448778 INFO: performing precursor FDR with 40 features
0:14:23.448900 INFO: Decoy channel: -1
0:14:23.448925 INFO: Competetive: True
0:14:23.521669 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:23.623260 INFO: Using random state 112349 for train-test-split
0:14:27.546823 INFO: Test AUC: 0.592
0:14:27.546941 INFO: Train AUC: 0.604
0:14:27.546971 INFO: AUC difference: 2.00%
0:14:27.860724 INFO: Resetting torch num_threads to 80
0:14:27.872461 PROGRESS: === Extracted 302120 precursors and 1609234 fragments ===
0:14:27.872838 INFO: === FDR correction performed with classifier version 8 ===
0:14:27.873330 PROGRESS: ============================= Precursor FDR =============================
0:14:27.873421 PROGRESS: Total precursors accumulated: 368
0:14:27.873483 PROGRESS: Target precursors: 365 (99.18%)
0:14:27.873535 PROGRESS: Decoy precursors: 3 (0.82%)
0:14:27.873582 PROGRESS: 
0:14:27.873627 PROGRESS: Precursor Summary:
0:14:27.874540 PROGRESS: Channel   0:	 0.050 FDR:   365; 0.010 FDR:   365; 0.001 FDR:   319
0:14:27.874627 PROGRESS: 
0:14:27.874683 PROGRESS: Protein Summary:
0:14:27.875778 PROGRESS: Channel   0:	 0.050 FDR:   343; 0.010 FDR:   343; 0.001 FDR:   300
0:14:27.875867 PROGRESS: =========================================================================
0:14:27.881087 INFO: Target number of precursors reached.
0:14:27.987936 INFO: fragments_df: keeping 4476 of 1609234 [sum(precursor_idx_mask)=9041 sum(mass_error_mask)=1609234 stop_rank=4476
0:14:28.194775 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:14:28.313610 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:14:28.905672 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:14:28.906080 INFO: Using score_cutoff 13.948942971038818 (fac=0.99, q=1)
0:14:28.906562 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:14:28.906641 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:14:28.906693 INFO: Updating optimization_manager: score_cutoff        : 14.170214281654358 -> 13.948942971038818
0:14:28.906752 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:28.968694 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:29.118769 INFO: === checking if optimization conditions were reached ===
0:14:29.121104 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:14:29.121227 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:14:29.121301 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:14:29.121367 INFO: ==============================================
0:14:29.121439 PROGRESS: Optimization finished for ms2_error.
0:14:29.333351 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:29.395590 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:29.546251 INFO: Starting optimization step 0.
0:14:29.546516 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:14:29.546606 INFO: Using ng extraction backend
0:14:29.546681 PROGRESS: Extracting batch of 100984 precursors
0:14:29.720953 INFO: === Search parameters used ===
0:14:29.721205 INFO: rt_error       : 805.6004638671875
0:14:29.721261 INFO: mobility_error : 0.1
0:14:29.721307 INFO: num_candidates : 3
0:14:29.721348 INFO: ms1_error      : 30
0:14:29.721386 INFO: ms2_error      : 10.0
0:14:29.721438 INFO: fwhm_rt        : 3.0
0:14:29.721479 INFO: quant_window   : 3
0:14:29.721517 INFO: ==============================================
0:14:30.905698 INFO: performing precursor FDR with 40 features
0:14:30.905816 INFO: Decoy channel: -1
0:14:30.905843 INFO: Competetive: True
0:14:30.978088 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:31.076343 INFO: Using random state 528574 for train-test-split
0:14:35.008069 INFO: Test AUC: 0.599
0:14:35.008191 INFO: Train AUC: 0.615
0:14:35.008223 INFO: AUC difference: 2.56%
0:14:35.314483 INFO: Resetting torch num_threads to 80
0:14:35.324914 PROGRESS: === Extracted 302117 precursors and 1609504 fragments ===
0:14:35.325296 INFO: === FDR correction performed with classifier version 9 ===
0:14:35.325782 PROGRESS: ============================= Precursor FDR =============================
0:14:35.325864 PROGRESS: Total precursors accumulated: 456
0:14:35.325919 PROGRESS: Target precursors: 452 (99.12%)
0:14:35.325967 PROGRESS: Decoy precursors: 4 (0.88%)
0:14:35.326010 PROGRESS: 
0:14:35.326053 PROGRESS: Precursor Summary:
0:14:35.326961 PROGRESS: Channel   0:	 0.050 FDR:   452; 0.010 FDR:   452; 0.001 FDR:   352
0:14:35.327045 PROGRESS: 
0:14:35.327098 PROGRESS: Protein Summary:
0:14:35.328219 PROGRESS: Channel   0:	 0.050 FDR:   427; 0.010 FDR:   427; 0.001 FDR:   332
0:14:35.328304 PROGRESS: =========================================================================
0:14:35.332735 INFO: Target number of precursors reached.
0:14:35.437205 INFO: fragments_df: keeping 5000 of 1609504 [sum(precursor_idx_mask)=11111 sum(mass_error_mask)=1609504 stop_rank=5000
0:14:35.576660 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:14:35.701482 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:14:36.403993 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:14:36.404944 INFO: Using score_cutoff 14.05003724756241 (fac=0.99, q=1)
0:14:36.405241 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:14:36.405331 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:14:36.405384 INFO: Updating optimization_manager: score_cutoff        : 13.948942971038818 -> 14.05003724756241
0:14:36.405437 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:36.436160 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:36.512239 INFO: === checking if optimization conditions were reached ===
0:14:36.512511 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:14:36.514733 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 107.41990921077091
0:14:36.514859 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 107.4199.
0:14:36.514935 INFO: ==============================================
0:14:36.515013 INFO: Starting optimization step 1.
0:14:36.515078 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:14:36.515149 INFO: Using ng extraction backend
0:14:36.515217 PROGRESS: Extracting batch of 50293 precursors
0:14:36.610180 INFO: === Search parameters used ===
0:14:36.610442 INFO: rt_error       : 107.41990921077091
0:14:36.610511 INFO: mobility_error : 0.1
0:14:36.610558 INFO: num_candidates : 3
0:14:36.610613 INFO: ms1_error      : 30
0:14:36.610659 INFO: ms2_error      : 10.0
0:14:36.610699 INFO: fwhm_rt        : 3.0
0:14:36.610739 INFO: quant_window   : 3
0:14:36.610778 INFO: ==============================================
0:14:37.187813 INFO: performing precursor FDR with 40 features
0:14:37.187921 INFO: Decoy channel: -1
0:14:37.187948 INFO: Competetive: True
0:14:37.225066 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:37.259887 INFO: Using random state 528574 for train-test-split
0:14:39.161155 INFO: Test AUC: 0.586
0:14:39.161267 INFO: Train AUC: 0.615
0:14:39.161297 INFO: AUC difference: 4.60%
0:14:39.418824 INFO: Resetting torch num_threads to 80
0:14:39.424659 PROGRESS: === Extracted 147243 precursors and 600864 fragments ===
0:14:39.425002 INFO: === FDR correction performed with classifier version 9 ===
0:14:39.425435 PROGRESS: ============================= Precursor FDR =============================
0:14:39.425519 PROGRESS: Total precursors accumulated: 238
0:14:39.425577 PROGRESS: Target precursors: 236 (99.16%)
0:14:39.425627 PROGRESS: Decoy precursors: 2 (0.84%)
0:14:39.425671 PROGRESS: 
0:14:39.425715 PROGRESS: Precursor Summary:
0:14:39.426585 PROGRESS: Channel   0:	 0.050 FDR:   236; 0.010 FDR:   236; 0.001 FDR:   186
0:14:39.426671 PROGRESS: 
0:14:39.426726 PROGRESS: Protein Summary:
0:14:39.427733 PROGRESS: Channel   0:	 0.050 FDR:   226; 0.010 FDR:   226; 0.001 FDR:   181
0:14:39.427819 PROGRESS: =========================================================================
0:14:39.429737 INFO: Target number of precursors reached.
0:14:39.470778 INFO: fragments_df: keeping 2689 of 600864 [sum(precursor_idx_mask)=5571 sum(mass_error_mask)=600864 stop_rank=2689
0:14:39.604532 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:14:39.700529 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:14:40.081280 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:14:40.081680 INFO: Using score_cutoff 13.93374899339676 (fac=0.99, q=1)
0:14:40.081956 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:14:40.082032 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:14:40.082086 INFO: Updating optimization_manager: score_cutoff        : 14.05003724756241 -> 13.93374899339676
0:14:40.082139 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:40.112452 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:40.177996 INFO: === checking if optimization conditions were reached ===
0:14:40.178235 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:14:40.180028 INFO: Updating optimization_manager: rt_error            : 107.41990921077091 -> 73.08411461029371
0:14:40.180128 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 73.0841.
0:14:40.180196 INFO: ==============================================
0:14:40.180264 INFO: Starting optimization step 2.
0:14:40.180322 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:14:40.180381 INFO: Using ng extraction backend
0:14:40.180439 PROGRESS: Extracting batch of 50293 precursors
0:14:40.267271 INFO: === Search parameters used ===
0:14:40.267527 INFO: rt_error       : 73.08411461029371
0:14:40.267594 INFO: mobility_error : 0.1
0:14:40.267646 INFO: num_candidates : 3
0:14:40.267690 INFO: ms1_error      : 30
0:14:40.267732 INFO: ms2_error      : 10.0
0:14:40.267771 INFO: fwhm_rt        : 3.0
0:14:40.267811 INFO: quant_window   : 3
0:14:40.267851 INFO: ==============================================
0:14:40.823890 INFO: performing precursor FDR with 40 features
0:14:40.824003 INFO: Decoy channel: -1
0:14:40.824032 INFO: Competetive: True
0:14:40.860130 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:40.894253 INFO: Using random state 528574 for train-test-split
0:14:42.783134 INFO: Test AUC: 0.594
0:14:42.783250 INFO: Train AUC: 0.612
0:14:42.783281 INFO: AUC difference: 3.02%
0:14:43.046225 INFO: Resetting torch num_threads to 80
0:14:43.052414 PROGRESS: === Extracted 144997 precursors and 555913 fragments ===
0:14:43.052761 INFO: === FDR correction performed with classifier version 9 ===
0:14:43.053212 PROGRESS: ============================= Precursor FDR =============================
0:14:43.053299 PROGRESS: Total precursors accumulated: 323
0:14:43.053357 PROGRESS: Target precursors: 320 (99.07%)
0:14:43.053407 PROGRESS: Decoy precursors: 3 (0.93%)
0:14:43.053451 PROGRESS: 
0:14:43.053493 PROGRESS: Precursor Summary:
0:14:43.054435 PROGRESS: Channel   0:	 0.050 FDR:   320; 0.010 FDR:   320; 0.001 FDR:   264
0:14:43.054524 PROGRESS: 
0:14:43.054580 PROGRESS: Protein Summary:
0:14:43.055652 PROGRESS: Channel   0:	 0.050 FDR:   307; 0.010 FDR:   307; 0.001 FDR:   254
0:14:43.055744 PROGRESS: =========================================================================
0:14:43.057687 INFO: Target number of precursors reached.
0:14:43.096699 INFO: fragments_df: keeping 3262 of 555913 [sum(precursor_idx_mask)=7212 sum(mass_error_mask)=555913 stop_rank=3262
0:14:43.231157 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:14:43.329438 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:14:43.686316 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:14:43.686714 INFO: Using score_cutoff 11.281741996192933 (fac=0.99, q=1)
0:14:43.686993 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:14:43.687073 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:14:43.687128 INFO: Updating optimization_manager: score_cutoff        : 13.93374899339676 -> 11.281741996192933
0:14:43.687181 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:43.718477 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:43.786387 INFO: === checking if optimization conditions were reached ===
0:14:43.786616 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:14:43.788567 INFO: Updating optimization_manager: rt_error            : 73.08411461029371 -> 58.55834386852392
0:14:43.788670 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 58.5583.
0:14:43.788738 INFO: ==============================================
0:14:43.788807 INFO: Starting optimization step 3.
0:14:43.788867 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:14:43.788929 INFO: Using ng extraction backend
0:14:43.788987 PROGRESS: Extracting batch of 50293 precursors
0:14:43.875731 INFO: === Search parameters used ===
0:14:43.875981 INFO: rt_error       : 58.55834386852392
0:14:43.876034 INFO: mobility_error : 0.1
0:14:43.876078 INFO: num_candidates : 3
0:14:43.876119 INFO: ms1_error      : 30
0:14:43.876159 INFO: ms2_error      : 10.0
0:14:43.876198 INFO: fwhm_rt        : 3.0
0:14:43.876237 INFO: quant_window   : 3
0:14:43.876276 INFO: ==============================================
0:14:44.432208 INFO: performing precursor FDR with 40 features
0:14:44.432537 INFO: Decoy channel: -1
0:14:44.432574 INFO: Competetive: True
0:14:44.467587 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:44.500387 INFO: Using random state 528574 for train-test-split
0:14:46.238334 INFO: Test AUC: 0.594
0:14:46.238446 INFO: Train AUC: 0.609
0:14:46.238476 INFO: AUC difference: 2.48%
0:14:46.497177 INFO: Resetting torch num_threads to 80
0:14:46.503195 PROGRESS: === Extracted 142324 precursors and 532138 fragments ===
0:14:46.503538 INFO: === FDR correction performed with classifier version 9 ===
0:14:46.503981 PROGRESS: ============================= Precursor FDR =============================
0:14:46.504070 PROGRESS: Total precursors accumulated: 304
0:14:46.504132 PROGRESS: Target precursors: 301 (99.01%)
0:14:46.504182 PROGRESS: Decoy precursors: 3 (0.99%)
0:14:46.504229 PROGRESS: 
0:14:46.504273 PROGRESS: Precursor Summary:
0:14:46.505170 PROGRESS: Channel   0:	 0.050 FDR:   301; 0.010 FDR:   301; 0.001 FDR:   235
0:14:46.505260 PROGRESS: 
0:14:46.505317 PROGRESS: Protein Summary:
0:14:46.506373 PROGRESS: Channel   0:	 0.050 FDR:   290; 0.010 FDR:   290; 0.001 FDR:   228
0:14:46.506462 PROGRESS: =========================================================================
0:14:46.508327 INFO: Target number of precursors reached.
0:14:46.544968 INFO: fragments_df: keeping 3075 of 532138 [sum(precursor_idx_mask)=6524 sum(mass_error_mask)=532138 stop_rank=3075
0:14:46.679514 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:14:46.791634 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:14:47.127627 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:14:47.128035 INFO: Using score_cutoff 12.49724410057068 (fac=0.99, q=1)
0:14:47.128316 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:14:47.128395 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:14:47.128447 INFO: Updating optimization_manager: score_cutoff        : 11.281741996192933 -> 12.49724410057068
0:14:47.128499 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:47.160432 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:47.229912 INFO: === checking if optimization conditions were reached ===
0:14:47.230134 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:14:47.232063 INFO: Updating optimization_manager: rt_error            : 58.55834386852392 -> 41.601385343646264
0:14:47.232164 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 41.6014.
0:14:47.232229 INFO: ==============================================
0:14:47.232296 INFO: Starting optimization step 4.
0:14:47.232353 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:14:47.232414 INFO: Using ng extraction backend
0:14:47.232480 PROGRESS: Extracting batch of 50293 precursors
0:14:47.320498 INFO: === Search parameters used ===
0:14:47.320741 INFO: rt_error       : 41.601385343646264
0:14:47.320797 INFO: mobility_error : 0.1
0:14:47.320841 INFO: num_candidates : 3
0:14:47.320883 INFO: ms1_error      : 30
0:14:47.320923 INFO: ms2_error      : 10.0
0:14:47.320962 INFO: fwhm_rt        : 3.0
0:14:47.321008 INFO: quant_window   : 3
0:14:47.321047 INFO: ==============================================
0:14:47.866465 INFO: performing precursor FDR with 40 features
0:14:47.866581 INFO: Decoy channel: -1
0:14:47.866607 INFO: Competetive: True
0:14:47.907395 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:47.937822 INFO: Using random state 528574 for train-test-split
0:14:49.821849 INFO: Test AUC: 0.593
0:14:49.821968 INFO: Train AUC: 0.611
0:14:49.821998 INFO: AUC difference: 2.91%
0:14:50.079557 INFO: Resetting torch num_threads to 80
0:14:50.085288 PROGRESS: === Extracted 134275 precursors and 491401 fragments ===
0:14:50.085631 INFO: === FDR correction performed with classifier version 9 ===
0:14:50.086097 PROGRESS: ============================= Precursor FDR =============================
0:14:50.086184 PROGRESS: Total precursors accumulated: 268
0:14:50.086240 PROGRESS: Target precursors: 266 (99.25%)
0:14:50.086289 PROGRESS: Decoy precursors: 2 (0.75%)
0:14:50.086332 PROGRESS: 
0:14:50.086373 PROGRESS: Precursor Summary:
0:14:50.087255 PROGRESS: Channel   0:	 0.050 FDR:   266; 0.010 FDR:   266; 0.001 FDR:   229
0:14:50.087340 PROGRESS: 
0:14:50.087393 PROGRESS: Protein Summary:
0:14:50.088442 PROGRESS: Channel   0:	 0.050 FDR:   256; 0.010 FDR:   256; 0.001 FDR:   221
0:14:50.088537 PROGRESS: =========================================================================
0:14:50.090364 INFO: Target number of precursors reached.
0:14:50.124262 INFO: fragments_df: keeping 2657 of 491401 [sum(precursor_idx_mask)=5439 sum(mass_error_mask)=491401 stop_rank=2657
0:14:50.258697 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:14:50.359143 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:14:50.648178 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:14:50.648595 INFO: Using score_cutoff 12.970321226119996 (fac=0.99, q=1)
0:14:50.648882 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:14:50.648966 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:14:50.649032 INFO: Updating optimization_manager: score_cutoff        : 12.49724410057068 -> 12.970321226119996
0:14:50.649087 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:50.681226 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:50.747525 INFO: === checking if optimization conditions were reached ===
0:14:50.747793 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:14:50.750082 INFO: Updating optimization_manager: rt_error            : 41.601385343646264 -> 33.07793835655655
0:14:50.750194 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 33.0779.
0:14:50.750268 INFO: ==============================================
0:14:50.750346 INFO: Starting optimization step 5.
0:14:50.750432 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:14:50.750504 INFO: Using ng extraction backend
0:14:50.750578 PROGRESS: Extracting batch of 50293 precursors
0:14:50.838297 INFO: === Search parameters used ===
0:14:50.838562 INFO: rt_error       : 33.07793835655655
0:14:50.838643 INFO: mobility_error : 0.1
0:14:50.838705 INFO: num_candidates : 3
0:14:50.838760 INFO: ms1_error      : 30
0:14:50.838811 INFO: ms2_error      : 10.0
0:14:50.838864 INFO: fwhm_rt        : 3.0
0:14:50.838916 INFO: quant_window   : 3
0:14:50.838968 INFO: ==============================================
0:14:51.352526 INFO: performing precursor FDR with 40 features
0:14:51.352641 INFO: Decoy channel: -1
0:14:51.352672 INFO: Competetive: True
0:14:51.385873 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:51.415631 INFO: Using random state 528574 for train-test-split
0:14:53.156119 INFO: Test AUC: 0.596
0:14:53.156235 INFO: Train AUC: 0.612
0:14:53.156272 INFO: AUC difference: 2.61%
0:14:53.418108 INFO: Resetting torch num_threads to 80
0:14:53.424615 PROGRESS: === Extracted 134347 precursors and 492604 fragments ===
0:14:53.425023 INFO: === FDR correction performed with classifier version 9 ===
0:14:53.425513 PROGRESS: ============================= Precursor FDR =============================
0:14:53.425607 PROGRESS: Total precursors accumulated: 312
0:14:53.425678 PROGRESS: Target precursors: 309 (99.04%)
0:14:53.425741 PROGRESS: Decoy precursors: 3 (0.96%)
0:14:53.425797 PROGRESS: 
0:14:53.425851 PROGRESS: Precursor Summary:
0:14:53.426842 PROGRESS: Channel   0:	 0.050 FDR:   309; 0.010 FDR:   309; 0.001 FDR:   237
0:14:53.426943 PROGRESS: 
0:14:53.427018 PROGRESS: Protein Summary:
0:14:53.428159 PROGRESS: Channel   0:	 0.050 FDR:   300; 0.010 FDR:   300; 0.001 FDR:   229
0:14:53.428255 PROGRESS: =========================================================================
0:14:53.430398 INFO: Target number of precursors reached.
0:14:53.464213 INFO: fragments_df: keeping 2914 of 492604 [sum(precursor_idx_mask)=6162 sum(mass_error_mask)=492604 stop_rank=2914
0:14:53.600891 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:14:53.783186 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:14:54.819538 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:14:54.819945 INFO: Using score_cutoff 10.800386804580688 (fac=0.99, q=1)
0:14:54.820225 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:14:54.820302 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:14:54.820356 INFO: Updating optimization_manager: score_cutoff        : 12.970321226119996 -> 10.800386804580688
0:14:54.820409 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:54.852046 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:54.918357 INFO: === checking if optimization conditions were reached ===
0:14:54.918618 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:14:54.920916 INFO: Updating optimization_manager: rt_error            : 33.07793835655655 -> 33.32485576649823
0:14:54.921044 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 33.3249.
0:14:54.921121 INFO: ==============================================
0:14:54.921216 INFO: Starting optimization step 6.
0:14:54.921285 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:14:54.921355 INFO: Using ng extraction backend
0:14:54.921423 PROGRESS: Extracting batch of 50293 precursors
0:14:55.011007 INFO: === Search parameters used ===
0:14:55.011252 INFO: rt_error       : 33.32485576649823
0:14:55.011305 INFO: mobility_error : 0.1
0:14:55.011351 INFO: num_candidates : 3
0:14:55.011393 INFO: ms1_error      : 30
0:14:55.011438 INFO: ms2_error      : 10.0
0:14:55.011478 INFO: fwhm_rt        : 3.0
0:14:55.011518 INFO: quant_window   : 3
0:14:55.011556 INFO: ==============================================
0:14:55.523318 INFO: performing precursor FDR with 40 features
0:14:55.523434 INFO: Decoy channel: -1
0:14:55.523460 INFO: Competetive: True
0:14:55.557164 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:55.588062 INFO: Using random state 528574 for train-test-split
0:14:57.306394 INFO: Test AUC: 0.595
0:14:57.306511 INFO: Train AUC: 0.611
0:14:57.306540 INFO: AUC difference: 2.55%
0:14:57.572274 INFO: Resetting torch num_threads to 80
0:14:57.578112 PROGRESS: === Extracted 134232 precursors and 489854 fragments ===
0:14:57.578446 INFO: === FDR correction performed with classifier version 9 ===
0:14:57.578917 PROGRESS: ============================= Precursor FDR =============================
0:14:57.579001 PROGRESS: Total precursors accumulated: 273
0:14:57.579058 PROGRESS: Target precursors: 271 (99.27%)
0:14:57.579106 PROGRESS: Decoy precursors: 2 (0.73%)
0:14:57.579150 PROGRESS: 
0:14:57.579192 PROGRESS: Precursor Summary:
0:14:57.580107 PROGRESS: Channel   0:	 0.050 FDR:   271; 0.010 FDR:   271; 0.001 FDR:   221
0:14:57.580193 PROGRESS: 
0:14:57.580246 PROGRESS: Protein Summary:
0:14:57.581290 PROGRESS: Channel   0:	 0.050 FDR:   262; 0.010 FDR:   262; 0.001 FDR:   214
0:14:57.581378 PROGRESS: =========================================================================
0:14:57.583181 INFO: Target number of precursors reached.
0:14:57.617639 INFO: fragments_df: keeping 2691 of 489854 [sum(precursor_idx_mask)=5538 sum(mass_error_mask)=489854 stop_rank=2691
0:14:57.751937 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:14:57.872201 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:14:58.253385 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:14:58.253794 INFO: Using score_cutoff 12.814653050422669 (fac=0.99, q=1)
0:14:58.254068 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:14:58.254144 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:14:58.254197 INFO: Updating optimization_manager: score_cutoff        : 10.800386804580688 -> 12.814653050422669
0:14:58.254250 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:58.286250 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:58.351060 INFO: === checking if optimization conditions were reached ===
0:14:58.351341 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:14:58.352566 INFO: Updating optimization_manager: rt_error            : 33.32485576649823 -> 33.07793835655655
0:14:58.352721 INFO: Updating optimization_manager: classifier_version  : 9 -> 15
0:14:58.352834 INFO: Updating optimization_manager: score_cutoff        : 12.814653050422669 -> 10.800386804580688
0:14:58.352931 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:14:58.353037 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:14:58.353136 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 33.0779 found after 7 searches.
0:14:58.353205 INFO: ==============================================
0:14:58.353279 PROGRESS: Optimization finished for rt_error.
0:14:58.499926 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:58.532470 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:58.629653 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:14:58.629879 PROGRESS: ==============================================
0:14:58.629953 PROGRESS: ms2_error      : 10.0000
0:14:58.630015 PROGRESS: rt_error       : 33.0779
0:14:58.630069 PROGRESS: ==============================================
0:14:58.630597 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:15:06.577181 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:15:24.340118 INFO: Using ng extraction backend
0:15:24.340397 PROGRESS: Extracting batch of 12001526 precursors
0:15:40.099898 INFO: === Search parameters used ===
0:15:40.100234 INFO: rt_error       : 33.07793835655655
0:15:40.100317 INFO: mobility_error : 0.1
0:15:40.100372 INFO: num_candidates : 3
0:15:40.100419 INFO: ms1_error      : 30
0:15:40.100462 INFO: ms2_error      : 10.0
0:15:40.100504 INFO: fwhm_rt        : 3.0
0:15:40.100543 INFO: quant_window   : 3
0:15:40.100585 INFO: ==============================================
0:16:03.253181 INFO: Removed 23627495 precursors with score below cutoff 10.800386804580688
0:16:13.913998 INFO: performing precursor FDR with 40 features
0:16:13.914145 INFO: Decoy channel: -1
0:16:13.914175 INFO: Competetive: True
0:16:14.887807 INFO: Setting torch num_threads to 2 for FDR classification task
0:16:18.395359 INFO: Using random state 626917 for train-test-split
0:18:27.709215 INFO: Test AUC: 0.622
0:18:27.709413 INFO: Train AUC: 0.624
0:18:27.709450 INFO: AUC difference: 0.25%
0:18:30.746381 INFO: Resetting torch num_threads to 80
0:18:32.282645 PROGRESS: ============================= Precursor FDR =============================
0:18:32.282923 PROGRESS: Total precursors accumulated: 72,717
0:18:32.282993 PROGRESS: Target precursors: 71,998 (99.01%)
0:18:32.283045 PROGRESS: Decoy precursors: 719 (0.99%)
0:18:32.283091 PROGRESS: 
0:18:32.283135 PROGRESS: Precursor Summary:
0:18:32.302028 PROGRESS: Channel   0:	 0.050 FDR: 71,998; 0.010 FDR: 71,998; 0.001 FDR: 51,934
0:18:32.302255 PROGRESS: 
0:18:32.302316 PROGRESS: Protein Summary:
0:18:32.330428 PROGRESS: Channel   0:	 0.050 FDR: 12,704; 0.010 FDR: 12,704; 0.001 FDR: 9,472
0:18:32.330647 PROGRESS: =========================================================================
0:18:32.389468 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/psm.parquet
0:18:32.533539 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.parquet
0:18:32.742879 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:18:33.337526 PROGRESS: 
0:18:33.337678 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant
0:18:33.337751 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/figures
0:18:33.337916 INFO: Initializing TimingManager
0:18:33.338357 INFO: Initializing RawFileManager
0:18:44.307563 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.
0:18:44.311556 INFO: Determining DIA cycle
0:18:44.326709 INFO: Found cycle with start 0.00 min and length 300.
0:18:44.495332 INFO: RT (min)            : 0.0 - 26.9
0:18:44.495423 INFO: RT duration (sec)   : 1611.2
0:18:44.495452 INFO: RT duration (min)   : 26.9
0:18:44.495480 INFO: Cycle len (scans)   : 300
0:18:44.495501 INFO: Cycle len (sec)     : 1.65
0:18:44.495521 INFO: Number of cycles    : 977
0:18:44.495543 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:18:44.495571 INFO: Creating DIA data object took: 11.157121658325195
0:18:45.210736 INFO: Creating DIA data NG object took: 0.7150611877441406
0:18:46.353765 INFO: Initializing CalibrationManager
0:18:46.354028 INFO: Setting up calibration estimators ..
0:18:46.354086 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:18:46.354166 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'}' ..
0:18:46.354265 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:18:46.354316 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:18:46.354371 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}}' ..
0:18:46.354421 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:18:46.354464 INFO: Done setting up calibration estimators.
0:18:46.354663 INFO: Initializing OptimizationManager
0:18:46.354805 INFO: initial parameter: ms1_error = 30
0:18:46.354856 INFO: initial parameter: ms2_error = 30
0:18:46.354901 INFO: initial parameter: rt_error = 805.5982666015625
0:18:46.354943 INFO: initial parameter: mobility_error = 0.1
0:18:46.354983 INFO: initial parameter: num_candidates = 1
0:18:46.355023 INFO: initial parameter: fwhm_rt = 5
0:18:46.355065 INFO: initial parameter: fwhm_mobility = 0.01
0:18:46.355104 INFO: initial parameter: score_cutoff = 0
0:18:46.355142 INFO: initial parameter: classifier_version = -1
0:18:46.355205 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:18:46.355437 INFO: FDRManager: loading saved state not requested, will be initialized.
0:18:46.355470 INFO: Initializing FDRManager
0:18:46.355506 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:18:47.553126 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:18:48.313035 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:18:48.314715 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
0:18:48.314856 PROGRESS: Starting initial search for precursors.
0:18:48.314944 INFO: Starting optimization step 0.
0:18:48.315010 PROGRESS: === Extracting elution groups 0 to 200 ===
0:18:48.315077 INFO: Using ng extraction backend
0:18:48.315140 PROGRESS: Extracting batch of 396 precursors
0:18:48.317184 INFO: === Search parameters used ===
0:18:48.317287 INFO: rt_error       : 805.5982666015625
0:18:48.317336 INFO: mobility_error : 0.1
0:18:48.317380 INFO: num_candidates : 1
0:18:48.317420 INFO: ms1_error      : 30
0:18:48.317460 INFO: ms2_error      : 30
0:18:48.317499 INFO: fwhm_rt        : 5
0:18:48.317538 INFO: quant_window   : 3
0:18:48.317575 INFO: ==============================================
0:18:48.342131 INFO: performing precursor FDR with 40 features
0:18:48.342237 INFO: Decoy channel: -1
0:18:48.342263 INFO: Competetive: True
0:18:48.343215 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:48.345360 INFO: Using random state 168413 for train-test-split
0:18:48.352479 INFO: Test AUC: 0.534
0:18:48.352540 INFO: Train AUC: 0.498
0:18:48.352572 INFO: AUC difference: 7.31%
0:18:48.352597 WARNING: AUC difference > 5%. This may indicate overfitting.
0:18:48.567740 INFO: Resetting torch num_threads to 80
0:18:48.569038 PROGRESS: === Extracted 392 precursors and 1853 fragments ===
0:18:48.569372 INFO: === FDR correction performed with classifier version -1 ===
0:18:48.569832 PROGRESS: ============================= Precursor FDR =============================
0:18:48.569919 PROGRESS: Total precursors accumulated: 1
0:18:48.569978 PROGRESS: Target precursors: 1 (100.00%)
0:18:48.570028 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:48.570073 PROGRESS: 
0:18:48.570115 PROGRESS: Precursor Summary:
0:18:48.571040 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:18:48.571128 PROGRESS: 
0:18:48.571182 PROGRESS: Protein Summary:
0:18:48.572225 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:18:48.572314 PROGRESS: =========================================================================
0:18:48.572479 INFO: Target number of precursors not reached yet.
0:18:48.636683 INFO: Starting optimization step 1.
0:18:48.636870 PROGRESS: === Extracting elution groups 200 to 600 ===
0:18:48.636949 INFO: Using ng extraction backend
0:18:48.637020 PROGRESS: Extracting batch of 786 precursors
0:18:48.639668 INFO: === Search parameters used ===
0:18:48.639764 INFO: rt_error       : 805.5982666015625
0:18:48.639814 INFO: mobility_error : 0.1
0:18:48.639860 INFO: num_candidates : 1
0:18:48.639902 INFO: ms1_error      : 30
0:18:48.639944 INFO: ms2_error      : 30
0:18:48.639983 INFO: fwhm_rt        : 5
0:18:48.640021 INFO: quant_window   : 3
0:18:48.640060 INFO: ==============================================
0:18:48.707568 INFO: performing precursor FDR with 40 features
0:18:48.707654 INFO: Decoy channel: -1
0:18:48.707679 INFO: Competetive: True
0:18:48.710482 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:48.712049 INFO: Using random state 818032 for train-test-split
0:18:48.720471 INFO: Test AUC: 0.523
0:18:48.720535 INFO: Train AUC: 0.495
0:18:48.720565 INFO: AUC difference: 5.74%
0:18:48.720587 WARNING: AUC difference > 5%. This may indicate overfitting.
0:18:48.926136 INFO: Resetting torch num_threads to 80
0:18:48.928132 PROGRESS: === Extracted 1171 precursors and 5469 fragments ===
0:18:48.928473 INFO: === FDR correction performed with classifier version -1 ===
0:18:48.928940 PROGRESS: ============================= Precursor FDR =============================
0:18:48.929041 PROGRESS: Total precursors accumulated: 1
0:18:48.929102 PROGRESS: Target precursors: 1 (100.00%)
0:18:48.929151 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:48.929196 PROGRESS: 
0:18:48.929238 PROGRESS: Precursor Summary:
0:18:48.930978 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:18:48.931069 PROGRESS: 
0:18:48.931126 PROGRESS: Protein Summary:
0:18:48.932132 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:18:48.932223 PROGRESS: =========================================================================
0:18:48.932418 INFO: Target number of precursors not reached yet.
0:18:48.999085 INFO: Starting optimization step 2.
0:18:48.999284 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:18:48.999363 INFO: Using ng extraction backend
0:18:48.999430 PROGRESS: Extracting batch of 1592 precursors
0:18:49.003619 INFO: === Search parameters used ===
0:18:49.003733 INFO: rt_error       : 805.5982666015625
0:18:49.003782 INFO: mobility_error : 0.1
0:18:49.003827 INFO: num_candidates : 1
0:18:49.003871 INFO: ms1_error      : 30
0:18:49.003912 INFO: ms2_error      : 30
0:18:49.003953 INFO: fwhm_rt        : 5
0:18:49.003994 INFO: quant_window   : 3
0:18:49.004035 INFO: ==============================================
0:18:49.046415 INFO: performing precursor FDR with 40 features
0:18:49.046507 INFO: Decoy channel: -1
0:18:49.046534 INFO: Competetive: True
0:18:49.050701 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:49.052469 INFO: Using random state 494326 for train-test-split
0:18:49.064286 INFO: Test AUC: 0.541
0:18:49.064350 INFO: Train AUC: 0.487
0:18:49.064379 INFO: AUC difference: 11.00%
0:18:49.064400 WARNING: AUC difference > 5%. This may indicate overfitting.
0:18:49.272781 INFO: Resetting torch num_threads to 80
0:18:49.275250 PROGRESS: === Extracted 2751 precursors and 13038 fragments ===
0:18:49.275595 INFO: === FDR correction performed with classifier version -1 ===
0:18:49.276063 PROGRESS: ============================= Precursor FDR =============================
0:18:49.276152 PROGRESS: Total precursors accumulated: 2
0:18:49.276213 PROGRESS: Target precursors: 2 (100.00%)
0:18:49.276263 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:49.276308 PROGRESS: 
0:18:49.276352 PROGRESS: Precursor Summary:
0:18:49.277275 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:18:49.277364 PROGRESS: 
0:18:49.277420 PROGRESS: Protein Summary:
0:18:49.278435 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:18:49.278526 PROGRESS: =========================================================================
0:18:49.278737 INFO: Target number of precursors not reached yet.
0:18:49.347867 INFO: Starting optimization step 3.
0:18:49.348078 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:18:49.348155 INFO: Using ng extraction backend
0:18:49.348215 PROGRESS: Extracting batch of 3177 precursors
0:18:49.355202 INFO: === Search parameters used ===
0:18:49.355325 INFO: rt_error       : 805.5982666015625
0:18:49.355375 INFO: mobility_error : 0.1
0:18:49.355422 INFO: num_candidates : 1
0:18:49.355464 INFO: ms1_error      : 30
0:18:49.355504 INFO: ms2_error      : 30
0:18:49.355560 INFO: fwhm_rt        : 5
0:18:49.355603 INFO: quant_window   : 3
0:18:49.355642 INFO: ==============================================
0:18:49.402581 INFO: performing precursor FDR with 40 features
0:18:49.402673 INFO: Decoy channel: -1
0:18:49.402697 INFO: Competetive: True
0:18:49.406769 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:49.408977 INFO: Using random state 29506 for train-test-split
0:18:49.428159 INFO: Test AUC: 0.488
0:18:49.428234 INFO: Train AUC: 0.503
0:18:49.428263 INFO: AUC difference: 3.10%
0:18:49.639965 INFO: Resetting torch num_threads to 80
0:18:49.643121 PROGRESS: === Extracted 5898 precursors and 28051 fragments ===
0:18:49.643466 INFO: === FDR correction performed with classifier version -1 ===
0:18:49.643923 PROGRESS: ============================= Precursor FDR =============================
0:18:49.644013 PROGRESS: Total precursors accumulated: 2
0:18:49.644073 PROGRESS: Target precursors: 2 (100.00%)
0:18:49.644123 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:49.644171 PROGRESS: 
0:18:49.644216 PROGRESS: Precursor Summary:
0:18:49.645147 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:18:49.645236 PROGRESS: 
0:18:49.645288 PROGRESS: Protein Summary:
0:18:49.646296 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:18:49.646387 PROGRESS: =========================================================================
0:18:49.646630 INFO: Target number of precursors not reached yet.
0:18:49.719840 INFO: Starting optimization step 4.
0:18:49.720061 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:18:49.720140 INFO: Using ng extraction backend
0:18:49.720206 PROGRESS: Extracting batch of 6340 precursors
0:18:49.732619 INFO: === Search parameters used ===
0:18:49.732758 INFO: rt_error       : 805.5982666015625
0:18:49.732810 INFO: mobility_error : 0.1
0:18:49.732858 INFO: num_candidates : 1
0:18:49.732901 INFO: ms1_error      : 30
0:18:49.732943 INFO: ms2_error      : 30
0:18:49.732984 INFO: fwhm_rt        : 5
0:18:49.733037 INFO: quant_window   : 3
0:18:49.733078 INFO: ==============================================
0:18:49.811372 INFO: performing precursor FDR with 40 features
0:18:49.811515 INFO: Decoy channel: -1
0:18:49.811543 INFO: Competetive: True
0:18:49.818430 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:49.822714 INFO: Using random state 600554 for train-test-split
0:18:49.862393 INFO: Test AUC: 0.501
0:18:49.862513 INFO: Train AUC: 0.499
0:18:49.862543 INFO: AUC difference: 0.24%
0:18:50.081374 INFO: Resetting torch num_threads to 80
0:18:50.085665 PROGRESS: === Extracted 12176 precursors and 57532 fragments ===
0:18:50.086021 INFO: === FDR correction performed with classifier version -1 ===
0:18:50.086462 PROGRESS: ============================= Precursor FDR =============================
0:18:50.086550 PROGRESS: Total precursors accumulated: 0
0:18:50.086610 PROGRESS: Target precursors: 0 (0.00%)
0:18:50.086661 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:50.086706 PROGRESS: 
0:18:50.086751 PROGRESS: Precursor Summary:
0:18:50.086855 PROGRESS: 
0:18:50.086916 PROGRESS: Protein Summary:
0:18:50.086987 PROGRESS: =========================================================================
0:18:50.087272 INFO: Target number of precursors not reached yet.
0:18:50.168930 INFO: Starting optimization step 5.
0:18:50.169175 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:18:50.169256 INFO: Using ng extraction backend
0:18:50.169318 PROGRESS: Extracting batch of 12663 precursors
0:18:50.192676 INFO: === Search parameters used ===
0:18:50.192840 INFO: rt_error       : 805.5982666015625
0:18:50.192891 INFO: mobility_error : 0.1
0:18:50.192937 INFO: num_candidates : 1
0:18:50.192979 INFO: ms1_error      : 30
0:18:50.193044 INFO: ms2_error      : 30
0:18:50.193086 INFO: fwhm_rt        : 5
0:18:50.193126 INFO: quant_window   : 3
0:18:50.193168 INFO: ==============================================
0:18:50.303705 INFO: performing precursor FDR with 40 features
0:18:50.303815 INFO: Decoy channel: -1
0:18:50.303841 INFO: Competetive: True
0:18:50.313587 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:50.319533 INFO: Using random state 314884 for train-test-split
0:18:50.547983 INFO: Test AUC: 0.527
0:18:50.548094 INFO: Train AUC: 0.540
0:18:50.548123 INFO: AUC difference: 2.35%
0:18:50.773683 INFO: Resetting torch num_threads to 80
0:18:50.779823 PROGRESS: === Extracted 24724 precursors and 116398 fragments ===
0:18:50.780241 INFO: === FDR correction performed with classifier version -1 ===
0:18:50.780736 PROGRESS: ============================= Precursor FDR =============================
0:18:50.780852 PROGRESS: Total precursors accumulated: 51
0:18:50.780914 PROGRESS: Target precursors: 51 (100.00%)
0:18:50.780965 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:50.781031 PROGRESS: 
0:18:50.781093 PROGRESS: Precursor Summary:
0:18:50.782030 PROGRESS: Channel   0:	 0.050 FDR:    51; 0.010 FDR:    51; 0.001 FDR:    51
0:18:50.782125 PROGRESS: 
0:18:50.782182 PROGRESS: Protein Summary:
0:18:50.783220 PROGRESS: Channel   0:	 0.050 FDR:    51; 0.010 FDR:    51; 0.001 FDR:    51
0:18:50.783309 PROGRESS: =========================================================================
0:18:50.783747 INFO: Target number of precursors not reached yet.
0:18:50.881089 INFO: Starting optimization step 6.
0:18:50.881322 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:18:50.881403 INFO: Using ng extraction backend
0:18:50.881467 PROGRESS: Extracting batch of 25339 precursors
0:18:50.926178 INFO: === Search parameters used ===
0:18:50.926380 INFO: rt_error       : 805.5982666015625
0:18:50.926435 INFO: mobility_error : 0.1
0:18:50.926483 INFO: num_candidates : 1
0:18:50.926527 INFO: ms1_error      : 30
0:18:50.926568 INFO: ms2_error      : 30
0:18:50.926609 INFO: fwhm_rt        : 5
0:18:50.926649 INFO: quant_window   : 3
0:18:50.926687 INFO: ==============================================
0:18:51.135039 INFO: performing precursor FDR with 40 features
0:18:51.135153 INFO: Decoy channel: -1
0:18:51.135179 INFO: Competetive: True
0:18:51.152832 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:51.164646 INFO: Using random state 944791 for train-test-split
0:18:51.725313 INFO: Test AUC: 0.558
0:18:51.725426 INFO: Train AUC: 0.583
0:18:51.725456 INFO: AUC difference: 4.27%
0:18:51.956187 INFO: Resetting torch num_threads to 80
0:18:51.965877 PROGRESS: === Extracted 49832 precursors and 234547 fragments ===
0:18:51.966427 INFO: === FDR correction performed with classifier version -1 ===
0:18:51.966924 PROGRESS: ============================= Precursor FDR =============================
0:18:51.967012 PROGRESS: Total precursors accumulated: 111
0:18:51.967086 PROGRESS: Target precursors: 110 (99.10%)
0:18:51.967141 PROGRESS: Decoy precursors: 1 (0.90%)
0:18:51.967186 PROGRESS: 
0:18:51.967232 PROGRESS: Precursor Summary:
0:18:51.968108 PROGRESS: Channel   0:	 0.050 FDR:   110; 0.010 FDR:   110; 0.001 FDR:   105
0:18:51.968200 PROGRESS: 
0:18:51.968256 PROGRESS: Protein Summary:
0:18:51.969260 PROGRESS: Channel   0:	 0.050 FDR:   108; 0.010 FDR:   108; 0.001 FDR:   103
0:18:51.969352 PROGRESS: =========================================================================
0:18:51.970126 INFO: Target number of precursors not reached yet.
0:18:52.102565 INFO: Starting optimization step 7.
0:18:52.102803 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:18:52.102884 INFO: Using ng extraction backend
0:18:52.102948 PROGRESS: Extracting batch of 50691 precursors
0:18:52.190133 INFO: === Search parameters used ===
0:18:52.190369 INFO: rt_error       : 805.5982666015625
0:18:52.190422 INFO: mobility_error : 0.1
0:18:52.190467 INFO: num_candidates : 1
0:18:52.190510 INFO: ms1_error      : 30
0:18:52.190552 INFO: ms2_error      : 30
0:18:52.190593 INFO: fwhm_rt        : 5
0:18:52.190634 INFO: quant_window   : 3
0:18:52.190688 INFO: ==============================================
0:18:52.523561 INFO: performing precursor FDR with 40 features
0:18:52.523687 INFO: Decoy channel: -1
0:18:52.523713 INFO: Competetive: True
0:18:52.559972 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:52.584313 INFO: Using random state 913985 for train-test-split
0:18:53.847198 INFO: Test AUC: 0.581
0:18:53.847319 INFO: Train AUC: 0.599
0:18:53.847350 INFO: AUC difference: 3.01%
0:18:54.102648 INFO: Resetting torch num_threads to 80
0:18:54.120726 PROGRESS: === Extracted 100023 precursors and 471000 fragments ===
0:18:54.121313 INFO: === FDR correction performed with classifier version -1 ===
0:18:54.121907 PROGRESS: ============================= Precursor FDR =============================
0:18:54.122009 PROGRESS: Total precursors accumulated: 285
0:18:54.122072 PROGRESS: Target precursors: 283 (99.30%)
0:18:54.122123 PROGRESS: Decoy precursors: 2 (0.70%)
0:18:54.122169 PROGRESS: 
0:18:54.122215 PROGRESS: Precursor Summary:
0:18:54.123167 PROGRESS: Channel   0:	 0.050 FDR:   283; 0.010 FDR:   283; 0.001 FDR:   271
0:18:54.123263 PROGRESS: 
0:18:54.123322 PROGRESS: Protein Summary:
0:18:54.124418 PROGRESS: Channel   0:	 0.050 FDR:   266; 0.010 FDR:   266; 0.001 FDR:   254
0:18:54.124509 PROGRESS: =========================================================================
0:18:54.125998 INFO: Target number of precursors reached.
0:18:54.161288 INFO: fragments_df: keeping 2413 of 471000 [sum(precursor_idx_mask)=3109 sum(mass_error_mask)=471000 stop_rank=2413
0:18:54.364786 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:54.484726 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:54.801351 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:18:54.801760 INFO: Using score_cutoff 14.510643231582641 (fac=0.99, q=1)
0:18:54.802069 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:18:54.802150 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:18:54.802204 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.510643231582641
0:18:54.802260 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:54.864700 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:55.020163 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:18:55.020403 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:18:55.020492 INFO: Starting optimization step 8.
0:18:55.020554 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:18:55.020621 INFO: Using ng extraction backend
0:18:55.020680 PROGRESS: Extracting batch of 100984 precursors
0:18:55.193456 INFO: === Search parameters used ===
0:18:55.193694 INFO: rt_error       : 805.5982666015625
0:18:55.193747 INFO: mobility_error : 0.1
0:18:55.193793 INFO: num_candidates : 3
0:18:55.193834 INFO: ms1_error      : 30
0:18:55.193873 INFO: ms2_error      : 30
0:18:55.193913 INFO: fwhm_rt        : 3.0
0:18:55.193954 INFO: quant_window   : 3
0:18:55.193997 INFO: ==============================================
0:18:56.445058 INFO: performing precursor FDR with 40 features
0:18:56.445171 INFO: Decoy channel: -1
0:18:56.445196 INFO: Competetive: True
0:18:56.523466 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:56.618295 INFO: Using random state 911501 for train-test-split
0:19:00.467468 INFO: Test AUC: 0.592
0:19:00.467590 INFO: Train AUC: 0.606
0:19:00.467621 INFO: AUC difference: 2.36%
0:19:00.778458 INFO: Resetting torch num_threads to 80
0:19:00.790205 PROGRESS: === Extracted 300250 precursors and 1383332 fragments ===
0:19:00.790596 INFO: === FDR correction performed with classifier version 7 ===
0:19:00.791064 PROGRESS: ============================= Precursor FDR =============================
0:19:00.791153 PROGRESS: Total precursors accumulated: 350
0:19:00.791211 PROGRESS: Target precursors: 347 (99.14%)
0:19:00.791260 PROGRESS: Decoy precursors: 3 (0.86%)
0:19:00.791304 PROGRESS: 
0:19:00.791348 PROGRESS: Precursor Summary:
0:19:00.792264 PROGRESS: Channel   0:	 0.050 FDR:   347; 0.010 FDR:   347; 0.001 FDR:   294
0:19:00.792352 PROGRESS: 
0:19:00.792407 PROGRESS: Protein Summary:
0:19:00.793507 PROGRESS: Channel   0:	 0.050 FDR:   324; 0.010 FDR:   324; 0.001 FDR:   276
0:19:00.793602 PROGRESS: =========================================================================
0:19:00.798266 INFO: Target number of precursors reached.
0:19:00.891848 INFO: fragments_df: keeping 4112 of 1383332 [sum(precursor_idx_mask)=7912 sum(mass_error_mask)=1383332 stop_rank=4112
0:19:01.103205 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:01.209552 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:01.680118 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:01.680532 INFO: Using score_cutoff 14.935311100387572 (fac=0.99, q=1)
0:19:01.680814 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:01.680894 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:01.680962 INFO: Updating optimization_manager: score_cutoff        : 14.510643231582641 -> 14.935311100387572
0:19:01.681029 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:01.743100 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:01.886053 INFO: === checking if optimization conditions were reached ===
0:19:01.888008 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:19:01.888109 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:19:01.888173 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:19:01.888233 INFO: ==============================================
0:19:01.888296 INFO: Starting optimization step 9.
0:19:01.888353 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:19:01.888411 INFO: Using ng extraction backend
0:19:01.888467 PROGRESS: Extracting batch of 100984 precursors
0:19:02.060438 INFO: === Search parameters used ===
0:19:02.060685 INFO: rt_error       : 805.5982666015625
0:19:02.060737 INFO: mobility_error : 0.1
0:19:02.060785 INFO: num_candidates : 3
0:19:02.060828 INFO: ms1_error      : 30
0:19:02.060871 INFO: ms2_error      : 10.0
0:19:02.060911 INFO: fwhm_rt        : 3.0
0:19:02.060952 INFO: quant_window   : 3
0:19:02.061016 INFO: ==============================================
0:19:03.262630 INFO: performing precursor FDR with 40 features
0:19:03.262744 INFO: Decoy channel: -1
0:19:03.262770 INFO: Competetive: True
0:19:03.335278 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:03.434355 INFO: Using random state 939702 for train-test-split
0:19:07.558925 INFO: Test AUC: 0.593
0:19:07.559049 INFO: Train AUC: 0.608
0:19:07.559081 INFO: AUC difference: 2.48%
0:19:07.872381 INFO: Resetting torch num_threads to 80
0:19:07.882883 PROGRESS: === Extracted 302362 precursors and 1621629 fragments ===
0:19:07.883271 INFO: === FDR correction performed with classifier version 8 ===
0:19:07.883741 PROGRESS: ============================= Precursor FDR =============================
0:19:07.883830 PROGRESS: Total precursors accumulated: 432
0:19:07.883887 PROGRESS: Target precursors: 428 (99.07%)
0:19:07.883937 PROGRESS: Decoy precursors: 4 (0.93%)
0:19:07.883980 PROGRESS: 
0:19:07.884023 PROGRESS: Precursor Summary:
0:19:07.884925 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   428; 0.001 FDR:    45
0:19:07.885026 PROGRESS: 
0:19:07.885082 PROGRESS: Protein Summary:
0:19:07.886141 PROGRESS: Channel   0:	 0.050 FDR:   395; 0.010 FDR:   395; 0.001 FDR:    45
0:19:07.886230 PROGRESS: =========================================================================
0:19:07.890864 INFO: Target number of precursors reached.
0:19:07.995916 INFO: fragments_df: keeping 5000 of 1621629 [sum(precursor_idx_mask)=10603 sum(mass_error_mask)=1621629 stop_rank=5000
0:19:08.136443 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:08.263099 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:08.937020 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:08.937431 INFO: Using score_cutoff 14.857107713127135 (fac=0.99, q=1)
0:19:08.937728 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:08.937817 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:08.937873 INFO: Updating optimization_manager: score_cutoff        : 14.935311100387572 -> 14.857107713127135
0:19:08.937927 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:08.968512 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:09.033973 INFO: === checking if optimization conditions were reached ===
0:19:09.035996 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:19:09.036099 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:19:09.036164 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:19:09.036223 INFO: ==============================================
0:19:09.036288 PROGRESS: Optimization finished for ms2_error.
0:19:09.168941 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:09.199848 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:09.265069 INFO: Starting optimization step 0.
0:19:09.265300 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:19:09.265379 INFO: Using ng extraction backend
0:19:09.265447 PROGRESS: Extracting batch of 50293 precursors
0:19:09.352469 INFO: === Search parameters used ===
0:19:09.352719 INFO: rt_error       : 805.5982666015625
0:19:09.352781 INFO: mobility_error : 0.1
0:19:09.352832 INFO: num_candidates : 3
0:19:09.352889 INFO: ms1_error      : 30
0:19:09.352934 INFO: ms2_error      : 10.0
0:19:09.352975 INFO: fwhm_rt        : 3.0
0:19:09.353026 INFO: quant_window   : 3
0:19:09.353067 INFO: ==============================================
0:19:09.973182 INFO: performing precursor FDR with 40 features
0:19:09.973299 INFO: Decoy channel: -1
0:19:09.973325 INFO: Competetive: True
0:19:10.011530 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:10.052299 INFO: Using random state 980416 for train-test-split
0:19:11.988683 INFO: Test AUC: 0.596
0:19:11.988789 INFO: Train AUC: 0.621
0:19:11.988818 INFO: AUC difference: 4.07%
0:19:12.255800 INFO: Resetting torch num_threads to 80
0:19:12.261537 PROGRESS: === Extracted 150570 precursors and 808305 fragments ===
0:19:12.261887 INFO: === FDR correction performed with classifier version 9 ===
0:19:12.262320 PROGRESS: ============================= Precursor FDR =============================
0:19:12.262407 PROGRESS: Total precursors accumulated: 209
0:19:12.262464 PROGRESS: Target precursors: 207 (99.04%)
0:19:12.262514 PROGRESS: Decoy precursors: 2 (0.96%)
0:19:12.262557 PROGRESS: 
0:19:12.262601 PROGRESS: Precursor Summary:
0:19:12.263435 PROGRESS: Channel   0:	 0.050 FDR:   207; 0.010 FDR:   207; 0.001 FDR:     0
0:19:12.263520 PROGRESS: 
0:19:12.263574 PROGRESS: Protein Summary:
0:19:12.264539 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   200; 0.001 FDR:     0
0:19:12.264627 PROGRESS: =========================================================================
0:19:12.266537 INFO: Target number of precursors reached.
0:19:12.321374 INFO: fragments_df: keeping 2435 of 808305 [sum(precursor_idx_mask)=5117 sum(mass_error_mask)=808305 stop_rank=2435
0:19:12.456933 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:12.574367 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:12.892315 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:12.892720 INFO: Using score_cutoff 15.055156921577453 (fac=0.99, q=1)
0:19:12.893009 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:12.893092 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:12.893147 INFO: Updating optimization_manager: score_cutoff        : 14.857107713127135 -> 15.055156921577453
0:19:12.893201 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:12.923740 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:12.991262 INFO: === checking if optimization conditions were reached ===
0:19:12.991507 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:19:12.993259 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 86.64777867784825
0:19:12.993361 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 86.6478.
0:19:12.993427 INFO: ==============================================
0:19:12.993495 INFO: Starting optimization step 1.
0:19:12.993556 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:19:12.993618 INFO: Using ng extraction backend
0:19:12.993673 PROGRESS: Extracting batch of 50293 precursors
0:19:13.080585 INFO: === Search parameters used ===
0:19:13.080822 INFO: rt_error       : 86.64777867784825
0:19:13.080889 INFO: mobility_error : 0.1
0:19:13.080936 INFO: num_candidates : 3
0:19:13.080979 INFO: ms1_error      : 30
0:19:13.081031 INFO: ms2_error      : 10.0
0:19:13.081071 INFO: fwhm_rt        : 3.0
0:19:13.081109 INFO: quant_window   : 3
0:19:13.081147 INFO: ==============================================
0:19:13.662050 INFO: performing precursor FDR with 40 features
0:19:13.662165 INFO: Decoy channel: -1
0:19:13.662192 INFO: Competetive: True
0:19:13.699070 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:13.733603 INFO: Using random state 980416 for train-test-split
0:19:15.857349 INFO: Test AUC: 0.594
0:19:15.857470 INFO: Train AUC: 0.611
0:19:15.857498 INFO: AUC difference: 2.77%
0:19:16.116498 INFO: Resetting torch num_threads to 80
0:19:16.122310 PROGRESS: === Extracted 146252 precursors and 582464 fragments ===
0:19:16.122652 INFO: === FDR correction performed with classifier version 9 ===
0:19:16.123094 PROGRESS: ============================= Precursor FDR =============================
0:19:16.123181 PROGRESS: Total precursors accumulated: 260
0:19:16.123238 PROGRESS: Target precursors: 258 (99.23%)
0:19:16.123288 PROGRESS: Decoy precursors: 2 (0.77%)
0:19:16.123331 PROGRESS: 
0:19:16.123375 PROGRESS: Precursor Summary:
0:19:16.124246 PROGRESS: Channel   0:	 0.050 FDR:   258; 0.010 FDR:   258; 0.001 FDR:   173
0:19:16.124333 PROGRESS: 
0:19:16.124386 PROGRESS: Protein Summary:
0:19:16.125421 PROGRESS: Channel   0:	 0.050 FDR:   249; 0.010 FDR:   249; 0.001 FDR:   165
0:19:16.125521 PROGRESS: =========================================================================
0:19:16.127424 INFO: Target number of precursors reached.
0:19:16.167662 INFO: fragments_df: keeping 2836 of 582464 [sum(precursor_idx_mask)=5966 sum(mass_error_mask)=582464 stop_rank=2836
0:19:16.301741 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:16.401236 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:16.725144 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:16.725559 INFO: Using score_cutoff 13.420294767093658 (fac=0.99, q=1)
0:19:16.725839 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:16.725916 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:16.725968 INFO: Updating optimization_manager: score_cutoff        : 15.055156921577453 -> 13.420294767093658
0:19:16.726023 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:16.756945 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:16.823395 INFO: === checking if optimization conditions were reached ===
0:19:16.823658 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:19:16.825824 INFO: Updating optimization_manager: rt_error            : 86.64777867784825 -> 67.75699942215172
0:19:16.825940 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 67.7570.
0:19:16.826016 INFO: ==============================================
0:19:16.826095 INFO: Starting optimization step 2.
0:19:16.826162 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:19:16.826231 INFO: Using ng extraction backend
0:19:16.826298 PROGRESS: Extracting batch of 50293 precursors
0:19:16.913687 INFO: === Search parameters used ===
0:19:16.913952 INFO: rt_error       : 67.75699942215172
0:19:16.914012 INFO: mobility_error : 0.1
0:19:16.914060 INFO: num_candidates : 3
0:19:16.914104 INFO: ms1_error      : 30
0:19:16.914144 INFO: ms2_error      : 10.0
0:19:16.914184 INFO: fwhm_rt        : 3.0
0:19:16.914222 INFO: quant_window   : 3
0:19:16.914260 INFO: ==============================================
0:19:17.483371 INFO: performing precursor FDR with 40 features
0:19:17.483488 INFO: Decoy channel: -1
0:19:17.483514 INFO: Competetive: True
0:19:17.519591 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:17.552320 INFO: Using random state 980416 for train-test-split
0:19:19.476058 INFO: Test AUC: 0.590
0:19:19.476179 INFO: Train AUC: 0.613
0:19:19.476209 INFO: AUC difference: 3.79%
0:19:19.736406 INFO: Resetting torch num_threads to 80
0:19:19.742302 PROGRESS: === Extracted 144302 precursors and 549706 fragments ===
0:19:19.742646 INFO: === FDR correction performed with classifier version 9 ===
0:19:19.743096 PROGRESS: ============================= Precursor FDR =============================
0:19:19.743184 PROGRESS: Total precursors accumulated: 254
0:19:19.743240 PROGRESS: Target precursors: 252 (99.21%)
0:19:19.743289 PROGRESS: Decoy precursors: 2 (0.79%)
0:19:19.743334 PROGRESS: 
0:19:19.743378 PROGRESS: Precursor Summary:
0:19:19.744256 PROGRESS: Channel   0:	 0.050 FDR:   252; 0.010 FDR:   252; 0.001 FDR:   185
0:19:19.744343 PROGRESS: 
0:19:19.744396 PROGRESS: Protein Summary:
0:19:19.745433 PROGRESS: Channel   0:	 0.050 FDR:   245; 0.010 FDR:   245; 0.001 FDR:   179
0:19:19.745523 PROGRESS: =========================================================================
0:19:19.747416 INFO: Target number of precursors reached.
0:19:19.784761 INFO: fragments_df: keeping 2721 of 549706 [sum(precursor_idx_mask)=5653 sum(mass_error_mask)=549706 stop_rank=2721
0:19:19.925061 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:20.024704 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:20.383347 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:20.383750 INFO: Using score_cutoff 12.860718665027617 (fac=0.99, q=1)
0:19:20.384029 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:20.384116 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:20.384170 INFO: Updating optimization_manager: score_cutoff        : 13.420294767093658 -> 12.860718665027617
0:19:20.384223 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:20.415241 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:20.482560 INFO: === checking if optimization conditions were reached ===
0:19:20.482822 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:19:20.485120 INFO: Updating optimization_manager: rt_error            : 67.75699942215172 -> 51.28906628467523
0:19:20.485237 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 51.2891.
0:19:20.485313 INFO: ==============================================
0:19:20.485392 INFO: Starting optimization step 3.
0:19:20.485462 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:19:20.485551 INFO: Using ng extraction backend
0:19:20.485618 PROGRESS: Extracting batch of 50293 precursors
0:19:20.574776 INFO: === Search parameters used ===
0:19:20.575016 INFO: rt_error       : 51.28906628467523
0:19:20.575073 INFO: mobility_error : 0.1
0:19:20.575123 INFO: num_candidates : 3
0:19:20.575166 INFO: ms1_error      : 30
0:19:20.575205 INFO: ms2_error      : 10.0
0:19:20.575245 INFO: fwhm_rt        : 3.0
0:19:20.575284 INFO: quant_window   : 3
0:19:20.575323 INFO: ==============================================
0:19:21.099826 INFO: performing precursor FDR with 40 features
0:19:21.099941 INFO: Decoy channel: -1
0:19:21.099967 INFO: Competetive: True
0:19:21.134722 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:21.165403 INFO: Using random state 980416 for train-test-split
0:19:23.030356 INFO: Test AUC: 0.590
0:19:23.030470 INFO: Train AUC: 0.612
0:19:23.030499 INFO: AUC difference: 3.55%
0:19:23.287349 INFO: Resetting torch num_threads to 80
0:19:23.293239 PROGRESS: === Extracted 136243 precursors and 492281 fragments ===
0:19:23.293589 INFO: === FDR correction performed with classifier version 9 ===
0:19:23.294036 PROGRESS: ============================= Precursor FDR =============================
0:19:23.294123 PROGRESS: Total precursors accumulated: 263
0:19:23.294180 PROGRESS: Target precursors: 261 (99.24%)
0:19:23.294242 PROGRESS: Decoy precursors: 2 (0.76%)
0:19:23.294313 PROGRESS: 
0:19:23.294362 PROGRESS: Precursor Summary:
0:19:23.295252 PROGRESS: Channel   0:	 0.050 FDR:   261; 0.010 FDR:   261; 0.001 FDR:   218
0:19:23.295340 PROGRESS: 
0:19:23.295393 PROGRESS: Protein Summary:
0:19:23.296486 PROGRESS: Channel   0:	 0.050 FDR:   250; 0.010 FDR:   250; 0.001 FDR:   212
0:19:23.296574 PROGRESS: =========================================================================
0:19:23.299055 INFO: Target number of precursors reached.
0:19:23.332229 INFO: fragments_df: keeping 2599 of 492281 [sum(precursor_idx_mask)=5453 sum(mass_error_mask)=492281 stop_rank=2599
0:19:23.495422 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:24.430523 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:24.715322 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:24.715731 INFO: Using score_cutoff 11.71250489616394 (fac=0.99, q=1)
0:19:24.716012 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:24.716092 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:24.716147 INFO: Updating optimization_manager: score_cutoff        : 12.860718665027617 -> 11.71250489616394
0:19:24.716202 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:24.746905 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:24.810870 INFO: === checking if optimization conditions were reached ===
0:19:24.811133 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:19:24.813408 INFO: Updating optimization_manager: rt_error            : 51.28906628467523 -> 40.04385502886187
0:19:24.813549 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 40.0439.
0:19:24.813628 INFO: ==============================================
0:19:24.813708 INFO: Starting optimization step 4.
0:19:24.813785 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:19:24.813860 INFO: Using ng extraction backend
0:19:24.813928 PROGRESS: Extracting batch of 50293 precursors
0:19:24.903323 INFO: === Search parameters used ===
0:19:24.903569 INFO: rt_error       : 40.04385502886187
0:19:24.903621 INFO: mobility_error : 0.1
0:19:24.903668 INFO: num_candidates : 3
0:19:24.903717 INFO: ms1_error      : 30
0:19:24.903760 INFO: ms2_error      : 10.0
0:19:24.903801 INFO: fwhm_rt        : 3.0
0:19:24.903840 INFO: quant_window   : 3
0:19:24.903878 INFO: ==============================================
0:19:25.426545 INFO: performing precursor FDR with 40 features
0:19:25.426670 INFO: Decoy channel: -1
0:19:25.426697 INFO: Competetive: True
0:19:25.459562 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:25.488866 INFO: Using random state 980416 for train-test-split
0:19:27.183607 INFO: Test AUC: 0.592
0:19:27.183729 INFO: Train AUC: 0.613
0:19:27.183760 INFO: AUC difference: 3.49%
0:19:27.446201 INFO: Resetting torch num_threads to 80
0:19:27.451839 PROGRESS: === Extracted 133794 precursors and 481263 fragments ===
0:19:27.452315 INFO: === FDR correction performed with classifier version 9 ===
0:19:27.452766 PROGRESS: ============================= Precursor FDR =============================
0:19:27.452854 PROGRESS: Total precursors accumulated: 261
0:19:27.452912 PROGRESS: Target precursors: 259 (99.23%)
0:19:27.452961 PROGRESS: Decoy precursors: 2 (0.77%)
0:19:27.453013 PROGRESS: 
0:19:27.453060 PROGRESS: Precursor Summary:
0:19:27.453951 PROGRESS: Channel   0:	 0.050 FDR:   259; 0.010 FDR:   259; 0.001 FDR:   210
0:19:27.454053 PROGRESS: 
0:19:27.454110 PROGRESS: Protein Summary:
0:19:27.455153 PROGRESS: Channel   0:	 0.050 FDR:   250; 0.010 FDR:   250; 0.001 FDR:   204
0:19:27.455241 PROGRESS: =========================================================================
0:19:27.457027 INFO: Target number of precursors reached.
0:19:27.489661 INFO: fragments_df: keeping 2527 of 481263 [sum(precursor_idx_mask)=5226 sum(mass_error_mask)=481263 stop_rank=2527
0:19:27.629333 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:27.729495 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:28.005572 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:28.005980 INFO: Using score_cutoff 11.116088734817506 (fac=0.99, q=1)
0:19:28.006261 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:28.006340 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:28.006395 INFO: Updating optimization_manager: score_cutoff        : 11.71250489616394 -> 11.116088734817506
0:19:28.006454 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:28.037391 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:28.102204 INFO: === checking if optimization conditions were reached ===
0:19:28.102434 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:19:28.104368 INFO: Updating optimization_manager: rt_error            : 40.04385502886187 -> 35.19741625414378
0:19:28.104479 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 35.1974.
0:19:28.104559 INFO: ==============================================
0:19:28.104637 INFO: Starting optimization step 5.
0:19:28.104703 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:19:28.104787 INFO: Using ng extraction backend
0:19:28.104863 PROGRESS: Extracting batch of 50293 precursors
0:19:28.191491 INFO: === Search parameters used ===
0:19:28.191727 INFO: rt_error       : 35.19741625414378
0:19:28.191781 INFO: mobility_error : 0.1
0:19:28.191828 INFO: num_candidates : 3
0:19:28.191871 INFO: ms1_error      : 30
0:19:28.192361 INFO: ms2_error      : 10.0
0:19:28.192408 INFO: fwhm_rt        : 3.0
0:19:28.192449 INFO: quant_window   : 3
0:19:28.192488 INFO: ==============================================
0:19:28.702657 INFO: performing precursor FDR with 40 features
0:19:28.702785 INFO: Decoy channel: -1
0:19:28.702811 INFO: Competetive: True
0:19:28.737683 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:28.772197 INFO: Using random state 980416 for train-test-split
0:19:30.457295 INFO: Test AUC: 0.590
0:19:30.457412 INFO: Train AUC: 0.612
0:19:30.457443 INFO: AUC difference: 3.61%
0:19:30.715226 INFO: Resetting torch num_threads to 80
0:19:30.720819 PROGRESS: === Extracted 134048 precursors and 483186 fragments ===
0:19:30.721175 INFO: === FDR correction performed with classifier version 9 ===
0:19:30.721625 PROGRESS: ============================= Precursor FDR =============================
0:19:30.721717 PROGRESS: Total precursors accumulated: 242
0:19:30.721781 PROGRESS: Target precursors: 240 (99.17%)
0:19:30.721832 PROGRESS: Decoy precursors: 2 (0.83%)
0:19:30.721877 PROGRESS: 
0:19:30.721920 PROGRESS: Precursor Summary:
0:19:30.722803 PROGRESS: Channel   0:	 0.050 FDR:   240; 0.010 FDR:   240; 0.001 FDR:   200
0:19:30.722902 PROGRESS: 
0:19:30.722956 PROGRESS: Protein Summary:
0:19:30.723971 PROGRESS: Channel   0:	 0.050 FDR:   232; 0.010 FDR:   232; 0.001 FDR:   194
0:19:30.724060 PROGRESS: =========================================================================
0:19:30.725861 INFO: Target number of precursors reached.
0:19:30.758980 INFO: fragments_df: keeping 2391 of 483186 [sum(precursor_idx_mask)=4862 sum(mass_error_mask)=483186 stop_rank=2391
0:19:30.892878 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:31.008971 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:31.323151 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:31.323559 INFO: Using score_cutoff 11.525616441822052 (fac=0.99, q=1)
0:19:31.323841 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:31.323920 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:31.323974 INFO: Updating optimization_manager: score_cutoff        : 11.116088734817506 -> 11.525616441822052
0:19:31.324027 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:31.356093 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:31.423195 INFO: === checking if optimization conditions were reached ===
0:19:31.423458 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:19:31.425828 INFO: Updating optimization_manager: rt_error            : 35.19741625414378 -> 32.73114674944846
0:19:31.425972 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 32.7311.
0:19:31.426052 INFO: ==============================================
0:19:31.426136 INFO: Starting optimization step 6.
0:19:31.426211 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:19:31.426292 INFO: Using ng extraction backend
0:19:31.426361 PROGRESS: Extracting batch of 50293 precursors
0:19:31.517082 INFO: === Search parameters used ===
0:19:31.517339 INFO: rt_error       : 32.73114674944846
0:19:31.517396 INFO: mobility_error : 0.1
0:19:31.517443 INFO: num_candidates : 3
0:19:31.517491 INFO: ms1_error      : 30
0:19:31.517534 INFO: ms2_error      : 10.0
0:19:31.517576 INFO: fwhm_rt        : 3.0
0:19:31.517616 INFO: quant_window   : 3
0:19:31.517657 INFO: ==============================================
0:19:32.038586 INFO: performing precursor FDR with 40 features
0:19:32.038701 INFO: Decoy channel: -1
0:19:32.038728 INFO: Competetive: True
0:19:32.071862 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:32.101832 INFO: Using random state 980416 for train-test-split
0:19:33.849771 INFO: Test AUC: 0.593
0:19:33.849921 INFO: Train AUC: 0.614
0:19:33.849952 INFO: AUC difference: 3.42%
0:19:34.113461 INFO: Resetting torch num_threads to 80
0:19:34.119242 PROGRESS: === Extracted 134432 precursors and 488625 fragments ===
0:19:34.119625 INFO: === FDR correction performed with classifier version 9 ===
0:19:34.120068 PROGRESS: ============================= Precursor FDR =============================
0:19:34.120156 PROGRESS: Total precursors accumulated: 260
0:19:34.120214 PROGRESS: Target precursors: 258 (99.23%)
0:19:34.120264 PROGRESS: Decoy precursors: 2 (0.77%)
0:19:34.120317 PROGRESS: 
0:19:34.120362 PROGRESS: Precursor Summary:
0:19:34.121266 PROGRESS: Channel   0:	 0.050 FDR:   258; 0.010 FDR:   258; 0.001 FDR:   182
0:19:34.121359 PROGRESS: 
0:19:34.121414 PROGRESS: Protein Summary:
0:19:34.122455 PROGRESS: Channel   0:	 0.050 FDR:   248; 0.010 FDR:   248; 0.001 FDR:   177
0:19:34.122543 PROGRESS: =========================================================================
0:19:34.124417 INFO: Target number of precursors reached.
0:19:34.158654 INFO: fragments_df: keeping 2504 of 488625 [sum(precursor_idx_mask)=5233 sum(mass_error_mask)=488625 stop_rank=2504
0:19:34.292760 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:34.396523 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:34.670406 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:34.670831 INFO: Using score_cutoff 10.205315104579926 (fac=0.99, q=1)
0:19:34.671152 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:34.671235 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:34.671295 INFO: Updating optimization_manager: score_cutoff        : 11.525616441822052 -> 10.205315104579926
0:19:34.671356 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:34.702948 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:34.767667 INFO: === checking if optimization conditions were reached ===
0:19:34.767908 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:19:34.770314 INFO: Updating optimization_manager: rt_error            : 32.73114674944846 -> 32.779623096468654
0:19:34.770432 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 32.7796.
0:19:34.770510 INFO: ==============================================
0:19:34.770592 INFO: Starting optimization step 7.
0:19:34.770663 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:19:34.770748 INFO: Using ng extraction backend
0:19:34.770825 PROGRESS: Extracting batch of 50293 precursors
0:19:34.861825 INFO: === Search parameters used ===
0:19:34.862060 INFO: rt_error       : 32.779623096468654
0:19:34.862114 INFO: mobility_error : 0.1
0:19:34.862159 INFO: num_candidates : 3
0:19:34.862205 INFO: ms1_error      : 30
0:19:34.862248 INFO: ms2_error      : 10.0
0:19:34.862289 INFO: fwhm_rt        : 3.0
0:19:34.862329 INFO: quant_window   : 3
0:19:34.862368 INFO: ==============================================
0:19:35.389829 INFO: performing precursor FDR with 40 features
0:19:35.389941 INFO: Decoy channel: -1
0:19:35.389966 INFO: Competetive: True
0:19:35.424236 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:35.454595 INFO: Using random state 980416 for train-test-split
0:19:37.195056 INFO: Test AUC: 0.597
0:19:37.195174 INFO: Train AUC: 0.611
0:19:37.195206 INFO: AUC difference: 2.27%
0:19:37.451658 INFO: Resetting torch num_threads to 80
0:19:37.457303 PROGRESS: === Extracted 134586 precursors and 490510 fragments ===
0:19:37.457653 INFO: === FDR correction performed with classifier version 9 ===
0:19:37.458097 PROGRESS: ============================= Precursor FDR =============================
0:19:37.458185 PROGRESS: Total precursors accumulated: 246
0:19:37.458254 PROGRESS: Target precursors: 244 (99.19%)
0:19:37.458306 PROGRESS: Decoy precursors: 2 (0.81%)
0:19:37.458351 PROGRESS: 
0:19:37.458396 PROGRESS: Precursor Summary:
0:19:37.459269 PROGRESS: Channel   0:	 0.050 FDR:   244; 0.010 FDR:   244; 0.001 FDR:   219
0:19:37.459355 PROGRESS: 
0:19:37.459410 PROGRESS: Protein Summary:
0:19:37.460422 PROGRESS: Channel   0:	 0.050 FDR:   237; 0.010 FDR:   237; 0.001 FDR:   214
0:19:37.460517 PROGRESS: =========================================================================
0:19:37.462276 INFO: Target number of precursors reached.
0:19:37.496918 INFO: fragments_df: keeping 2430 of 490510 [sum(precursor_idx_mask)=4998 sum(mass_error_mask)=490510 stop_rank=2430
0:19:37.631108 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:37.729053 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:37.993947 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:37.994360 INFO: Using score_cutoff 12.22518070936203 (fac=0.99, q=1)
0:19:37.994644 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:37.994723 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:37.994777 INFO: Updating optimization_manager: score_cutoff        : 10.205315104579926 -> 12.22518070936203
0:19:37.994831 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:38.026228 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:38.089844 INFO: === checking if optimization conditions were reached ===
0:19:38.090105 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
0:19:38.091402 INFO: Updating optimization_manager: rt_error            : 32.779623096468654 -> 32.73114674944846
0:19:38.091548 INFO: Updating optimization_manager: classifier_version  : 9 -> 16
0:19:38.091655 INFO: Updating optimization_manager: score_cutoff        : 12.22518070936203 -> 10.205315104579926
0:19:38.091757 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:38.091853 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:38.091953 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 32.7311 found after 8 searches.
0:19:38.092025 INFO: ==============================================
0:19:38.092101 PROGRESS: Optimization finished for rt_error.
0:19:38.242370 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:38.274115 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:38.369549 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:19:38.369780 PROGRESS: ==============================================
0:19:38.369861 PROGRESS: ms2_error      : 10.0000
0:19:38.369927 PROGRESS: rt_error       : 32.7311
0:19:38.369982 PROGRESS: ==============================================
0:19:38.370544 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:46.319591 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:20:03.565365 INFO: Using ng extraction backend
0:20:03.565629 PROGRESS: Extracting batch of 12001526 precursors
0:20:19.321235 INFO: === Search parameters used ===
0:20:19.321483 INFO: rt_error       : 32.73114674944846
0:20:19.321547 INFO: mobility_error : 0.1
0:20:19.321598 INFO: num_candidates : 3
0:20:19.321642 INFO: ms1_error      : 30
0:20:19.321686 INFO: ms2_error      : 10.0
0:20:19.321728 INFO: fwhm_rt        : 3.0
0:20:19.321769 INFO: quant_window   : 3
0:20:19.321809 INFO: ==============================================
0:20:41.579327 INFO: Removed 22710272 precursors with score below cutoff 10.205315104579926
0:20:53.294692 INFO: performing precursor FDR with 40 features
0:20:53.294812 INFO: Decoy channel: -1
0:20:53.294838 INFO: Competetive: True
0:20:54.419399 INFO: Setting torch num_threads to 2 for FDR classification task
0:20:58.441218 INFO: Using random state 38098 for train-test-split
0:23:31.639521 INFO: Test AUC: 0.623
0:23:31.639652 INFO: Train AUC: 0.625
0:23:31.639686 INFO: AUC difference: 0.26%
0:23:34.809762 INFO: Resetting torch num_threads to 80
0:23:36.256449 PROGRESS: ============================= Precursor FDR =============================
0:23:36.256682 PROGRESS: Total precursors accumulated: 73,750
0:23:36.256747 PROGRESS: Target precursors: 73,020 (99.01%)
0:23:36.256801 PROGRESS: Decoy precursors: 730 (0.99%)
0:23:36.256848 PROGRESS: 
0:23:36.256907 PROGRESS: Precursor Summary:
0:23:36.277719 PROGRESS: Channel   0:	 0.050 FDR: 73,020; 0.010 FDR: 73,020; 0.001 FDR: 52,312
0:23:36.277950 PROGRESS: 
0:23:36.278012 PROGRESS: Protein Summary:
0:23:36.306457 PROGRESS: Channel   0:	 0.050 FDR: 12,281; 0.010 FDR: 12,281; 0.001 FDR: 9,170
0:23:36.306692 PROGRESS: =========================================================================
0:23:36.366897 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/psm.parquet
0:23:36.518563 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.parquet
0:23:36.727412 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:23:37.379249 PROGRESS: 
0:23:37.379398 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant
0:23:37.379466 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/figures
0:23:37.379627 INFO: Initializing TimingManager
0:23:37.380025 INFO: Initializing RawFileManager
0:23:53.304968 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.
0:23:53.309531 INFO: Determining DIA cycle
0:23:53.325150 INFO: Found cycle with start 0.00 min and length 300.
0:23:53.526357 INFO: RT (min)            : 0.0 - 26.9
0:23:53.526480 INFO: RT duration (sec)   : 1611.2
0:23:53.526509 INFO: RT duration (min)   : 26.9
0:23:53.526535 INFO: Cycle len (scans)   : 300
0:23:53.526555 INFO: Cycle len (sec)     : 1.65
0:23:53.526575 INFO: Number of cycles    : 977
0:23:53.526596 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:23:53.526664 INFO: Creating DIA data object took: 16.146532773971558
0:23:54.712926 INFO: Creating DIA data NG object took: 1.1861107349395752
0:24:07.566900 INFO: Initializing CalibrationManager
0:24:07.567359 INFO: Setting up calibration estimators ..
0:24:07.567427 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:24:07.567541 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'}' ..
0:24:07.567653 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:24:07.567714 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:24:07.567778 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}}' ..
0:24:07.567828 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:24:07.567877 INFO: Done setting up calibration estimators.
0:24:07.568177 INFO: Initializing OptimizationManager
0:24:07.568371 INFO: initial parameter: ms1_error = 30
0:24:07.568432 INFO: initial parameter: ms2_error = 30
0:24:07.568502 INFO: initial parameter: rt_error = 805.6002197265625
0:24:07.568548 INFO: initial parameter: mobility_error = 0.1
0:24:07.568592 INFO: initial parameter: num_candidates = 1
0:24:07.568634 INFO: initial parameter: fwhm_rt = 5
0:24:07.568674 INFO: initial parameter: fwhm_mobility = 0.01
0:24:07.568714 INFO: initial parameter: score_cutoff = 0
0:24:07.568755 INFO: initial parameter: classifier_version = -1
0:24:07.568847 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:24:07.569305 INFO: FDRManager: loading saved state not requested, will be initialized.
0:24:07.569364 INFO: Initializing FDRManager
0:24:07.569425 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:24:11.475165 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:24:12.220355 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:24:12.220758 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
0:24:12.220873 PROGRESS: Starting initial search for precursors.
0:24:12.220958 INFO: Starting optimization step 0.
0:24:12.221033 PROGRESS: === Extracting elution groups 0 to 200 ===
0:24:12.221104 INFO: Using ng extraction backend
0:24:12.221169 PROGRESS: Extracting batch of 396 precursors
0:24:12.223239 INFO: === Search parameters used ===
0:24:12.223336 INFO: rt_error       : 805.6002197265625
0:24:12.223387 INFO: mobility_error : 0.1
0:24:12.223435 INFO: num_candidates : 1
0:24:12.223481 INFO: ms1_error      : 30
0:24:12.223530 INFO: ms2_error      : 30
0:24:12.223576 INFO: fwhm_rt        : 5
0:24:12.223617 INFO: quant_window   : 3
0:24:12.223658 INFO: ==============================================
0:24:12.242752 INFO: performing precursor FDR with 40 features
0:24:12.242858 INFO: Decoy channel: -1
0:24:12.242884 INFO: Competetive: True
0:24:12.243886 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:12.246338 INFO: Using random state 162350 for train-test-split
0:24:12.253789 INFO: Test AUC: 0.554
0:24:12.253844 INFO: Train AUC: 0.482
0:24:12.253875 INFO: AUC difference: 14.92%
0:24:12.253899 WARNING: AUC difference > 5%. This may indicate overfitting.
0:24:12.466380 INFO: Resetting torch num_threads to 80
0:24:12.467729 PROGRESS: === Extracted 393 precursors and 1847 fragments ===
0:24:12.468067 INFO: === FDR correction performed with classifier version -1 ===
0:24:12.468495 PROGRESS: ============================= Precursor FDR =============================
0:24:12.468582 PROGRESS: Total precursors accumulated: 0
0:24:12.468642 PROGRESS: Target precursors: 0 (0.00%)
0:24:12.468693 PROGRESS: Decoy precursors: 0 (0.00%)
0:24:12.468738 PROGRESS: 
0:24:12.468783 PROGRESS: Precursor Summary:
0:24:12.468888 PROGRESS: 
0:24:12.468950 PROGRESS: Protein Summary:
0:24:12.469037 PROGRESS: =========================================================================
0:24:12.469236 INFO: Target number of precursors not reached yet.
0:24:12.533369 INFO: Starting optimization step 1.
0:24:12.533573 PROGRESS: === Extracting elution groups 200 to 600 ===
0:24:12.533652 INFO: Using ng extraction backend
0:24:12.533712 PROGRESS: Extracting batch of 786 precursors
0:24:12.536520 INFO: === Search parameters used ===
0:24:12.536619 INFO: rt_error       : 805.6002197265625
0:24:12.536669 INFO: mobility_error : 0.1
0:24:12.536713 INFO: num_candidates : 1
0:24:12.536756 INFO: ms1_error      : 30
0:24:12.536797 INFO: ms2_error      : 30
0:24:12.536837 INFO: fwhm_rt        : 5
0:24:12.536880 INFO: quant_window   : 3
0:24:12.536918 INFO: ==============================================
0:24:12.581261 INFO: performing precursor FDR with 40 features
0:24:12.581399 INFO: Decoy channel: -1
0:24:12.581437 INFO: Competetive: True
0:24:12.585561 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:12.587165 INFO: Using random state 121758 for train-test-split
0:24:12.595617 INFO: Test AUC: 0.508
0:24:12.595683 INFO: Train AUC: 0.495
0:24:12.595712 INFO: AUC difference: 2.63%
0:24:12.811121 INFO: Resetting torch num_threads to 80
0:24:12.813205 PROGRESS: === Extracted 1172 precursors and 5527 fragments ===
0:24:12.813540 INFO: === FDR correction performed with classifier version -1 ===
0:24:12.813991 PROGRESS: ============================= Precursor FDR =============================
0:24:12.814079 PROGRESS: Total precursors accumulated: 1
0:24:12.814135 PROGRESS: Target precursors: 1 (100.00%)
0:24:12.814184 PROGRESS: Decoy precursors: 0 (0.00%)
0:24:12.814229 PROGRESS: 
0:24:12.814273 PROGRESS: Precursor Summary:
0:24:12.815189 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:24:12.815273 PROGRESS: 
0:24:12.815335 PROGRESS: Protein Summary:
0:24:12.816338 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:24:12.816440 PROGRESS: =========================================================================
0:24:12.816661 INFO: Target number of precursors not reached yet.
0:24:12.883440 INFO: Starting optimization step 2.
0:24:12.883630 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:24:12.883708 INFO: Using ng extraction backend
0:24:12.883769 PROGRESS: Extracting batch of 1592 precursors
0:24:12.888013 INFO: === Search parameters used ===
0:24:12.888122 INFO: rt_error       : 805.6002197265625
0:24:12.888171 INFO: mobility_error : 0.1
0:24:12.888215 INFO: num_candidates : 1
0:24:12.888259 INFO: ms1_error      : 30
0:24:12.888299 INFO: ms2_error      : 30
0:24:12.888340 INFO: fwhm_rt        : 5
0:24:12.888379 INFO: quant_window   : 3
0:24:12.888418 INFO: ==============================================
0:24:12.918883 INFO: performing precursor FDR with 40 features
0:24:12.918960 INFO: Decoy channel: -1
0:24:12.918986 INFO: Competetive: True
0:24:12.922241 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:12.924078 INFO: Using random state 983056 for train-test-split
0:24:12.936472 INFO: Test AUC: 0.504
0:24:12.936545 INFO: Train AUC: 0.498
0:24:12.936579 INFO: AUC difference: 1.28%
0:24:13.144083 INFO: Resetting torch num_threads to 80
0:24:13.146564 PROGRESS: === Extracted 2754 precursors and 13075 fragments ===
0:24:13.146897 INFO: === FDR correction performed with classifier version -1 ===
0:24:13.147351 PROGRESS: ============================= Precursor FDR =============================
0:24:13.147439 PROGRESS: Total precursors accumulated: 1
0:24:13.147498 PROGRESS: Target precursors: 1 (100.00%)
0:24:13.147558 PROGRESS: Decoy precursors: 0 (0.00%)
0:24:13.147607 PROGRESS: 
0:24:13.147651 PROGRESS: Precursor Summary:
0:24:13.148554 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:24:13.148642 PROGRESS: 
0:24:13.148697 PROGRESS: Protein Summary:
0:24:13.149704 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:24:13.149798 PROGRESS: =========================================================================
0:24:13.150041 INFO: Target number of precursors not reached yet.
0:24:13.219365 INFO: Starting optimization step 3.
0:24:13.219573 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:24:13.219651 INFO: Using ng extraction backend
0:24:13.219712 PROGRESS: Extracting batch of 3177 precursors
0:24:13.226784 INFO: === Search parameters used ===
0:24:13.226901 INFO: rt_error       : 805.6002197265625
0:24:13.226952 INFO: mobility_error : 0.1
0:24:13.226997 INFO: num_candidates : 1
0:24:13.227039 INFO: ms1_error      : 30
0:24:13.227078 INFO: ms2_error      : 30
0:24:13.227120 INFO: fwhm_rt        : 5
0:24:13.227161 INFO: quant_window   : 3
0:24:13.227201 INFO: ==============================================
0:24:13.273340 INFO: performing precursor FDR with 40 features
0:24:13.273428 INFO: Decoy channel: -1
0:24:13.273457 INFO: Competetive: True
0:24:13.277454 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:13.279618 INFO: Using random state 693963 for train-test-split
0:24:13.299049 INFO: Test AUC: 0.500
0:24:13.299124 INFO: Train AUC: 0.495
0:24:13.299154 INFO: AUC difference: 0.87%
0:24:13.516129 INFO: Resetting torch num_threads to 80
0:24:13.519416 PROGRESS: === Extracted 5901 precursors and 27847 fragments ===
0:24:13.519756 INFO: === FDR correction performed with classifier version -1 ===
0:24:13.520213 PROGRESS: ============================= Precursor FDR =============================
0:24:13.520302 PROGRESS: Total precursors accumulated: 3
0:24:13.520360 PROGRESS: Target precursors: 3 (100.00%)
0:24:13.520410 PROGRESS: Decoy precursors: 0 (0.00%)
0:24:13.520454 PROGRESS: 
0:24:13.520497 PROGRESS: Precursor Summary:
0:24:13.521423 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
0:24:13.521518 PROGRESS: 
0:24:13.521573 PROGRESS: Protein Summary:
0:24:13.522586 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
0:24:13.522696 PROGRESS: =========================================================================
0:24:13.522965 INFO: Target number of precursors not reached yet.
0:24:13.596625 INFO: Starting optimization step 4.
0:24:13.596841 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:24:13.596922 INFO: Using ng extraction backend
0:24:13.596982 PROGRESS: Extracting batch of 6340 precursors
0:24:13.609483 INFO: === Search parameters used ===
0:24:13.609620 INFO: rt_error       : 805.6002197265625
0:24:13.609671 INFO: mobility_error : 0.1
0:24:13.609729 INFO: num_candidates : 1
0:24:13.609773 INFO: ms1_error      : 30
0:24:13.609813 INFO: ms2_error      : 30
0:24:13.609855 INFO: fwhm_rt        : 5
0:24:13.609894 INFO: quant_window   : 3
0:24:13.609935 INFO: ==============================================
0:24:13.680436 INFO: performing precursor FDR with 40 features
0:24:13.680546 INFO: Decoy channel: -1
0:24:13.680572 INFO: Competetive: True
0:24:13.686750 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:13.689939 INFO: Using random state 368948 for train-test-split
0:24:13.726519 INFO: Test AUC: 0.508
0:24:13.726615 INFO: Train AUC: 0.494
0:24:13.726645 INFO: AUC difference: 2.86%
0:24:13.940147 INFO: Resetting torch num_threads to 80
0:24:13.944440 PROGRESS: === Extracted 12165 precursors and 57133 fragments ===
0:24:13.944809 INFO: === FDR correction performed with classifier version -1 ===
0:24:13.945256 PROGRESS: ============================= Precursor FDR =============================
0:24:13.945348 PROGRESS: Total precursors accumulated: 0
0:24:13.945407 PROGRESS: Target precursors: 0 (0.00%)
0:24:13.945457 PROGRESS: Decoy precursors: 0 (0.00%)
0:24:13.945502 PROGRESS: 
0:24:13.945545 PROGRESS: Precursor Summary:
0:24:13.945651 PROGRESS: 
0:24:13.945710 PROGRESS: Protein Summary:
0:24:13.945782 PROGRESS: =========================================================================
0:24:13.946082 INFO: Target number of precursors not reached yet.
0:24:14.027889 INFO: Starting optimization step 5.
0:24:14.028108 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:24:14.028188 INFO: Using ng extraction backend
0:24:14.028262 PROGRESS: Extracting batch of 12663 precursors
0:24:14.051762 INFO: === Search parameters used ===
0:24:14.051918 INFO: rt_error       : 805.6002197265625
0:24:14.051969 INFO: mobility_error : 0.1
0:24:14.052016 INFO: num_candidates : 1
0:24:14.052058 INFO: ms1_error      : 30
0:24:14.052100 INFO: ms2_error      : 30
0:24:14.052143 INFO: fwhm_rt        : 5
0:24:14.052183 INFO: quant_window   : 3
0:24:14.052224 INFO: ==============================================
0:24:14.178491 INFO: performing precursor FDR with 40 features
0:24:14.178612 INFO: Decoy channel: -1
0:24:14.178640 INFO: Competetive: True
0:24:14.188997 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:14.195001 INFO: Using random state 377746 for train-test-split
0:24:14.421480 INFO: Test AUC: 0.527
0:24:14.421593 INFO: Train AUC: 0.542
0:24:14.421623 INFO: AUC difference: 2.83%
0:24:14.647255 INFO: Resetting torch num_threads to 80
0:24:14.653703 PROGRESS: === Extracted 24723 precursors and 116071 fragments ===
0:24:14.654135 INFO: === FDR correction performed with classifier version -1 ===
0:24:14.654648 PROGRESS: ============================= Precursor FDR =============================
0:24:14.654759 PROGRESS: Total precursors accumulated: 47
0:24:14.654819 PROGRESS: Target precursors: 47 (100.00%)
0:24:14.654870 PROGRESS: Decoy precursors: 0 (0.00%)
0:24:14.654917 PROGRESS: 
0:24:14.654962 PROGRESS: Precursor Summary:
0:24:14.655877 PROGRESS: Channel   0:	 0.050 FDR:    47; 0.010 FDR:    47; 0.001 FDR:    47
0:24:14.655963 PROGRESS: 
0:24:14.656019 PROGRESS: Protein Summary:
0:24:14.657056 PROGRESS: Channel   0:	 0.050 FDR:    47; 0.010 FDR:    47; 0.001 FDR:    47
0:24:14.657158 PROGRESS: =========================================================================
0:24:14.657627 INFO: Target number of precursors not reached yet.
0:24:14.756197 INFO: Starting optimization step 6.
0:24:14.756449 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:24:14.756531 INFO: Using ng extraction backend
0:24:14.756596 PROGRESS: Extracting batch of 25339 precursors
0:24:14.802286 INFO: === Search parameters used ===
0:24:14.802481 INFO: rt_error       : 805.6002197265625
0:24:14.802535 INFO: mobility_error : 0.1
0:24:14.802581 INFO: num_candidates : 1
0:24:14.802625 INFO: ms1_error      : 30
0:24:14.802666 INFO: ms2_error      : 30
0:24:14.802705 INFO: fwhm_rt        : 5
0:24:14.802746 INFO: quant_window   : 3
0:24:14.802787 INFO: ==============================================
0:24:15.040769 INFO: performing precursor FDR with 40 features
0:24:15.040926 INFO: Decoy channel: -1
0:24:15.040954 INFO: Competetive: True
0:24:15.063956 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:15.079781 INFO: Using random state 689188 for train-test-split
0:24:15.719332 INFO: Test AUC: 0.558
0:24:15.719444 INFO: Train AUC: 0.577
0:24:15.719474 INFO: AUC difference: 3.39%
0:24:15.948593 INFO: Resetting torch num_threads to 80
0:24:15.959043 PROGRESS: === Extracted 49768 precursors and 233056 fragments ===
0:24:15.959600 INFO: === FDR correction performed with classifier version -1 ===
0:24:15.960109 PROGRESS: ============================= Precursor FDR =============================
0:24:15.960198 PROGRESS: Total precursors accumulated: 101
0:24:15.960257 PROGRESS: Target precursors: 100 (99.01%)
0:24:15.960310 PROGRESS: Decoy precursors: 1 (0.99%)
0:24:15.960355 PROGRESS: 
0:24:15.960410 PROGRESS: Precursor Summary:
0:24:15.961312 PROGRESS: Channel   0:	 0.050 FDR:   100; 0.010 FDR:    10; 0.001 FDR:    10
0:24:15.961402 PROGRESS: 
0:24:15.961457 PROGRESS: Protein Summary:
0:24:15.962417 PROGRESS: Channel   0:	 0.050 FDR:    98; 0.010 FDR:    10; 0.001 FDR:    10
0:24:15.962506 PROGRESS: =========================================================================
0:24:15.963314 INFO: Target number of precursors not reached yet.
0:24:16.097843 INFO: Starting optimization step 7.
0:24:16.098074 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:24:16.098155 INFO: Using ng extraction backend
0:24:16.098220 PROGRESS: Extracting batch of 50691 precursors
0:24:16.187251 INFO: === Search parameters used ===
0:24:16.187490 INFO: rt_error       : 805.6002197265625
0:24:16.187543 INFO: mobility_error : 0.1
0:24:16.187592 INFO: num_candidates : 1
0:24:16.187635 INFO: ms1_error      : 30
0:24:16.187680 INFO: ms2_error      : 30
0:24:16.187725 INFO: fwhm_rt        : 5
0:24:16.187765 INFO: quant_window   : 3
0:24:16.187807 INFO: ==============================================
0:24:16.543965 INFO: performing precursor FDR with 40 features
0:24:16.544075 INFO: Decoy channel: -1
0:24:16.544101 INFO: Competetive: True
0:24:16.581396 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:16.609478 INFO: Using random state 559366 for train-test-split
0:24:18.079216 INFO: Test AUC: 0.579
0:24:18.079329 INFO: Train AUC: 0.598
0:24:18.079361 INFO: AUC difference: 3.20%
0:24:18.321103 INFO: Resetting torch num_threads to 80
0:24:18.340234 PROGRESS: === Extracted 99957 precursors and 468918 fragments ===
0:24:18.340805 INFO: === FDR correction performed with classifier version -1 ===
0:24:18.341435 PROGRESS: ============================= Precursor FDR =============================
0:24:18.341540 PROGRESS: Total precursors accumulated: 330
0:24:18.341600 PROGRESS: Target precursors: 327 (99.09%)
0:24:18.341652 PROGRESS: Decoy precursors: 3 (0.91%)
0:24:18.341697 PROGRESS: 
0:24:18.341741 PROGRESS: Precursor Summary:
0:24:18.342718 PROGRESS: Channel   0:	 0.050 FDR:   327; 0.010 FDR:   327; 0.001 FDR:   260
0:24:18.342809 PROGRESS: 
0:24:18.342864 PROGRESS: Protein Summary:
0:24:18.343963 PROGRESS: Channel   0:	 0.050 FDR:   304; 0.010 FDR:   304; 0.001 FDR:   243
0:24:18.344056 PROGRESS: =========================================================================
0:24:18.345497 INFO: Target number of precursors reached.
0:24:18.382648 INFO: fragments_df: keeping 2711 of 468918 [sum(precursor_idx_mask)=3510 sum(mass_error_mask)=468918 stop_rank=2711
0:24:18.591108 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:24:18.715392 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:24:19.072463 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:24:19.072876 INFO: Using score_cutoff 13.071926781463624 (fac=0.99, q=1)
0:24:19.073185 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:24:19.073267 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:24:19.073328 INFO: Updating optimization_manager: score_cutoff        : 0 -> 13.071926781463624
0:24:19.073386 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:24:19.137048 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:19.295706 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:24:19.295959 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:24:19.296059 INFO: Starting optimization step 8.
0:24:19.296128 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:24:19.296202 INFO: Using ng extraction backend
0:24:19.296268 PROGRESS: Extracting batch of 100984 precursors
0:24:19.477871 INFO: === Search parameters used ===
0:24:19.478127 INFO: rt_error       : 805.6002197265625
0:24:19.478188 INFO: mobility_error : 0.1
0:24:19.478236 INFO: num_candidates : 3
0:24:19.478279 INFO: ms1_error      : 30
0:24:19.478320 INFO: ms2_error      : 30
0:24:19.478358 INFO: fwhm_rt        : 3.0
0:24:19.478395 INFO: quant_window   : 3
0:24:19.478432 INFO: ==============================================
0:24:20.751020 INFO: performing precursor FDR with 40 features
0:24:20.751137 INFO: Decoy channel: -1
0:24:20.751164 INFO: Competetive: True
0:24:20.830362 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:20.931479 INFO: Using random state 574095 for train-test-split
0:24:25.229172 INFO: Test AUC: 0.588
0:24:25.229294 INFO: Train AUC: 0.606
0:24:25.229326 INFO: AUC difference: 2.89%
0:24:25.539717 INFO: Resetting torch num_threads to 80
0:24:25.551946 PROGRESS: === Extracted 300116 precursors and 1379199 fragments ===
0:24:25.552346 INFO: === FDR correction performed with classifier version 7 ===
0:24:25.552825 PROGRESS: ============================= Precursor FDR =============================
0:24:25.552924 PROGRESS: Total precursors accumulated: 370
0:24:25.552984 PROGRESS: Target precursors: 367 (99.19%)
0:24:25.553056 PROGRESS: Decoy precursors: 3 (0.81%)
0:24:25.553102 PROGRESS: 
0:24:25.553145 PROGRESS: Precursor Summary:
0:24:25.554060 PROGRESS: Channel   0:	 0.050 FDR:   367; 0.010 FDR:   367; 0.001 FDR:   242
0:24:25.554151 PROGRESS: 
0:24:25.554204 PROGRESS: Protein Summary:
0:24:25.555284 PROGRESS: Channel   0:	 0.050 FDR:   342; 0.010 FDR:   342; 0.001 FDR:   225
0:24:25.555373 PROGRESS: =========================================================================
0:24:25.560377 INFO: Target number of precursors reached.
0:24:25.651498 INFO: fragments_df: keeping 4097 of 1379199 [sum(precursor_idx_mask)=7891 sum(mass_error_mask)=1379199 stop_rank=4097
0:24:25.866304 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:24:25.968260 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:24:26.436649 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:24:26.437072 INFO: Using score_cutoff 6.370630937862396 (fac=0.99, q=1)
0:24:26.437375 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:24:26.437456 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:24:26.437511 INFO: Updating optimization_manager: score_cutoff        : 13.071926781463624 -> 6.370630937862396
0:24:26.437566 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:24:26.499105 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:26.649071 INFO: === checking if optimization conditions were reached ===
0:24:26.651033 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:24:26.651137 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:24:26.651221 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:24:26.651283 INFO: ==============================================
0:24:26.651347 INFO: Starting optimization step 9.
0:24:26.651402 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:24:26.651465 INFO: Using ng extraction backend
0:24:26.651524 PROGRESS: Extracting batch of 100984 precursors
0:24:26.826458 INFO: === Search parameters used ===
0:24:26.826695 INFO: rt_error       : 805.6002197265625
0:24:26.826748 INFO: mobility_error : 0.1
0:24:26.826793 INFO: num_candidates : 3
0:24:26.826835 INFO: ms1_error      : 30
0:24:26.826875 INFO: ms2_error      : 10.0
0:24:26.826914 INFO: fwhm_rt        : 3.0
0:24:26.826953 INFO: quant_window   : 3
0:24:26.826993 INFO: ==============================================
0:24:28.096440 INFO: performing precursor FDR with 40 features
0:24:28.096560 INFO: Decoy channel: -1
0:24:28.096586 INFO: Competetive: True
0:24:28.179388 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:28.285405 INFO: Using random state 848153 for train-test-split
0:24:32.340436 INFO: Test AUC: 0.595
0:24:32.340559 INFO: Train AUC: 0.608
0:24:32.340590 INFO: AUC difference: 2.20%
0:24:32.661978 INFO: Resetting torch num_threads to 80
0:24:32.672898 PROGRESS: === Extracted 302331 precursors and 1617873 fragments ===
0:24:32.673312 INFO: === FDR correction performed with classifier version 8 ===
0:24:32.673814 PROGRESS: ============================= Precursor FDR =============================
0:24:32.673904 PROGRESS: Total precursors accumulated: 513
0:24:32.673962 PROGRESS: Target precursors: 508 (99.03%)
0:24:32.674013 PROGRESS: Decoy precursors: 5 (0.97%)
0:24:32.674058 PROGRESS: 
0:24:32.674103 PROGRESS: Precursor Summary:
0:24:32.675052 PROGRESS: Channel   0:	 0.050 FDR:   508; 0.010 FDR:   508; 0.001 FDR:   380
0:24:32.675140 PROGRESS: 
0:24:32.675194 PROGRESS: Protein Summary:
0:24:32.676346 PROGRESS: Channel   0:	 0.050 FDR:   473; 0.010 FDR:   473; 0.001 FDR:   354
0:24:32.676435 PROGRESS: =========================================================================
0:24:32.681418 INFO: Target number of precursors reached.
0:24:32.789031 INFO: fragments_df: keeping 5000 of 1617873 [sum(precursor_idx_mask)=12258 sum(mass_error_mask)=1617873 stop_rank=5000
0:24:32.932595 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:24:33.047474 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:24:33.657438 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:24:33.657853 INFO: Using score_cutoff 12.84779404478073 (fac=0.99, q=1)
0:24:33.658139 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:24:33.658218 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:24:33.658269 INFO: Updating optimization_manager: score_cutoff        : 6.370630937862396 -> 12.84779404478073
0:24:33.658331 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:24:33.688962 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:33.755652 INFO: === checking if optimization conditions were reached ===
0:24:33.757667 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:24:33.757775 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:24:33.757838 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:24:33.757898 INFO: ==============================================
0:24:33.757962 PROGRESS: Optimization finished for ms2_error.
0:24:33.893391 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:24:33.924244 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:33.991611 INFO: Starting optimization step 0.
0:24:33.991837 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:33.991915 INFO: Using ng extraction backend
0:24:33.991976 PROGRESS: Extracting batch of 50293 precursors
0:24:34.079739 INFO: === Search parameters used ===
0:24:34.079989 INFO: rt_error       : 805.6002197265625
0:24:34.080059 INFO: mobility_error : 0.1
0:24:34.080109 INFO: num_candidates : 3
0:24:34.080152 INFO: ms1_error      : 30
0:24:34.080193 INFO: ms2_error      : 10.0
0:24:34.080235 INFO: fwhm_rt        : 3.0
0:24:34.080290 INFO: quant_window   : 3
0:24:34.080331 INFO: ==============================================
0:24:34.724511 INFO: performing precursor FDR with 40 features
0:24:34.724630 INFO: Decoy channel: -1
0:24:34.724656 INFO: Competetive: True
0:24:34.767191 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:34.808935 INFO: Using random state 439991 for train-test-split
0:24:36.952183 INFO: Test AUC: 0.594
0:24:36.952303 INFO: Train AUC: 0.619
0:24:36.952334 INFO: AUC difference: 4.06%
0:24:37.212414 INFO: Resetting torch num_threads to 80
0:24:37.218441 PROGRESS: === Extracted 150569 precursors and 805058 fragments ===
0:24:37.218791 INFO: === FDR correction performed with classifier version 9 ===
0:24:37.219233 PROGRESS: ============================= Precursor FDR =============================
0:24:37.219319 PROGRESS: Total precursors accumulated: 225
0:24:37.219376 PROGRESS: Target precursors: 223 (99.11%)
0:24:37.219427 PROGRESS: Decoy precursors: 2 (0.89%)
0:24:37.219473 PROGRESS: 
0:24:37.219517 PROGRESS: Precursor Summary:
0:24:37.220368 PROGRESS: Channel   0:	 0.050 FDR:   223; 0.010 FDR:   223; 0.001 FDR:   178
0:24:37.220455 PROGRESS: 
0:24:37.220509 PROGRESS: Protein Summary:
0:24:37.221521 PROGRESS: Channel   0:	 0.050 FDR:   215; 0.010 FDR:   215; 0.001 FDR:   171
0:24:37.221615 PROGRESS: =========================================================================
0:24:37.223699 INFO: Target number of precursors reached.
0:24:37.277955 INFO: fragments_df: keeping 2581 of 805058 [sum(precursor_idx_mask)=5406 sum(mass_error_mask)=805058 stop_rank=2581
0:24:37.415119 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:24:37.503589 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:24:37.784491 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:24:37.784901 INFO: Using score_cutoff 13.205436331558227 (fac=0.99, q=1)
0:24:37.785191 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:24:37.785274 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:24:37.785328 INFO: Updating optimization_manager: score_cutoff        : 12.84779404478073 -> 13.205436331558227
0:24:37.785382 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:24:37.816185 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:37.883832 INFO: === checking if optimization conditions were reached ===
0:24:37.884081 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:24:37.885832 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 118.98713837444228
0:24:37.885938 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 118.9871.
0:24:37.886005 INFO: ==============================================
0:24:37.886073 INFO: Starting optimization step 1.
0:24:37.886133 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:37.886193 INFO: Using ng extraction backend
0:24:37.886249 PROGRESS: Extracting batch of 50293 precursors
0:24:37.973709 INFO: === Search parameters used ===
0:24:37.973951 INFO: rt_error       : 118.98713837444228
0:24:37.974003 INFO: mobility_error : 0.1
0:24:37.974050 INFO: num_candidates : 3
0:24:37.974094 INFO: ms1_error      : 30
0:24:37.974148 INFO: ms2_error      : 10.0
0:24:37.974192 INFO: fwhm_rt        : 3.0
0:24:37.974238 INFO: quant_window   : 3
0:24:37.974283 INFO: ==============================================
0:24:38.573248 INFO: performing precursor FDR with 40 features
0:24:38.573368 INFO: Decoy channel: -1
0:24:38.573393 INFO: Competetive: True
0:24:38.613739 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:38.656411 INFO: Using random state 439991 for train-test-split
0:24:40.812786 INFO: Test AUC: 0.588
0:24:40.812906 INFO: Train AUC: 0.610
0:24:40.812951 INFO: AUC difference: 3.61%
0:24:41.084158 INFO: Resetting torch num_threads to 80
0:24:41.090609 PROGRESS: === Extracted 147571 precursors and 615146 fragments ===
0:24:41.090955 INFO: === FDR correction performed with classifier version 9 ===
0:24:41.091408 PROGRESS: ============================= Precursor FDR =============================
0:24:41.091494 PROGRESS: Total precursors accumulated: 313
0:24:41.091552 PROGRESS: Target precursors: 310 (99.04%)
0:24:41.091601 PROGRESS: Decoy precursors: 3 (0.96%)
0:24:41.091648 PROGRESS: 
0:24:41.091691 PROGRESS: Precursor Summary:
0:24:41.092578 PROGRESS: Channel   0:	 0.050 FDR:   310; 0.010 FDR:   310; 0.001 FDR:   180
0:24:41.092664 PROGRESS: 
0:24:41.092718 PROGRESS: Protein Summary:
0:24:41.093786 PROGRESS: Channel   0:	 0.050 FDR:   299; 0.010 FDR:   299; 0.001 FDR:   174
0:24:41.093878 PROGRESS: =========================================================================
0:24:41.095914 INFO: Target number of precursors reached.
0:24:41.137840 INFO: fragments_df: keeping 3327 of 615146 [sum(precursor_idx_mask)=7106 sum(mass_error_mask)=615146 stop_rank=3327
0:24:41.275072 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:24:41.370530 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:24:41.737202 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:24:41.737610 INFO: Using score_cutoff 11.572084438419342 (fac=0.99, q=1)
0:24:41.737891 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:24:41.737971 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:24:41.738027 INFO: Updating optimization_manager: score_cutoff        : 13.205436331558227 -> 11.572084438419342
0:24:41.738080 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:24:41.769259 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:41.837110 INFO: === checking if optimization conditions were reached ===
0:24:41.837342 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:24:41.839193 INFO: Updating optimization_manager: rt_error            : 118.98713837444228 -> 100.70119306976116
0:24:41.839295 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 100.7012.
0:24:41.839363 INFO: ==============================================
0:24:41.839431 INFO: Starting optimization step 2.
0:24:41.839491 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:41.839552 INFO: Using ng extraction backend
0:24:41.839608 PROGRESS: Extracting batch of 50293 precursors
0:24:41.926713 INFO: === Search parameters used ===
0:24:41.926949 INFO: rt_error       : 100.70119306976116
0:24:41.927003 INFO: mobility_error : 0.1
0:24:41.927063 INFO: num_candidates : 3
0:24:41.927112 INFO: ms1_error      : 30
0:24:41.927153 INFO: ms2_error      : 10.0
0:24:41.927193 INFO: fwhm_rt        : 3.0
0:24:41.927232 INFO: quant_window   : 3
0:24:41.927271 INFO: ==============================================
0:24:42.519812 INFO: performing precursor FDR with 40 features
0:24:42.519925 INFO: Decoy channel: -1
0:24:42.519952 INFO: Competetive: True
0:24:42.560088 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:42.607497 INFO: Using random state 439991 for train-test-split
0:24:45.564910 INFO: Test AUC: 0.590
0:24:45.565076 INFO: Train AUC: 0.612
0:24:45.565109 INFO: AUC difference: 3.50%
0:24:47.436752 INFO: Resetting torch num_threads to 80
0:24:47.444287 PROGRESS: === Extracted 146859 precursors and 594887 fragments ===
0:24:47.444747 INFO: === FDR correction performed with classifier version 9 ===
0:24:47.445245 PROGRESS: ============================= Precursor FDR =============================
0:24:47.445337 PROGRESS: Total precursors accumulated: 321
0:24:47.445396 PROGRESS: Target precursors: 318 (99.07%)
0:24:47.445447 PROGRESS: Decoy precursors: 3 (0.93%)
0:24:47.445495 PROGRESS: 
0:24:47.445544 PROGRESS: Precursor Summary:
0:24:47.446495 PROGRESS: Channel   0:	 0.050 FDR:   318; 0.010 FDR:   318; 0.001 FDR:   211
0:24:47.446599 PROGRESS: 
0:24:47.446656 PROGRESS: Protein Summary:
0:24:47.447756 PROGRESS: Channel   0:	 0.050 FDR:   304; 0.010 FDR:   304; 0.001 FDR:   202
0:24:47.447855 PROGRESS: =========================================================================
0:24:47.450403 INFO: Target number of precursors reached.
0:24:47.491122 INFO: fragments_df: keeping 3368 of 594887 [sum(precursor_idx_mask)=7265 sum(mass_error_mask)=594887 stop_rank=3368
0:24:47.657264 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:24:47.782621 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:24:48.232494 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:24:48.233059 INFO: Using score_cutoff 11.813965195941925 (fac=0.99, q=1)
0:24:48.233420 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:24:48.233500 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:24:48.233553 INFO: Updating optimization_manager: score_cutoff        : 11.572084438419342 -> 11.813965195941925
0:24:48.233610 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:24:48.265193 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:48.332315 INFO: === checking if optimization conditions were reached ===
0:24:48.332685 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:24:48.335542 INFO: Updating optimization_manager: rt_error            : 100.70119306976116 -> 75.09132207254807
0:24:48.335666 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 75.0913.
0:24:48.335747 INFO: ==============================================
0:24:48.335829 INFO: Starting optimization step 3.
0:24:48.335899 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:48.335973 INFO: Using ng extraction backend
0:24:48.336044 PROGRESS: Extracting batch of 50293 precursors
0:24:48.429807 INFO: === Search parameters used ===
0:24:48.430167 INFO: rt_error       : 75.09132207254807
0:24:48.430242 INFO: mobility_error : 0.1
0:24:48.430294 INFO: num_candidates : 3
0:24:48.430342 INFO: ms1_error      : 30
0:24:48.430388 INFO: ms2_error      : 10.0
0:24:48.430429 INFO: fwhm_rt        : 3.0
0:24:48.430470 INFO: quant_window   : 3
0:24:48.430510 INFO: ==============================================
0:24:49.050491 INFO: performing precursor FDR with 40 features
0:24:49.050671 INFO: Decoy channel: -1
0:24:49.050700 INFO: Competetive: True
0:24:49.100494 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:49.143537 INFO: Using random state 439991 for train-test-split
0:24:51.768412 INFO: Test AUC: 0.591
0:24:51.768573 INFO: Train AUC: 0.609
0:24:51.768605 INFO: AUC difference: 2.90%
0:24:52.033113 INFO: Resetting torch num_threads to 80
0:24:52.040588 PROGRESS: === Extracted 145063 precursors and 560061 fragments ===
0:24:52.041061 INFO: === FDR correction performed with classifier version 9 ===
0:24:52.041542 PROGRESS: ============================= Precursor FDR =============================
0:24:52.041633 PROGRESS: Total precursors accumulated: 324
0:24:52.041693 PROGRESS: Target precursors: 321 (99.07%)
0:24:52.041745 PROGRESS: Decoy precursors: 3 (0.93%)
0:24:52.041792 PROGRESS: 
0:24:52.041839 PROGRESS: Precursor Summary:
0:24:52.042804 PROGRESS: Channel   0:	 0.050 FDR:   321; 0.010 FDR:   321; 0.001 FDR:   267
0:24:52.042895 PROGRESS: 
0:24:52.042953 PROGRESS: Protein Summary:
0:24:52.044109 PROGRESS: Channel   0:	 0.050 FDR:   310; 0.010 FDR:   310; 0.001 FDR:   258
0:24:52.044203 PROGRESS: =========================================================================
0:24:52.046763 INFO: Target number of precursors reached.
0:24:52.086253 INFO: fragments_df: keeping 3281 of 560061 [sum(precursor_idx_mask)=7163 sum(mass_error_mask)=560061 stop_rank=3281
0:24:52.259830 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:24:52.363327 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:24:52.736207 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:24:52.736764 INFO: Using score_cutoff 11.1610150680542 (fac=0.99, q=1)
0:24:52.737104 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:24:52.737187 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:24:52.737241 INFO: Updating optimization_manager: score_cutoff        : 11.813965195941925 -> 11.1610150680542
0:24:52.737298 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:24:52.768735 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:52.834416 INFO: === checking if optimization conditions were reached ===
0:24:52.834766 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:24:52.837393 INFO: Updating optimization_manager: rt_error            : 75.09132207254807 -> 58.61961804785068
0:24:52.837508 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 58.6196.
0:24:52.837580 INFO: ==============================================
0:24:52.837653 INFO: Starting optimization step 4.
0:24:52.837715 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:52.837780 INFO: Using ng extraction backend
0:24:52.837840 PROGRESS: Extracting batch of 50293 precursors
0:24:52.930001 INFO: === Search parameters used ===
0:24:52.930366 INFO: rt_error       : 58.61961804785068
0:24:52.930425 INFO: mobility_error : 0.1
0:24:52.930472 INFO: num_candidates : 3
0:24:52.930517 INFO: ms1_error      : 30
0:24:52.930557 INFO: ms2_error      : 10.0
0:24:52.930599 INFO: fwhm_rt        : 3.0
0:24:52.930641 INFO: quant_window   : 3
0:24:52.930681 INFO: ==============================================
0:24:53.540162 INFO: performing precursor FDR with 40 features
0:24:53.540328 INFO: Decoy channel: -1
0:24:53.540354 INFO: Competetive: True
0:24:53.588434 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:53.633630 INFO: Using random state 439991 for train-test-split
0:24:56.105073 INFO: Test AUC: 0.594
0:24:56.105241 INFO: Train AUC: 0.609
0:24:56.105273 INFO: AUC difference: 2.36%
0:24:56.374450 INFO: Resetting torch num_threads to 80
0:24:56.381578 PROGRESS: === Extracted 141459 precursors and 521617 fragments ===
0:24:56.382017 INFO: === FDR correction performed with classifier version 9 ===
0:24:56.382473 PROGRESS: ============================= Precursor FDR =============================
0:24:56.382559 PROGRESS: Total precursors accumulated: 277
0:24:56.382618 PROGRESS: Target precursors: 275 (99.28%)
0:24:56.382666 PROGRESS: Decoy precursors: 2 (0.72%)
0:24:56.382710 PROGRESS: 
0:24:56.382754 PROGRESS: Precursor Summary:
0:24:56.383664 PROGRESS: Channel   0:	 0.050 FDR:   275; 0.010 FDR:   275; 0.001 FDR:   231
0:24:56.383752 PROGRESS: 
0:24:56.383806 PROGRESS: Protein Summary:
0:24:56.384881 PROGRESS: Channel   0:	 0.050 FDR:   267; 0.010 FDR:   267; 0.001 FDR:   225
0:24:56.384969 PROGRESS: =========================================================================
0:24:56.387424 INFO: Target number of precursors reached.
0:24:56.423663 INFO: fragments_df: keeping 2836 of 521617 [sum(precursor_idx_mask)=5955 sum(mass_error_mask)=521617 stop_rank=2836
0:24:56.590055 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:24:56.694537 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:24:57.009853 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:24:57.010412 INFO: Using score_cutoff 12.680532605552672 (fac=0.99, q=1)
0:24:57.010736 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:24:57.010817 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:24:57.010873 INFO: Updating optimization_manager: score_cutoff        : 11.1610150680542 -> 12.680532605552672
0:24:57.010933 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:24:57.042333 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:57.112430 INFO: === checking if optimization conditions were reached ===
0:24:57.112764 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:24:57.115172 INFO: Updating optimization_manager: rt_error            : 58.61961804785068 -> 45.7879394712203
0:24:57.115285 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 45.7879.
0:24:57.115354 INFO: ==============================================
0:24:57.115427 INFO: Starting optimization step 5.
0:24:57.115489 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:24:57.115559 INFO: Using ng extraction backend
0:24:57.115623 PROGRESS: Extracting batch of 50293 precursors
0:24:57.207687 INFO: === Search parameters used ===
0:24:57.208053 INFO: rt_error       : 45.7879394712203
0:24:57.208114 INFO: mobility_error : 0.1
0:24:57.208163 INFO: num_candidates : 3
0:24:57.208207 INFO: ms1_error      : 30
0:24:57.208247 INFO: ms2_error      : 10.0
0:24:57.208286 INFO: fwhm_rt        : 3.0
0:24:57.208324 INFO: quant_window   : 3
0:24:57.208364 INFO: ==============================================
0:24:57.767078 INFO: performing precursor FDR with 40 features
0:24:57.767243 INFO: Decoy channel: -1
0:24:57.767270 INFO: Competetive: True
0:24:57.817463 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:57.858748 INFO: Using random state 439991 for train-test-split
0:25:00.229788 INFO: Test AUC: 0.592
0:25:00.229955 INFO: Train AUC: 0.609
0:25:00.229987 INFO: AUC difference: 2.74%
0:25:00.501134 INFO: Resetting torch num_threads to 80
0:25:00.507941 PROGRESS: === Extracted 132822 precursors and 474083 fragments ===
0:25:00.508390 INFO: === FDR correction performed with classifier version 9 ===
0:25:00.508857 PROGRESS: ============================= Precursor FDR =============================
0:25:00.508947 PROGRESS: Total precursors accumulated: 279
0:25:00.509017 PROGRESS: Target precursors: 277 (99.28%)
0:25:00.509072 PROGRESS: Decoy precursors: 2 (0.72%)
0:25:00.509120 PROGRESS: 
0:25:00.509169 PROGRESS: Precursor Summary:
0:25:00.510117 PROGRESS: Channel   0:	 0.050 FDR:   277; 0.010 FDR:   277; 0.001 FDR:   243
0:25:00.510209 PROGRESS: 
0:25:00.510264 PROGRESS: Protein Summary:
0:25:00.511411 PROGRESS: Channel   0:	 0.050 FDR:   268; 0.010 FDR:   268; 0.001 FDR:   236
0:25:00.511503 PROGRESS: =========================================================================
0:25:00.513833 INFO: Target number of precursors reached.
0:25:00.547012 INFO: fragments_df: keeping 2688 of 474083 [sum(precursor_idx_mask)=5496 sum(mass_error_mask)=474083 stop_rank=2688
0:25:00.713362 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:25:00.817143 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:25:01.118940 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:25:01.119474 INFO: Using score_cutoff 11.076447381591796 (fac=0.99, q=1)
0:25:01.119799 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:25:01.119880 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:25:01.119935 INFO: Updating optimization_manager: score_cutoff        : 12.680532605552672 -> 11.076447381591796
0:25:01.119991 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:25:01.151631 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:25:01.214881 INFO: === checking if optimization conditions were reached ===
0:25:01.215207 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:25:01.217608 INFO: Updating optimization_manager: rt_error            : 45.7879394712203 -> 37.49671062146517
0:25:01.217721 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 37.4967.
0:25:01.217791 INFO: ==============================================
0:25:01.217863 INFO: Starting optimization step 6.
0:25:01.217941 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:25:01.218008 INFO: Using ng extraction backend
0:25:01.218071 PROGRESS: Extracting batch of 50293 precursors
0:25:01.309314 INFO: === Search parameters used ===
0:25:01.309689 INFO: rt_error       : 37.49671062146517
0:25:01.309767 INFO: mobility_error : 0.1
0:25:01.309816 INFO: num_candidates : 3
0:25:01.309861 INFO: ms1_error      : 30
0:25:01.309903 INFO: ms2_error      : 10.0
0:25:01.309945 INFO: fwhm_rt        : 3.0
0:25:01.309986 INFO: quant_window   : 3
0:25:01.310026 INFO: ==============================================
0:25:01.882545 INFO: performing precursor FDR with 40 features
0:25:01.882706 INFO: Decoy channel: -1
0:25:01.882733 INFO: Competetive: True
0:25:01.930089 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:01.971586 INFO: Using random state 439991 for train-test-split
0:25:04.266589 INFO: Test AUC: 0.589
0:25:04.266754 INFO: Train AUC: 0.611
0:25:04.266786 INFO: AUC difference: 3.57%
0:25:04.541109 INFO: Resetting torch num_threads to 80
0:25:04.548030 PROGRESS: === Extracted 133431 precursors and 476416 fragments ===
0:25:04.548450 INFO: === FDR correction performed with classifier version 9 ===
0:25:04.548913 PROGRESS: ============================= Precursor FDR =============================
0:25:04.549009 PROGRESS: Total precursors accumulated: 268
0:25:04.549074 PROGRESS: Target precursors: 266 (99.25%)
0:25:04.549126 PROGRESS: Decoy precursors: 2 (0.75%)
0:25:04.549174 PROGRESS: 
0:25:04.549217 PROGRESS: Precursor Summary:
0:25:04.550148 PROGRESS: Channel   0:	 0.050 FDR:   266; 0.010 FDR:   266; 0.001 FDR:   233
0:25:04.550248 PROGRESS: 
0:25:04.550307 PROGRESS: Protein Summary:
0:25:04.551401 PROGRESS: Channel   0:	 0.050 FDR:   256; 0.010 FDR:   256; 0.001 FDR:   225
0:25:04.551496 PROGRESS: =========================================================================
0:25:04.553800 INFO: Target number of precursors reached.
0:25:04.587215 INFO: fragments_df: keeping 2575 of 476416 [sum(precursor_idx_mask)=5340 sum(mass_error_mask)=476416 stop_rank=2575
0:25:04.753484 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:25:04.880942 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:25:05.224577 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:25:05.225135 INFO: Using score_cutoff 10.789107901096344 (fac=0.99, q=1)
0:25:05.225464 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:25:05.225544 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:25:05.225599 INFO: Updating optimization_manager: score_cutoff        : 11.076447381591796 -> 10.789107901096344
0:25:05.225656 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:25:05.256907 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:25:05.324830 INFO: === checking if optimization conditions were reached ===
0:25:05.325203 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:25:05.327866 INFO: Updating optimization_manager: rt_error            : 37.49671062146517 -> 34.57965655020026
0:25:05.328012 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 34.5797.
0:25:05.328103 INFO: ==============================================
0:25:05.328179 INFO: Starting optimization step 7.
0:25:05.328241 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:25:05.328307 INFO: Using ng extraction backend
0:25:05.328368 PROGRESS: Extracting batch of 50293 precursors
0:25:05.421896 INFO: === Search parameters used ===
0:25:05.422239 INFO: rt_error       : 34.57965655020026
0:25:05.422297 INFO: mobility_error : 0.1
0:25:05.422345 INFO: num_candidates : 3
0:25:05.422391 INFO: ms1_error      : 30
0:25:05.422435 INFO: ms2_error      : 10.0
0:25:05.422477 INFO: fwhm_rt        : 3.0
0:25:05.422517 INFO: quant_window   : 3
0:25:05.422558 INFO: ==============================================
0:25:05.987334 INFO: performing precursor FDR with 40 features
0:25:05.987468 INFO: Decoy channel: -1
0:25:05.987494 INFO: Competetive: True
0:25:06.034440 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:06.073328 INFO: Using random state 439991 for train-test-split
0:25:08.583096 INFO: Test AUC: 0.592
0:25:08.583267 INFO: Train AUC: 0.612
0:25:08.583316 INFO: AUC difference: 3.12%
0:25:08.843145 INFO: Resetting torch num_threads to 80
0:25:08.850821 PROGRESS: === Extracted 133963 precursors and 479997 fragments ===
0:25:08.851256 INFO: === FDR correction performed with classifier version 9 ===
0:25:08.851722 PROGRESS: ============================= Precursor FDR =============================
0:25:08.851812 PROGRESS: Total precursors accumulated: 272
0:25:08.851871 PROGRESS: Target precursors: 270 (99.26%)
0:25:08.851923 PROGRESS: Decoy precursors: 2 (0.74%)
0:25:08.851969 PROGRESS: 
0:25:08.852014 PROGRESS: Precursor Summary:
0:25:08.852940 PROGRESS: Channel   0:	 0.050 FDR:   270; 0.010 FDR:   270; 0.001 FDR:   246
0:25:08.853036 PROGRESS: 
0:25:08.853094 PROGRESS: Protein Summary:
0:25:08.854162 PROGRESS: Channel   0:	 0.050 FDR:   260; 0.010 FDR:   260; 0.001 FDR:   237
0:25:08.854251 PROGRESS: =========================================================================
0:25:08.857064 INFO: Target number of precursors reached.
0:25:08.889675 INFO: fragments_df: keeping 2608 of 479997 [sum(precursor_idx_mask)=5377 sum(mass_error_mask)=479997 stop_rank=2608
0:25:09.055682 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:25:09.246652 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:25:09.612762 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:25:09.613321 INFO: Using score_cutoff 11.068552710914611 (fac=0.99, q=1)
0:25:09.613649 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:25:09.613734 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:25:09.613794 INFO: Updating optimization_manager: score_cutoff        : 10.789107901096344 -> 11.068552710914611
0:25:09.613856 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:25:09.645576 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:25:09.715374 INFO: === checking if optimization conditions were reached ===
0:25:09.715785 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
0:25:09.719115 INFO: Updating optimization_manager: rt_error            : 34.57965655020026 -> 34.91156659494393
0:25:09.719293 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 34.9116.
0:25:09.719393 INFO: ==============================================
0:25:09.719501 INFO: Starting optimization step 8.
0:25:09.719595 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:25:09.719689 INFO: Using ng extraction backend
0:25:09.719782 PROGRESS: Extracting batch of 50293 precursors
0:25:09.821511 INFO: === Search parameters used ===
0:25:09.821873 INFO: rt_error       : 34.91156659494393
0:25:09.821935 INFO: mobility_error : 0.1
0:25:09.821986 INFO: num_candidates : 3
0:25:09.822032 INFO: ms1_error      : 30
0:25:09.822073 INFO: ms2_error      : 10.0
0:25:09.822115 INFO: fwhm_rt        : 3.0
0:25:09.822160 INFO: quant_window   : 3
0:25:09.822201 INFO: ==============================================
0:25:10.403317 INFO: performing precursor FDR with 40 features
0:25:10.403478 INFO: Decoy channel: -1
0:25:10.403506 INFO: Competetive: True
0:25:10.447518 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:10.496040 INFO: Using random state 439991 for train-test-split
0:25:12.616174 INFO: Test AUC: 0.593
0:25:12.616343 INFO: Train AUC: 0.611
0:25:12.616375 INFO: AUC difference: 2.90%
0:25:12.876004 INFO: Resetting torch num_threads to 80
0:25:12.882783 PROGRESS: === Extracted 134144 precursors and 481653 fragments ===
0:25:12.883200 INFO: === FDR correction performed with classifier version 9 ===
0:25:12.883652 PROGRESS: ============================= Precursor FDR =============================
0:25:12.883740 PROGRESS: Total precursors accumulated: 265
0:25:12.883798 PROGRESS: Target precursors: 263 (99.25%)
0:25:12.883848 PROGRESS: Decoy precursors: 2 (0.75%)
0:25:12.883903 PROGRESS: 
0:25:12.883948 PROGRESS: Precursor Summary:
0:25:12.884859 PROGRESS: Channel   0:	 0.050 FDR:   263; 0.010 FDR:   263; 0.001 FDR:   222
0:25:12.884953 PROGRESS: 
0:25:12.885016 PROGRESS: Protein Summary:
0:25:12.886055 PROGRESS: Channel   0:	 0.050 FDR:   256; 0.010 FDR:   256; 0.001 FDR:   217
0:25:12.886147 PROGRESS: =========================================================================
0:25:12.888376 INFO: Target number of precursors reached.
0:25:12.921417 INFO: fragments_df: keeping 2487 of 481653 [sum(precursor_idx_mask)=5154 sum(mass_error_mask)=481653 stop_rank=2487
0:25:13.086334 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:25:13.217870 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:25:13.550215 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:25:13.550760 INFO: Using score_cutoff 8.778694501304628 (fac=0.99, q=1)
0:25:13.551081 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:25:13.551160 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:25:13.551212 INFO: Updating optimization_manager: score_cutoff        : 11.068552710914611 -> 8.778694501304628
0:25:13.551268 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:25:13.583469 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:25:13.650006 INFO: === checking if optimization conditions were reached ===
0:25:13.650373 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
0:25:13.651940 INFO: Updating optimization_manager: rt_error            : 34.91156659494393 -> 75.09132207254807
0:25:13.652088 INFO: Updating optimization_manager: classifier_version  : 9 -> 13
0:25:13.652196 INFO: Updating optimization_manager: score_cutoff        : 8.778694501304628 -> 11.1610150680542
0:25:13.652291 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:25:13.652386 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:25:13.652480 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 75.0913 found after 9 searches.
0:25:13.652558 INFO: ==============================================
0:25:13.652638 PROGRESS: Optimization finished for rt_error.
0:25:13.830113 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:25:13.862929 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:25:13.962803 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:25:13.963125 PROGRESS: ==============================================
0:25:13.963207 PROGRESS: ms2_error      : 10.0000
0:25:13.963273 PROGRESS: rt_error       : 75.0913
0:25:13.963329 PROGRESS: ==============================================
0:25:13.963953 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:25:25.138676 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:22.883944 INFO: Using ng extraction backend
0:26:22.884315 PROGRESS: Extracting batch of 12001526 precursors
0:26:44.479198 INFO: === Search parameters used ===
0:26:44.479569 INFO: rt_error       : 75.09132207254807
0:26:44.479634 INFO: mobility_error : 0.1
0:26:44.479684 INFO: num_candidates : 3
0:26:44.479734 INFO: ms1_error      : 30
0:26:44.479777 INFO: ms2_error      : 10.0
0:26:44.479819 INFO: fwhm_rt        : 3.0
0:26:44.479863 INFO: quant_window   : 3
0:26:44.479904 INFO: ==============================================
0:27:35.184409 INFO: Removed 23980971 precursors with score below cutoff 11.1610150680542
0:27:56.586831 INFO: performing precursor FDR with 40 features
0:27:56.587004 INFO: Decoy channel: -1
0:27:56.587033 INFO: Competetive: True
0:28:02.183313 INFO: Setting torch num_threads to 2 for FDR classification task
0:28:07.181962 INFO: Using random state 447845 for train-test-split
0:31:24.338632 INFO: Test AUC: 0.622
0:31:24.338863 INFO: Train AUC: 0.624
0:31:24.338902 INFO: AUC difference: 0.20%
0:31:27.899475 INFO: Resetting torch num_threads to 80
0:31:29.559514 PROGRESS: ============================= Precursor FDR =============================
0:31:29.559803 PROGRESS: Total precursors accumulated: 86,283
0:31:29.559891 PROGRESS: Target precursors: 85,429 (99.01%)
0:31:29.559948 PROGRESS: Decoy precursors: 854 (0.99%)
0:31:29.559996 PROGRESS: 
0:31:29.560043 PROGRESS: Precursor Summary:
0:31:29.588192 PROGRESS: Channel   0:	 0.050 FDR: 85,429; 0.010 FDR: 85,429; 0.001 FDR: 58,310
0:31:29.588437 PROGRESS: 
0:31:29.588497 PROGRESS: Protein Summary:
0:31:29.624035 PROGRESS: Channel   0:	 0.050 FDR: 12,772; 0.010 FDR: 12,772; 0.001 FDR: 9,194
0:31:29.624279 PROGRESS: =========================================================================
0:31:30.078812 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/psm.parquet
0:31:30.259981 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.parquet
0:31:30.512627 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:31:31.086629 PROGRESS: 
0:31:31.086784 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant
0:31:31.086853 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/figures
0:31:31.087018 INFO: Initializing TimingManager
0:31:31.088411 INFO: Initializing RawFileManager
0:31:41.614084 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.
0:31:41.618394 INFO: Determining DIA cycle
0:31:41.634699 INFO: Found cycle with start 0.00 min and length 300.
0:31:41.800221 INFO: RT (min)            : 0.0 - 26.9
0:31:41.800312 INFO: RT duration (sec)   : 1611.2
0:31:41.800341 INFO: RT duration (min)   : 26.9
0:31:41.800366 INFO: Cycle len (scans)   : 300
0:31:41.800386 INFO: Cycle len (sec)     : 1.65
0:31:41.800405 INFO: Number of cycles    : 978
0:31:41.800425 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:31:41.800454 INFO: Creating DIA data object took: 10.71194863319397
0:31:42.484851 INFO: Creating DIA data NG object took: 0.6842916011810303
0:31:43.677286 INFO: Initializing CalibrationManager
0:31:43.677555 INFO: Setting up calibration estimators ..
0:31:43.677616 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:31:43.677701 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'}' ..
0:31:43.677778 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:31:43.677831 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:31:43.677889 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}}' ..
0:31:43.677939 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:31:43.677984 INFO: Done setting up calibration estimators.
0:31:43.678181 INFO: Initializing OptimizationManager
0:31:43.678329 INFO: initial parameter: ms1_error = 30
0:31:43.678383 INFO: initial parameter: ms2_error = 30
0:31:43.678433 INFO: initial parameter: rt_error = 805.611083984375
0:31:43.678480 INFO: initial parameter: mobility_error = 0.1
0:31:43.678521 INFO: initial parameter: num_candidates = 1
0:31:43.678560 INFO: initial parameter: fwhm_rt = 5
0:31:43.678603 INFO: initial parameter: fwhm_mobility = 0.01
0:31:43.678647 INFO: initial parameter: score_cutoff = 0
0:31:43.678686 INFO: initial parameter: classifier_version = -1
0:31:43.678755 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:31:43.678989 INFO: FDRManager: loading saved state not requested, will be initialized.
0:31:43.679022 INFO: Initializing FDRManager
0:31:43.679057 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:31:44.906595 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:31:45.658243 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:31:45.658625 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
0:31:45.658728 PROGRESS: Starting initial search for precursors.
0:31:45.658810 INFO: Starting optimization step 0.
0:31:45.658871 PROGRESS: === Extracting elution groups 0 to 200 ===
0:31:45.658934 INFO: Using ng extraction backend
0:31:45.658994 PROGRESS: Extracting batch of 396 precursors
0:31:45.660886 INFO: === Search parameters used ===
0:31:45.660974 INFO: rt_error       : 805.611083984375
0:31:45.661041 INFO: mobility_error : 0.1
0:31:45.661088 INFO: num_candidates : 1
0:31:45.661131 INFO: ms1_error      : 30
0:31:45.661170 INFO: ms2_error      : 30
0:31:45.661213 INFO: fwhm_rt        : 5
0:31:45.661253 INFO: quant_window   : 3
0:31:45.661292 INFO: ==============================================
0:31:45.677626 INFO: performing precursor FDR with 40 features
0:31:45.677699 INFO: Decoy channel: -1
0:31:45.677726 INFO: Competetive: True
0:31:45.678634 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:45.680808 INFO: Using random state 276512 for train-test-split
0:31:45.687227 INFO: Test AUC: 0.582
0:31:45.687283 INFO: Train AUC: 0.460
0:31:45.687312 INFO: AUC difference: 26.74%
0:31:45.687335 WARNING: AUC difference > 5%. This may indicate overfitting.
0:31:45.893079 INFO: Resetting torch num_threads to 80
0:31:45.894393 PROGRESS: === Extracted 393 precursors and 1907 fragments ===
0:31:45.894726 INFO: === FDR correction performed with classifier version -1 ===
0:31:45.895174 PROGRESS: ============================= Precursor FDR =============================
0:31:45.895262 PROGRESS: Total precursors accumulated: 1
0:31:45.895327 PROGRESS: Target precursors: 1 (100.00%)
0:31:45.895379 PROGRESS: Decoy precursors: 0 (0.00%)
0:31:45.895423 PROGRESS: 
0:31:45.895467 PROGRESS: Precursor Summary:
0:31:45.896375 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:31:45.896463 PROGRESS: 
0:31:45.896518 PROGRESS: Protein Summary:
0:31:45.897522 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:31:45.897612 PROGRESS: =========================================================================
0:31:45.897807 INFO: Target number of precursors not reached yet.
0:31:45.962238 INFO: Starting optimization step 1.
0:31:45.962431 PROGRESS: === Extracting elution groups 200 to 600 ===
0:31:45.962512 INFO: Using ng extraction backend
0:31:45.962575 PROGRESS: Extracting batch of 786 precursors
0:31:45.965255 INFO: === Search parameters used ===
0:31:45.965356 INFO: rt_error       : 805.611083984375
0:31:45.965406 INFO: mobility_error : 0.1
0:31:45.965452 INFO: num_candidates : 1
0:31:45.965496 INFO: ms1_error      : 30
0:31:45.965535 INFO: ms2_error      : 30
0:31:45.965575 INFO: fwhm_rt        : 5
0:31:45.965620 INFO: quant_window   : 3
0:31:45.965659 INFO: ==============================================
0:31:45.987795 INFO: performing precursor FDR with 40 features
0:31:45.987866 INFO: Decoy channel: -1
0:31:45.987892 INFO: Competetive: True
0:31:45.990686 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:45.992115 INFO: Using random state 7416 for train-test-split
0:31:45.999888 INFO: Test AUC: 0.445
0:31:45.999945 INFO: Train AUC: 0.496
0:31:45.999976 INFO: AUC difference: 10.23%
0:31:46 WARNING: AUC difference > 5%. This may indicate overfitting.
0:31:46.220440 INFO: Resetting torch num_threads to 80
0:31:46.222507 PROGRESS: === Extracted 1172 precursors and 5583 fragments ===
0:31:46.222842 INFO: === FDR correction performed with classifier version -1 ===
0:31:46.223291 PROGRESS: ============================= Precursor FDR =============================
0:31:46.223379 PROGRESS: Total precursors accumulated: 3
0:31:46.223447 PROGRESS: Target precursors: 3 (100.00%)
0:31:46.223497 PROGRESS: Decoy precursors: 0 (0.00%)
0:31:46.223549 PROGRESS: 
0:31:46.223591 PROGRESS: Precursor Summary:
0:31:46.224503 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
0:31:46.224590 PROGRESS: 
0:31:46.224645 PROGRESS: Protein Summary:
0:31:46.225652 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
0:31:46.225743 PROGRESS: =========================================================================
0:31:46.225960 INFO: Target number of precursors not reached yet.
0:31:46.293101 INFO: Starting optimization step 2.
0:31:46.293292 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:31:46.293374 INFO: Using ng extraction backend
0:31:46.293437 PROGRESS: Extracting batch of 1592 precursors
0:31:46.298015 INFO: === Search parameters used ===
0:31:46.298129 INFO: rt_error       : 805.611083984375
0:31:46.298181 INFO: mobility_error : 0.1
0:31:46.298226 INFO: num_candidates : 1
0:31:46.298270 INFO: ms1_error      : 30
0:31:46.298311 INFO: ms2_error      : 30
0:31:46.298350 INFO: fwhm_rt        : 5
0:31:46.298393 INFO: quant_window   : 3
0:31:46.298432 INFO: ==============================================
0:31:46.329771 INFO: performing precursor FDR with 40 features
0:31:46.329851 INFO: Decoy channel: -1
0:31:46.329885 INFO: Competetive: True
0:31:46.333121 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:46.334917 INFO: Using random state 490649 for train-test-split
0:31:46.346630 INFO: Test AUC: 0.449
0:31:46.346689 INFO: Train AUC: 0.497
0:31:46.346726 INFO: AUC difference: 9.72%
0:31:46.346760 WARNING: AUC difference > 5%. This may indicate overfitting.
0:31:46.559880 INFO: Resetting torch num_threads to 80
0:31:46.562357 PROGRESS: === Extracted 2760 precursors and 13238 fragments ===
0:31:46.562701 INFO: === FDR correction performed with classifier version -1 ===
0:31:46.563163 PROGRESS: ============================= Precursor FDR =============================
0:31:46.563251 PROGRESS: Total precursors accumulated: 2
0:31:46.563311 PROGRESS: Target precursors: 2 (100.00%)
0:31:46.563361 PROGRESS: Decoy precursors: 0 (0.00%)
0:31:46.563407 PROGRESS: 
0:31:46.563452 PROGRESS: Precursor Summary:
0:31:46.564361 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:31:46.564449 PROGRESS: 
0:31:46.564507 PROGRESS: Protein Summary:
0:31:46.565545 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:31:46.565637 PROGRESS: =========================================================================
0:31:46.565865 INFO: Target number of precursors not reached yet.
0:31:46.634988 INFO: Starting optimization step 3.
0:31:46.635191 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:31:46.635272 INFO: Using ng extraction backend
0:31:46.635333 PROGRESS: Extracting batch of 3177 precursors
0:31:46.642346 INFO: === Search parameters used ===
0:31:46.642460 INFO: rt_error       : 805.611083984375
0:31:46.642509 INFO: mobility_error : 0.1
0:31:46.642554 INFO: num_candidates : 1
0:31:46.642597 INFO: ms1_error      : 30
0:31:46.642637 INFO: ms2_error      : 30
0:31:46.642693 INFO: fwhm_rt        : 5
0:31:46.642736 INFO: quant_window   : 3
0:31:46.642776 INFO: ==============================================
0:31:46.697728 INFO: performing precursor FDR with 40 features
0:31:46.697821 INFO: Decoy channel: -1
0:31:46.697847 INFO: Competetive: True
0:31:46.701925 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:46.704159 INFO: Using random state 673723 for train-test-split
0:31:46.722903 INFO: Test AUC: 0.460
0:31:46.722983 INFO: Train AUC: 0.496
0:31:46.723013 INFO: AUC difference: 7.29%
0:31:46.723034 WARNING: AUC difference > 5%. This may indicate overfitting.
0:31:46.935286 INFO: Resetting torch num_threads to 80
0:31:46.938514 PROGRESS: === Extracted 5916 precursors and 28236 fragments ===
0:31:46.938856 INFO: === FDR correction performed with classifier version -1 ===
0:31:46.939315 PROGRESS: ============================= Precursor FDR =============================
0:31:46.939411 PROGRESS: Total precursors accumulated: 1
0:31:46.939469 PROGRESS: Target precursors: 1 (100.00%)
0:31:46.939519 PROGRESS: Decoy precursors: 0 (0.00%)
0:31:46.939564 PROGRESS: 
0:31:46.939610 PROGRESS: Precursor Summary:
0:31:46.940525 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:31:46.940614 PROGRESS: 
0:31:46.940670 PROGRESS: Protein Summary:
0:31:46.941682 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:31:46.941776 PROGRESS: =========================================================================
0:31:46.942037 INFO: Target number of precursors not reached yet.
0:31:47.015331 INFO: Starting optimization step 4.
0:31:47.015546 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:31:47.015625 INFO: Using ng extraction backend
0:31:47.015686 PROGRESS: Extracting batch of 6340 precursors
0:31:47.028015 INFO: === Search parameters used ===
0:31:47.028141 INFO: rt_error       : 805.611083984375
0:31:47.028191 INFO: mobility_error : 0.1
0:31:47.028237 INFO: num_candidates : 1
0:31:47.028279 INFO: ms1_error      : 30
0:31:47.028318 INFO: ms2_error      : 30
0:31:47.028359 INFO: fwhm_rt        : 5
0:31:47.028397 INFO: quant_window   : 3
0:31:47.028435 INFO: ==============================================
0:31:47.101588 INFO: performing precursor FDR with 40 features
0:31:47.101691 INFO: Decoy channel: -1
0:31:47.101719 INFO: Competetive: True
0:31:47.107758 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:47.111034 INFO: Using random state 136468 for train-test-split
0:31:47.145868 INFO: Test AUC: 0.507
0:31:47.145977 INFO: Train AUC: 0.486
0:31:47.146008 INFO: AUC difference: 4.26%
0:31:47.363141 INFO: Resetting torch num_threads to 80
0:31:47.367487 PROGRESS: === Extracted 12186 precursors and 57773 fragments ===
0:31:47.367842 INFO: === FDR correction performed with classifier version -1 ===
0:31:47.368304 PROGRESS: ============================= Precursor FDR =============================
0:31:47.368392 PROGRESS: Total precursors accumulated: 1
0:31:47.368452 PROGRESS: Target precursors: 1 (100.00%)
0:31:47.368502 PROGRESS: Decoy precursors: 0 (0.00%)
0:31:47.368546 PROGRESS: 
0:31:47.368590 PROGRESS: Precursor Summary:
0:31:47.369504 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:31:47.369594 PROGRESS: 
0:31:47.369649 PROGRESS: Protein Summary:
0:31:47.370642 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:31:47.370731 PROGRESS: =========================================================================
0:31:47.371058 INFO: Target number of precursors not reached yet.
0:31:47.452710 INFO: Starting optimization step 5.
0:31:47.452933 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:31:47.453022 INFO: Using ng extraction backend
0:31:47.453089 PROGRESS: Extracting batch of 12663 precursors
0:31:47.476260 INFO: === Search parameters used ===
0:31:47.476418 INFO: rt_error       : 805.611083984375
0:31:47.476468 INFO: mobility_error : 0.1
0:31:47.476518 INFO: num_candidates : 1
0:31:47.476562 INFO: ms1_error      : 30
0:31:47.476604 INFO: ms2_error      : 30
0:31:47.476644 INFO: fwhm_rt        : 5
0:31:47.476689 INFO: quant_window   : 3
0:31:47.476730 INFO: ==============================================
0:31:47.602280 INFO: performing precursor FDR with 40 features
0:31:47.602391 INFO: Decoy channel: -1
0:31:47.602417 INFO: Competetive: True
0:31:47.612258 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:47.618154 INFO: Using random state 113562 for train-test-split
0:31:47.796635 INFO: Test AUC: 0.537
0:31:47.796749 INFO: Train AUC: 0.546
0:31:47.796780 INFO: AUC difference: 1.62%
0:31:48.018575 INFO: Resetting torch num_threads to 80
0:31:48.024883 PROGRESS: === Extracted 24708 precursors and 116540 fragments ===
0:31:48.025331 INFO: === FDR correction performed with classifier version -1 ===
0:31:48.025844 PROGRESS: ============================= Precursor FDR =============================
0:31:48.027160 PROGRESS: Total precursors accumulated: 26
0:31:48.027226 PROGRESS: Target precursors: 26 (100.00%)
0:31:48.027279 PROGRESS: Decoy precursors: 0 (0.00%)
0:31:48.027328 PROGRESS: 
0:31:48.027384 PROGRESS: Precursor Summary:
0:31:48.028332 PROGRESS: Channel   0:	 0.050 FDR:    26; 0.010 FDR:    26; 0.001 FDR:    26
0:31:48.028420 PROGRESS: 
0:31:48.028477 PROGRESS: Protein Summary:
0:31:48.029511 PROGRESS: Channel   0:	 0.050 FDR:    26; 0.010 FDR:    26; 0.001 FDR:    26
0:31:48.029602 PROGRESS: =========================================================================
0:31:48.030081 INFO: Target number of precursors not reached yet.
0:31:48.128135 INFO: Starting optimization step 6.
0:31:48.128371 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:31:48.128452 INFO: Using ng extraction backend
0:31:48.128516 PROGRESS: Extracting batch of 25339 precursors
0:31:48.173005 INFO: === Search parameters used ===
0:31:48.173207 INFO: rt_error       : 805.611083984375
0:31:48.173258 INFO: mobility_error : 0.1
0:31:48.173303 INFO: num_candidates : 1
0:31:48.173345 INFO: ms1_error      : 30
0:31:48.173387 INFO: ms2_error      : 30
0:31:48.173427 INFO: fwhm_rt        : 5
0:31:48.173466 INFO: quant_window   : 3
0:31:48.173505 INFO: ==============================================
0:31:48.399121 INFO: performing precursor FDR with 40 features
0:31:48.399238 INFO: Decoy channel: -1
0:31:48.399264 INFO: Competetive: True
0:31:48.418187 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:48.431088 INFO: Using random state 670238 for train-test-split
0:31:49.082243 INFO: Test AUC: 0.563
0:31:49.082363 INFO: Train AUC: 0.580
0:31:49.082393 INFO: AUC difference: 3.03%
0:31:49.322846 INFO: Resetting torch num_threads to 80
0:31:49.332628 PROGRESS: === Extracted 49785 precursors and 233156 fragments ===
0:31:49.333123 INFO: === FDR correction performed with classifier version -1 ===
0:31:49.333611 PROGRESS: ============================= Precursor FDR =============================
0:31:49.333699 PROGRESS: Total precursors accumulated: 111
0:31:49.333758 PROGRESS: Target precursors: 110 (99.10%)
0:31:49.333808 PROGRESS: Decoy precursors: 1 (0.90%)
0:31:49.333853 PROGRESS: 
0:31:49.333897 PROGRESS: Precursor Summary:
0:31:49.334761 PROGRESS: Channel   0:	 0.050 FDR:   110; 0.010 FDR:   110; 0.001 FDR:    96
0:31:49.334849 PROGRESS: 
0:31:49.334904 PROGRESS: Protein Summary:
0:31:49.335875 PROGRESS: Channel   0:	 0.050 FDR:   108; 0.010 FDR:   108; 0.001 FDR:    94
0:31:49.335965 PROGRESS: =========================================================================
0:31:49.336637 INFO: Target number of precursors not reached yet.
0:31:49.470671 INFO: Starting optimization step 7.
0:31:49.470911 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:31:49.470994 INFO: Using ng extraction backend
0:31:49.471059 PROGRESS: Extracting batch of 50691 precursors
0:31:49.558460 INFO: === Search parameters used ===
0:31:49.558691 INFO: rt_error       : 805.611083984375
0:31:49.558743 INFO: mobility_error : 0.1
0:31:49.558791 INFO: num_candidates : 1
0:31:49.558836 INFO: ms1_error      : 30
0:31:49.558889 INFO: ms2_error      : 30
0:31:49.558933 INFO: fwhm_rt        : 5
0:31:49.558974 INFO: quant_window   : 3
0:31:49.559014 INFO: ==============================================
0:31:49.920803 INFO: performing precursor FDR with 40 features
0:31:49.920919 INFO: Decoy channel: -1
0:31:49.920945 INFO: Competetive: True
0:31:49.961140 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:49.992920 INFO: Using random state 962745 for train-test-split
0:31:51.578376 INFO: Test AUC: 0.585
0:31:51.578492 INFO: Train AUC: 0.594
0:31:51.578523 INFO: AUC difference: 1.54%
0:31:51.823662 INFO: Resetting torch num_threads to 80
0:31:51.842474 PROGRESS: === Extracted 99985 precursors and 468362 fragments ===
0:31:51.842936 INFO: === FDR correction performed with classifier version -1 ===
0:31:51.843466 PROGRESS: ============================= Precursor FDR =============================
0:31:51.843561 PROGRESS: Total precursors accumulated: 251
0:31:51.843641 PROGRESS: Target precursors: 249 (99.20%)
0:31:51.843693 PROGRESS: Decoy precursors: 2 (0.80%)
0:31:51.843740 PROGRESS: 
0:31:51.843786 PROGRESS: Precursor Summary:
0:31:51.844712 PROGRESS: Channel   0:	 0.050 FDR:   249; 0.010 FDR:   249; 0.001 FDR:   125
0:31:51.844803 PROGRESS: 
0:31:51.844860 PROGRESS: Protein Summary:
0:31:51.845935 PROGRESS: Channel   0:	 0.050 FDR:   232; 0.010 FDR:   232; 0.001 FDR:   116
0:31:51.846028 PROGRESS: =========================================================================
0:31:51.847345 INFO: Target number of precursors reached.
0:31:51.883782 INFO: fragments_df: keeping 2237 of 468362 [sum(precursor_idx_mask)=2718 sum(mass_error_mask)=468362 stop_rank=2237
0:31:52.089374 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:52.199837 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:52.446119 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:31:52.446530 INFO: Using score_cutoff 14.869808421707154 (fac=0.99, q=1)
0:31:52.446829 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:31:52.446908 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:31:52.446964 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.869808421707154
0:31:52.447021 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:52.509503 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:52.669291 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:31:52.669516 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:31:52.669603 INFO: Starting optimization step 8.
0:31:52.669664 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:31:52.669730 INFO: Using ng extraction backend
0:31:52.669788 PROGRESS: Extracting batch of 100984 precursors
0:31:52.843651 INFO: === Search parameters used ===
0:31:52.843892 INFO: rt_error       : 805.611083984375
0:31:52.843944 INFO: mobility_error : 0.1
0:31:52.843992 INFO: num_candidates : 3
0:31:52.844034 INFO: ms1_error      : 30
0:31:52.844076 INFO: ms2_error      : 30
0:31:52.844119 INFO: fwhm_rt        : 3.0
0:31:52.844171 INFO: quant_window   : 3
0:31:52.844218 INFO: ==============================================
0:31:54.124832 INFO: performing precursor FDR with 40 features
0:31:54.124955 INFO: Decoy channel: -1
0:31:54.124981 INFO: Competetive: True
0:31:54.205420 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:54.310923 INFO: Using random state 867136 for train-test-split
0:31:58.688951 INFO: Test AUC: 0.594
0:31:58.689085 INFO: Train AUC: 0.604
0:31:58.689115 INFO: AUC difference: 1.64%
0:31:58.994666 INFO: Resetting torch num_threads to 80
0:31:59.005829 PROGRESS: === Extracted 300163 precursors and 1376589 fragments ===
0:31:59.006202 INFO: === FDR correction performed with classifier version 7 ===
0:31:59.006654 PROGRESS: ============================= Precursor FDR =============================
0:31:59.006741 PROGRESS: Total precursors accumulated: 274
0:31:59.006800 PROGRESS: Target precursors: 272 (99.27%)
0:31:59.006851 PROGRESS: Decoy precursors: 2 (0.73%)
0:31:59.006898 PROGRESS: 
0:31:59.006944 PROGRESS: Precursor Summary:
0:31:59.007813 PROGRESS: Channel   0:	 0.050 FDR:   272; 0.010 FDR:   272; 0.001 FDR:   154
0:31:59.007901 PROGRESS: 
0:31:59.007956 PROGRESS: Protein Summary:
0:31:59.008980 PROGRESS: Channel   0:	 0.050 FDR:   255; 0.010 FDR:   255; 0.001 FDR:   144
0:31:59.009079 PROGRESS: =========================================================================
0:31:59.014144 INFO: Target number of precursors reached.
0:31:59.103148 INFO: fragments_df: keeping 3051 of 1376589 [sum(precursor_idx_mask)=5698 sum(mass_error_mask)=1376589 stop_rank=3051
0:31:59.361927 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:59.467278 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:59.802303 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:59.802723 INFO: Using score_cutoff 8.478266668224334 (fac=0.99, q=1)
0:31:59.803004 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:59.803085 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:59.803140 INFO: Updating optimization_manager: score_cutoff        : 14.869808421707154 -> 8.478266668224334
0:31:59.803196 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:59.866068 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:00.029321 INFO: === checking if optimization conditions were reached ===
0:32:00.031433 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:32:00.031545 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:32:00.031620 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:32:00.031688 INFO: ==============================================
0:32:00.031764 INFO: Starting optimization step 9.
0:32:00.031830 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:32:00.031900 INFO: Using ng extraction backend
0:32:00.031967 PROGRESS: Extracting batch of 100984 precursors
0:32:00.207353 INFO: === Search parameters used ===
0:32:00.207593 INFO: rt_error       : 805.611083984375
0:32:00.207649 INFO: mobility_error : 0.1
0:32:00.207695 INFO: num_candidates : 3
0:32:00.207750 INFO: ms1_error      : 30
0:32:00.207794 INFO: ms2_error      : 10.0
0:32:00.207845 INFO: fwhm_rt        : 3.0
0:32:00.207886 INFO: quant_window   : 3
0:32:00.207926 INFO: ==============================================
0:32:01.466763 INFO: performing precursor FDR with 40 features
0:32:01.466881 INFO: Decoy channel: -1
0:32:01.466906 INFO: Competetive: True
0:32:01.549123 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:01.661790 INFO: Using random state 831643 for train-test-split
0:32:06.088850 INFO: Test AUC: 0.596
0:32:06.088976 INFO: Train AUC: 0.608
0:32:06.089016 INFO: AUC difference: 1.92%
0:32:06.403507 INFO: Resetting torch num_threads to 80
0:32:06.414005 PROGRESS: === Extracted 302270 precursors and 1615177 fragments ===
0:32:06.414383 INFO: === FDR correction performed with classifier version 8 ===
0:32:06.414857 PROGRESS: ============================= Precursor FDR =============================
0:32:06.414944 PROGRESS: Total precursors accumulated: 425
0:32:06.415002 PROGRESS: Target precursors: 421 (99.06%)
0:32:06.415052 PROGRESS: Decoy precursors: 4 (0.94%)
0:32:06.415095 PROGRESS: 
0:32:06.415140 PROGRESS: Precursor Summary:
0:32:06.416051 PROGRESS: Channel   0:	 0.050 FDR:   421; 0.010 FDR:   421; 0.001 FDR:   247
0:32:06.416140 PROGRESS: 
0:32:06.416194 PROGRESS: Protein Summary:
0:32:06.417298 PROGRESS: Channel   0:	 0.050 FDR:   392; 0.010 FDR:   392; 0.001 FDR:   228
0:32:06.417390 PROGRESS: =========================================================================
0:32:06.422372 INFO: Target number of precursors reached.
0:32:06.528710 INFO: fragments_df: keeping 4920 of 1615177 [sum(precursor_idx_mask)=10202 sum(mass_error_mask)=1615177 stop_rank=4920
0:32:06.695662 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:32:06.803863 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:32:07.483444 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:32:07.483859 INFO: Using score_cutoff 8.958398757934571 (fac=0.99, q=1)
0:32:07.484142 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:32:07.484223 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:32:07.484278 INFO: Updating optimization_manager: score_cutoff        : 8.478266668224334 -> 8.958398757934571
0:32:07.484333 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:07.515329 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:07.580265 INFO: === checking if optimization conditions were reached ===
0:32:07.582611 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:32:07.582728 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:32:07.583844 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:32:07.583919 INFO: ==============================================
0:32:07.583995 PROGRESS: Optimization finished for ms2_error.
0:32:07.733894 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:07.765119 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:07.830153 INFO: Starting optimization step 0.
0:32:07.830411 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:32:07.830503 INFO: Using ng extraction backend
0:32:07.830576 PROGRESS: Extracting batch of 50293 precursors
0:32:07.921172 INFO: === Search parameters used ===
0:32:07.921465 INFO: rt_error       : 805.611083984375
0:32:07.921526 INFO: mobility_error : 0.1
0:32:07.921574 INFO: num_candidates : 3
0:32:07.921622 INFO: ms1_error      : 30
0:32:07.921667 INFO: ms2_error      : 10.0
0:32:07.921712 INFO: fwhm_rt        : 3.0
0:32:07.921757 INFO: quant_window   : 3
0:32:07.921797 INFO: ==============================================
0:32:08.566212 INFO: performing precursor FDR with 40 features
0:32:08.566341 INFO: Decoy channel: -1
0:32:08.566367 INFO: Competetive: True
0:32:08.609849 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:08.651402 INFO: Using random state 34812 for train-test-split
0:32:11.168760 INFO: Test AUC: 0.600
0:32:11.168882 INFO: Train AUC: 0.619
0:32:11.168913 INFO: AUC difference: 3.06%
0:32:11.446971 INFO: Resetting torch num_threads to 80
0:32:11.452861 PROGRESS: === Extracted 150547 precursors and 804500 fragments ===
0:32:11.453783 INFO: === FDR correction performed with classifier version 9 ===
0:32:11.455159 PROGRESS: ============================= Precursor FDR =============================
0:32:11.455366 PROGRESS: Total precursors accumulated: 220
0:32:11.455505 PROGRESS: Target precursors: 218 (99.09%)
0:32:11.455622 PROGRESS: Decoy precursors: 2 (0.91%)
0:32:11.455731 PROGRESS: 
0:32:11.455834 PROGRESS: Precursor Summary:
0:32:11.457522 PROGRESS: Channel   0:	 0.050 FDR:   218; 0.010 FDR:   218; 0.001 FDR:   145
0:32:11.457615 PROGRESS: 
0:32:11.457668 PROGRESS: Protein Summary:
0:32:11.458660 PROGRESS: Channel   0:	 0.050 FDR:   212; 0.010 FDR:   212; 0.001 FDR:   141
0:32:11.458754 PROGRESS: =========================================================================
0:32:11.462832 INFO: Target number of precursors reached.
0:32:11.517642 INFO: fragments_df: keeping 2559 of 804500 [sum(precursor_idx_mask)=5277 sum(mass_error_mask)=804500 stop_rank=2559
0:32:11.654154 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:32:11.745595 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:32:12.025997 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:32:12.026404 INFO: Using score_cutoff 8.473787896728515 (fac=0.99, q=1)
0:32:12.026682 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:32:12.026762 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:32:12.026815 INFO: Updating optimization_manager: score_cutoff        : 8.958398757934571 -> 8.473787896728515
0:32:12.026871 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:12.057760 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:12.166758 INFO: === checking if optimization conditions were reached ===
0:32:12.167047 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:32:12.169111 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 356.17460223641814
0:32:12.169230 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 356.1746.
0:32:12.169311 INFO: ==============================================
0:32:12.169391 INFO: Starting optimization step 1.
0:32:12.169459 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:32:12.169530 INFO: Using ng extraction backend
0:32:12.169613 PROGRESS: Extracting batch of 50293 precursors
0:32:12.258466 INFO: === Search parameters used ===
0:32:12.258714 INFO: rt_error       : 356.17460223641814
0:32:12.258802 INFO: mobility_error : 0.1
0:32:12.258849 INFO: num_candidates : 3
0:32:12.258893 INFO: ms1_error      : 30
0:32:12.258936 INFO: ms2_error      : 10.0
0:32:12.258980 INFO: fwhm_rt        : 3.0
0:32:12.259021 INFO: quant_window   : 3
0:32:12.259061 INFO: ==============================================
0:32:12.898495 INFO: performing precursor FDR with 40 features
0:32:12.898618 INFO: Decoy channel: -1
0:32:12.898644 INFO: Competetive: True
0:32:12.941969 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:12.994393 INFO: Using random state 34812 for train-test-split
0:32:15.741180 INFO: Test AUC: 0.603
0:32:15.741302 INFO: Train AUC: 0.614
0:32:15.741332 INFO: AUC difference: 1.90%
0:32:16.006335 INFO: Resetting torch num_threads to 80
0:32:16.012264 PROGRESS: === Extracted 150369 precursors and 777060 fragments ===
0:32:16.012610 INFO: === FDR correction performed with classifier version 9 ===
0:32:16.013051 PROGRESS: ============================= Precursor FDR =============================
0:32:16.013142 PROGRESS: Total precursors accumulated: 202
0:32:16.013202 PROGRESS: Target precursors: 200 (99.01%)
0:32:16.013254 PROGRESS: Decoy precursors: 2 (0.99%)
0:32:16.013299 PROGRESS: 
0:32:16.013343 PROGRESS: Precursor Summary:
0:32:16.014199 PROGRESS: Channel   0:	 0.050 FDR:   200; 0.010 FDR:   194; 0.001 FDR:   148
0:32:16.014287 PROGRESS: 
0:32:16.014341 PROGRESS: Protein Summary:
0:32:16.015337 PROGRESS: Channel   0:	 0.050 FDR:   196; 0.010 FDR:   190; 0.001 FDR:   144
0:32:16.015434 PROGRESS: =========================================================================
0:32:16.017502 INFO: Target number of precursors not reached yet.
0:32:16.159292 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:16.190825 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:16.259243 INFO: === skipping optimization until target number of precursors are found ===
0:32:16.259490 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
0:32:16.259583 INFO: Starting optimization step 2.
0:32:16.259649 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:32:16.259716 INFO: Using ng extraction backend
0:32:16.259777 PROGRESS: Extracting batch of 50691 precursors
0:32:16.348341 INFO: === Search parameters used ===
0:32:16.348590 INFO: rt_error       : 356.17460223641814
0:32:16.348642 INFO: mobility_error : 0.1
0:32:16.348690 INFO: num_candidates : 3
0:32:16.348734 INFO: ms1_error      : 30
0:32:16.348774 INFO: ms2_error      : 10.0
0:32:16.348817 INFO: fwhm_rt        : 3.0
0:32:16.348857 INFO: quant_window   : 3
0:32:16.348896 INFO: ==============================================
0:32:17.029905 INFO: performing precursor FDR with 40 features
0:32:17.030036 INFO: Decoy channel: -1
0:32:17.030068 INFO: Competetive: True
0:32:17.141855 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:17.246689 INFO: Using random state 34812 for train-test-split
0:32:22.432708 INFO: Test AUC: 0.601
0:32:22.432834 INFO: Train AUC: 0.612
0:32:22.432865 INFO: AUC difference: 1.72%
0:32:22.749057 INFO: Resetting torch num_threads to 80
0:32:22.799834 PROGRESS: === Extracted 301966 precursors and 1561064 fragments ===
0:32:22.800440 INFO: === FDR correction performed with classifier version 9 ===
0:32:22.801067 PROGRESS: ============================= Precursor FDR =============================
0:32:22.801158 PROGRESS: Total precursors accumulated: 308
0:32:22.801218 PROGRESS: Target precursors: 305 (99.03%)
0:32:22.801269 PROGRESS: Decoy precursors: 3 (0.97%)
0:32:22.801314 PROGRESS: 
0:32:22.801356 PROGRESS: Precursor Summary:
0:32:22.802272 PROGRESS: Channel   0:	 0.050 FDR:   305; 0.010 FDR:   305; 0.001 FDR:    34
0:32:22.802363 PROGRESS: 
0:32:22.802418 PROGRESS: Protein Summary:
0:32:22.803481 PROGRESS: Channel   0:	 0.050 FDR:   286; 0.010 FDR:   286; 0.001 FDR:    34
0:32:22.803578 PROGRESS: =========================================================================
0:32:22.807731 INFO: Target number of precursors reached.
0:32:22.920941 INFO: fragments_df: keeping 3825 of 1561064 [sum(precursor_idx_mask)=7595 sum(mass_error_mask)=1561064 stop_rank=3825
0:32:23.133495 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:32:23.233999 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:32:23.665986 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:32:23.666406 INFO: Using score_cutoff 12.93795822944641 (fac=0.99, q=1)
0:32:23.666689 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:32:23.666768 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:32:23.666822 INFO: Updating optimization_manager: score_cutoff        : 8.473787896728515 -> 12.93795822944641
0:32:23.666884 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:23.729424 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:23.874899 INFO: === checking if optimization conditions were reached ===
0:32:23.875135 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:32:23.877043 INFO: Updating optimization_manager: rt_error            : 356.17460223641814 -> 120.1476404869537
0:32:23.877151 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 120.1476.
0:32:23.877215 INFO: ==============================================
0:32:23.877282 INFO: Starting optimization step 3.
0:32:23.877339 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:32:23.877401 INFO: Using ng extraction backend
0:32:23.877458 PROGRESS: Extracting batch of 100984 precursors
0:32:24.051404 INFO: === Search parameters used ===
0:32:24.051656 INFO: rt_error       : 120.1476404869537
0:32:24.051711 INFO: mobility_error : 0.1
0:32:24.051759 INFO: num_candidates : 3
0:32:24.051800 INFO: ms1_error      : 30
0:32:24.051842 INFO: ms2_error      : 10.0
0:32:24.051883 INFO: fwhm_rt        : 3.0
0:32:24.051921 INFO: quant_window   : 3
0:32:24.051960 INFO: ==============================================
0:32:25.216844 INFO: performing precursor FDR with 40 features
0:32:25.216963 INFO: Decoy channel: -1
0:32:25.216995 INFO: Competetive: True
0:32:25.296107 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:25.403326 INFO: Using random state 34812 for train-test-split
0:32:30.607166 INFO: Test AUC: 0.591
0:32:30.607308 INFO: Train AUC: 0.607
0:32:30.607356 INFO: AUC difference: 2.63%
0:32:32.186282 INFO: Resetting torch num_threads to 80
0:32:32.197640 PROGRESS: === Extracted 296711 precursors and 1242193 fragments ===
0:32:32.198025 INFO: === FDR correction performed with classifier version 9 ===
0:32:32.198526 PROGRESS: ============================= Precursor FDR =============================
0:32:32.198617 PROGRESS: Total precursors accumulated: 510
0:32:32.198677 PROGRESS: Target precursors: 505 (99.02%)
0:32:32.198727 PROGRESS: Decoy precursors: 5 (0.98%)
0:32:32.198773 PROGRESS: 
0:32:32.198816 PROGRESS: Precursor Summary:
0:32:32.199775 PROGRESS: Channel   0:	 0.050 FDR:   505; 0.010 FDR:   505; 0.001 FDR:   386
0:32:32.199868 PROGRESS: 
0:32:32.199924 PROGRESS: Protein Summary:
0:32:32.201108 PROGRESS: Channel   0:	 0.050 FDR:   470; 0.010 FDR:   470; 0.001 FDR:   361
0:32:32.201201 PROGRESS: =========================================================================
0:32:32.206281 INFO: Target number of precursors reached.
0:32:32.290743 INFO: fragments_df: keeping 5000 of 1242193 [sum(precursor_idx_mask)=11896 sum(mass_error_mask)=1242193 stop_rank=5000
0:32:32.433290 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:32:32.579074 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:32:33.373791 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:32:33.374212 INFO: Using score_cutoff 12.899028378295899 (fac=0.99, q=1)
0:32:33.374502 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:32:33.375580 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:32:33.375645 INFO: Updating optimization_manager: score_cutoff        : 12.93795822944641 -> 12.899028378295899
0:32:33.375710 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:33.406557 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:33.476793 INFO: === checking if optimization conditions were reached ===
0:32:33.477032 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:32:33.479154 INFO: Updating optimization_manager: rt_error            : 120.1476404869537 -> 90.8361682359718
0:32:33.479256 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 90.8362.
0:32:33.479321 INFO: ==============================================
0:32:33.479391 INFO: Starting optimization step 4.
0:32:33.479451 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:32:33.479526 INFO: Using ng extraction backend
0:32:33.479587 PROGRESS: Extracting batch of 50293 precursors
0:32:33.568226 INFO: === Search parameters used ===
0:32:33.568489 INFO: rt_error       : 90.8361682359718
0:32:33.568549 INFO: mobility_error : 0.1
0:32:33.568598 INFO: num_candidates : 3
0:32:33.568640 INFO: ms1_error      : 30
0:32:33.568681 INFO: ms2_error      : 10.0
0:32:33.568721 INFO: fwhm_rt        : 3.0
0:32:33.568761 INFO: quant_window   : 3
0:32:33.568812 INFO: ==============================================
0:32:34.170846 INFO: performing precursor FDR with 40 features
0:32:34.170968 INFO: Decoy channel: -1
0:32:34.170993 INFO: Competetive: True
0:32:34.214414 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:34.255632 INFO: Using random state 34812 for train-test-split
0:32:36.542477 INFO: Test AUC: 0.590
0:32:36.542598 INFO: Train AUC: 0.610
0:32:36.542630 INFO: AUC difference: 3.31%
0:32:36.807314 INFO: Resetting torch num_threads to 80
0:32:36.813430 PROGRESS: === Extracted 146628 precursors and 584861 fragments ===
0:32:36.813784 INFO: === FDR correction performed with classifier version 9 ===
0:32:36.814226 PROGRESS: ============================= Precursor FDR =============================
0:32:36.814317 PROGRESS: Total precursors accumulated: 244
0:32:36.814377 PROGRESS: Target precursors: 242 (99.18%)
0:32:36.814426 PROGRESS: Decoy precursors: 2 (0.82%)
0:32:36.814471 PROGRESS: 
0:32:36.814513 PROGRESS: Precursor Summary:
0:32:36.815393 PROGRESS: Channel   0:	 0.050 FDR:   242; 0.010 FDR:   242; 0.001 FDR:   185
0:32:36.815483 PROGRESS: 
0:32:36.815538 PROGRESS: Protein Summary:
0:32:36.816565 PROGRESS: Channel   0:	 0.050 FDR:   235; 0.010 FDR:   235; 0.001 FDR:   181
0:32:36.816657 PROGRESS: =========================================================================
0:32:36.818741 INFO: Target number of precursors reached.
0:32:36.859217 INFO: fragments_df: keeping 2723 of 584861 [sum(precursor_idx_mask)=5674 sum(mass_error_mask)=584861 stop_rank=2723
0:32:36.996128 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:32:37.094419 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:32:37.395650 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:32:37.396060 INFO: Using score_cutoff 13.109954065418243 (fac=0.99, q=1)
0:32:37.396355 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:32:37.396439 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:32:37.396493 INFO: Updating optimization_manager: score_cutoff        : 12.899028378295899 -> 13.109954065418243
0:32:37.396547 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:37.427595 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:37.495364 INFO: === checking if optimization conditions were reached ===
0:32:37.495626 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:32:37.497916 INFO: Updating optimization_manager: rt_error            : 90.8361682359718 -> 74.41628773529804
0:32:37.498034 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 74.4163.
0:32:37.498112 INFO: ==============================================
0:32:37.498211 INFO: Starting optimization step 5.
0:32:37.498280 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:32:37.498351 INFO: Using ng extraction backend
0:32:37.498419 PROGRESS: Extracting batch of 50293 precursors
0:32:37.588878 INFO: === Search parameters used ===
0:32:37.589137 INFO: rt_error       : 74.41628773529804
0:32:37.589197 INFO: mobility_error : 0.1
0:32:37.589244 INFO: num_candidates : 3
0:32:37.589289 INFO: ms1_error      : 30
0:32:37.589329 INFO: ms2_error      : 10.0
0:32:37.589383 INFO: fwhm_rt        : 3.0
0:32:37.589427 INFO: quant_window   : 3
0:32:37.589466 INFO: ==============================================
0:32:38.174958 INFO: performing precursor FDR with 40 features
0:32:38.175072 INFO: Decoy channel: -1
0:32:38.175098 INFO: Competetive: True
0:32:38.217118 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:38.258400 INFO: Using random state 34812 for train-test-split
0:32:40.334829 INFO: Test AUC: 0.589
0:32:40.334948 INFO: Train AUC: 0.607
0:32:40.334980 INFO: AUC difference: 2.92%
0:32:40.600015 INFO: Resetting torch num_threads to 80
0:32:40.606114 PROGRESS: === Extracted 145362 precursors and 559699 fragments ===
0:32:40.606463 INFO: === FDR correction performed with classifier version 9 ===
0:32:40.606916 PROGRESS: ============================= Precursor FDR =============================
0:32:40.607010 PROGRESS: Total precursors accumulated: 243
0:32:40.607068 PROGRESS: Target precursors: 241 (99.18%)
0:32:40.607118 PROGRESS: Decoy precursors: 2 (0.82%)
0:32:40.607164 PROGRESS: 
0:32:40.607206 PROGRESS: Precursor Summary:
0:32:40.608115 PROGRESS: Channel   0:	 0.050 FDR:   241; 0.010 FDR:   241; 0.001 FDR:   202
0:32:40.608206 PROGRESS: 
0:32:40.608261 PROGRESS: Protein Summary:
0:32:40.609338 PROGRESS: Channel   0:	 0.050 FDR:   235; 0.010 FDR:   235; 0.001 FDR:   198
0:32:40.609432 PROGRESS: =========================================================================
0:32:40.611549 INFO: Target number of precursors reached.
0:32:40.651901 INFO: fragments_df: keeping 2704 of 559699 [sum(precursor_idx_mask)=5548 sum(mass_error_mask)=559699 stop_rank=2704
0:32:40.788736 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:32:40.880088 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:32:41.194811 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:32:41.195235 INFO: Using score_cutoff 12.989094835281373 (fac=0.99, q=1)
0:32:41.195523 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:32:41.195608 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:32:41.195668 INFO: Updating optimization_manager: score_cutoff        : 13.109954065418243 -> 12.989094835281373
0:32:41.195729 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:41.226681 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:41.297156 INFO: === checking if optimization conditions were reached ===
0:32:41.297391 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:32:41.299329 INFO: Updating optimization_manager: rt_error            : 74.41628773529804 -> 55.12223530175282
0:32:41.299434 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 55.1222.
0:32:41.299507 INFO: ==============================================
0:32:41.299584 INFO: Starting optimization step 6.
0:32:41.299651 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:32:41.299718 INFO: Using ng extraction backend
0:32:41.299784 PROGRESS: Extracting batch of 50293 precursors
0:32:41.387200 INFO: === Search parameters used ===
0:32:41.387459 INFO: rt_error       : 55.12223530175282
0:32:41.387522 INFO: mobility_error : 0.1
0:32:41.387577 INFO: num_candidates : 3
0:32:41.387645 INFO: ms1_error      : 30
0:32:41.387700 INFO: ms2_error      : 10.0
0:32:41.387748 INFO: fwhm_rt        : 3.0
0:32:41.387796 INFO: quant_window   : 3
0:32:41.387843 INFO: ==============================================
0:32:41.944538 INFO: performing precursor FDR with 40 features
0:32:41.944655 INFO: Decoy channel: -1
0:32:41.944682 INFO: Competetive: True
0:32:41.986137 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:42.035578 INFO: Using random state 34812 for train-test-split
0:32:44.023005 INFO: Test AUC: 0.590
0:32:44.023123 INFO: Train AUC: 0.610
0:32:44.023153 INFO: AUC difference: 3.20%
0:32:44.288947 INFO: Resetting torch num_threads to 80
0:32:44.294891 PROGRESS: === Extracted 139713 precursors and 506608 fragments ===
0:32:44.295239 INFO: === FDR correction performed with classifier version 9 ===
0:32:44.295695 PROGRESS: ============================= Precursor FDR =============================
0:32:44.295784 PROGRESS: Total precursors accumulated: 240
0:32:44.295847 PROGRESS: Target precursors: 238 (99.17%)
0:32:44.295897 PROGRESS: Decoy precursors: 2 (0.83%)
0:32:44.295940 PROGRESS: 
0:32:44.295984 PROGRESS: Precursor Summary:
0:32:44.296854 PROGRESS: Channel   0:	 0.050 FDR:   238; 0.010 FDR:   238; 0.001 FDR:   112
0:32:44.296941 PROGRESS: 
0:32:44.297005 PROGRESS: Protein Summary:
0:32:44.298021 PROGRESS: Channel   0:	 0.050 FDR:   235; 0.010 FDR:   235; 0.001 FDR:   110
0:32:44.298112 PROGRESS: =========================================================================
0:32:44.300122 INFO: Target number of precursors reached.
0:32:44.335439 INFO: fragments_df: keeping 2512 of 506608 [sum(precursor_idx_mask)=5128 sum(mass_error_mask)=506608 stop_rank=2512
0:32:44.472199 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:32:44.575003 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:32:44.850314 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:32:44.850735 INFO: Using score_cutoff 13.132203535938263 (fac=0.99, q=1)
0:32:44.851027 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:32:44.851113 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:32:44.851176 INFO: Updating optimization_manager: score_cutoff        : 12.989094835281373 -> 13.132203535938263
0:32:44.851237 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:44.882099 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:44.947644 INFO: === checking if optimization conditions were reached ===
0:32:44.947879 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:32:44.949854 INFO: Updating optimization_manager: rt_error            : 55.12223530175282 -> 38.1247046502407
0:32:44.949968 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 38.1247.
0:32:44.950040 INFO: ==============================================
0:32:44.950116 INFO: Starting optimization step 7.
0:32:44.950181 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:32:44.950250 INFO: Using ng extraction backend
0:32:44.950313 PROGRESS: Extracting batch of 50293 precursors
0:32:45.037822 INFO: === Search parameters used ===
0:32:45.038087 INFO: rt_error       : 38.1247046502407
0:32:45.038164 INFO: mobility_error : 0.1
0:32:45.038220 INFO: num_candidates : 3
0:32:45.038269 INFO: ms1_error      : 30
0:32:45.038317 INFO: ms2_error      : 10.0
0:32:45.038363 INFO: fwhm_rt        : 3.0
0:32:45.038409 INFO: quant_window   : 3
0:32:45.038454 INFO: ==============================================
0:32:45.565117 INFO: performing precursor FDR with 40 features
0:32:45.565238 INFO: Decoy channel: -1
0:32:45.565268 INFO: Competetive: True
0:32:45.604785 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:45.647688 INFO: Using random state 34812 for train-test-split
0:32:47.638641 INFO: Test AUC: 0.591
0:32:47.638759 INFO: Train AUC: 0.610
0:32:47.638789 INFO: AUC difference: 3.06%
0:32:47.896586 INFO: Resetting torch num_threads to 80
0:32:47.902589 PROGRESS: === Extracted 133184 precursors and 473883 fragments ===
0:32:47.902934 INFO: === FDR correction performed with classifier version 9 ===
0:32:47.903383 PROGRESS: ============================= Precursor FDR =============================
0:32:47.903478 PROGRESS: Total precursors accumulated: 274
0:32:47.903537 PROGRESS: Target precursors: 272 (99.27%)
0:32:47.903587 PROGRESS: Decoy precursors: 2 (0.73%)
0:32:47.903632 PROGRESS: 
0:32:47.903676 PROGRESS: Precursor Summary:
0:32:47.904559 PROGRESS: Channel   0:	 0.050 FDR:   272; 0.010 FDR:   272; 0.001 FDR:   190
0:32:47.904646 PROGRESS: 
0:32:47.904703 PROGRESS: Protein Summary:
0:32:47.905867 PROGRESS: Channel   0:	 0.050 FDR:   266; 0.010 FDR:   266; 0.001 FDR:   188
0:32:47.905967 PROGRESS: =========================================================================
0:32:47.907971 INFO: Target number of precursors reached.
0:32:47.941818 INFO: fragments_df: keeping 2616 of 473883 [sum(precursor_idx_mask)=5451 sum(mass_error_mask)=473883 stop_rank=2616
0:32:48.078161 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:32:48.180005 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:32:48.472246 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:32:48.472662 INFO: Using score_cutoff 11.745475690841674 (fac=0.99, q=1)
0:32:48.472950 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:32:48.473042 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:32:48.473102 INFO: Updating optimization_manager: score_cutoff        : 13.132203535938263 -> 11.745475690841674
0:32:48.473160 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:48.503991 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:48.569852 INFO: === checking if optimization conditions were reached ===
0:32:48.570090 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:32:48.572037 INFO: Updating optimization_manager: rt_error            : 38.1247046502407 -> 36.561625310339785
0:32:48.572138 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 36.5616.
0:32:48.572205 INFO: ==============================================
0:32:48.572274 INFO: Starting optimization step 8.
0:32:48.572335 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:32:48.572396 INFO: Using ng extraction backend
0:32:48.572455 PROGRESS: Extracting batch of 50293 precursors
0:32:48.659938 INFO: === Search parameters used ===
0:32:48.660198 INFO: rt_error       : 36.561625310339785
0:32:48.660261 INFO: mobility_error : 0.1
0:32:48.660311 INFO: num_candidates : 3
0:32:48.660355 INFO: ms1_error      : 30
0:32:48.660395 INFO: ms2_error      : 10.0
0:32:48.660435 INFO: fwhm_rt        : 3.0
0:32:48.660475 INFO: quant_window   : 3
0:32:48.660515 INFO: ==============================================
0:32:49.198660 INFO: performing precursor FDR with 40 features
0:32:49.198779 INFO: Decoy channel: -1
0:32:49.198805 INFO: Competetive: True
0:32:49.238004 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:49.285791 INFO: Using random state 34812 for train-test-split
0:32:51.271699 INFO: Test AUC: 0.595
0:32:51.271818 INFO: Train AUC: 0.612
0:32:51.271848 INFO: AUC difference: 2.85%
0:32:51.533481 INFO: Resetting torch num_threads to 80
0:32:51.539806 PROGRESS: === Extracted 133479 precursors and 474852 fragments ===
0:32:51.540160 INFO: === FDR correction performed with classifier version 9 ===
0:32:51.540620 PROGRESS: ============================= Precursor FDR =============================
0:32:51.540709 PROGRESS: Total precursors accumulated: 180
0:32:51.540767 PROGRESS: Target precursors: 179 (99.44%)
0:32:51.540821 PROGRESS: Decoy precursors: 1 (0.56%)
0:32:51.540868 PROGRESS: 
0:32:51.540911 PROGRESS: Precursor Summary:
0:32:51.541769 PROGRESS: Channel   0:	 0.050 FDR:   179; 0.010 FDR:   179; 0.001 FDR:   106
0:32:51.541858 PROGRESS: 
0:32:51.541914 PROGRESS: Protein Summary:
0:32:51.542922 PROGRESS: Channel   0:	 0.050 FDR:   177; 0.010 FDR:   177; 0.001 FDR:   104
0:32:51.543015 PROGRESS: =========================================================================
0:32:51.544940 INFO: Target number of precursors not reached yet.
0:32:51.679144 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:51.710920 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:51.777785 INFO: === skipping optimization until target number of precursors are found ===
0:32:51.778024 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
0:32:51.778113 INFO: Starting optimization step 9.
0:32:51.778177 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:32:51.778243 INFO: Using ng extraction backend
0:32:51.778301 PROGRESS: Extracting batch of 50691 precursors
0:32:51.866189 INFO: === Search parameters used ===
0:32:51.866439 INFO: rt_error       : 36.561625310339785
0:32:51.866494 INFO: mobility_error : 0.1
0:32:51.866540 INFO: num_candidates : 3
0:32:51.866584 INFO: ms1_error      : 30
0:32:51.866625 INFO: ms2_error      : 10.0
0:32:51.866668 INFO: fwhm_rt        : 3.0
0:32:51.866709 INFO: quant_window   : 3
0:32:51.866751 INFO: ==============================================
0:32:52.445167 INFO: performing precursor FDR with 40 features
0:32:52.445294 INFO: Decoy channel: -1
0:32:52.445320 INFO: Competetive: True
0:32:52.544408 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:52.643470 INFO: Using random state 34812 for train-test-split
0:32:57.483594 INFO: Test AUC: 0.600
0:32:57.483722 INFO: Train AUC: 0.606
0:32:57.483753 INFO: AUC difference: 1.05%
0:32:57.787076 INFO: Resetting torch num_threads to 80
0:32:57.826687 PROGRESS: === Extracted 267932 precursors and 951571 fragments ===
0:32:57.827297 INFO: === FDR correction performed with classifier version 9 ===
0:32:57.827932 PROGRESS: ============================= Precursor FDR =============================
0:32:57.828033 PROGRESS: Total precursors accumulated: 515
0:32:57.828099 PROGRESS: Target precursors: 510 (99.03%)
0:32:57.828150 PROGRESS: Decoy precursors: 5 (0.97%)
0:32:57.828194 PROGRESS: 
0:32:57.828235 PROGRESS: Precursor Summary:
0:32:57.829253 PROGRESS: Channel   0:	 0.050 FDR:   510; 0.010 FDR:   510; 0.001 FDR:   431
0:32:57.829344 PROGRESS: 
0:32:57.829399 PROGRESS: Protein Summary:
0:32:57.830621 PROGRESS: Channel   0:	 0.050 FDR:   481; 0.010 FDR:   481; 0.001 FDR:   405
0:32:57.830714 PROGRESS: =========================================================================
0:32:57.834507 INFO: Target number of precursors reached.
0:32:57.904861 INFO: fragments_df: keeping 4899 of 951571 [sum(precursor_idx_mask)=9984 sum(mass_error_mask)=951571 stop_rank=4899
0:32:58.045719 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:32:58.186097 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:32:58.842411 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:32:58.842839 INFO: Using score_cutoff 5.482032729434967 (fac=0.99, q=1)
0:32:58.843118 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:32:58.843195 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:32:58.843249 INFO: Updating optimization_manager: score_cutoff        : 11.745475690841674 -> 5.482032729434967
0:32:58.843301 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:58.874263 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:58.940591 INFO: === checking if optimization conditions were reached ===
0:32:58.940834 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
0:32:58.941875 INFO: Updating optimization_manager: rt_error            : 36.561625310339785 -> 36.561625310339785
0:32:58.942010 INFO: Updating optimization_manager: classifier_version  : 9 -> 19
0:32:58.942113 INFO: Updating optimization_manager: score_cutoff        : 5.482032729434967 -> 5.482032729434967
0:32:58.942206 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:32:58.942297 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:32:58.942386 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 36.5616 found after 8 searches.
0:32:58.942917 INFO: ==============================================
0:32:58.942993 PROGRESS: Optimization finished for rt_error.
0:32:59.077801 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:59.109067 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:59.199686 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:32:59.199890 PROGRESS: ==============================================
0:32:59.199961 PROGRESS: ms2_error      : 10.0000
0:32:59.200022 PROGRESS: rt_error       : 36.5616
0:32:59.200074 PROGRESS: ==============================================
0:32:59.200545 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:33:06.917821 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:33:25.120081 INFO: Using ng extraction backend
0:33:25.120363 PROGRESS: Extracting batch of 12001526 precursors
0:33:40.943069 INFO: === Search parameters used ===
0:33:40.943334 INFO: rt_error       : 36.561625310339785
0:33:40.943398 INFO: mobility_error : 0.1
0:33:40.943448 INFO: num_candidates : 3
0:33:40.943492 INFO: ms1_error      : 30
0:33:40.943533 INFO: ms2_error      : 10.0
0:33:40.943576 INFO: fwhm_rt        : 3.0
0:33:40.943615 INFO: quant_window   : 3
0:33:40.943656 INFO: ==============================================
0:34:00.319181 INFO: Removed 12274281 precursors with score below cutoff 5.482032729434967
0:34:18.109850 INFO: performing precursor FDR with 40 features
0:34:18.109973 INFO: Decoy channel: -1
0:34:18.110000 INFO: Competetive: True
0:34:20.318554 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:28.469718 INFO: Using random state 396108 for train-test-split
0:39:43.549820 INFO: Test AUC: 0.621
0:39:43.550058 INFO: Train AUC: 0.622
0:39:43.550100 INFO: AUC difference: 0.11%
0:39:48.685268 INFO: Resetting torch num_threads to 80
0:39:50.543603 PROGRESS: ============================= Precursor FDR =============================
0:39:50.543877 PROGRESS: Total precursors accumulated: 71,080
0:39:50.543947 PROGRESS: Target precursors: 70,377 (99.01%)
0:39:50.543998 PROGRESS: Decoy precursors: 703 (0.99%)
0:39:50.544043 PROGRESS: 
0:39:50.544086 PROGRESS: Precursor Summary:
0:39:50.570192 PROGRESS: Channel   0:	 0.050 FDR: 70,377; 0.010 FDR: 70,377; 0.001 FDR: 38,210
0:39:50.570536 PROGRESS: 
0:39:50.570605 PROGRESS: Protein Summary:
0:39:50.603362 PROGRESS: Channel   0:	 0.050 FDR: 12,375; 0.010 FDR: 12,375; 0.001 FDR: 7,723
0:39:50.603671 PROGRESS: =========================================================================
0:39:50.751734 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/psm.parquet
0:39:50.900910 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.parquet
0:39:51.111250 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:40:18.952423 PROGRESS: Processing search outputs
0:40:18.952536 PROGRESS: Performing protein grouping and FDR
0:40:18.952571 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:40:18.998055 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:40:19.027343 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:40:19.055233 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:40:19.088139 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:40:19.124904 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:40:19.154137 INFO: Building combined output
0:40:19.174534 INFO: Performing protein inference
0:40:19.670667 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
0:40:58.867910 INFO: Performing protein FDR
0:41:05.399106 INFO: Normalizing q-values using 17,652 targets and 3,258 decoys
0:41:05.403164 INFO: Test AUC: 0.853
0:41:05.403224 INFO: Train AUC: 0.861
0:41:05.403258 INFO: AUC difference: 0.95%
0:41:05.935341 PROGRESS: ================ Protein FDR =================
0:41:05.935472 PROGRESS: Unique protein groups in output
0:41:05.935501 PROGRESS:   1% protein FDR: 9,993
0:41:05.935525 PROGRESS: 
0:41:05.935544 PROGRESS: Unique precursor in output
0:41:05.935563 PROGRESS:   1% protein FDR: 115,864
0:41:05.935579 PROGRESS: ================================================
0:41:05.990757 PROGRESS: Building search statistics
0:41:06.070220 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
0:41:06.070400 INFO: Initializing OptimizationManager
0:41:06.070621 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
0:41:06.070692 INFO: Initializing CalibrationManager
0:41:06.070890 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
0:41:06.070962 INFO: Initializing RawFileManager
0:41:06.097961 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
0:41:06.098141 INFO: Initializing OptimizationManager
0:41:06.098331 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
0:41:06.098402 INFO: Initializing CalibrationManager
0:41:06.098590 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
0:41:06.098661 INFO: Initializing RawFileManager
0:41:06.126100 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
0:41:06.126280 INFO: Initializing OptimizationManager
0:41:06.126467 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
0:41:06.126537 INFO: Initializing CalibrationManager
0:41:06.126723 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
0:41:06.126791 INFO: Initializing RawFileManager
0:41:06.154151 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
0:41:06.154330 INFO: Initializing OptimizationManager
0:41:06.154516 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
0:41:06.154584 INFO: Initializing CalibrationManager
0:41:06.154769 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
0:41:06.154839 INFO: Initializing RawFileManager
0:41:06.184216 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
0:41:06.184400 INFO: Initializing OptimizationManager
0:41:06.184591 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
0:41:06.184661 INFO: Initializing CalibrationManager
0:41:06.184850 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
0:41:06.184920 INFO: Initializing RawFileManager
0:41:06.212343 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
0:41:06.212538 INFO: Initializing OptimizationManager
0:41:06.212739 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
0:41:06.212810 INFO: Initializing CalibrationManager
0:41:06.213003 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
0:41:06.213079 INFO: Initializing RawFileManager
0:41:06.215606 INFO: Writing stat output to disk
0:41:06.215668 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/stat.tsv to disk
0:41:06.223323 PROGRESS: Building internal statistics
0:41:06.223586 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
0:41:06.223633 INFO: Initializing TimingManager
0:41:06.223993 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
0:41:06.224038 INFO: Initializing TimingManager
0:41:06.224244 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
0:41:06.224284 INFO: Initializing TimingManager
0:41:06.224461 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
0:41:06.224498 INFO: Initializing TimingManager
0:41:06.224671 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
0:41:06.224708 INFO: Initializing TimingManager
0:41:06.224874 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
0:41:06.224910 INFO: Initializing TimingManager
0:41:06.225325 INFO: Writing internal output to disk
0:41:06.225372 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/internal.tsv to disk
0:41:06.225867 PROGRESS: Performing label free quantification
0:41:06.280280 INFO: Accumulating fragment data
0:41:06.280428 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:41:06.494151 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:41:07.686142 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:41:08.769511 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:41:09.976876 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:41:11.398626 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:41:13.129875 PROGRESS: Performing label free quantification on the precursor level
0:41:13.130002 INFO: Filtering fragments by quality
0:41:13.503482 INFO: Performing label-free quantification using directLFQ
0:41:15.129711 INFO: 115864 lfq-groups total
0:42:02.083278 INFO: using 80 processes
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0:43:20.201161 INFO: Writing precursor output to disk
0:43:20.201315 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/precursor.matrix.tsv to disk
0:43:20.695607 PROGRESS: Performing label free quantification on the pg level
0:43:20.695714 INFO: Filtering fragments by quality
0:43:21.023726 INFO: Performing label-free quantification using directLFQ
0:43:21.332659 INFO: 9993 lfq-groups total
0:43:49.307926 INFO: using 80 processes
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0:43:50.962650 INFO: lfq-object 3600
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0:43:51.052752 INFO: lfq-object 3800
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0:43:51.126325 INFO: lfq-object 3700
0:43:52.550159 INFO: lfq-object 4000
0:43:52.607874 INFO: lfq-object 4100
0:43:52.695971 INFO: lfq-object 4200
0:43:52.728605 INFO: lfq-object 4300
0:43:52.783364 INFO: lfq-object 4400
0:43:52.802013 INFO: lfq-object 4500
0:43:52.828614 INFO: lfq-object 4800
0:43:52.876296 INFO: lfq-object 4900
0:43:52.910132 INFO: lfq-object 5000
0:43:52.942688 INFO: lfq-object 4700
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0:43:53.031111 INFO: lfq-object 5100
0:43:53.098781 INFO: lfq-object 5200
0:43:53.109623 INFO: lfq-object 5600
0:43:53.141327 INFO: lfq-object 5400
0:43:53.174778 INFO: lfq-object 5700
0:43:53.196920 INFO: lfq-object 5500
0:43:53.205492 INFO: lfq-object 5300
0:43:53.221967 INFO: lfq-object 5800
0:43:53.331908 INFO: lfq-object 5900
0:43:53.335403 INFO: lfq-object 6000
0:43:53.424583 INFO: lfq-object 6200
0:43:53.459263 INFO: lfq-object 6400
0:43:53.509280 INFO: lfq-object 6500
0:43:53.589403 INFO: lfq-object 6600
0:43:53.590534 INFO: lfq-object 6700
0:43:53.611359 INFO: lfq-object 6100
0:43:53.640689 INFO: lfq-object 6300
0:43:53.669969 INFO: lfq-object 6900
0:43:53.748626 INFO: lfq-object 6800
0:43:53.768764 INFO: lfq-object 7000
0:43:53.776082 INFO: lfq-object 7200
0:43:53.794268 INFO: lfq-object 7100
0:43:53.846069 INFO: lfq-object 7300
0:43:53.881094 INFO: lfq-object 7400
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0:43:54.019814 INFO: lfq-object 7700
0:43:54.029640 INFO: lfq-object 7600
0:43:54.055572 INFO: lfq-object 7800
0:43:54.084883 INFO: lfq-object 8000
0:43:54.152256 INFO: lfq-object 8100
0:43:54.198714 INFO: lfq-object 8200
0:43:54.242282 INFO: lfq-object 7900
0:43:54.244957 INFO: lfq-object 8300
0:43:54.284534 INFO: lfq-object 8400
0:43:54.452480 INFO: lfq-object 8600
0:43:54.470389 INFO: lfq-object 8800
0:43:54.500892 INFO: lfq-object 8900
0:43:54.514789 INFO: lfq-object 8500
0:43:54.525423 INFO: lfq-object 8700
0:43:54.595666 INFO: lfq-object 9000
0:43:54.614841 INFO: lfq-object 9100
0:43:54.678677 INFO: lfq-object 9300
0:43:54.745343 INFO: lfq-object 9400
0:43:54.760163 INFO: lfq-object 9600
0:43:54.803798 INFO: lfq-object 9500
0:43:54.808131 INFO: lfq-object 9200
0:43:54.832011 INFO: lfq-object 9700
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0:43:54.917661 INFO: lfq-object 9900
0:43:56.901801 INFO: Writing pg output to disk
0:43:56.901955 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/pg.matrix.tsv to disk
0:43:57.089996 INFO: Writing psm output to disk
0:43:57.090132 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/precursors.tsv to disk
0:44:04.993016 PROGRESS: Building MBR spectral library
0:44:05.055374 INFO: Running MbrLibraryBuilder
0:44:07.191339 INFO: MBR spectral library contains 115,864 precursors, 9,993 proteins
0:44:07.191469 INFO: Writing MBR spectral library to disk
0:44:08.604625 PROGRESS: =================== Search Finished ===================
0:44:10.026278 INFO: Running step 'mbr'
0:44:10.028736 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 30.0, 'target_ms2_tolerance': 10.0}})
0:44:10.028866 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:44:10.041334 INFO: loading additional config provided via CLI
0:44:10.041547 INFO: loading additional config provided via CLI parameters
0:44:10.041955 INFO: Updating config with 'user defined'
0:44:10.042193 INFO: Updating config with 'user defined (cli)'
0:44:10.042248 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default_ng.yaml
0:44:10.042916 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': 5, 'target_ms2_tolerance': 10, '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': 10.0}, '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/library/speclib.mbr.hdf', 'output_directory': 'run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR'}]
0:44:10.043224 INFO: Updating config with 'ng_default'
0:44:10.043263 INFO: Updating config with 'user defined'
0:44:10.043380 INFO: Updating config with 'user defined (cli)'
0:44:10.043461 INFO: Updating config with 'multistep search'
0:44:10.043507 INFO: ├──version: 1
0:44:10.043536 INFO: ├──workflow_name: None
0:44:10.043564 INFO: [32;20m├──output_directory: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR [multistep search, default: None][0m
0:44:10.043585 INFO: [32;20m├──library_path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/speclib.mbr.hdf [multistep search, default: None][0m
0:44:10.043606 INFO: ├──raw_paths:
0:44:10.043627 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:44:10.043648 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:44:10.043667 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:44:10.043687 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:44:10.043706 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:44:10.045403 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:44:10.045440 INFO: ├──fasta_paths:
0:44:10.045464 INFO: ├──quant_directory: None
0:44:10.045488 INFO: ├──general
0:44:10.045511 INFO: │   [32;20m├──thread_count: 80 [user defined, default: 10][0m
0:44:10.045535 INFO: │   ├──transfer_step_enabled: False
0:44:10.045558 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
0:44:10.045581 INFO: │   ├──reuse_calibration: False
0:44:10.045600 INFO: │   ├──reuse_quant: False
0:44:10.045621 INFO: │   ├──astral_ms1: False
0:44:10.045642 INFO: │   ├──log_level: INFO
0:44:10.045667 INFO: │   ├──mmap_detector_events: False
0:44:10.045689 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:44:10.045711 INFO: │   ├──save_figures: True
0:44:10.045731 INFO: │   ├──save_library: True
0:44:10.045752 INFO: │   ├──save_flat_library: False
0:44:10.045772 INFO: │   ├──input_library_type: base
0:44:10.045793 INFO: │   ├──save_mbr_library: True
0:44:10.045814 INFO: │   └──random_state: None
0:44:10.045834 INFO: ├──library_loading
0:44:10.045855 INFO: │   └──rt_heuristic: 180
0:44:10.045877 INFO: ├──library_prediction
0:44:10.045898 INFO: │   ├──enabled: False
0:44:10.045917 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:44:10.045937 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:44:10.045955 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:44:10.045978 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:44:10.046000 INFO: │   ├──missed_cleavages: 1
0:44:10.046023 INFO: │   ├──precursor_len:
0:44:10.046043 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:44:10.046064 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:44:10.046085 INFO: │   ├──precursor_charge:
0:44:10.046106 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:44:10.046125 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:44:10.046145 INFO: │   ├──precursor_mz:
0:44:10.046164 INFO: │   │   - 400
0:44:10.046183 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
0:44:10.046202 INFO: │   ├──fragment_mz:
0:44:10.046221 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
0:44:10.046241 INFO: │   │   - 2000
0:44:10.046260 INFO: │   ├──nce: 25.0
0:44:10.046280 INFO: │   ├──fragment_types:
0:44:10.046300 INFO: │   │   - b
0:44:10.046321 INFO: │   │   - y
0:44:10.046340 INFO: │   ├──max_fragment_charge: 2
0:44:10.046362 INFO: │   [32;20m├──instrument: Astral [user defined, default: Lumos][0m
0:44:10.046382 INFO: │   ├──peptdeep_model_path: None
0:44:10.046402 INFO: │   └──peptdeep_model_type: generic
0:44:10.046423 INFO: ├──custom_modifications:
0:44:10.046443 INFO: │   ├──name: Dimethyl:d12@K
0:44:10.046465 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:44:10.046486 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:44:10.046508 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:44:10.046528 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:44:10.046549 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:44:10.046569 INFO: │   ├──name: mTRAQ:d12@K
0:44:10.046590 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:44:10.046610 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:44:10.046631 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:44:10.046651 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:44:10.046674 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:44:10.046694 INFO: │   ├──name: Label:13C(12)@K
0:44:10.046715 INFO: │   └──composition: C(12)
0:44:10.046742 INFO: ├──search
0:44:10.046764 INFO: │   [32;20m├──extraction_backend: ng [user defined, default: classic][0m
0:44:10.046786 INFO: │   [32;20m├──target_ms1_tolerance: 30.0 [multistep search, default: 5][0m
0:44:10.046808 INFO: │   ├──target_ms2_tolerance: 10.0
0:44:10.046829 INFO: │   ├──target_rt_tolerance: 0.0
0:44:10.046850 INFO: │   ├──target_mobility_tolerance: 0.0
0:44:10.046870 INFO: │   ├──quant_window: 3
0:44:10.046891 INFO: │   ├──target_num_candidates: 3
0:44:10.046911 INFO: │   ├──channel_filter: 
0:44:10.046931 INFO: │   ├──exclude_shared_ions: True
0:44:10.046952 INFO: │   ├──compete_for_fragments: True
0:44:10.046972 INFO: │   ├──quant_all: True
0:44:10.046993 INFO: │   ├──top_k_fragments_selection: 12
0:44:10.047012 INFO: │   ├──top_k_fragments_scoring: 12
0:44:10.047032 INFO: │   ├──min_fragment_intensity: 0.01
0:44:10.047051 INFO: │   ├──experimental_xic: True
0:44:10.047072 INFO: │   └──optimized_peak_group_score: False
0:44:10.047091 INFO: ├──calibration
0:44:10.047113 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
0:44:10.047133 INFO: │   ├──optimization_lock_target: 200
0:44:10.047152 INFO: │   ├──max_steps: 20
0:44:10.047172 INFO: │   ├──min_steps: 2
0:44:10.047190 INFO: │   ├──max_skips: 1
0:44:10.047211 INFO: │   ├──max_fragments: 5000
0:44:10.047231 INFO: │   └──min_correlation: 0.7
0:44:10.047259 INFO: ├──search_initial
0:44:10.047298 INFO: │   ├──initial_num_candidates: 1
0:44:10.047337 INFO: │   ├──initial_ms1_tolerance: 30
0:44:10.047358 INFO: │   ├──initial_ms2_tolerance: 30
0:44:10.047380 INFO: │   ├──initial_mobility_tolerance: 0.1
0:44:10.047401 INFO: │   └──initial_rt_tolerance: 0.5
0:44:10.047420 INFO: ├──selection_config
0:44:10.047442 INFO: │   ├──peak_len_rt: 10.0
0:44:10.047463 INFO: │   ├──sigma_scale_rt: 0.5
0:44:10.047483 INFO: │   ├──peak_len_mobility: 0.01
0:44:10.047506 INFO: │   ├──sigma_scale_mobility: 1.0
0:44:10.047534 INFO: │   ├──top_k_precursors: 3
0:44:10.047578 INFO: │   ├──kernel_size: 30
0:44:10.047619 INFO: │   ├──f_mobility: 1.0
0:44:10.047655 INFO: │   ├──f_rt: 0.99
0:44:10.047695 INFO: │   ├──center_fraction: 0.5
0:44:10.047732 INFO: │   ├──min_size_mobility: 8
0:44:10.047769 INFO: │   ├──min_size_rt: 3
0:44:10.047807 INFO: │   ├──max_size_mobility: 20
0:44:10.047846 INFO: │   ├──max_size_rt: 15
0:44:10.047884 INFO: │   ├──group_channels: False
0:44:10.047923 INFO: │   ├──use_weighted_score: True
0:44:10.047962 INFO: │   ├──join_close_candidates: False
0:44:10.048002 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:44:10.048042 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:44:10.048079 INFO: ├──scoring_config
0:44:10.048118 INFO: │   ├──score_grouped: False
0:44:10.048171 INFO: │   ├──top_k_isotopes: 3
0:44:10.048199 INFO: │   ├──reference_channel: -1
0:44:10.048226 INFO: │   ├──precursor_mz_tolerance: 10
0:44:10.048253 INFO: │   └──fragment_mz_tolerance: 15
0:44:10.048278 INFO: ├──library_multiplexing
0:44:10.048302 INFO: │   ├──enabled: False
0:44:10.048326 INFO: │   ├──input_channel: 0
0:44:10.048352 INFO: │   └──multiplex_mapping:
0:44:10.048375 INFO: ├──multiplexing
0:44:10.048399 INFO: │   ├──enabled: False
0:44:10.048422 INFO: │   ├──target_channels: 4,8
0:44:10.048450 INFO: │   ├──decoy_channel: 12
0:44:10.048472 INFO: │   ├──reference_channel: 0
0:44:10.048496 INFO: │   └──competetive_scoring: True
0:44:10.048522 INFO: ├──fdr
0:44:10.048547 INFO: │   ├──fdr: 0.01
0:44:10.048568 INFO: │   ├──group_level: proteins
0:44:10.048587 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
0:44:10.048611 INFO: │   ├──competetive_scoring: True
0:44:10.048630 INFO: │   ├──keep_decoys: False
0:44:10.048648 INFO: │   ├──channel_wise_fdr: False
0:44:10.048666 INFO: │   ├──enable_two_step_classifier: False
0:44:10.048685 INFO: │   ├──two_step_classifier_max_iterations: 5
0:44:10.048702 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:44:10.048720 INFO: ├──search_output
0:44:10.048740 INFO: │   ├──file_format: tsv
0:44:10.048764 INFO: │   ├──peptide_level_lfq: False
0:44:10.048794 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:44:10.048827 INFO: │   ├──save_fragment_quant_matrix: False
0:44:10.048882 INFO: │   ├──min_k_fragments: 12
0:44:10.048952 INFO: │   ├──min_correlation: 0.9
0:44:10.049227 INFO: │   ├──num_samples_quadratic: 50
0:44:10.049343 INFO: │   ├──min_nonnan: 3
0:44:10.049456 INFO: │   └──normalize_lfq: True
0:44:10.049563 INFO: ├──optimization
0:44:10.049658 INFO: │   ├──order_of_optimization: None
0:44:10.049759 INFO: │   ├──ms2_error
0:44:10.049860 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:44:10.049960 INFO: │   │   ├──targeted_update_factor: 1.0
0:44:10.050036 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:44:10.050082 INFO: │   │   ├──automatic_update_factor: 1.1
0:44:10.050112 INFO: │   │   ├──try_narrower_values: True
0:44:10.050140 INFO: │   │   ├──maximal_decrease: 0.5
0:44:10.050168 INFO: │   │   ├──favour_narrower_optimum: False
0:44:10.050195 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:44:10.050251 INFO: │   ├──ms1_error
0:44:10.050286 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:44:10.050319 INFO: │   │   ├──targeted_update_factor: 1.0
0:44:10.050352 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:44:10.050389 INFO: │   │   ├──automatic_update_factor: 1.1
0:44:10.050424 INFO: │   │   ├──try_narrower_values: False
0:44:10.050462 INFO: │   │   ├──maximal_decrease: 0.2
0:44:10.050510 INFO: │   │   ├──favour_narrower_optimum: False
0:44:10.050659 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:44:10.050744 INFO: │   ├──mobility_error
0:44:10.050826 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:44:10.050898 INFO: │   │   ├──targeted_update_factor: 1.0
0:44:10.050972 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:44:10.051304 INFO: │   │   ├──automatic_update_factor: 1.1
0:44:10.051384 INFO: │   │   ├──try_narrower_values: False
0:44:10.051457 INFO: │   │   ├──maximal_decrease: 0.2
0:44:10.051531 INFO: │   │   ├──favour_narrower_optimum: False
0:44:10.051604 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:44:10.051670 INFO: │   └──rt_error
0:44:10.051741 INFO: │       ├──targeted_update_percentile_range: 0.95
0:44:10.051812 INFO: │       ├──targeted_update_factor: 1.0
0:44:10.051878 INFO: │       ├──automatic_update_percentile_range: 0.99
0:44:10.051948 INFO: │       ├──automatic_update_factor: 1.1
0:44:10.053071 INFO: │       ├──try_narrower_values: True
0:44:10.053183 INFO: │       ├──maximal_decrease: 0.2
0:44:10.053254 INFO: │       ├──favour_narrower_optimum: True
0:44:10.053322 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:44:10.053387 INFO: ├──optimization_manager
0:44:10.053453 INFO: │   ├──fwhm_rt: 5
0:44:10.053521 INFO: │   ├──fwhm_mobility: 0.01
0:44:10.053588 INFO: │   └──score_cutoff: 0
0:44:10.053650 INFO: ├──transfer_library
0:44:10.053719 INFO: │   ├──enabled: False
0:44:10.053784 INFO: │   ├──fragment_types:
0:44:10.053847 INFO: │   │   - b
0:44:10.053919 INFO: │   │   - y
0:44:10.053986 INFO: │   ├──max_charge: 2
0:44:10.054051 INFO: │   ├──top_k_samples: 3
0:44:10.054117 INFO: │   ├──norm_delta_max: True
0:44:10.054183 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:44:10.054251 INFO: │   └──fragment_correlation_ratio: 0.75
0:44:10.054316 INFO: └──transfer_learning
0:44:10.054381 INFO:     ├──enabled: False
0:44:10.054445 INFO:     ├──batch_size: 2000
0:44:10.054512 INFO:     ├──max_lr: 0.0001
0:44:10.054577 INFO:     ├──train_fraction: 0.7
0:44:10.054643 INFO:     ├──validation_fraction: 0.2
0:44:10.054708 INFO:     ├──test_fraction: 0.1
0:44:10.054771 INFO:     ├──test_interval: 1
0:44:10.054835 INFO:     ├──lr_patience: 3
0:44:10.054898 INFO:     ├──epochs: 51
0:44:10.054960 INFO:     ├──warmup_epochs: 5
0:44:10.055022 INFO:     ├──nce: 25
0:44:10.055087 INFO:     [32;20m└──instrument: Astral [user defined, default: Lumos][0m
0:44:10.061835 INFO: Moved existing config file run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/frozen_config.yaml to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/frozen_config.yaml
0:44:10.062068 INFO: Registering 7 custom modifications
0:44:10.085997 INFO: Searching 6 files:
0:44:10.086089 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:44:10.086126 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:44:10.086151 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:44:10.086178 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:44:10.086204 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:44:10.086228 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:44:10.086252 INFO: Using 0 fasta files:
0:44:10.086277 INFO: Using library: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/speclib.mbr.hdf
0:44:10.086303 INFO: Saving output to: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR
0:44:10.086345 PROGRESS: Loading spectral library
0:44:10.086387 PROGRESS: Loading library (type: base) from disk..
0:44:10.086424 INFO: Running DynamicLoader
0:44:10.086495 INFO: Loading .hdf library from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/library/speclib.mbr.hdf
0:44:10.723725 INFO: Running PrecursorInitializer
0:44:10.723894 INFO: Running AnnotateFasta
0:44:10.724180 INFO: Dropping decoys from input library before annotation
0:44:10.739809 INFO: Running IsotopeGenerator
0:44:10.740045 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
0:44:10.740091 INFO: Running RTNormalization
0:44:10.743912 INFO: Saving library to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/speclib.hdf
0:44:11.539283 INFO: Running DecoyGenerator
0:44:19.574086 INFO: Running FlattenLibrary
0:44:20.621514 INFO: Running InitFlatColumns
0:44:20.627737 INFO: Running LogFlatLibraryStats
0:44:20.627853 INFO: ============ Library Stats ============
0:44:20.627883 INFO: Number of precursors: 231,699
0:44:20.676272 INFO: 	thereof targets:115,864
0:44:20.676424 INFO: 	thereof decoys: 115,835
0:44:20.678499 INFO: Number of elution groups: 115,864
0:44:20.678569 INFO: 	average size: 2.00
0:44:20.687641 INFO: Number of proteins: 9,993
0:44:20.688997 INFO: Number of channels: 1 ([0])
0:44:20.689112 INFO: Isotopes Distribution for 4 isotopes
0:44:20.689148 INFO: =======================================
0:44:20.689607 PROGRESS: Starting Search Workflows
0:44:20.689677 PROGRESS: 
0:44:20.689734 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant
0:44:20.689804 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/figures
0:44:20.690026 INFO: Initializing TimingManager
0:44:20.690419 INFO: Initializing RawFileManager
0:44:31.577209 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.
0:44:31.581230 INFO: Determining DIA cycle
0:44:31.597583 INFO: Found cycle with start 0.00 min and length 300.
0:44:31.754512 INFO: RT (min)            : 0.0 - 26.9
0:44:31.754603 INFO: RT duration (sec)   : 1611.2
0:44:31.754632 INFO: RT duration (min)   : 26.9
0:44:31.754653 INFO: Cycle len (scans)   : 300
0:44:31.754672 INFO: Cycle len (sec)     : 1.65
0:44:31.754690 INFO: Number of cycles    : 977
0:44:31.754709 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:44:31.754737 INFO: Creating DIA data object took: 11.064205408096313
0:44:32.461598 INFO: Creating DIA data NG object took: 0.7067563533782959
0:44:32.479294 INFO: Initializing CalibrationManager
0:44:32.479559 INFO: Setting up calibration estimators ..
0:44:32.479617 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:44:32.479683 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'}' ..
0:44:32.479748 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:44:32.479796 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:44:32.479847 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}}' ..
0:44:32.479896 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:44:32.479940 INFO: Done setting up calibration estimators.
0:44:32.480126 INFO: Initializing OptimizationManager
0:44:32.480250 INFO: initial parameter: ms1_error = 30
0:44:32.480300 INFO: initial parameter: ms2_error = 30
0:44:32.480346 INFO: initial parameter: rt_error = 805.5992431640625
0:44:32.480389 INFO: initial parameter: mobility_error = 0.1
0:44:32.480431 INFO: initial parameter: num_candidates = 1
0:44:32.480473 INFO: initial parameter: fwhm_rt = 5
0:44:32.480518 INFO: initial parameter: fwhm_mobility = 0.01
0:44:32.480559 INFO: initial parameter: score_cutoff = 0
0:44:32.480598 INFO: initial parameter: classifier_version = -1
0:44:32.480664 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:44:32.480875 INFO: FDRManager: loading saved state not requested, will be initialized.
0:44:32.480908 INFO: Initializing FDRManager
0:44:32.480941 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:44:32.505357 PROGRESS: Initializing spectral library: 115,864 target precursors potentially observable (0 removed)
0:44:32.522243 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:44:32.522576 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
0:44:32.522670 PROGRESS: Starting initial search for precursors.
0:44:32.522749 INFO: Starting optimization step 0.
0:44:32.522805 PROGRESS: === Extracting elution groups 0 to 200 ===
0:44:32.522859 INFO: Using ng extraction backend
0:44:32.522915 PROGRESS: Extracting batch of 397 precursors
0:44:32.524895 INFO: === Search parameters used ===
0:44:32.525016 INFO: rt_error       : 805.5992431640625
0:44:32.525085 INFO: mobility_error : 0.1
0:44:32.525144 INFO: num_candidates : 1
0:44:32.525198 INFO: ms1_error      : 30
0:44:32.525248 INFO: ms2_error      : 30
0:44:32.525290 INFO: fwhm_rt        : 5
0:44:32.525331 INFO: quant_window   : 3
0:44:32.525369 INFO: ==============================================
0:44:32.541404 INFO: performing precursor FDR with 40 features
0:44:32.541503 INFO: Decoy channel: -1
0:44:32.541528 INFO: Competetive: True
0:44:32.542438 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:32.544459 INFO: Using random state 742421 for train-test-split
0:44:32.551076 INFO: Test AUC: 0.580
0:44:32.551127 INFO: Train AUC: 0.506
0:44:32.551167 INFO: AUC difference: 14.52%
0:44:32.551189 WARNING: AUC difference > 5%. This may indicate overfitting.
0:44:32.786496 INFO: Resetting torch num_threads to 80
0:44:32.787746 PROGRESS: === Extracted 397 precursors and 2796 fragments ===
0:44:32.788074 INFO: === FDR correction performed with classifier version -1 ===
0:44:32.788494 PROGRESS: ============================= Precursor FDR =============================
0:44:32.788577 PROGRESS: Total precursors accumulated: 0
0:44:32.788636 PROGRESS: Target precursors: 0 (0.00%)
0:44:32.788683 PROGRESS: Decoy precursors: 0 (0.00%)
0:44:32.788727 PROGRESS: 
0:44:32.788770 PROGRESS: Precursor Summary:
0:44:32.788872 PROGRESS: 
0:44:32.788931 PROGRESS: Protein Summary:
0:44:32.789011 PROGRESS: =========================================================================
0:44:32.789158 INFO: Target number of precursors not reached yet.
0:44:32.792805 INFO: Starting optimization step 1.
0:44:32.792913 PROGRESS: === Extracting elution groups 200 to 600 ===
0:44:32.792986 INFO: Using ng extraction backend
0:44:32.793059 PROGRESS: Extracting batch of 797 precursors
0:44:32.795664 INFO: === Search parameters used ===
0:44:32.795746 INFO: rt_error       : 805.5992431640625
0:44:32.795797 INFO: mobility_error : 0.1
0:44:32.795840 INFO: num_candidates : 1
0:44:32.795880 INFO: ms1_error      : 30
0:44:32.795918 INFO: ms2_error      : 30
0:44:32.795957 INFO: fwhm_rt        : 5
0:44:32.795995 INFO: quant_window   : 3
0:44:32.796032 INFO: ==============================================
0:44:32.849980 INFO: performing precursor FDR with 40 features
0:44:32.850058 INFO: Decoy channel: -1
0:44:32.850084 INFO: Competetive: True
0:44:32.852953 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:32.854557 INFO: Using random state 628602 for train-test-split
0:44:32.863887 INFO: Test AUC: 0.490
0:44:32.863946 INFO: Train AUC: 0.531
0:44:32.863976 INFO: AUC difference: 7.74%
0:44:32.863998 WARNING: AUC difference > 5%. This may indicate overfitting.
0:44:33.067472 INFO: Resetting torch num_threads to 80
0:44:33.069484 PROGRESS: === Extracted 1191 precursors and 8298 fragments ===
0:44:33.069812 INFO: === FDR correction performed with classifier version -1 ===
0:44:33.070232 PROGRESS: ============================= Precursor FDR =============================
0:44:33.070316 PROGRESS: Total precursors accumulated: 0
0:44:33.070371 PROGRESS: Target precursors: 0 (0.00%)
0:44:33.070420 PROGRESS: Decoy precursors: 0 (0.00%)
0:44:33.070464 PROGRESS: 
0:44:33.070507 PROGRESS: Precursor Summary:
0:44:33.070609 PROGRESS: 
0:44:33.070670 PROGRESS: Protein Summary:
0:44:33.070746 PROGRESS: =========================================================================
0:44:33.070921 INFO: Target number of precursors not reached yet.
0:44:33.075502 INFO: Starting optimization step 2.
0:44:33.075611 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:44:33.075681 INFO: Using ng extraction backend
0:44:33.075741 PROGRESS: Extracting batch of 1593 precursors
0:44:33.079916 INFO: === Search parameters used ===
0:44:33.080012 INFO: rt_error       : 805.5992431640625
0:44:33.080061 INFO: mobility_error : 0.1
0:44:33.080104 INFO: num_candidates : 1
0:44:33.080145 INFO: ms1_error      : 30
0:44:33.080184 INFO: ms2_error      : 30
0:44:33.080222 INFO: fwhm_rt        : 5
0:44:33.080259 INFO: quant_window   : 3
0:44:33.080296 INFO: ==============================================
0:44:33.111748 INFO: performing precursor FDR with 40 features
0:44:33.111822 INFO: Decoy channel: -1
0:44:33.111847 INFO: Competetive: True
0:44:33.115018 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:33.116835 INFO: Using random state 417942 for train-test-split
0:44:33.128427 INFO: Test AUC: 0.551
0:44:33.128491 INFO: Train AUC: 0.521
0:44:33.128519 INFO: AUC difference: 5.64%
0:44:33.128542 WARNING: AUC difference > 5%. This may indicate overfitting.
0:44:33.338073 INFO: Resetting torch num_threads to 80
0:44:33.340405 PROGRESS: === Extracted 2780 precursors and 19530 fragments ===
0:44:33.340748 INFO: === FDR correction performed with classifier version -1 ===
0:44:33.341182 PROGRESS: ============================= Precursor FDR =============================
0:44:33.341268 PROGRESS: Total precursors accumulated: 0
0:44:33.341326 PROGRESS: Target precursors: 0 (0.00%)
0:44:33.341376 PROGRESS: Decoy precursors: 0 (0.00%)
0:44:33.341421 PROGRESS: 
0:44:33.341471 PROGRESS: Precursor Summary:
0:44:33.341576 PROGRESS: 
0:44:33.341637 PROGRESS: Protein Summary:
0:44:33.341708 PROGRESS: =========================================================================
0:44:33.341894 INFO: Target number of precursors not reached yet.
0:44:33.348300 INFO: Starting optimization step 3.
0:44:33.348406 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:44:33.348477 INFO: Using ng extraction backend
0:44:33.348534 PROGRESS: Extracting batch of 3185 precursors
0:44:33.355559 INFO: === Search parameters used ===
0:44:33.355666 INFO: rt_error       : 805.5992431640625
0:44:33.355717 INFO: mobility_error : 0.1
0:44:33.355762 INFO: num_candidates : 1
0:44:33.355803 INFO: ms1_error      : 30
0:44:33.355845 INFO: ms2_error      : 30
0:44:33.355884 INFO: fwhm_rt        : 5
0:44:33.355922 INFO: quant_window   : 3
0:44:33.355961 INFO: ==============================================
0:44:33.410935 INFO: performing precursor FDR with 40 features
0:44:33.411022 INFO: Decoy channel: -1
0:44:33.411048 INFO: Competetive: True
0:44:33.415583 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:33.418193 INFO: Using random state 541721 for train-test-split
0:44:33.437824 INFO: Test AUC: 0.500
0:44:33.437900 INFO: Train AUC: 0.526
0:44:33.437931 INFO: AUC difference: 5.05%
0:44:33.437955 WARNING: AUC difference > 5%. This may indicate overfitting.
0:44:33.646766 INFO: Resetting torch num_threads to 80
0:44:33.649764 PROGRESS: === Extracted 5961 precursors and 41508 fragments ===
0:44:33.650108 INFO: === FDR correction performed with classifier version -1 ===
0:44:33.650552 PROGRESS: ============================= Precursor FDR =============================
0:44:33.650638 PROGRESS: Total precursors accumulated: 2
0:44:33.650701 PROGRESS: Target precursors: 2 (100.00%)
0:44:33.650753 PROGRESS: Decoy precursors: 0 (0.00%)
0:44:33.650798 PROGRESS: 
0:44:33.650841 PROGRESS: Precursor Summary:
0:44:33.651757 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:44:33.651841 PROGRESS: 
0:44:33.651896 PROGRESS: Protein Summary:
0:44:33.652891 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:44:33.652978 PROGRESS: =========================================================================
0:44:33.653220 INFO: Target number of precursors not reached yet.
0:44:33.663042 INFO: Starting optimization step 4.
0:44:33.663160 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:44:33.663234 INFO: Using ng extraction backend
0:44:33.663291 PROGRESS: Extracting batch of 6366 precursors
0:44:33.675414 INFO: === Search parameters used ===
0:44:33.675530 INFO: rt_error       : 805.5992431640625
0:44:33.675578 INFO: mobility_error : 0.1
0:44:33.675620 INFO: num_candidates : 1
0:44:33.675663 INFO: ms1_error      : 30
0:44:33.675704 INFO: ms2_error      : 30
0:44:33.675743 INFO: fwhm_rt        : 5
0:44:33.676532 INFO: quant_window   : 3
0:44:33.676589 INFO: ==============================================
0:44:33.750491 INFO: performing precursor FDR with 40 features
0:44:33.750598 INFO: Decoy channel: -1
0:44:33.750623 INFO: Competetive: True
0:44:33.756775 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:33.760090 INFO: Using random state 713246 for train-test-split
0:44:33.796977 INFO: Test AUC: 0.518
0:44:33.797092 INFO: Train AUC: 0.516
0:44:33.797122 INFO: AUC difference: 0.45%
0:44:34.014879 INFO: Resetting torch num_threads to 80
0:44:34.018856 PROGRESS: === Extracted 12316 precursors and 85957 fragments ===
0:44:34.019216 INFO: === FDR correction performed with classifier version -1 ===
0:44:34.019679 PROGRESS: ============================= Precursor FDR =============================
0:44:34.019774 PROGRESS: Total precursors accumulated: 3
0:44:34.019830 PROGRESS: Target precursors: 3 (100.00%)
0:44:34.019879 PROGRESS: Decoy precursors: 0 (0.00%)
0:44:34.019923 PROGRESS: 
0:44:34.019964 PROGRESS: Precursor Summary:
0:44:34.020871 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
0:44:34.020955 PROGRESS: 
0:44:34.021018 PROGRESS: Protein Summary:
0:44:34.022028 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
0:44:34.022115 PROGRESS: =========================================================================
0:44:34.022395 INFO: Target number of precursors not reached yet.
0:44:34.037247 INFO: Starting optimization step 5.
0:44:34.037426 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:44:34.037502 INFO: Using ng extraction backend
0:44:34.037563 PROGRESS: Extracting batch of 12747 precursors
0:44:34.059793 INFO: === Search parameters used ===
0:44:34.059954 INFO: rt_error       : 805.5992431640625
0:44:34.060006 INFO: mobility_error : 0.1
0:44:34.060053 INFO: num_candidates : 1
0:44:34.060094 INFO: ms1_error      : 30
0:44:34.060135 INFO: ms2_error      : 30
0:44:34.060172 INFO: fwhm_rt        : 5
0:44:34.060210 INFO: quant_window   : 3
0:44:34.060248 INFO: ==============================================
0:44:34.191159 INFO: performing precursor FDR with 40 features
0:44:34.191273 INFO: Decoy channel: -1
0:44:34.191299 INFO: Competetive: True
0:44:34.200692 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:34.206299 INFO: Using random state 701913 for train-test-split
0:44:34.457023 INFO: Test AUC: 0.807
0:44:34.457137 INFO: Train AUC: 0.805
0:44:34.457167 INFO: AUC difference: 0.30%
0:44:34.684557 INFO: Resetting torch num_threads to 80
0:44:34.690670 PROGRESS: === Extracted 25048 precursors and 175539 fragments ===
0:44:34.691120 INFO: === FDR correction performed with classifier version -1 ===
0:44:34.692043 PROGRESS: ============================= Precursor FDR =============================
0:44:34.692141 PROGRESS: Total precursors accumulated: 4,274
0:44:34.692198 PROGRESS: Target precursors: 4,232 (99.02%)
0:44:34.692247 PROGRESS: Decoy precursors: 42 (0.98%)
0:44:34.692291 PROGRESS: 
0:44:34.692336 PROGRESS: Precursor Summary:
0:44:34.694184 PROGRESS: Channel   0:	 0.050 FDR: 4,232; 0.010 FDR: 4,232; 0.001 FDR: 2,179
0:44:34.694278 PROGRESS: 
0:44:34.694334 PROGRESS: Protein Summary:
0:44:34.696918 PROGRESS: Channel   0:	 0.050 FDR: 2,553; 0.010 FDR: 2,553; 0.001 FDR: 1,482
0:44:34.697029 PROGRESS: =========================================================================
0:44:34.697423 INFO: Target number of precursors reached.
0:44:34.723501 INFO: fragments_df: keeping 5000 of 175539 [sum(precursor_idx_mask)=46478 sum(mass_error_mask)=175539 stop_rank=5000
0:44:34.729506 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:35.301729 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:35.979655 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:44:35.980115 INFO: Using score_cutoff 14.028855303955078 (fac=0.99, q=1)
0:44:35.980455 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:44:35.980534 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:44:35.980591 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.028855303955078
0:44:35.980645 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:35.982197 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:35.984235 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
0:44:35.984327 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:44:35.984403 INFO: Starting optimization step 6.
0:44:35.984463 PROGRESS: === Extracting elution groups 0 to 600 ===
0:44:35.984524 INFO: Using ng extraction backend
0:44:35.984577 PROGRESS: Extracting batch of 1194 precursors
0:44:35.987876 INFO: === Search parameters used ===
0:44:35.987968 INFO: rt_error       : 805.5992431640625
0:44:35.988029 INFO: mobility_error : 0.1
0:44:35.988075 INFO: num_candidates : 3
0:44:35.988123 INFO: ms1_error      : 30
0:44:35.988167 INFO: ms2_error      : 30
0:44:35.988208 INFO: fwhm_rt        : 3.0
0:44:35.988246 INFO: quant_window   : 3
0:44:35.988286 INFO: ==============================================
0:44:36.025713 INFO: performing precursor FDR with 40 features
0:44:36.025794 INFO: Decoy channel: -1
0:44:36.025820 INFO: Competetive: True
0:44:36.028543 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:36.030288 INFO: Using random state 452285 for train-test-split
0:44:36.041950 INFO: Test AUC: 0.654
0:44:36.042015 INFO: Train AUC: 0.653
0:44:36.042043 INFO: AUC difference: 0.18%
0:44:36.252126 INFO: Resetting torch num_threads to 80
0:44:36.253625 PROGRESS: === Extracted 3573 precursors and 21741 fragments ===
0:44:36.253960 INFO: === FDR correction performed with classifier version 5 ===
0:44:36.254400 PROGRESS: ============================= Precursor FDR =============================
0:44:36.254483 PROGRESS: Total precursors accumulated: 213
0:44:36.254540 PROGRESS: Target precursors: 211 (99.06%)
0:44:36.254590 PROGRESS: Decoy precursors: 2 (0.94%)
0:44:36.254635 PROGRESS: 
0:44:36.254676 PROGRESS: Precursor Summary:
0:44:36.255559 PROGRESS: Channel   0:	 0.050 FDR:   211; 0.010 FDR:   211; 0.001 FDR:   173
0:44:36.255644 PROGRESS: 
0:44:36.255696 PROGRESS: Protein Summary:
0:44:36.256705 PROGRESS: Channel   0:	 0.050 FDR:   202; 0.010 FDR:   202; 0.001 FDR:   167
0:44:36.256790 PROGRESS: =========================================================================
0:44:36.257146 INFO: Target number of precursors reached.
0:44:36.260485 INFO: fragments_df: keeping 2530 of 21741 [sum(precursor_idx_mask)=4819 sum(mass_error_mask)=21741 stop_rank=2530
0:44:36.265342 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:36.379859 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:36.711089 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:44:36.711499 INFO: Using score_cutoff 14.292624607086182 (fac=0.99, q=1)
0:44:36.711777 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:44:36.711854 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:44:36.711908 INFO: Updating optimization_manager: score_cutoff        : 14.028855303955078 -> 14.292624607086182
0:44:36.711961 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:36.713554 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:36.715730 INFO: === checking if optimization conditions were reached ===
0:44:36.716985 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:44:36.717091 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
0:44:36.717151 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:44:36.717208 INFO: ==============================================
0:44:36.717268 INFO: Starting optimization step 7.
0:44:36.717323 PROGRESS: === Extracting elution groups 0 to 600 ===
0:44:36.717381 INFO: Using ng extraction backend
0:44:36.717435 PROGRESS: Extracting batch of 1194 precursors
0:44:36.720823 INFO: === Search parameters used ===
0:44:36.720920 INFO: rt_error       : 805.5992431640625
0:44:36.721198 INFO: mobility_error : 0.1
0:44:36.721256 INFO: num_candidates : 3
0:44:36.721297 INFO: ms1_error      : 30
0:44:36.721336 INFO: ms2_error      : 10.0
0:44:36.721374 INFO: fwhm_rt        : 3.0
0:44:36.721411 INFO: quant_window   : 3
0:44:36.721448 INFO: ==============================================
0:44:36.757919 INFO: performing precursor FDR with 40 features
0:44:36.757992 INFO: Decoy channel: -1
0:44:36.758017 INFO: Competetive: True
0:44:36.760759 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:36.762659 INFO: Using random state 348590 for train-test-split
0:44:36.773951 INFO: Test AUC: 0.660
0:44:36.774017 INFO: Train AUC: 0.689
0:44:36.774045 INFO: AUC difference: 4.21%
0:44:36.986940 INFO: Resetting torch num_threads to 80
0:44:36.988507 PROGRESS: === Extracted 3582 precursors and 24575 fragments ===
0:44:36.988836 INFO: === FDR correction performed with classifier version 6 ===
0:44:36.989305 PROGRESS: ============================= Precursor FDR =============================
0:44:36.989393 PROGRESS: Total precursors accumulated: 380
0:44:36.989450 PROGRESS: Target precursors: 377 (99.21%)
0:44:36.989499 PROGRESS: Decoy precursors: 3 (0.79%)
0:44:36.989543 PROGRESS: 
0:44:36.989586 PROGRESS: Precursor Summary:
0:44:36.990497 PROGRESS: Channel   0:	 0.050 FDR:   377; 0.010 FDR:   377; 0.001 FDR:   170
0:44:36.990582 PROGRESS: 
0:44:36.990636 PROGRESS: Protein Summary:
0:44:36.991716 PROGRESS: Channel   0:	 0.050 FDR:   359; 0.010 FDR:   359; 0.001 FDR:   165
0:44:36.991802 PROGRESS: =========================================================================
0:44:36.992004 INFO: Target number of precursors reached.
0:44:36.996157 INFO: fragments_df: keeping 4077 of 24575 [sum(precursor_idx_mask)=9090 sum(mass_error_mask)=24575 stop_rank=4077
0:44:37.000946 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:37.122578 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:37.656789 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:44:37.657208 INFO: Using score_cutoff 12.131102602386473 (fac=0.99, q=1)
0:44:37.657488 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:44:37.657566 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:44:37.657619 INFO: Updating optimization_manager: score_cutoff        : 14.292624607086182 -> 12.131102602386473
0:44:37.657673 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:37.659208 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:37.661357 INFO: === checking if optimization conditions were reached ===
0:44:37.662792 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:44:37.662887 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:44:37.662949 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:44:37.663007 INFO: ==============================================
0:44:37.663070 PROGRESS: Optimization finished for ms2_error.
0:44:37.667722 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:37.669075 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:37.671177 INFO: Starting optimization step 0.
0:44:37.671270 PROGRESS: === Extracting elution groups 0 to 600 ===
0:44:37.671347 INFO: Using ng extraction backend
0:44:37.671408 PROGRESS: Extracting batch of 1194 precursors
0:44:37.674825 INFO: === Search parameters used ===
0:44:37.674920 INFO: rt_error       : 805.5992431640625
0:44:37.674969 INFO: mobility_error : 0.1
0:44:37.675013 INFO: num_candidates : 3
0:44:37.675055 INFO: ms1_error      : 30
0:44:37.675097 INFO: ms2_error      : 10.0
0:44:37.675135 INFO: fwhm_rt        : 3.0
0:44:37.675174 INFO: quant_window   : 3
0:44:37.675213 INFO: ==============================================
0:44:37.711542 INFO: performing precursor FDR with 40 features
0:44:37.711620 INFO: Decoy channel: -1
0:44:37.711646 INFO: Competetive: True
0:44:37.714309 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:37.716067 INFO: Using random state 468789 for train-test-split
0:44:37.727651 INFO: Test AUC: 0.676
0:44:37.727714 INFO: Train AUC: 0.685
0:44:37.727743 INFO: AUC difference: 1.38%
0:44:37.939300 INFO: Resetting torch num_threads to 80
0:44:37.940804 PROGRESS: === Extracted 3582 precursors and 24575 fragments ===
0:44:37.941142 INFO: === FDR correction performed with classifier version 7 ===
0:44:37.941594 PROGRESS: ============================= Precursor FDR =============================
0:44:37.941678 PROGRESS: Total precursors accumulated: 387
0:44:37.941735 PROGRESS: Target precursors: 384 (99.22%)
0:44:37.941784 PROGRESS: Decoy precursors: 3 (0.78%)
0:44:37.941830 PROGRESS: 
0:44:37.941871 PROGRESS: Precursor Summary:
0:44:37.942772 PROGRESS: Channel   0:	 0.050 FDR:   384; 0.010 FDR:   384; 0.001 FDR:   170
0:44:37.942866 PROGRESS: 
0:44:37.942919 PROGRESS: Protein Summary:
0:44:37.944023 PROGRESS: Channel   0:	 0.050 FDR:   366; 0.010 FDR:   366; 0.001 FDR:   165
0:44:37.944110 PROGRESS: =========================================================================
0:44:37.944307 INFO: Target number of precursors reached.
0:44:37.948422 INFO: fragments_df: keeping 4129 of 24575 [sum(precursor_idx_mask)=9229 sum(mass_error_mask)=24575 stop_rank=4129
0:44:37.953249 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:38.073485 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:38.611900 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:44:38.612315 INFO: Using score_cutoff 12.158895010185242 (fac=0.99, q=1)
0:44:38.612596 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:44:38.612671 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:44:38.612723 INFO: Updating optimization_manager: score_cutoff        : 12.131102602386473 -> 12.158895010185242
0:44:38.612775 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:38.614336 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:38.616497 INFO: === checking if optimization conditions were reached ===
0:44:38.616590 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:44:38.618056 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 112.36674831918614
0:44:38.618155 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 112.3667.
0:44:38.618217 INFO: ==============================================
0:44:38.618303 INFO: Starting optimization step 1.
0:44:38.618362 PROGRESS: === Extracting elution groups 0 to 600 ===
0:44:38.618420 INFO: Using ng extraction backend
0:44:38.618473 PROGRESS: Extracting batch of 1194 precursors
0:44:38.621869 INFO: === Search parameters used ===
0:44:38.621964 INFO: rt_error       : 112.36674831918614
0:44:38.622013 INFO: mobility_error : 0.1
0:44:38.622055 INFO: num_candidates : 3
0:44:38.622097 INFO: ms1_error      : 30
0:44:38.622139 INFO: ms2_error      : 10.0
0:44:38.622176 INFO: fwhm_rt        : 3.0
0:44:38.622216 INFO: quant_window   : 3
0:44:38.622254 INFO: ==============================================
0:44:38.656488 INFO: performing precursor FDR with 40 features
0:44:38.656602 INFO: Decoy channel: -1
0:44:38.656664 INFO: Competetive: True
0:44:38.659362 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:38.661155 INFO: Using random state 468789 for train-test-split
0:44:38.672234 INFO: Test AUC: 0.698
0:44:38.672293 INFO: Train AUC: 0.699
0:44:38.672321 INFO: AUC difference: 0.09%
0:44:38.884774 INFO: Resetting torch num_threads to 80
0:44:38.886255 PROGRESS: === Extracted 3580 precursors and 22798 fragments ===
0:44:38.886574 INFO: === FDR correction performed with classifier version 7 ===
0:44:38.887031 PROGRESS: ============================= Precursor FDR =============================
0:44:38.887114 PROGRESS: Total precursors accumulated: 478
0:44:38.887169 PROGRESS: Target precursors: 474 (99.16%)
0:44:38.887217 PROGRESS: Decoy precursors: 4 (0.84%)
0:44:38.887259 PROGRESS: 
0:44:38.887300 PROGRESS: Precursor Summary:
0:44:38.888232 PROGRESS: Channel   0:	 0.050 FDR:   474; 0.010 FDR:   474; 0.001 FDR:   422
0:44:38.888323 PROGRESS: 
0:44:38.888375 PROGRESS: Protein Summary:
0:44:38.889534 PROGRESS: Channel   0:	 0.050 FDR:   450; 0.010 FDR:   450; 0.001 FDR:   401
0:44:38.889622 PROGRESS: =========================================================================
0:44:38.889804 INFO: Target number of precursors reached.
0:44:38.893928 INFO: fragments_df: keeping 4638 of 22798 [sum(precursor_idx_mask)=10742 sum(mass_error_mask)=22798 stop_rank=4638
0:44:38.898636 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:39.023073 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:39.648481 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:44:39.648893 INFO: Using score_cutoff 11.605779339408874 (fac=0.99, q=1)
0:44:39.649183 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:44:39.649264 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:44:39.649318 INFO: Updating optimization_manager: score_cutoff        : 12.158895010185242 -> 11.605779339408874
0:44:39.649371 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:39.650905 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:39.653115 INFO: === checking if optimization conditions were reached ===
0:44:39.653210 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:44:39.654800 INFO: Updating optimization_manager: rt_error            : 112.36674831918614 -> 65.91177912124434
0:44:39.654896 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 65.9118.
0:44:39.654966 INFO: ==============================================
0:44:39.655034 INFO: Starting optimization step 2.
0:44:39.655089 PROGRESS: === Extracting elution groups 0 to 600 ===
0:44:39.655147 INFO: Using ng extraction backend
0:44:39.655199 PROGRESS: Extracting batch of 1194 precursors
0:44:39.658502 INFO: === Search parameters used ===
0:44:39.658596 INFO: rt_error       : 65.91177912124434
0:44:39.658643 INFO: mobility_error : 0.1
0:44:39.658685 INFO: num_candidates : 3
0:44:39.658726 INFO: ms1_error      : 30
0:44:39.658765 INFO: ms2_error      : 10.0
0:44:39.658802 INFO: fwhm_rt        : 3.0
0:44:39.658839 INFO: quant_window   : 3
0:44:39.658876 INFO: ==============================================
0:44:39.696652 INFO: performing precursor FDR with 40 features
0:44:39.696727 INFO: Decoy channel: -1
0:44:39.696752 INFO: Competetive: True
0:44:39.699417 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:39.701247 INFO: Using random state 468789 for train-test-split
0:44:39.713426 INFO: Test AUC: 0.668
0:44:39.713490 INFO: Train AUC: 0.692
0:44:39.713519 INFO: AUC difference: 3.48%
0:44:39.925972 INFO: Resetting torch num_threads to 80
0:44:39.927438 PROGRESS: === Extracted 3569 precursors and 21447 fragments ===
0:44:39.927783 INFO: === FDR correction performed with classifier version 7 ===
0:44:39.928242 PROGRESS: ============================= Precursor FDR =============================
0:44:39.928325 PROGRESS: Total precursors accumulated: 494
0:44:39.928380 PROGRESS: Target precursors: 490 (99.19%)
0:44:39.928427 PROGRESS: Decoy precursors: 4 (0.81%)
0:44:39.928472 PROGRESS: 
0:44:39.928520 PROGRESS: Precursor Summary:
0:44:39.929459 PROGRESS: Channel   0:	 0.050 FDR:   490; 0.010 FDR:   490; 0.001 FDR:   401
0:44:39.929546 PROGRESS: 
0:44:39.929597 PROGRESS: Protein Summary:
0:44:39.930726 PROGRESS: Channel   0:	 0.050 FDR:   464; 0.010 FDR:   464; 0.001 FDR:   383
0:44:39.930811 PROGRESS: =========================================================================
0:44:39.930995 INFO: Target number of precursors reached.
0:44:39.935009 INFO: fragments_df: keeping 4565 of 21447 [sum(precursor_idx_mask)=10583 sum(mass_error_mask)=21447 stop_rank=4565
0:44:39.939689 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:40.073609 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:40.675657 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:44:40.676049 INFO: Using score_cutoff 11.545997294139863 (fac=0.99, q=1)
0:44:40.676327 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:44:40.676404 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:44:40.676455 INFO: Updating optimization_manager: score_cutoff        : 11.605779339408874 -> 11.545997294139863
0:44:40.676508 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:40.678033 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:40.680155 INFO: === checking if optimization conditions were reached ===
0:44:40.680247 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:44:40.681947 INFO: Updating optimization_manager: rt_error            : 65.91177912124434 -> 31.999568946424993
0:44:40.682044 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 31.9996.
0:44:40.682105 INFO: ==============================================
0:44:40.682168 INFO: Starting optimization step 3.
0:44:40.682225 PROGRESS: === Extracting elution groups 0 to 600 ===
0:44:40.682281 INFO: Using ng extraction backend
0:44:40.682334 PROGRESS: Extracting batch of 1194 precursors
0:44:40.685534 INFO: === Search parameters used ===
0:44:40.685622 INFO: rt_error       : 31.999568946424993
0:44:40.685669 INFO: mobility_error : 0.1
0:44:40.685711 INFO: num_candidates : 3
0:44:40.685751 INFO: ms1_error      : 30
0:44:40.685790 INFO: ms2_error      : 10.0
0:44:40.685827 INFO: fwhm_rt        : 3.0
0:44:40.685864 INFO: quant_window   : 3
0:44:40.685899 INFO: ==============================================
0:44:40.718040 INFO: performing precursor FDR with 40 features
0:44:40.718116 INFO: Decoy channel: -1
0:44:40.718142 INFO: Competetive: True
0:44:40.720598 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:40.722318 INFO: Using random state 468789 for train-test-split
0:44:40.733668 INFO: Test AUC: 0.708
0:44:40.733727 INFO: Train AUC: 0.713
0:44:40.733755 INFO: AUC difference: 0.81%
0:44:40.945980 INFO: Resetting torch num_threads to 80
0:44:40.947482 PROGRESS: === Extracted 3295 precursors and 19314 fragments ===
0:44:40.947814 INFO: === FDR correction performed with classifier version 7 ===
0:44:40.948287 PROGRESS: ============================= Precursor FDR =============================
0:44:40.948368 PROGRESS: Total precursors accumulated: 491
0:44:40.948425 PROGRESS: Target precursors: 487 (99.19%)
0:44:40.948478 PROGRESS: Decoy precursors: 4 (0.81%)
0:44:40.948523 PROGRESS: 
0:44:40.948564 PROGRESS: Precursor Summary:
0:44:40.949554 PROGRESS: Channel   0:	 0.050 FDR:   487; 0.010 FDR:   487; 0.001 FDR:   398
0:44:40.949640 PROGRESS: 
0:44:40.949692 PROGRESS: Protein Summary:
0:44:40.950862 PROGRESS: Channel   0:	 0.050 FDR:   462; 0.010 FDR:   462; 0.001 FDR:   380
0:44:40.950946 PROGRESS: =========================================================================
0:44:40.951133 INFO: Target number of precursors reached.
0:44:40.954844 INFO: fragments_df: keeping 4258 of 19314 [sum(precursor_idx_mask)=9474 sum(mass_error_mask)=19314 stop_rank=4258
0:44:40.959562 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:41.094171 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:41.797385 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:44:41.797794 INFO: Using score_cutoff 11.69855014629364 (fac=0.99, q=1)
0:44:41.798073 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:44:41.798147 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:44:41.798200 INFO: Updating optimization_manager: score_cutoff        : 11.545997294139863 -> 11.69855014629364
0:44:41.798252 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:41.800323 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:41.803195 INFO: === checking if optimization conditions were reached ===
0:44:41.803298 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:44:41.805206 INFO: Updating optimization_manager: rt_error            : 31.999568946424993 -> 23.67085481407434
0:44:41.805567 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 23.6709.
0:44:41.805798 INFO: ==============================================
0:44:41.806044 INFO: Starting optimization step 4.
0:44:41.806131 PROGRESS: === Extracting elution groups 0 to 600 ===
0:44:41.806215 INFO: Using ng extraction backend
0:44:41.806274 PROGRESS: Extracting batch of 1194 precursors
0:44:41.810056 INFO: === Search parameters used ===
0:44:41.810162 INFO: rt_error       : 23.67085481407434
0:44:41.810224 INFO: mobility_error : 0.1
0:44:41.810269 INFO: num_candidates : 3
0:44:41.810308 INFO: ms1_error      : 30
0:44:41.810344 INFO: ms2_error      : 10.0
0:44:41.810381 INFO: fwhm_rt        : 3.0
0:44:41.810417 INFO: quant_window   : 3
0:44:41.810452 INFO: ==============================================
0:44:41.863695 INFO: performing precursor FDR with 40 features
0:44:41.863790 INFO: Decoy channel: -1
0:44:41.863815 INFO: Competetive: True
0:44:41.867547 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:41.869890 INFO: Using random state 468789 for train-test-split
0:44:41.883813 INFO: Test AUC: 0.710
0:44:41.883954 INFO: Train AUC: 0.711
0:44:41.883997 INFO: AUC difference: 0.10%
0:44:42.165979 INFO: Resetting torch num_threads to 80
0:44:42.167640 PROGRESS: === Extracted 3286 precursors and 19280 fragments ===
0:44:42.167984 INFO: === FDR correction performed with classifier version 7 ===
0:44:42.168452 PROGRESS: ============================= Precursor FDR =============================
0:44:42.170493 PROGRESS: Total precursors accumulated: 492
0:44:42.170578 PROGRESS: Target precursors: 488 (99.19%)
0:44:42.170648 PROGRESS: Decoy precursors: 4 (0.81%)
0:44:42.170714 PROGRESS: 
0:44:42.170761 PROGRESS: Precursor Summary:
0:44:42.172821 PROGRESS: Channel   0:	 0.050 FDR:   488; 0.010 FDR:   488; 0.001 FDR:   396
0:44:42.172935 PROGRESS: 
0:44:42.173047 PROGRESS: Protein Summary:
0:44:42.174804 PROGRESS: Channel   0:	 0.050 FDR:   463; 0.010 FDR:   463; 0.001 FDR:   378
0:44:42.174939 PROGRESS: =========================================================================
0:44:42.175237 INFO: Target number of precursors reached.
0:44:42.181387 INFO: fragments_df: keeping 4248 of 19280 [sum(precursor_idx_mask)=9451 sum(mass_error_mask)=19280 stop_rank=4248
0:44:42.186502 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:42.347121 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:43.046630 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:44:43.047137 INFO: Using score_cutoff 11.613955684089662 (fac=0.99, q=1)
0:44:43.047485 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:44:43.047564 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:44:43.047630 INFO: Updating optimization_manager: score_cutoff        : 11.69855014629364 -> 11.613955684089662
0:44:43.047731 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:43.049491 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:43.051641 INFO: === checking if optimization conditions were reached ===
0:44:43.051739 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:44:43.054016 INFO: Updating optimization_manager: rt_error            : 23.67085481407434 -> 23.687025018493625
0:44:43.054348 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 23.6870.
0:44:43.054472 INFO: ==============================================
0:44:43.054602 INFO: Starting optimization step 5.
0:44:43.054715 PROGRESS: === Extracting elution groups 0 to 600 ===
0:44:43.054843 INFO: Using ng extraction backend
0:44:43.054936 PROGRESS: Extracting batch of 1194 precursors
0:44:43.058975 INFO: === Search parameters used ===
0:44:43.059098 INFO: rt_error       : 23.687025018493625
0:44:43.059167 INFO: mobility_error : 0.1
0:44:43.059229 INFO: num_candidates : 3
0:44:43.059294 INFO: ms1_error      : 30
0:44:43.059354 INFO: ms2_error      : 10.0
0:44:43.059410 INFO: fwhm_rt        : 3.0
0:44:43.059464 INFO: quant_window   : 3
0:44:43.059519 INFO: ==============================================
0:44:43.113039 INFO: performing precursor FDR with 40 features
0:44:43.113159 INFO: Decoy channel: -1
0:44:43.113197 INFO: Competetive: True
0:44:43.115937 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:43.117707 INFO: Using random state 468789 for train-test-split
0:44:43.130531 INFO: Test AUC: 0.694
0:44:43.130606 INFO: Train AUC: 0.715
0:44:43.130637 INFO: AUC difference: 2.83%
0:44:43.404112 INFO: Resetting torch num_threads to 80
0:44:43.406160 PROGRESS: === Extracted 3286 precursors and 19268 fragments ===
0:44:43.406847 INFO: === FDR correction performed with classifier version 7 ===
0:44:43.407457 PROGRESS: ============================= Precursor FDR =============================
0:44:43.407542 PROGRESS: Total precursors accumulated: 492
0:44:43.407597 PROGRESS: Target precursors: 488 (99.19%)
0:44:43.407644 PROGRESS: Decoy precursors: 4 (0.81%)
0:44:43.407687 PROGRESS: 
0:44:43.407728 PROGRESS: Precursor Summary:
0:44:43.408717 PROGRESS: Channel   0:	 0.050 FDR:   488; 0.010 FDR:   488; 0.001 FDR:   396
0:44:43.408801 PROGRESS: 
0:44:43.408854 PROGRESS: Protein Summary:
0:44:43.410468 PROGRESS: Channel   0:	 0.050 FDR:   463; 0.010 FDR:   463; 0.001 FDR:   378
0:44:43.410562 PROGRESS: =========================================================================
0:44:43.410774 INFO: Target number of precursors reached.
0:44:43.415050 INFO: fragments_df: keeping 4243 of 19268 [sum(precursor_idx_mask)=9447 sum(mass_error_mask)=19268 stop_rank=4243
0:44:43.421202 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:43.569332 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:44.229766 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:44:44.230269 INFO: Using score_cutoff 11.613955684089662 (fac=0.99, q=1)
0:44:44.230556 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:44:44.230637 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:44:44.230699 INFO: Updating optimization_manager: score_cutoff        : 11.613955684089662 -> 11.613955684089662
0:44:44.230760 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:44.232426 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:44.235303 INFO: === checking if optimization conditions were reached ===
0:44:44.235426 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:44:44.236570 INFO: Updating optimization_manager: rt_error            : 23.687025018493625 -> 23.67085481407434
0:44:44.236724 INFO: Updating optimization_manager: classifier_version  : 7 -> 12
0:44:44.236844 INFO: Updating optimization_manager: score_cutoff        : 11.613955684089662 -> 11.613955684089662
0:44:44.236956 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:44:44.237077 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:44:44.237191 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 23.6709 found after 6 searches.
0:44:44.237274 INFO: ==============================================
0:44:44.237371 PROGRESS: Optimization finished for rt_error.
0:44:44.242461 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:44.244040 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:44.272667 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:44:44.272817 PROGRESS: ==============================================
0:44:44.272898 PROGRESS: ms2_error      : 10.0000
0:44:44.272964 PROGRESS: rt_error       : 23.6709
0:44:44.273032 PROGRESS: ==============================================
0:44:44.274440 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:44.399036 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:44.729700 INFO: Using ng extraction backend
0:44:44.729963 PROGRESS: Extracting batch of 230645 precursors
0:44:45.093765 INFO: === Search parameters used ===
0:44:45.094018 INFO: rt_error       : 23.67085481407434
0:44:45.094093 INFO: mobility_error : 0.1
0:44:45.094157 INFO: num_candidates : 3
0:44:45.094215 INFO: ms1_error      : 30
0:44:45.094272 INFO: ms2_error      : 10.0
0:44:45.094329 INFO: fwhm_rt        : 3.0
0:44:45.094384 INFO: quant_window   : 3
0:44:45.094438 INFO: ==============================================
0:44:45.334396 INFO: Removed 305359 precursors with score below cutoff 11.613955684089662
0:44:45.657287 INFO: performing precursor FDR with 40 features
0:44:45.657393 INFO: Decoy channel: -1
0:44:45.657424 INFO: Competetive: True
0:44:45.684088 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:45.700420 WARNING: FDR calculation for 204149 target and 125752 decoy PSMs
0:44:45.700549 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
0:44:45.768494 INFO: Using random state 335063 for train-test-split
0:44:50.110828 INFO: Test AUC: 0.871
0:44:50.110950 INFO: Train AUC: 0.874
0:44:50.110986 INFO: AUC difference: 0.31%
0:44:50.417546 INFO: Resetting torch num_threads to 80
0:44:50.702335 PROGRESS: ============================= Precursor FDR =============================
0:44:50.702591 PROGRESS: Total precursors accumulated: 104,868
0:44:50.702674 PROGRESS: Target precursors: 103,830 (99.01%)
0:44:50.702740 PROGRESS: Decoy precursors: 1,038 (0.99%)
0:44:50.702801 PROGRESS: 
0:44:50.702862 PROGRESS: Precursor Summary:
0:44:50.727891 PROGRESS: Channel   0:	 0.050 FDR: 103,830; 0.010 FDR: 103,830; 0.001 FDR: 94,421
0:44:50.728166 PROGRESS: 
0:44:50.728249 PROGRESS: Protein Summary:
0:44:50.763437 PROGRESS: Channel   0:	 0.050 FDR: 9,962; 0.010 FDR: 9,962; 0.001 FDR: 9,833
0:44:50.763689 PROGRESS: =========================================================================
0:44:50.765280 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/psm.parquet
0:44:50.930547 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.parquet
0:44:51.203303 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:44:51.393335 PROGRESS: 
0:44:51.393480 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant
0:44:51.393565 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/figures
0:44:51.393749 INFO: Initializing TimingManager
0:44:51.394203 INFO: Initializing RawFileManager
0:45:02.134499 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.
0:45:02.138475 INFO: Determining DIA cycle
0:45:02.153562 INFO: Found cycle with start 0.00 min and length 300.
0:45:02.316127 INFO: RT (min)            : 0.0 - 26.9
0:45:02.316219 INFO: RT duration (sec)   : 1611.2
0:45:02.316247 INFO: RT duration (min)   : 26.9
0:45:02.316271 INFO: Cycle len (scans)   : 300
0:45:02.316292 INFO: Cycle len (sec)     : 1.65
0:45:02.316313 INFO: Number of cycles    : 978
0:45:02.316333 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:45:02.316363 INFO: Creating DIA data object took: 10.922069311141968
0:45:02.979316 INFO: Creating DIA data NG object took: 0.6628413200378418
0:45:02.997220 INFO: Initializing CalibrationManager
0:45:02.997488 INFO: Setting up calibration estimators ..
0:45:02.997550 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:45:02.997616 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'}' ..
0:45:02.997680 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:45:02.997729 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:45:02.997781 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}}' ..
0:45:02.997828 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:45:02.997873 INFO: Done setting up calibration estimators.
0:45:02.998086 INFO: Initializing OptimizationManager
0:45:02.998206 INFO: initial parameter: ms1_error = 30
0:45:02.998260 INFO: initial parameter: ms2_error = 30
0:45:02.998306 INFO: initial parameter: rt_error = 805.6019897460938
0:45:02.998349 INFO: initial parameter: mobility_error = 0.1
0:45:02.998390 INFO: initial parameter: num_candidates = 1
0:45:02.998429 INFO: initial parameter: fwhm_rt = 5
0:45:02.998470 INFO: initial parameter: fwhm_mobility = 0.01
0:45:02.998509 INFO: initial parameter: score_cutoff = 0
0:45:02.998549 INFO: initial parameter: classifier_version = -1
0:45:02.998618 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:45:02.998819 INFO: FDRManager: loading saved state not requested, will be initialized.
0:45:02.998851 INFO: Initializing FDRManager
0:45:02.998882 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:45:03.022208 PROGRESS: Initializing spectral library: 115,864 target precursors potentially observable (0 removed)
0:45:03.038607 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:45:03.038947 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
0:45:03.039043 PROGRESS: Starting initial search for precursors.
0:45:03.039123 INFO: Starting optimization step 0.
0:45:03.039183 PROGRESS: === Extracting elution groups 0 to 200 ===
0:45:03.039238 INFO: Using ng extraction backend
0:45:03.039292 PROGRESS: Extracting batch of 397 precursors
0:45:03.041299 INFO: === Search parameters used ===
0:45:03.041397 INFO: rt_error       : 805.6019897460938
0:45:03.041448 INFO: mobility_error : 0.1
0:45:03.041494 INFO: num_candidates : 1
0:45:03.041538 INFO: ms1_error      : 30
0:45:03.041579 INFO: ms2_error      : 30
0:45:03.041623 INFO: fwhm_rt        : 5
0:45:03.041667 INFO: quant_window   : 3
0:45:03.041708 INFO: ==============================================
0:45:03.058342 INFO: performing precursor FDR with 40 features
0:45:03.058421 INFO: Decoy channel: -1
0:45:03.058446 INFO: Competetive: True
0:45:03.059312 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:03.061990 INFO: Using random state 242517 for train-test-split
0:45:03.068427 INFO: Test AUC: 0.381
0:45:03.068482 INFO: Train AUC: 0.464
0:45:03.068511 INFO: AUC difference: 17.93%
0:45:03.068533 WARNING: AUC difference > 5%. This may indicate overfitting.
0:45:03.276122 INFO: Resetting torch num_threads to 80
0:45:03.277405 PROGRESS: === Extracted 397 precursors and 2787 fragments ===
0:45:03.277733 INFO: === FDR correction performed with classifier version -1 ===
0:45:03.278177 PROGRESS: ============================= Precursor FDR =============================
0:45:03.278265 PROGRESS: Total precursors accumulated: 1
0:45:03.278322 PROGRESS: Target precursors: 1 (100.00%)
0:45:03.278371 PROGRESS: Decoy precursors: 0 (0.00%)
0:45:03.278416 PROGRESS: 
0:45:03.278457 PROGRESS: Precursor Summary:
0:45:03.279363 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:45:03.279449 PROGRESS: 
0:45:03.279503 PROGRESS: Protein Summary:
0:45:03.280505 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:45:03.280593 PROGRESS: =========================================================================
0:45:03.280760 INFO: Target number of precursors not reached yet.
0:45:03.284387 INFO: Starting optimization step 1.
0:45:03.284490 PROGRESS: === Extracting elution groups 200 to 600 ===
0:45:03.284564 INFO: Using ng extraction backend
0:45:03.284621 PROGRESS: Extracting batch of 797 precursors
0:45:03.287221 INFO: === Search parameters used ===
0:45:03.287306 INFO: rt_error       : 805.6019897460938
0:45:03.287356 INFO: mobility_error : 0.1
0:45:03.287402 INFO: num_candidates : 1
0:45:03.287443 INFO: ms1_error      : 30
0:45:03.287485 INFO: ms2_error      : 30
0:45:03.287525 INFO: fwhm_rt        : 5
0:45:03.287565 INFO: quant_window   : 3
0:45:03.287603 INFO: ==============================================
0:45:03.308278 INFO: performing precursor FDR with 40 features
0:45:03.308347 INFO: Decoy channel: -1
0:45:03.308373 INFO: Competetive: True
0:45:03.311026 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:03.312467 INFO: Using random state 802887 for train-test-split
0:45:03.320383 INFO: Test AUC: 0.451
0:45:03.320445 INFO: Train AUC: 0.470
0:45:03.320475 INFO: AUC difference: 4.15%
0:45:03.530243 INFO: Resetting torch num_threads to 80
0:45:03.532189 PROGRESS: === Extracted 1194 precursors and 8259 fragments ===
0:45:03.532517 INFO: === FDR correction performed with classifier version -1 ===
0:45:03.532971 PROGRESS: ============================= Precursor FDR =============================
0:45:03.533067 PROGRESS: Total precursors accumulated: 1
0:45:03.533126 PROGRESS: Target precursors: 1 (100.00%)
0:45:03.533175 PROGRESS: Decoy precursors: 0 (0.00%)
0:45:03.533221 PROGRESS: 
0:45:03.533264 PROGRESS: Precursor Summary:
0:45:03.534182 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:45:03.534271 PROGRESS: 
0:45:03.534326 PROGRESS: Protein Summary:
0:45:03.535336 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:45:03.535423 PROGRESS: =========================================================================
0:45:03.535614 INFO: Target number of precursors not reached yet.
0:45:03.540086 INFO: Starting optimization step 2.
0:45:03.540191 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:45:03.540264 INFO: Using ng extraction backend
0:45:03.540324 PROGRESS: Extracting batch of 1593 precursors
0:45:03.544408 INFO: === Search parameters used ===
0:45:03.544499 INFO: rt_error       : 805.6019897460938
0:45:03.544551 INFO: mobility_error : 0.1
0:45:03.544599 INFO: num_candidates : 1
0:45:03.544641 INFO: ms1_error      : 30
0:45:03.544683 INFO: ms2_error      : 30
0:45:03.544724 INFO: fwhm_rt        : 5
0:45:03.544762 INFO: quant_window   : 3
0:45:03.544801 INFO: ==============================================
0:45:03.574533 INFO: performing precursor FDR with 40 features
0:45:03.574609 INFO: Decoy channel: -1
0:45:03.574634 INFO: Competetive: True
0:45:03.577693 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:03.579475 INFO: Using random state 347799 for train-test-split
0:45:03.591206 INFO: Test AUC: 0.449
0:45:03.591264 INFO: Train AUC: 0.468
0:45:03.591292 INFO: AUC difference: 4.05%
0:45:03.798207 INFO: Resetting torch num_threads to 80
0:45:03.800547 PROGRESS: === Extracted 2786 precursors and 19407 fragments ===
0:45:03.800879 INFO: === FDR correction performed with classifier version -1 ===
0:45:03.801322 PROGRESS: ============================= Precursor FDR =============================
0:45:03.801410 PROGRESS: Total precursors accumulated: 0
0:45:03.801469 PROGRESS: Target precursors: 0 (0.00%)
0:45:03.801519 PROGRESS: Decoy precursors: 0 (0.00%)
0:45:03.801565 PROGRESS: 
0:45:03.801610 PROGRESS: Precursor Summary:
0:45:03.801716 PROGRESS: 
0:45:03.801776 PROGRESS: Protein Summary:
0:45:03.801846 PROGRESS: =========================================================================
0:45:03.802046 INFO: Target number of precursors not reached yet.
0:45:03.808266 INFO: Starting optimization step 3.
0:45:03.808379 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:45:03.808450 INFO: Using ng extraction backend
0:45:03.808509 PROGRESS: Extracting batch of 3185 precursors
0:45:03.815537 INFO: === Search parameters used ===
0:45:03.815634 INFO: rt_error       : 805.6019897460938
0:45:03.815683 INFO: mobility_error : 0.1
0:45:03.815727 INFO: num_candidates : 1
0:45:03.815770 INFO: ms1_error      : 30
0:45:03.815809 INFO: ms2_error      : 30
0:45:03.815851 INFO: fwhm_rt        : 5
0:45:03.815890 INFO: quant_window   : 3
0:45:03.815938 INFO: ==============================================
0:45:03.878444 INFO: performing precursor FDR with 40 features
0:45:03.878551 INFO: Decoy channel: -1
0:45:03.878577 INFO: Competetive: True
0:45:03.883264 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:03.885525 INFO: Using random state 322790 for train-test-split
0:45:03.905655 INFO: Test AUC: 0.473
0:45:03.905728 INFO: Train AUC: 0.464
0:45:03.905760 INFO: AUC difference: 1.94%
0:45:04.121112 INFO: Resetting torch num_threads to 80
0:45:04.124017 PROGRESS: === Extracted 5967 precursors and 41394 fragments ===
0:45:04.124361 INFO: === FDR correction performed with classifier version -1 ===
0:45:04.124789 PROGRESS: ============================= Precursor FDR =============================
0:45:04.124875 PROGRESS: Total precursors accumulated: 0
0:45:04.124932 PROGRESS: Target precursors: 0 (0.00%)
0:45:04.124981 PROGRESS: Decoy precursors: 0 (0.00%)
0:45:04.125050 PROGRESS: 
0:45:04.125106 PROGRESS: Precursor Summary:
0:45:04.125227 PROGRESS: 
0:45:04.125289 PROGRESS: Protein Summary:
0:45:04.125361 PROGRESS: =========================================================================
0:45:04.125578 INFO: Target number of precursors not reached yet.
0:45:04.135314 INFO: Starting optimization step 4.
0:45:04.135432 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:45:04.135503 INFO: Using ng extraction backend
0:45:04.135562 PROGRESS: Extracting batch of 6366 precursors
0:45:04.147597 INFO: === Search parameters used ===
0:45:04.147721 INFO: rt_error       : 805.6019897460938
0:45:04.147773 INFO: mobility_error : 0.1
0:45:04.147822 INFO: num_candidates : 1
0:45:04.147864 INFO: ms1_error      : 30
0:45:04.147920 INFO: ms2_error      : 30
0:45:04.147962 INFO: fwhm_rt        : 5
0:45:04.148002 INFO: quant_window   : 3
0:45:04.148041 INFO: ==============================================
0:45:04.222388 INFO: performing precursor FDR with 40 features
0:45:04.222492 INFO: Decoy channel: -1
0:45:04.222518 INFO: Competetive: True
0:45:04.227567 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:04.230839 INFO: Using random state 247367 for train-test-split
0:45:04.264779 INFO: Test AUC: 0.467
0:45:04.264874 INFO: Train AUC: 0.466
0:45:04.264903 INFO: AUC difference: 0.25%
0:45:05.707862 INFO: Resetting torch num_threads to 80
0:45:05.711782 PROGRESS: === Extracted 12325 precursors and 85540 fragments ===
0:45:05.712144 INFO: === FDR correction performed with classifier version -1 ===
0:45:05.712584 PROGRESS: ============================= Precursor FDR =============================
0:45:05.712673 PROGRESS: Total precursors accumulated: 0
0:45:05.712731 PROGRESS: Target precursors: 0 (0.00%)
0:45:05.712782 PROGRESS: Decoy precursors: 0 (0.00%)
0:45:05.712828 PROGRESS: 
0:45:05.712874 PROGRESS: Precursor Summary:
0:45:05.712978 PROGRESS: 
0:45:05.713060 PROGRESS: Protein Summary:
0:45:05.713134 PROGRESS: =========================================================================
0:45:05.713389 INFO: Target number of precursors not reached yet.
0:45:05.728360 INFO: Starting optimization step 5.
0:45:05.728546 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:45:05.728626 INFO: Using ng extraction backend
0:45:05.728689 PROGRESS: Extracting batch of 12747 precursors
0:45:05.751045 INFO: === Search parameters used ===
0:45:05.751211 INFO: rt_error       : 805.6019897460938
0:45:05.751266 INFO: mobility_error : 0.1
0:45:05.751312 INFO: num_candidates : 1
0:45:05.751355 INFO: ms1_error      : 30
0:45:05.751397 INFO: ms2_error      : 30
0:45:05.751436 INFO: fwhm_rt        : 5
0:45:05.751476 INFO: quant_window   : 3
0:45:05.751513 INFO: ==============================================
0:45:05.881705 INFO: performing precursor FDR with 40 features
0:45:05.881813 INFO: Decoy channel: -1
0:45:05.881839 INFO: Competetive: True
0:45:05.890590 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:05.896095 INFO: Using random state 495432 for train-test-split
0:45:06.204052 INFO: Test AUC: 0.807
0:45:06.204161 INFO: Train AUC: 0.809
0:45:06.204190 INFO: AUC difference: 0.24%
0:45:06.434408 INFO: Resetting torch num_threads to 80
0:45:06.440967 PROGRESS: === Extracted 25063 precursors and 174557 fragments ===
0:45:06.441471 INFO: === FDR correction performed with classifier version -1 ===
0:45:06.442423 PROGRESS: ============================= Precursor FDR =============================
0:45:06.442515 PROGRESS: Total precursors accumulated: 4,144
0:45:06.442573 PROGRESS: Target precursors: 4,103 (99.01%)
0:45:06.442623 PROGRESS: Decoy precursors: 41 (0.99%)
0:45:06.442669 PROGRESS: 
0:45:06.442712 PROGRESS: Precursor Summary:
0:45:06.444565 PROGRESS: Channel   0:	 0.050 FDR: 4,103; 0.010 FDR: 4,103; 0.001 FDR: 2,153
0:45:06.444662 PROGRESS: 
0:45:06.444719 PROGRESS: Protein Summary:
0:45:06.447325 PROGRESS: Channel   0:	 0.050 FDR: 2,524; 0.010 FDR: 2,524; 0.001 FDR: 1,462
0:45:06.447425 PROGRESS: =========================================================================
0:45:06.447810 INFO: Target number of precursors reached.
0:45:06.473574 INFO: fragments_df: keeping 5000 of 174557 [sum(precursor_idx_mask)=45215 sum(mass_error_mask)=174557 stop_rank=5000
0:45:06.481562 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:07.082840 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:07.805506 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:45:07.805938 INFO: Using score_cutoff 13.988602753829957 (fac=0.99, q=1)
0:45:07.806251 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:45:07.806330 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:45:07.806384 INFO: Updating optimization_manager: score_cutoff        : 0 -> 13.988602753829957
0:45:07.806437 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:07.808774 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:07.812895 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
0:45:07.813007 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:45:07.813089 INFO: Starting optimization step 6.
0:45:07.813149 PROGRESS: === Extracting elution groups 0 to 1400 ===
0:45:07.813211 INFO: Using ng extraction backend
0:45:07.813265 PROGRESS: Extracting batch of 2787 precursors
0:45:07.819309 INFO: === Search parameters used ===
0:45:07.819408 INFO: rt_error       : 805.6019897460938
0:45:07.819459 INFO: mobility_error : 0.1
0:45:07.819502 INFO: num_candidates : 3
0:45:07.819556 INFO: ms1_error      : 30
0:45:07.819600 INFO: ms2_error      : 30
0:45:07.819642 INFO: fwhm_rt        : 3.0
0:45:07.819680 INFO: quant_window   : 3
0:45:07.819718 INFO: ==============================================
0:45:07.884201 INFO: performing precursor FDR with 40 features
0:45:07.884304 INFO: Decoy channel: -1
0:45:07.884330 INFO: Competetive: True
0:45:07.887832 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:07.890373 INFO: Using random state 208442 for train-test-split
0:45:07.910004 INFO: Test AUC: 0.688
0:45:07.910087 INFO: Train AUC: 0.653
0:45:07.910117 INFO: AUC difference: 5.38%
0:45:07.910139 WARNING: AUC difference > 5%. This may indicate overfitting.
0:45:08.123553 INFO: Resetting torch num_threads to 80
0:45:08.125259 PROGRESS: === Extracted 8338 precursors and 50726 fragments ===
0:45:08.125585 INFO: === FDR correction performed with classifier version 5 ===
0:45:08.126047 PROGRESS: ============================= Precursor FDR =============================
0:45:08.126135 PROGRESS: Total precursors accumulated: 442
0:45:08.126192 PROGRESS: Target precursors: 438 (99.10%)
0:45:08.126243 PROGRESS: Decoy precursors: 4 (0.90%)
0:45:08.126287 PROGRESS: 
0:45:08.126329 PROGRESS: Precursor Summary:
0:45:08.127318 PROGRESS: Channel   0:	 0.050 FDR:   438; 0.010 FDR:   438; 0.001 FDR:   285
0:45:08.127407 PROGRESS: 
0:45:08.127462 PROGRESS: Protein Summary:
0:45:08.128611 PROGRESS: Channel   0:	 0.050 FDR:   397; 0.010 FDR:   397; 0.001 FDR:   269
0:45:08.128699 PROGRESS: =========================================================================
0:45:08.129083 INFO: Target number of precursors reached.
0:45:08.135113 INFO: fragments_df: keeping 5000 of 50726 [sum(precursor_idx_mask)=10215 sum(mass_error_mask)=50726 stop_rank=5000
0:45:08.142020 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:08.276097 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:08.950909 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:08.951319 INFO: Using score_cutoff 15.841123325443267 (fac=0.99, q=1)
0:45:08.951605 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:08.951682 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:08.951739 INFO: Updating optimization_manager: score_cutoff        : 13.988602753829957 -> 15.841123325443267
0:45:08.951793 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:08.954172 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:08.958434 INFO: === checking if optimization conditions were reached ===
0:45:08.960028 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:45:08.960124 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
0:45:08.960186 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:45:08.960243 INFO: ==============================================
0:45:08.960304 INFO: Starting optimization step 7.
0:45:08.960359 PROGRESS: === Extracting elution groups 0 to 1400 ===
0:45:08.960417 INFO: Using ng extraction backend
0:45:08.960472 PROGRESS: Extracting batch of 2787 precursors
0:45:08.966644 INFO: === Search parameters used ===
0:45:08.966738 INFO: rt_error       : 805.6019897460938
0:45:08.966796 INFO: mobility_error : 0.1
0:45:08.966842 INFO: num_candidates : 3
0:45:08.966885 INFO: ms1_error      : 30
0:45:08.966927 INFO: ms2_error      : 10.0
0:45:08.966969 INFO: fwhm_rt        : 3.0
0:45:08.967009 INFO: quant_window   : 3
0:45:08.967048 INFO: ==============================================
0:45:09.045520 INFO: performing precursor FDR with 40 features
0:45:09.045632 INFO: Decoy channel: -1
0:45:09.045658 INFO: Competetive: True
0:45:09.049065 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:09.051519 INFO: Using random state 354347 for train-test-split
0:45:09.071617 INFO: Test AUC: 0.690
0:45:09.071700 INFO: Train AUC: 0.677
0:45:09.071729 INFO: AUC difference: 1.96%
0:45:09.288448 INFO: Resetting torch num_threads to 80
0:45:09.290196 PROGRESS: === Extracted 8354 precursors and 57052 fragments ===
0:45:09.290527 INFO: === FDR correction performed with classifier version 6 ===
0:45:09.291062 PROGRESS: ============================= Precursor FDR =============================
0:45:09.291149 PROGRESS: Total precursors accumulated: 912
0:45:09.291207 PROGRESS: Target precursors: 903 (99.01%)
0:45:09.291255 PROGRESS: Decoy precursors: 9 (0.99%)
0:45:09.291299 PROGRESS: 
0:45:09.291341 PROGRESS: Precursor Summary:
0:45:09.292406 PROGRESS: Channel   0:	 0.050 FDR:   903; 0.010 FDR:   903; 0.001 FDR:   633
0:45:09.292496 PROGRESS: 
0:45:09.292550 PROGRESS: Protein Summary:
0:45:09.293930 PROGRESS: Channel   0:	 0.050 FDR:   802; 0.010 FDR:   802; 0.001 FDR:   572
0:45:09.294023 PROGRESS: =========================================================================
0:45:09.294271 INFO: Target number of precursors reached.
0:45:09.302497 INFO: fragments_df: keeping 5000 of 57052 [sum(precursor_idx_mask)=21734 sum(mass_error_mask)=57052 stop_rank=5000
0:45:09.307359 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:09.472662 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:10.149039 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:10.149448 INFO: Using score_cutoff 12.881207158470154 (fac=0.99, q=1)
0:45:10.149740 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:10.149822 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:10.149877 INFO: Updating optimization_manager: score_cutoff        : 15.841123325443267 -> 12.881207158470154
0:45:10.149931 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:10.151436 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:10.153554 INFO: === checking if optimization conditions were reached ===
0:45:10.155148 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:45:10.155246 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:45:10.155308 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:45:10.155365 INFO: ==============================================
0:45:10.155425 PROGRESS: Optimization finished for ms2_error.
0:45:10.160026 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:10.161320 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:10.163386 INFO: Starting optimization step 0.
0:45:10.163480 PROGRESS: === Extracting elution groups 0 to 600 ===
0:45:10.163558 INFO: Using ng extraction backend
0:45:10.163619 PROGRESS: Extracting batch of 1194 precursors
0:45:10.166951 INFO: === Search parameters used ===
0:45:10.167044 INFO: rt_error       : 805.6019897460938
0:45:10.167094 INFO: mobility_error : 0.1
0:45:10.167139 INFO: num_candidates : 3
0:45:10.167181 INFO: ms1_error      : 30
0:45:10.167222 INFO: ms2_error      : 10.0
0:45:10.167264 INFO: fwhm_rt        : 3.0
0:45:10.167303 INFO: quant_window   : 3
0:45:10.167342 INFO: ==============================================
0:45:10.212998 INFO: performing precursor FDR with 40 features
0:45:10.213086 INFO: Decoy channel: -1
0:45:10.213113 INFO: Competetive: True
0:45:10.215687 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:10.217444 INFO: Using random state 857681 for train-test-split
0:45:10.229277 INFO: Test AUC: 0.659
0:45:10.229335 INFO: Train AUC: 0.679
0:45:10.229363 INFO: AUC difference: 2.96%
0:45:10.443061 INFO: Resetting torch num_threads to 80
0:45:10.444580 PROGRESS: === Extracted 3577 precursors and 24464 fragments ===
0:45:10.444910 INFO: === FDR correction performed with classifier version 7 ===
0:45:10.445374 PROGRESS: ============================= Precursor FDR =============================
0:45:10.445461 PROGRESS: Total precursors accumulated: 379
0:45:10.445518 PROGRESS: Target precursors: 376 (99.21%)
0:45:10.445566 PROGRESS: Decoy precursors: 3 (0.79%)
0:45:10.445609 PROGRESS: 
0:45:10.445651 PROGRESS: Precursor Summary:
0:45:10.446568 PROGRESS: Channel   0:	 0.050 FDR:   376; 0.010 FDR:   376; 0.001 FDR:   285
0:45:10.446657 PROGRESS: 
0:45:10.446717 PROGRESS: Protein Summary:
0:45:10.447847 PROGRESS: Channel   0:	 0.050 FDR:   355; 0.010 FDR:   355; 0.001 FDR:   274
0:45:10.447937 PROGRESS: =========================================================================
0:45:10.448169 INFO: Target number of precursors reached.
0:45:10.452195 INFO: fragments_df: keeping 4065 of 24464 [sum(precursor_idx_mask)=9016 sum(mass_error_mask)=24464 stop_rank=4065
0:45:10.456926 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:10.581586 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:11.118014 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:11.119213 INFO: Using score_cutoff 12.84535871744156 (fac=0.99, q=1)
0:45:11.119499 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:11.119578 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:11.119632 INFO: Updating optimization_manager: score_cutoff        : 12.881207158470154 -> 12.84535871744156
0:45:11.119687 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:11.121344 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:11.123727 INFO: === checking if optimization conditions were reached ===
0:45:11.123830 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:45:11.125348 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 49.39682098895065
0:45:11.125475 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 49.3968.
0:45:11.125540 INFO: ==============================================
0:45:11.125616 INFO: Starting optimization step 1.
0:45:11.125675 PROGRESS: === Extracting elution groups 0 to 600 ===
0:45:11.125733 INFO: Using ng extraction backend
0:45:11.125795 PROGRESS: Extracting batch of 1194 precursors
0:45:11.129342 INFO: === Search parameters used ===
0:45:11.129440 INFO: rt_error       : 49.39682098895065
0:45:11.129489 INFO: mobility_error : 0.1
0:45:11.129533 INFO: num_candidates : 3
0:45:11.129574 INFO: ms1_error      : 30
0:45:11.129615 INFO: ms2_error      : 10.0
0:45:11.129655 INFO: fwhm_rt        : 3.0
0:45:11.129694 INFO: quant_window   : 3
0:45:11.129732 INFO: ==============================================
0:45:11.162937 INFO: performing precursor FDR with 40 features
0:45:11.163744 INFO: Decoy channel: -1
0:45:11.163777 INFO: Competetive: True
0:45:11.166475 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:11.168305 INFO: Using random state 857681 for train-test-split
0:45:11.180128 INFO: Test AUC: 0.712
0:45:11.180191 INFO: Train AUC: 0.708
0:45:11.180220 INFO: AUC difference: 0.45%
0:45:11.393051 INFO: Resetting torch num_threads to 80
0:45:11.394542 PROGRESS: === Extracted 3308 precursors and 19264 fragments ===
0:45:11.394864 INFO: === FDR correction performed with classifier version 7 ===
0:45:11.395322 PROGRESS: ============================= Precursor FDR =============================
0:45:11.395406 PROGRESS: Total precursors accumulated: 444
0:45:11.395463 PROGRESS: Target precursors: 440 (99.10%)
0:45:11.395512 PROGRESS: Decoy precursors: 4 (0.90%)
0:45:11.395557 PROGRESS: 
0:45:11.395598 PROGRESS: Precursor Summary:
0:45:11.396531 PROGRESS: Channel   0:	 0.050 FDR:   440; 0.010 FDR:   440; 0.001 FDR:   284
0:45:11.396624 PROGRESS: 
0:45:11.396682 PROGRESS: Protein Summary:
0:45:11.397815 PROGRESS: Channel   0:	 0.050 FDR:   416; 0.010 FDR:   416; 0.001 FDR:   273
0:45:11.397904 PROGRESS: =========================================================================
0:45:11.398101 INFO: Target number of precursors reached.
0:45:11.401695 INFO: fragments_df: keeping 3934 of 19264 [sum(precursor_idx_mask)=8548 sum(mass_error_mask)=19264 stop_rank=3934
0:45:11.406388 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:11.534441 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:12.055531 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:12.056092 INFO: Using score_cutoff 12.252117756843566 (fac=0.99, q=1)
0:45:12.056417 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:12.056498 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:12.056552 INFO: Updating optimization_manager: score_cutoff        : 12.84535871744156 -> 12.252117756843566
0:45:12.056606 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:12.058431 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:12.060647 INFO: === checking if optimization conditions were reached ===
0:45:12.060749 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:45:12.062476 INFO: Updating optimization_manager: rt_error            : 49.39682098895065 -> 9.84983164292501
0:45:12.062583 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 9.8498.
0:45:12.062657 INFO: ==============================================
0:45:12.062725 INFO: Starting optimization step 2.
0:45:12.062785 PROGRESS: === Extracting elution groups 0 to 600 ===
0:45:12.062845 INFO: Using ng extraction backend
0:45:12.062901 PROGRESS: Extracting batch of 1194 precursors
0:45:12.067124 INFO: === Search parameters used ===
0:45:12.067227 INFO: rt_error       : 9.84983164292501
0:45:12.067278 INFO: mobility_error : 0.1
0:45:12.067325 INFO: num_candidates : 3
0:45:12.067367 INFO: ms1_error      : 30
0:45:12.067407 INFO: ms2_error      : 10.0
0:45:12.067446 INFO: fwhm_rt        : 3.0
0:45:12.067483 INFO: quant_window   : 3
0:45:12.067521 INFO: ==============================================
0:45:12.102739 INFO: performing precursor FDR with 40 features
0:45:12.102881 INFO: Decoy channel: -1
0:45:12.102907 INFO: Competetive: True
0:45:12.105777 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:12.107729 INFO: Using random state 857681 for train-test-split
0:45:12.121076 INFO: Test AUC: 0.720
0:45:12.121173 INFO: Train AUC: 0.705
0:45:12.121207 INFO: AUC difference: 2.08%
0:45:12.363198 INFO: Resetting torch num_threads to 80
0:45:12.366212 PROGRESS: === Extracted 3307 precursors and 19304 fragments ===
0:45:12.366717 INFO: === FDR correction performed with classifier version 7 ===
0:45:12.367188 PROGRESS: ============================= Precursor FDR =============================
0:45:12.367279 PROGRESS: Total precursors accumulated: 436
0:45:12.367338 PROGRESS: Target precursors: 432 (99.08%)
0:45:12.367390 PROGRESS: Decoy precursors: 4 (0.92%)
0:45:12.367436 PROGRESS: 
0:45:12.367493 PROGRESS: Precursor Summary:
0:45:12.368450 PROGRESS: Channel   0:	 0.050 FDR:   432; 0.010 FDR:   432; 0.001 FDR:   284
0:45:12.368541 PROGRESS: 
0:45:12.368597 PROGRESS: Protein Summary:
0:45:12.369745 PROGRESS: Channel   0:	 0.050 FDR:   409; 0.010 FDR:   409; 0.001 FDR:   273
0:45:12.369839 PROGRESS: =========================================================================
0:45:12.370109 INFO: Target number of precursors reached.
0:45:12.373906 INFO: fragments_df: keeping 3893 of 19304 [sum(precursor_idx_mask)=8467 sum(mass_error_mask)=19304 stop_rank=3893
0:45:12.378698 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:12.505909 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:13.014610 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:13.015015 INFO: Using score_cutoff 12.21477598285675 (fac=0.99, q=1)
0:45:13.015298 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:13.015380 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:13.015437 INFO: Updating optimization_manager: score_cutoff        : 12.252117756843566 -> 12.21477598285675
0:45:13.015491 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:13.017034 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:13.019216 INFO: === checking if optimization conditions were reached ===
0:45:13.019315 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:45:13.020981 INFO: Updating optimization_manager: rt_error            : 9.84983164292501 -> 9.949782516718747
0:45:13.021089 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 9.9498.
0:45:13.021155 INFO: ==============================================
0:45:13.021220 INFO: Starting optimization step 3.
0:45:13.021276 PROGRESS: === Extracting elution groups 0 to 600 ===
0:45:13.021335 INFO: Using ng extraction backend
0:45:13.021390 PROGRESS: Extracting batch of 1194 precursors
0:45:13.024605 INFO: === Search parameters used ===
0:45:13.024696 INFO: rt_error       : 9.949782516718747
0:45:13.024746 INFO: mobility_error : 0.1
0:45:13.024793 INFO: num_candidates : 3
0:45:13.024840 INFO: ms1_error      : 30
0:45:13.024882 INFO: ms2_error      : 10.0
0:45:13.024922 INFO: fwhm_rt        : 3.0
0:45:13.024962 INFO: quant_window   : 3
0:45:13.025010 INFO: ==============================================
0:45:13.056386 INFO: performing precursor FDR with 40 features
0:45:13.056473 INFO: Decoy channel: -1
0:45:13.056499 INFO: Competetive: True
0:45:13.059115 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:13.060852 INFO: Using random state 857681 for train-test-split
0:45:13.072111 INFO: Test AUC: 0.683
0:45:13.072170 INFO: Train AUC: 0.716
0:45:13.072199 INFO: AUC difference: 4.55%
0:45:13.289324 INFO: Resetting torch num_threads to 80
0:45:13.290834 PROGRESS: === Extracted 3305 precursors and 19300 fragments ===
0:45:13.291158 INFO: === FDR correction performed with classifier version 7 ===
0:45:13.291631 PROGRESS: ============================= Precursor FDR =============================
0:45:13.291714 PROGRESS: Total precursors accumulated: 436
0:45:13.291771 PROGRESS: Target precursors: 432 (99.08%)
0:45:13.291828 PROGRESS: Decoy precursors: 4 (0.92%)
0:45:13.291880 PROGRESS: 
0:45:13.291924 PROGRESS: Precursor Summary:
0:45:13.292863 PROGRESS: Channel   0:	 0.050 FDR:   432; 0.010 FDR:   432; 0.001 FDR:   284
0:45:13.292949 PROGRESS: 
0:45:13.293013 PROGRESS: Protein Summary:
0:45:13.294142 PROGRESS: Channel   0:	 0.050 FDR:   409; 0.010 FDR:   409; 0.001 FDR:   273
0:45:13.294230 PROGRESS: =========================================================================
0:45:13.294429 INFO: Target number of precursors reached.
0:45:13.297981 INFO: fragments_df: keeping 3895 of 19300 [sum(precursor_idx_mask)=8454 sum(mass_error_mask)=19300 stop_rank=3895
0:45:13.302911 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:13.437824 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:13.949420 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:13.949831 INFO: Using score_cutoff 12.21477598285675 (fac=0.99, q=1)
0:45:13.950114 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:13.950191 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:13.950243 INFO: Updating optimization_manager: score_cutoff        : 12.21477598285675 -> 12.21477598285675
0:45:13.950294 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:13.951837 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:13.954019 INFO: === checking if optimization conditions were reached ===
0:45:13.954121 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:45:13.954976 INFO: Updating optimization_manager: rt_error            : 9.949782516718747 -> 9.84983164292501
0:45:13.955098 INFO: Updating optimization_manager: classifier_version  : 7 -> 10
0:45:13.955191 INFO: Updating optimization_manager: score_cutoff        : 12.21477598285675 -> 12.21477598285675
0:45:13.955279 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:13.955362 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:13.955445 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 9.8498 found after 4 searches.
0:45:13.955504 INFO: ==============================================
0:45:13.955565 PROGRESS: Optimization finished for rt_error.
0:45:13.960073 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:13.961422 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:13.988710 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:45:13.988851 PROGRESS: ==============================================
0:45:13.988916 PROGRESS: ms2_error      : 10.0000
0:45:13.988969 PROGRESS: rt_error       : 9.8498
0:45:13.989037 PROGRESS: ==============================================
0:45:13.989433 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:14.113680 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:14.449606 INFO: Using ng extraction backend
0:45:14.449892 PROGRESS: Extracting batch of 230645 precursors
0:45:14.813504 INFO: === Search parameters used ===
0:45:14.813735 INFO: rt_error       : 9.84983164292501
0:45:14.813791 INFO: mobility_error : 0.1
0:45:14.813837 INFO: num_candidates : 3
0:45:14.813879 INFO: ms1_error      : 30
0:45:14.813921 INFO: ms2_error      : 10.0
0:45:14.813961 INFO: fwhm_rt        : 3.0
0:45:23.142316 INFO: quant_window   : 3
0:45:23.142493 INFO: ==============================================
0:45:23.374194 INFO: Removed 326122 precursors with score below cutoff 12.21477598285675
0:45:23.665445 INFO: performing precursor FDR with 40 features
0:45:23.665569 INFO: Decoy channel: -1
0:45:23.665595 INFO: Competetive: True
0:45:23.691713 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:23.706573 WARNING: FDR calculation for 196305 target and 112997 decoy PSMs
0:45:23.706702 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
0:45:23.769567 INFO: Using random state 446951 for train-test-split
0:45:27.981052 INFO: Test AUC: 0.872
0:45:27.981177 INFO: Train AUC: 0.874
0:45:27.981208 INFO: AUC difference: 0.22%
0:45:28.265058 INFO: Resetting torch num_threads to 80
0:45:28.547488 PROGRESS: ============================= Precursor FDR =============================
0:45:28.547728 PROGRESS: Total precursors accumulated: 105,407
0:45:28.547797 PROGRESS: Target precursors: 104,364 (99.01%)
0:45:28.547851 PROGRESS: Decoy precursors: 1,043 (0.99%)
0:45:28.547898 PROGRESS: 
0:45:28.547945 PROGRESS: Precursor Summary:
0:45:28.573481 PROGRESS: Channel   0:	 0.050 FDR: 104,364; 0.010 FDR: 104,364; 0.001 FDR: 91,439
0:45:28.573711 PROGRESS: 
0:45:28.573777 PROGRESS: Protein Summary:
0:45:28.609576 PROGRESS: Channel   0:	 0.050 FDR: 9,952; 0.010 FDR: 9,952; 0.001 FDR: 9,746
0:45:28.609814 PROGRESS: =========================================================================
0:45:28.611497 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/psm.parquet
0:45:28.781484 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.parquet
0:45:29.055070 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:45:29.176336 PROGRESS: 
0:45:29.176473 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant
0:45:29.176539 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/figures
0:45:29.176684 INFO: Initializing TimingManager
0:45:29.177097 INFO: Initializing RawFileManager
0:45:39.301892 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.
0:45:39.307001 INFO: Determining DIA cycle
0:45:39.323263 INFO: Found cycle with start 0.00 min and length 300.
0:45:39.481448 INFO: RT (min)            : 0.0 - 26.9
0:45:39.481542 INFO: RT duration (sec)   : 1611.2
0:45:39.481572 INFO: RT duration (min)   : 26.9
0:45:39.481595 INFO: Cycle len (scans)   : 300
0:45:39.481614 INFO: Cycle len (sec)     : 1.65
0:45:39.481633 INFO: Number of cycles    : 977
0:45:39.481652 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:45:39.481680 INFO: Creating DIA data object took: 10.304484605789185
0:45:40.108640 INFO: Creating DIA data NG object took: 0.6268496513366699
0:45:40.144833 INFO: Initializing CalibrationManager
0:45:40.145112 INFO: Setting up calibration estimators ..
0:45:40.145175 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:45:40.145239 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'}' ..
0:45:40.145309 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:45:40.145361 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:45:40.145413 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}}' ..
0:45:40.145463 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:45:40.145509 INFO: Done setting up calibration estimators.
0:45:40.145690 INFO: Initializing OptimizationManager
0:45:40.146232 INFO: initial parameter: ms1_error = 30
0:45:40.146286 INFO: initial parameter: ms2_error = 30
0:45:40.146334 INFO: initial parameter: rt_error = 805.6004638671875
0:45:40.146378 INFO: initial parameter: mobility_error = 0.1
0:45:40.146418 INFO: initial parameter: num_candidates = 1
0:45:40.146457 INFO: initial parameter: fwhm_rt = 5
0:45:40.146497 INFO: initial parameter: fwhm_mobility = 0.01
0:45:40.146536 INFO: initial parameter: score_cutoff = 0
0:45:40.146584 INFO: initial parameter: classifier_version = -1
0:45:40.146649 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:45:40.146861 INFO: FDRManager: loading saved state not requested, will be initialized.
0:45:40.146895 INFO: Initializing FDRManager
0:45:40.146924 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:45:40.170873 PROGRESS: Initializing spectral library: 115,864 target precursors potentially observable (0 removed)
0:45:40.189041 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:45:40.189370 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
0:45:40.189463 PROGRESS: Starting initial search for precursors.
0:45:40.189538 INFO: Starting optimization step 0.
0:45:40.189594 PROGRESS: === Extracting elution groups 0 to 200 ===
0:45:40.189648 INFO: Using ng extraction backend
0:45:40.189700 PROGRESS: Extracting batch of 397 precursors
0:45:40.191573 INFO: === Search parameters used ===
0:45:40.191669 INFO: rt_error       : 805.6004638671875
0:45:40.191718 INFO: mobility_error : 0.1
0:45:40.191760 INFO: num_candidates : 1
0:45:40.191800 INFO: ms1_error      : 30
0:45:40.191842 INFO: ms2_error      : 30
0:45:40.191882 INFO: fwhm_rt        : 5
0:45:40.191923 INFO: quant_window   : 3
0:45:40.191963 INFO: ==============================================
0:45:40.207066 INFO: performing precursor FDR with 40 features
0:45:40.207130 INFO: Decoy channel: -1
0:45:40.207156 INFO: Competetive: True
0:45:40.208040 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:40.210100 INFO: Using random state 316750 for train-test-split
0:45:40.216731 INFO: Test AUC: 0.365
0:45:40.216788 INFO: Train AUC: 0.471
0:45:40.216818 INFO: AUC difference: 22.57%
0:45:40.216841 WARNING: AUC difference > 5%. This may indicate overfitting.
0:45:40.429934 INFO: Resetting torch num_threads to 80
0:45:40.431214 PROGRESS: === Extracted 397 precursors and 2773 fragments ===
0:45:40.431538 INFO: === FDR correction performed with classifier version -1 ===
0:45:40.431982 PROGRESS: ============================= Precursor FDR =============================
0:45:40.432070 PROGRESS: Total precursors accumulated: 1
0:45:40.432127 PROGRESS: Target precursors: 1 (100.00%)
0:45:40.432178 PROGRESS: Decoy precursors: 0 (0.00%)
0:45:40.432221 PROGRESS: 
0:45:40.432265 PROGRESS: Precursor Summary:
0:45:40.433172 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:45:40.433259 PROGRESS: 
0:45:40.433314 PROGRESS: Protein Summary:
0:45:40.434304 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:45:40.434391 PROGRESS: =========================================================================
0:45:40.434560 INFO: Target number of precursors not reached yet.
0:45:40.438178 INFO: Starting optimization step 1.
0:45:40.438278 PROGRESS: === Extracting elution groups 200 to 600 ===
0:45:40.438349 INFO: Using ng extraction backend
0:45:40.438407 PROGRESS: Extracting batch of 797 precursors
0:45:40.440940 INFO: === Search parameters used ===
0:45:40.441033 INFO: rt_error       : 805.6004638671875
0:45:40.441087 INFO: mobility_error : 0.1
0:45:40.441135 INFO: num_candidates : 1
0:45:40.441177 INFO: ms1_error      : 30
0:45:40.441218 INFO: ms2_error      : 30
0:45:40.441260 INFO: fwhm_rt        : 5
0:45:40.441299 INFO: quant_window   : 3
0:45:40.441338 INFO: ==============================================
0:45:40.463494 INFO: performing precursor FDR with 40 features
0:45:40.463562 INFO: Decoy channel: -1
0:45:40.463588 INFO: Competetive: True
0:45:40.466258 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:40.467687 INFO: Using random state 798697 for train-test-split
0:45:40.475605 INFO: Test AUC: 0.457
0:45:40.475661 INFO: Train AUC: 0.451
0:45:40.475690 INFO: AUC difference: 1.33%
0:45:40.682265 INFO: Resetting torch num_threads to 80
0:45:40.684233 PROGRESS: === Extracted 1192 precursors and 8267 fragments ===
0:45:40.684764 INFO: === FDR correction performed with classifier version -1 ===
0:45:40.685225 PROGRESS: ============================= Precursor FDR =============================
0:45:40.685316 PROGRESS: Total precursors accumulated: 2
0:45:40.685375 PROGRESS: Target precursors: 2 (100.00%)
0:45:40.685426 PROGRESS: Decoy precursors: 0 (0.00%)
0:45:40.685472 PROGRESS: 
0:45:40.685515 PROGRESS: Precursor Summary:
0:45:40.686433 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:45:40.686522 PROGRESS: 
0:45:40.686577 PROGRESS: Protein Summary:
0:45:40.687590 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:45:40.687678 PROGRESS: =========================================================================
0:45:40.687868 INFO: Target number of precursors not reached yet.
0:45:40.692396 INFO: Starting optimization step 2.
0:45:40.692496 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:45:40.692566 INFO: Using ng extraction backend
0:45:40.692624 PROGRESS: Extracting batch of 1593 precursors
0:45:40.696708 INFO: === Search parameters used ===
0:45:40.696802 INFO: rt_error       : 805.6004638671875
0:45:40.696852 INFO: mobility_error : 0.1
0:45:40.696899 INFO: num_candidates : 1
0:45:40.696941 INFO: ms1_error      : 30
0:45:40.696986 INFO: ms2_error      : 30
0:45:40.697041 INFO: fwhm_rt        : 5
0:45:40.697082 INFO: quant_window   : 3
0:45:40.697122 INFO: ==============================================
0:45:40.727375 INFO: performing precursor FDR with 40 features
0:45:40.727449 INFO: Decoy channel: -1
0:45:40.727475 INFO: Competetive: True
0:45:40.730537 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:40.732400 INFO: Using random state 958850 for train-test-split
0:45:40.743619 INFO: Test AUC: 0.486
0:45:40.743681 INFO: Train AUC: 0.450
0:45:40.743711 INFO: AUC difference: 8.12%
0:45:40.743733 WARNING: AUC difference > 5%. This may indicate overfitting.
0:45:40.951184 INFO: Resetting torch num_threads to 80
0:45:40.953508 PROGRESS: === Extracted 2782 precursors and 19605 fragments ===
0:45:40.953841 INFO: === FDR correction performed with classifier version -1 ===
0:45:40.954298 PROGRESS: ============================= Precursor FDR =============================
0:45:40.954386 PROGRESS: Total precursors accumulated: 1
0:45:40.954445 PROGRESS: Target precursors: 1 (100.00%)
0:45:40.954495 PROGRESS: Decoy precursors: 0 (0.00%)
0:45:40.954541 PROGRESS: 
0:45:40.954584 PROGRESS: Precursor Summary:
0:45:40.955482 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:45:40.955571 PROGRESS: 
0:45:40.955626 PROGRESS: Protein Summary:
0:45:40.956615 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:45:40.956702 PROGRESS: =========================================================================
0:45:40.956912 INFO: Target number of precursors not reached yet.
0:45:40.963032 INFO: Starting optimization step 3.
0:45:40.963140 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:45:40.963211 INFO: Using ng extraction backend
0:45:40.963270 PROGRESS: Extracting batch of 3185 precursors
0:45:40.970190 INFO: === Search parameters used ===
0:45:40.970288 INFO: rt_error       : 805.6004638671875
0:45:40.970338 INFO: mobility_error : 0.1
0:45:40.970381 INFO: num_candidates : 1
0:45:40.970423 INFO: ms1_error      : 30
0:45:40.970463 INFO: ms2_error      : 30
0:45:40.970512 INFO: fwhm_rt        : 5
0:45:40.970553 INFO: quant_window   : 3
0:45:40.970593 INFO: ==============================================
0:45:41.015448 INFO: performing precursor FDR with 40 features
0:45:41.015543 INFO: Decoy channel: -1
0:45:41.015568 INFO: Competetive: True
0:45:41.019975 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:41.022358 INFO: Using random state 137440 for train-test-split
0:45:41.040914 INFO: Test AUC: 0.448
0:45:41.040998 INFO: Train AUC: 0.460
0:45:41.041029 INFO: AUC difference: 2.53%
0:45:41.252826 INFO: Resetting torch num_threads to 80
0:45:41.255749 PROGRESS: === Extracted 5961 precursors and 41716 fragments ===
0:45:41.256102 INFO: === FDR correction performed with classifier version -1 ===
0:45:41.256544 PROGRESS: ============================= Precursor FDR =============================
0:45:41.256633 PROGRESS: Total precursors accumulated: 2
0:45:41.256694 PROGRESS: Target precursors: 2 (100.00%)
0:45:41.256744 PROGRESS: Decoy precursors: 0 (0.00%)
0:45:41.256788 PROGRESS: 
0:45:41.256833 PROGRESS: Precursor Summary:
0:45:41.257742 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:45:41.257829 PROGRESS: 
0:45:41.257883 PROGRESS: Protein Summary:
0:45:41.258880 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:45:41.258967 PROGRESS: =========================================================================
0:45:41.259191 INFO: Target number of precursors not reached yet.
0:45:41.268945 INFO: Starting optimization step 4.
0:45:41.269068 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:45:41.269143 INFO: Using ng extraction backend
0:45:41.269202 PROGRESS: Extracting batch of 6366 precursors
0:45:41.281482 INFO: === Search parameters used ===
0:45:41.281590 INFO: rt_error       : 805.6004638671875
0:45:41.281643 INFO: mobility_error : 0.1
0:45:41.281688 INFO: num_candidates : 1
0:45:41.281730 INFO: ms1_error      : 30
0:45:41.281769 INFO: ms2_error      : 30
0:45:41.281809 INFO: fwhm_rt        : 5
0:45:41.281850 INFO: quant_window   : 3
0:45:41.281888 INFO: ==============================================
0:45:41.354006 INFO: performing precursor FDR with 40 features
0:45:41.354108 INFO: Decoy channel: -1
0:45:41.354134 INFO: Competetive: True
0:45:41.359304 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:41.362856 INFO: Using random state 922915 for train-test-split
0:45:41.400382 INFO: Test AUC: 0.458
0:45:41.400486 INFO: Train AUC: 0.458
0:45:41.400516 INFO: AUC difference: 0.07%
0:45:41.620580 INFO: Resetting torch num_threads to 80
0:45:41.624237 PROGRESS: === Extracted 12318 precursors and 86044 fragments ===
0:45:41.624591 INFO: === FDR correction performed with classifier version -1 ===
0:45:41.625062 PROGRESS: ============================= Precursor FDR =============================
0:45:41.625154 PROGRESS: Total precursors accumulated: 3
0:45:41.625212 PROGRESS: Target precursors: 3 (100.00%)
0:45:41.625262 PROGRESS: Decoy precursors: 0 (0.00%)
0:45:41.625307 PROGRESS: 
0:45:41.625352 PROGRESS: Precursor Summary:
0:45:41.626256 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
0:45:41.626343 PROGRESS: 
0:45:41.626398 PROGRESS: Protein Summary:
0:45:41.627399 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
0:45:41.627486 PROGRESS: =========================================================================
0:45:41.627771 INFO: Target number of precursors not reached yet.
0:45:41.642310 INFO: Starting optimization step 5.
0:45:41.642484 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:45:41.642560 INFO: Using ng extraction backend
0:45:41.642622 PROGRESS: Extracting batch of 12747 precursors
0:45:41.664766 INFO: === Search parameters used ===
0:45:41.664924 INFO: rt_error       : 805.6004638671875
0:45:41.664973 INFO: mobility_error : 0.1
0:45:41.665061 INFO: num_candidates : 1
0:45:41.665105 INFO: ms1_error      : 30
0:45:41.665146 INFO: ms2_error      : 30
0:45:41.665188 INFO: fwhm_rt        : 5
0:45:41.665226 INFO: quant_window   : 3
0:45:41.665266 INFO: ==============================================
0:45:41.809380 INFO: performing precursor FDR with 40 features
0:45:41.809531 INFO: Decoy channel: -1
0:45:41.809558 INFO: Competetive: True
0:45:41.821290 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:41.829223 INFO: Using random state 622493 for train-test-split
0:45:42.220016 INFO: Test AUC: 0.807
0:45:42.220129 INFO: Train AUC: 0.810
0:45:42.220158 INFO: AUC difference: 0.36%
0:45:42.441027 INFO: Resetting torch num_threads to 80
0:45:42.447121 PROGRESS: === Extracted 25046 precursors and 175328 fragments ===
0:45:42.447516 INFO: === FDR correction performed with classifier version -1 ===
0:45:42.448459 PROGRESS: ============================= Precursor FDR =============================
0:45:42.448557 PROGRESS: Total precursors accumulated: 4,557
0:45:42.448617 PROGRESS: Target precursors: 4,512 (99.01%)
0:45:42.448667 PROGRESS: Decoy precursors: 45 (0.99%)
0:45:42.448714 PROGRESS: 
0:45:42.448763 PROGRESS: Precursor Summary:
0:45:42.450790 PROGRESS: Channel   0:	 0.050 FDR: 4,512; 0.010 FDR: 4,512; 0.001 FDR: 2,868
0:45:42.450887 PROGRESS: 
0:45:42.450942 PROGRESS: Protein Summary:
0:45:42.453817 PROGRESS: Channel   0:	 0.050 FDR: 2,664; 0.010 FDR: 2,664; 0.001 FDR: 1,845
0:45:42.453915 PROGRESS: =========================================================================
0:45:42.454293 INFO: Target number of precursors reached.
0:45:42.481298 INFO: fragments_df: keeping 5000 of 175328 [sum(precursor_idx_mask)=49093 sum(mass_error_mask)=175328 stop_rank=5000
0:45:42.487280 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:43.100415 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:43.775045 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:45:43.775512 INFO: Using score_cutoff 13.699023061466217 (fac=0.99, q=1)
0:45:43.775836 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:45:43.775916 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:45:43.775971 INFO: Updating optimization_manager: score_cutoff        : 0 -> 13.699023061466217
0:45:43.776025 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:43.777565 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:43.779652 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
0:45:43.779744 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:45:43.779827 INFO: Starting optimization step 6.
0:45:43.779889 PROGRESS: === Extracting elution groups 0 to 600 ===
0:45:43.779949 INFO: Using ng extraction backend
0:45:43.780004 PROGRESS: Extracting batch of 1194 precursors
0:45:43.783283 INFO: === Search parameters used ===
0:45:43.783369 INFO: rt_error       : 805.6004638671875
0:45:43.783419 INFO: mobility_error : 0.1
0:45:43.783463 INFO: num_candidates : 3
0:45:43.783506 INFO: ms1_error      : 30
0:45:43.783547 INFO: ms2_error      : 30
0:45:43.783587 INFO: fwhm_rt        : 3.0
0:45:43.783627 INFO: quant_window   : 3
0:45:43.783666 INFO: ==============================================
0:45:43.819885 INFO: performing precursor FDR with 40 features
0:45:43.819963 INFO: Decoy channel: -1
0:45:43.819989 INFO: Competetive: True
0:45:43.822506 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:43.824228 INFO: Using random state 945363 for train-test-split
0:45:43.835648 INFO: Test AUC: 0.645
0:45:43.835711 INFO: Train AUC: 0.653
0:45:43.835739 INFO: AUC difference: 1.25%
0:45:44.046596 INFO: Resetting torch num_threads to 80
0:45:44.048019 PROGRESS: === Extracted 3572 precursors and 21677 fragments ===
0:45:44.048341 INFO: === FDR correction performed with classifier version 5 ===
0:45:44.048773 PROGRESS: ============================= Precursor FDR =============================
0:45:44.048857 PROGRESS: Total precursors accumulated: 232
0:45:44.048915 PROGRESS: Target precursors: 230 (99.14%)
0:45:44.048967 PROGRESS: Decoy precursors: 2 (0.86%)
0:45:44.049028 PROGRESS: 
0:45:44.049074 PROGRESS: Precursor Summary:
0:45:44.049937 PROGRESS: Channel   0:	 0.050 FDR:   230; 0.010 FDR:   230; 0.001 FDR:   199
0:45:44.050029 PROGRESS: 
0:45:44.050085 PROGRESS: Protein Summary:
0:45:44.051087 PROGRESS: Channel   0:	 0.050 FDR:   223; 0.010 FDR:   223; 0.001 FDR:   192
0:45:44.051176 PROGRESS: =========================================================================
0:45:44.051509 INFO: Target number of precursors reached.
0:45:44.054796 INFO: fragments_df: keeping 2732 of 21677 [sum(precursor_idx_mask)=5276 sum(mass_error_mask)=21677 stop_rank=2732
0:45:44.059535 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:44.178522 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:44.538060 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:44.538465 INFO: Using score_cutoff 13.903972669315337 (fac=0.99, q=1)
0:45:44.538746 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:44.538826 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:44.538883 INFO: Updating optimization_manager: score_cutoff        : 13.699023061466217 -> 13.903972669315337
0:45:44.538935 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:44.540472 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:44.542578 INFO: === checking if optimization conditions were reached ===
0:45:44.543837 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:45:44.543936 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
0:45:44.543999 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:45:44.544064 INFO: ==============================================
0:45:44.544128 INFO: Starting optimization step 7.
0:45:44.544186 PROGRESS: === Extracting elution groups 0 to 600 ===
0:45:44.544245 INFO: Using ng extraction backend
0:45:44.544297 PROGRESS: Extracting batch of 1194 precursors
0:45:44.547573 INFO: === Search parameters used ===
0:45:44.547659 INFO: rt_error       : 805.6004638671875
0:45:44.547709 INFO: mobility_error : 0.1
0:45:44.547755 INFO: num_candidates : 3
0:45:44.547799 INFO: ms1_error      : 30
0:45:44.547841 INFO: ms2_error      : 10.0
0:45:44.547883 INFO: fwhm_rt        : 3.0
0:45:44.547921 INFO: quant_window   : 3
0:45:44.547960 INFO: ==============================================
0:45:44.583467 INFO: performing precursor FDR with 40 features
0:45:44.583541 INFO: Decoy channel: -1
0:45:44.583567 INFO: Competetive: True
0:45:44.586118 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:44.587879 INFO: Using random state 712861 for train-test-split
0:45:44.599259 INFO: Test AUC: 0.665
0:45:44.599324 INFO: Train AUC: 0.665
0:45:44.599353 INFO: AUC difference: 0.05%
0:45:44.812695 INFO: Resetting torch num_threads to 80
0:45:44.814164 PROGRESS: === Extracted 3582 precursors and 24443 fragments ===
0:45:44.814486 INFO: === FDR correction performed with classifier version 6 ===
0:45:44.814937 PROGRESS: ============================= Precursor FDR =============================
0:45:44.815022 PROGRESS: Total precursors accumulated: 410
0:45:44.815080 PROGRESS: Target precursors: 406 (99.02%)
0:45:44.815131 PROGRESS: Decoy precursors: 4 (0.98%)
0:45:44.815176 PROGRESS: 
0:45:44.815221 PROGRESS: Precursor Summary:
0:45:44.816917 PROGRESS: Channel   0:	 0.050 FDR:   406; 0.010 FDR:   406; 0.001 FDR:   362
0:45:44.817016 PROGRESS: 
0:45:44.817074 PROGRESS: Protein Summary:
0:45:44.818206 PROGRESS: Channel   0:	 0.050 FDR:   387; 0.010 FDR:   387; 0.001 FDR:   348
0:45:44.818296 PROGRESS: =========================================================================
0:45:44.818486 INFO: Target number of precursors reached.
0:45:44.822526 INFO: fragments_df: keeping 4301 of 24443 [sum(precursor_idx_mask)=9624 sum(mass_error_mask)=24443 stop_rank=4301
0:45:44.827206 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:44.951751 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:45.516916 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:45.517337 INFO: Using score_cutoff 12.524165569782257 (fac=0.99, q=1)
0:45:45.517624 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:45.517703 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:45.517756 INFO: Updating optimization_manager: score_cutoff        : 13.903972669315337 -> 12.524165569782257
0:45:45.517808 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:45.519358 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:45.521507 INFO: === checking if optimization conditions were reached ===
0:45:45.522979 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:45:45.523078 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:45:45.523146 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:45:45.523204 INFO: ==============================================
0:45:45.523266 PROGRESS: Optimization finished for ms2_error.
0:45:45.527909 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:45.529241 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:45.531402 INFO: Starting optimization step 0.
0:45:45.531500 PROGRESS: === Extracting elution groups 0 to 600 ===
0:45:45.531570 INFO: Using ng extraction backend
0:45:45.531629 PROGRESS: Extracting batch of 1194 precursors
0:45:45.534971 INFO: === Search parameters used ===
0:45:45.535074 INFO: rt_error       : 805.6004638671875
0:45:45.535139 INFO: mobility_error : 0.1
0:45:45.535192 INFO: num_candidates : 3
0:45:45.535235 INFO: ms1_error      : 30
0:45:45.535276 INFO: ms2_error      : 10.0
0:45:45.535317 INFO: fwhm_rt        : 3.0
0:45:45.535355 INFO: quant_window   : 3
0:45:45.535393 INFO: ==============================================
0:45:45.572247 INFO: performing precursor FDR with 40 features
0:45:45.572322 INFO: Decoy channel: -1
0:45:45.572347 INFO: Competetive: True
0:45:45.574891 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:45.576645 INFO: Using random state 334166 for train-test-split
0:45:45.589375 INFO: Test AUC: 0.648
0:45:45.589439 INFO: Train AUC: 0.670
0:45:45.589468 INFO: AUC difference: 3.36%
0:45:45.802402 INFO: Resetting torch num_threads to 80
0:45:45.803890 PROGRESS: === Extracted 3582 precursors and 24419 fragments ===
0:45:45.804215 INFO: === FDR correction performed with classifier version 7 ===
0:45:45.804672 PROGRESS: ============================= Precursor FDR =============================
0:45:45.804764 PROGRESS: Total precursors accumulated: 408
0:45:45.804824 PROGRESS: Target precursors: 404 (99.02%)
0:45:45.804872 PROGRESS: Decoy precursors: 4 (0.98%)
0:45:45.804916 PROGRESS: 
0:45:45.804958 PROGRESS: Precursor Summary:
0:45:45.805899 PROGRESS: Channel   0:	 0.050 FDR:   404; 0.010 FDR:   404; 0.001 FDR:   364
0:45:45.805989 PROGRESS: 
0:45:45.806043 PROGRESS: Protein Summary:
0:45:45.807167 PROGRESS: Channel   0:	 0.050 FDR:   385; 0.010 FDR:   385; 0.001 FDR:   350
0:45:45.807255 PROGRESS: =========================================================================
0:45:45.807451 INFO: Target number of precursors reached.
0:45:45.811510 INFO: fragments_df: keeping 4289 of 24419 [sum(precursor_idx_mask)=9567 sum(mass_error_mask)=24419 stop_rank=4289
0:45:45.816226 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:45.935799 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:46.496394 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:46.496804 INFO: Using score_cutoff 12.517678079509734 (fac=0.99, q=1)
0:45:46.497104 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:46.497188 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:46.497241 INFO: Updating optimization_manager: score_cutoff        : 12.524165569782257 -> 12.517678079509734
0:45:46.497293 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:46.498982 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:46.501197 INFO: === checking if optimization conditions were reached ===
0:45:46.501295 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:45:46.502759 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 132.0739447173305
0:45:46.502857 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 132.0739.
0:45:46.502920 INFO: ==============================================
0:45:46.502986 INFO: Starting optimization step 1.
0:45:46.503041 PROGRESS: === Extracting elution groups 0 to 600 ===
0:45:46.503110 INFO: Using ng extraction backend
0:45:46.503163 PROGRESS: Extracting batch of 1194 precursors
0:45:46.506392 INFO: === Search parameters used ===
0:45:46.506480 INFO: rt_error       : 132.0739447173305
0:45:46.506532 INFO: mobility_error : 0.1
0:45:46.506576 INFO: num_candidates : 3
0:45:46.506620 INFO: ms1_error      : 30
0:45:46.506659 INFO: ms2_error      : 10.0
0:45:46.506699 INFO: fwhm_rt        : 3.0
0:45:46.506742 INFO: quant_window   : 3
0:45:46.506781 INFO: ==============================================
0:45:46.542535 INFO: performing precursor FDR with 40 features
0:45:46.542646 INFO: Decoy channel: -1
0:45:46.542673 INFO: Competetive: True
0:45:46.545160 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:46.546861 INFO: Using random state 334166 for train-test-split
0:45:46.558696 INFO: Test AUC: 0.690
0:45:46.558756 INFO: Train AUC: 0.701
0:45:46.558786 INFO: AUC difference: 1.58%
0:45:46.771007 INFO: Resetting torch num_threads to 80
0:45:46.772433 PROGRESS: === Extracted 3578 precursors and 23104 fragments ===
0:45:46.772758 INFO: === FDR correction performed with classifier version 7 ===
0:45:46.773247 PROGRESS: ============================= Precursor FDR =============================
0:45:46.773338 PROGRESS: Total precursors accumulated: 416
0:45:46.773396 PROGRESS: Target precursors: 412 (99.04%)
0:45:46.773446 PROGRESS: Decoy precursors: 4 (0.96%)
0:45:46.773492 PROGRESS: 
0:45:46.773535 PROGRESS: Precursor Summary:
0:45:46.774461 PROGRESS: Channel   0:	 0.050 FDR:   412; 0.010 FDR:   412; 0.001 FDR:   389
0:45:46.774550 PROGRESS: 
0:45:46.774603 PROGRESS: Protein Summary:
0:45:46.775724 PROGRESS: Channel   0:	 0.050 FDR:   392; 0.010 FDR:   392; 0.001 FDR:   371
0:45:46.775815 PROGRESS: =========================================================================
0:45:46.776003 INFO: Target number of precursors reached.
0:45:46.779933 INFO: fragments_df: keeping 4258 of 23104 [sum(precursor_idx_mask)=9501 sum(mass_error_mask)=23104 stop_rank=4258
0:45:46.784623 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:46.914079 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:47.471055 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:47.471466 INFO: Using score_cutoff 12.832972737121581 (fac=0.99, q=1)
0:45:47.471748 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:47.471829 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:47.471882 INFO: Updating optimization_manager: score_cutoff        : 12.517678079509734 -> 12.832972737121581
0:45:47.471941 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:47.473498 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:47.475606 INFO: === checking if optimization conditions were reached ===
0:45:47.475703 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:45:47.477271 INFO: Updating optimization_manager: rt_error            : 132.0739447173305 -> 39.61184781385519
0:45:47.477373 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 39.6118.
0:45:47.477437 INFO: ==============================================
0:45:47.477504 INFO: Starting optimization step 2.
0:45:47.477562 PROGRESS: === Extracting elution groups 0 to 600 ===
0:45:47.477622 INFO: Using ng extraction backend
0:45:47.477677 PROGRESS: Extracting batch of 1194 precursors
0:45:47.480986 INFO: === Search parameters used ===
0:45:47.481082 INFO: rt_error       : 39.61184781385519
0:45:47.481133 INFO: mobility_error : 0.1
0:45:47.481179 INFO: num_candidates : 3
0:45:47.481221 INFO: ms1_error      : 30
0:45:47.481264 INFO: ms2_error      : 10.0
0:45:47.481305 INFO: fwhm_rt        : 3.0
0:45:47.481346 INFO: quant_window   : 3
0:45:47.481384 INFO: ==============================================
0:45:47.511918 INFO: performing precursor FDR with 40 features
0:45:47.511991 INFO: Decoy channel: -1
0:45:47.512016 INFO: Competetive: True
0:45:47.515111 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:47.516775 INFO: Using random state 334166 for train-test-split
0:45:47.528729 INFO: Test AUC: 0.728
0:45:47.528793 INFO: Train AUC: 0.710
0:45:47.528822 INFO: AUC difference: 2.48%
0:45:47.745236 INFO: Resetting torch num_threads to 80
0:45:47.746701 PROGRESS: === Extracted 3301 precursors and 19461 fragments ===
0:45:47.747029 INFO: === FDR correction performed with classifier version 7 ===
0:45:47.747491 PROGRESS: ============================= Precursor FDR =============================
0:45:47.747578 PROGRESS: Total precursors accumulated: 462
0:45:47.747634 PROGRESS: Target precursors: 458 (99.13%)
0:45:47.747684 PROGRESS: Decoy precursors: 4 (0.87%)
0:45:47.747727 PROGRESS: 
0:45:47.747769 PROGRESS: Precursor Summary:
0:45:47.748715 PROGRESS: Channel   0:	 0.050 FDR:   458; 0.010 FDR:   458; 0.001 FDR:   386
0:45:47.748805 PROGRESS: 
0:45:47.748858 PROGRESS: Protein Summary:
0:45:47.750008 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   433; 0.001 FDR:   368
0:45:47.750101 PROGRESS: =========================================================================
0:45:47.750291 INFO: Target number of precursors reached.
0:45:47.753944 INFO: fragments_df: keeping 4144 of 19461 [sum(precursor_idx_mask)=8947 sum(mass_error_mask)=19461 stop_rank=4144
0:45:47.758637 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:47.886521 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:48.427754 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:48.428165 INFO: Using score_cutoff 11.664232378864288 (fac=0.99, q=1)
0:45:48.428450 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:48.428541 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:48.428599 INFO: Updating optimization_manager: score_cutoff        : 12.832972737121581 -> 11.664232378864288
0:45:48.428653 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:48.430197 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:48.432316 INFO: === checking if optimization conditions were reached ===
0:45:48.432413 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:45:48.434086 INFO: Updating optimization_manager: rt_error            : 39.61184781385519 -> 20.084021900431107
0:45:48.434188 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 20.0840.
0:45:48.434252 INFO: ==============================================
0:45:48.434316 INFO: Starting optimization step 3.
0:45:48.434375 PROGRESS: === Extracting elution groups 0 to 600 ===
0:45:48.434433 INFO: Using ng extraction backend
0:45:48.434485 PROGRESS: Extracting batch of 1194 precursors
0:45:48.437765 INFO: === Search parameters used ===
0:45:48.437852 INFO: rt_error       : 20.084021900431107
0:45:48.437902 INFO: mobility_error : 0.1
0:45:48.437948 INFO: num_candidates : 3
0:45:48.437987 INFO: ms1_error      : 30
0:45:48.438027 INFO: ms2_error      : 10.0
0:45:48.438067 INFO: fwhm_rt        : 3.0
0:45:48.438113 INFO: quant_window   : 3
0:45:48.438154 INFO: ==============================================
0:45:48.469970 INFO: performing precursor FDR with 40 features
0:45:48.470053 INFO: Decoy channel: -1
0:45:48.470077 INFO: Competetive: True
0:45:48.472535 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:48.474188 INFO: Using random state 334166 for train-test-split
0:45:48.486320 INFO: Test AUC: 0.696
0:45:48.486381 INFO: Train AUC: 0.719
0:45:48.486410 INFO: AUC difference: 3.30%
0:45:48.700607 INFO: Resetting torch num_threads to 80
0:45:48.702083 PROGRESS: === Extracted 3307 precursors and 19539 fragments ===
0:45:48.702412 INFO: === FDR correction performed with classifier version 7 ===
0:45:48.702867 PROGRESS: ============================= Precursor FDR =============================
0:45:48.702954 PROGRESS: Total precursors accumulated: 462
0:45:48.703012 PROGRESS: Target precursors: 458 (99.13%)
0:45:48.703069 PROGRESS: Decoy precursors: 4 (0.87%)
0:45:48.703115 PROGRESS: 
0:45:48.703158 PROGRESS: Precursor Summary:
0:45:48.704091 PROGRESS: Channel   0:	 0.050 FDR:   458; 0.010 FDR:   458; 0.001 FDR:   387
0:45:48.704179 PROGRESS: 
0:45:48.704234 PROGRESS: Protein Summary:
0:45:48.705388 PROGRESS: Channel   0:	 0.050 FDR:   433; 0.010 FDR:   433; 0.001 FDR:   369
0:45:48.705482 PROGRESS: =========================================================================
0:45:48.705669 INFO: Target number of precursors reached.
0:45:48.709242 INFO: fragments_df: keeping 4157 of 19539 [sum(precursor_idx_mask)=8979 sum(mass_error_mask)=19539 stop_rank=4157
0:45:48.713921 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:48.840664 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:49.382589 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:49.383002 INFO: Using score_cutoff 11.664232378864288 (fac=0.99, q=1)
0:45:49.383297 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:49.383378 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:49.383432 INFO: Updating optimization_manager: score_cutoff        : 11.664232378864288 -> 11.664232378864288
0:45:49.383487 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:49.385025 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:49.387213 INFO: === checking if optimization conditions were reached ===
0:45:49.387312 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:45:49.388967 INFO: Updating optimization_manager: rt_error            : 20.084021900431107 -> 20.08402190019506
0:45:49.389083 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 20.0840.
0:45:49.389146 INFO: ==============================================
0:45:49.389213 INFO: Starting optimization step 4.
0:45:49.389273 PROGRESS: === Extracting elution groups 0 to 600 ===
0:45:49.389332 INFO: Using ng extraction backend
0:45:49.389388 PROGRESS: Extracting batch of 1194 precursors
0:45:49.392639 INFO: === Search parameters used ===
0:45:49.392725 INFO: rt_error       : 20.08402190019506
0:45:49.392775 INFO: mobility_error : 0.1
0:45:49.392819 INFO: num_candidates : 3
0:45:49.392863 INFO: ms1_error      : 30
0:45:49.392914 INFO: ms2_error      : 10.0
0:45:49.392956 INFO: fwhm_rt        : 3.0
0:45:49.393006 INFO: quant_window   : 3
0:45:49.393047 INFO: ==============================================
0:45:49.425424 INFO: performing precursor FDR with 40 features
0:45:49.425502 INFO: Decoy channel: -1
0:45:49.425527 INFO: Competetive: True
0:45:49.427955 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:49.429625 INFO: Using random state 334166 for train-test-split
0:45:49.441854 INFO: Test AUC: 0.744
0:45:49.441916 INFO: Train AUC: 0.706
0:45:49.441945 INFO: AUC difference: 5.36%
0:45:49.441967 WARNING: AUC difference > 5%. This may indicate overfitting.
0:45:49.659218 INFO: Resetting torch num_threads to 80
0:45:49.660688 PROGRESS: === Extracted 3309 precursors and 19543 fragments ===
0:45:49.661028 INFO: === FDR correction performed with classifier version 7 ===
0:45:49.661492 PROGRESS: ============================= Precursor FDR =============================
0:45:49.661579 PROGRESS: Total precursors accumulated: 463
0:45:49.661636 PROGRESS: Target precursors: 459 (99.14%)
0:45:49.661684 PROGRESS: Decoy precursors: 4 (0.86%)
0:45:49.661728 PROGRESS: 
0:45:49.661771 PROGRESS: Precursor Summary:
0:45:49.662704 PROGRESS: Channel   0:	 0.050 FDR:   459; 0.010 FDR:   459; 0.001 FDR:   386
0:45:49.662792 PROGRESS: 
0:45:49.662846 PROGRESS: Protein Summary:
0:45:49.663988 PROGRESS: Channel   0:	 0.050 FDR:   434; 0.010 FDR:   434; 0.001 FDR:   368
0:45:49.664078 PROGRESS: =========================================================================
0:45:49.664267 INFO: Target number of precursors reached.
0:45:49.667895 INFO: fragments_df: keeping 4168 of 19543 [sum(precursor_idx_mask)=9002 sum(mass_error_mask)=19543 stop_rank=4168
0:45:49.672588 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:49.799433 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:50.346410 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:50.346825 INFO: Using score_cutoff 11.670151772117613 (fac=0.99, q=1)
0:45:50.347116 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:50.347201 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:50.347261 INFO: Updating optimization_manager: score_cutoff        : 11.664232378864288 -> 11.670151772117613
0:45:50.347319 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:50.348859 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:50.351080 INFO: === checking if optimization conditions were reached ===
0:45:50.351183 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:45:50.352048 INFO: Updating optimization_manager: rt_error            : 20.08402190019506 -> 20.08402190019506
0:45:50.352176 INFO: Updating optimization_manager: classifier_version  : 7 -> 12
0:45:50.352276 INFO: Updating optimization_manager: score_cutoff        : 11.670151772117613 -> 11.670151772117613
0:45:50.352370 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:50.352458 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:50.352549 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 20.0840 found after 5 searches.
0:45:50.352613 INFO: ==============================================
0:45:50.352684 PROGRESS: Optimization finished for rt_error.
0:45:50.357209 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:50.358581 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:50.386390 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:45:50.386534 PROGRESS: ==============================================
0:45:50.386606 PROGRESS: ms2_error      : 10.0000
0:45:50.386667 PROGRESS: rt_error       : 20.0840
0:45:50.386721 PROGRESS: ==============================================
0:45:50.387116 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:50.514570 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:50.857439 INFO: Using ng extraction backend
0:45:50.857687 PROGRESS: Extracting batch of 230645 precursors
0:45:51.222425 INFO: === Search parameters used ===
0:45:51.222646 INFO: rt_error       : 20.08402190019506
0:45:51.222701 INFO: mobility_error : 0.1
0:45:51.222749 INFO: num_candidates : 3
0:45:51.222793 INFO: ms1_error      : 30
0:45:51.222834 INFO: ms2_error      : 10.0
0:45:51.222877 INFO: fwhm_rt        : 3.0
0:45:51.222916 INFO: quant_window   : 3
0:45:51.222957 INFO: ==============================================
0:45:51.462530 INFO: Removed 304532 precursors with score below cutoff 11.670151772117613
0:45:51.780287 INFO: performing precursor FDR with 40 features
0:45:51.780398 INFO: Decoy channel: -1
0:45:51.780423 INFO: Competetive: True
0:45:51.806916 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:51.822820 WARNING: FDR calculation for 205855 target and 125326 decoy PSMs
0:45:51.822937 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
0:45:51.891623 INFO: Using random state 299906 for train-test-split
0:45:56.360155 INFO: Test AUC: 0.870
0:45:56.360271 INFO: Train AUC: 0.873
0:45:56.360301 INFO: AUC difference: 0.25%
0:45:56.674342 INFO: Resetting torch num_threads to 80
0:45:57.002562 PROGRESS: ============================= Precursor FDR =============================
0:45:57.002842 PROGRESS: Total precursors accumulated: 105,769
0:45:57.002916 PROGRESS: Target precursors: 104,722 (99.01%)
0:45:57.002974 PROGRESS: Decoy precursors: 1,047 (0.99%)
0:45:57.003028 PROGRESS: 
0:45:57.003079 PROGRESS: Precursor Summary:
0:45:57.034361 PROGRESS: Channel   0:	 0.050 FDR: 104,722; 0.010 FDR: 104,722; 0.001 FDR: 95,679
0:45:57.034649 PROGRESS: 
0:45:57.034737 PROGRESS: Protein Summary:
0:45:57.075224 PROGRESS: Channel   0:	 0.050 FDR: 9,958; 0.010 FDR: 9,958; 0.001 FDR: 9,842
0:45:57.075485 PROGRESS: =========================================================================
0:45:57.077644 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/psm.parquet
0:45:57.246760 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.parquet
0:45:57.518441 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:45:57.597476 PROGRESS: 
0:45:57.597615 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant
0:45:57.597684 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/figures
0:45:57.597828 INFO: Initializing TimingManager
0:45:57.598233 INFO: Initializing RawFileManager
0:46:09.200620 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.
0:46:09.204822 INFO: Determining DIA cycle
0:46:09.221174 INFO: Found cycle with start 0.00 min and length 300.
0:46:09.388840 INFO: RT (min)            : 0.0 - 26.9
0:46:09.388932 INFO: RT duration (sec)   : 1611.2
0:46:09.388961 INFO: RT duration (min)   : 26.9
0:46:09.388985 INFO: Cycle len (scans)   : 300
0:46:09.389014 INFO: Cycle len (sec)     : 1.65
0:46:09.389034 INFO: Number of cycles    : 977
0:46:09.389054 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:46:09.389096 INFO: Creating DIA data object took: 11.79075026512146
0:46:10.046706 INFO: Creating DIA data NG object took: 0.6574759483337402
0:46:10.080338 INFO: Initializing CalibrationManager
0:46:10.080615 INFO: Setting up calibration estimators ..
0:46:10.080679 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:46:10.080779 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
0:46:10.080870 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:46:10.080923 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:46:10.080980 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
0:46:10.081047 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:46:10.081094 INFO: Done setting up calibration estimators.
0:46:10.081279 INFO: Initializing OptimizationManager
0:46:10.081409 INFO: initial parameter: ms1_error = 30
0:46:10.081462 INFO: initial parameter: ms2_error = 30
0:46:10.081508 INFO: initial parameter: rt_error = 805.5982666015625
0:46:10.081551 INFO: initial parameter: mobility_error = 0.1
0:46:10.081594 INFO: initial parameter: num_candidates = 1
0:46:10.081634 INFO: initial parameter: fwhm_rt = 5
0:46:10.081674 INFO: initial parameter: fwhm_mobility = 0.01
0:46:10.081716 INFO: initial parameter: score_cutoff = 0
0:46:10.081757 INFO: initial parameter: classifier_version = -1
0:46:10.081831 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:46:10.082170 INFO: FDRManager: loading saved state not requested, will be initialized.
0:46:10.082206 INFO: Initializing FDRManager
0:46:10.082241 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:46:10.107324 PROGRESS: Initializing spectral library: 115,864 target precursors potentially observable (0 removed)
0:46:10.124449 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:46:10.124807 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
0:46:10.124912 PROGRESS: Starting initial search for precursors.
0:46:10.125003 INFO: Starting optimization step 0.
0:46:10.125068 PROGRESS: === Extracting elution groups 0 to 200 ===
0:46:10.125134 INFO: Using ng extraction backend
0:46:10.125203 PROGRESS: Extracting batch of 397 precursors
0:46:10.127216 INFO: === Search parameters used ===
0:46:10.127306 INFO: rt_error       : 805.5982666015625
0:46:10.127355 INFO: mobility_error : 0.1
0:46:10.127400 INFO: num_candidates : 1
0:46:10.127443 INFO: ms1_error      : 30
0:46:10.127483 INFO: ms2_error      : 30
0:46:10.127523 INFO: fwhm_rt        : 5
0:46:10.127563 INFO: quant_window   : 3
0:46:10.127601 INFO: ==============================================
0:46:10.144977 INFO: performing precursor FDR with 40 features
0:46:10.145091 INFO: Decoy channel: -1
0:46:10.145118 INFO: Competetive: True
0:46:10.146076 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:10.148548 INFO: Using random state 962155 for train-test-split
0:46:10.156133 INFO: Test AUC: 0.581
0:46:10.156188 INFO: Train AUC: 0.566
0:46:10.156220 INFO: AUC difference: 2.56%
0:46:10.369304 INFO: Resetting torch num_threads to 80
0:46:10.370603 PROGRESS: === Extracted 397 precursors and 2773 fragments ===
0:46:10.370938 INFO: === FDR correction performed with classifier version -1 ===
0:46:10.371377 PROGRESS: ============================= Precursor FDR =============================
0:46:10.371462 PROGRESS: Total precursors accumulated: 0
0:46:10.371523 PROGRESS: Target precursors: 0 (0.00%)
0:46:10.371575 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:10.371620 PROGRESS: 
0:46:10.371664 PROGRESS: Precursor Summary:
0:46:10.371773 PROGRESS: 
0:46:10.371833 PROGRESS: Protein Summary:
0:46:10.371905 PROGRESS: =========================================================================
0:46:10.372070 INFO: Target number of precursors not reached yet.
0:46:10.375697 INFO: Starting optimization step 1.
0:46:10.375805 PROGRESS: === Extracting elution groups 200 to 600 ===
0:46:10.375878 INFO: Using ng extraction backend
0:46:10.375936 PROGRESS: Extracting batch of 797 precursors
0:46:10.378481 INFO: === Search parameters used ===
0:46:10.378567 INFO: rt_error       : 805.5982666015625
0:46:10.378616 INFO: mobility_error : 0.1
0:46:10.378661 INFO: num_candidates : 1
0:46:10.378707 INFO: ms1_error      : 30
0:46:10.378748 INFO: ms2_error      : 30
0:46:10.378790 INFO: fwhm_rt        : 5
0:46:10.378829 INFO: quant_window   : 3
0:46:10.378869 INFO: ==============================================
0:46:10.401104 INFO: performing precursor FDR with 40 features
0:46:10.401175 INFO: Decoy channel: -1
0:46:10.401202 INFO: Competetive: True
0:46:10.403921 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:10.405431 INFO: Using random state 127409 for train-test-split
0:46:10.413715 INFO: Test AUC: 0.573
0:46:10.413770 INFO: Train AUC: 0.601
0:46:10.413799 INFO: AUC difference: 4.63%
0:46:10.628083 INFO: Resetting torch num_threads to 80
0:46:10.630040 PROGRESS: === Extracted 1190 precursors and 8296 fragments ===
0:46:10.630373 INFO: === FDR correction performed with classifier version -1 ===
0:46:10.630799 PROGRESS: ============================= Precursor FDR =============================
0:46:10.630885 PROGRESS: Total precursors accumulated: 0
0:46:10.630942 PROGRESS: Target precursors: 0 (0.00%)
0:46:10.630992 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:10.631037 PROGRESS: 
0:46:10.631082 PROGRESS: Precursor Summary:
0:46:10.631186 PROGRESS: 
0:46:10.631246 PROGRESS: Protein Summary:
0:46:10.631329 PROGRESS: =========================================================================
0:46:10.631519 INFO: Target number of precursors not reached yet.
0:46:10.636002 INFO: Starting optimization step 2.
0:46:10.636106 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:46:10.636178 INFO: Using ng extraction backend
0:46:10.636246 PROGRESS: Extracting batch of 1593 precursors
0:46:10.640259 INFO: === Search parameters used ===
0:46:10.640348 INFO: rt_error       : 805.5982666015625
0:46:10.640398 INFO: mobility_error : 0.1
0:46:10.640442 INFO: num_candidates : 1
0:46:10.640486 INFO: ms1_error      : 30
0:46:10.640526 INFO: ms2_error      : 30
0:46:10.640568 INFO: fwhm_rt        : 5
0:46:10.640608 INFO: quant_window   : 3
0:46:10.640646 INFO: ==============================================
0:46:10.671115 INFO: performing precursor FDR with 40 features
0:46:10.671189 INFO: Decoy channel: -1
0:46:10.671215 INFO: Competetive: True
0:46:10.674226 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:10.675879 INFO: Using random state 13626 for train-test-split
0:46:10.687644 INFO: Test AUC: 0.595
0:46:10.687705 INFO: Train AUC: 0.592
0:46:10.687735 INFO: AUC difference: 0.50%
0:46:10.904545 INFO: Resetting torch num_threads to 80
0:46:10.906855 PROGRESS: === Extracted 2783 precursors and 19658 fragments ===
0:46:10.907192 INFO: === FDR correction performed with classifier version -1 ===
0:46:10.907626 PROGRESS: ============================= Precursor FDR =============================
0:46:10.907712 PROGRESS: Total precursors accumulated: 0
0:46:10.907769 PROGRESS: Target precursors: 0 (0.00%)
0:46:10.907818 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:10.907862 PROGRESS: 
0:46:10.907912 PROGRESS: Precursor Summary:
0:46:10.908020 PROGRESS: 
0:46:10.908082 PROGRESS: Protein Summary:
0:46:10.908155 PROGRESS: =========================================================================
0:46:10.908353 INFO: Target number of precursors not reached yet.
0:46:10.914621 INFO: Starting optimization step 3.
0:46:10.914728 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:46:10.914800 INFO: Using ng extraction backend
0:46:10.914859 PROGRESS: Extracting batch of 3185 precursors
0:46:10.921775 INFO: === Search parameters used ===
0:46:10.921874 INFO: rt_error       : 805.5982666015625
0:46:10.921926 INFO: mobility_error : 0.1
0:46:10.921972 INFO: num_candidates : 1
0:46:10.922014 INFO: ms1_error      : 30
0:46:10.922054 INFO: ms2_error      : 30
0:46:10.922095 INFO: fwhm_rt        : 5
0:46:10.922140 INFO: quant_window   : 3
0:46:10.922179 INFO: ==============================================
0:46:10.967713 INFO: performing precursor FDR with 40 features
0:46:10.967803 INFO: Decoy channel: -1
0:46:10.967829 INFO: Competetive: True
0:46:10.972216 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:10.974321 INFO: Using random state 646405 for train-test-split
0:46:10.993351 INFO: Test AUC: 0.586
0:46:10.993419 INFO: Train AUC: 0.585
0:46:10.993448 INFO: AUC difference: 0.25%
0:46:11.213977 INFO: Resetting torch num_threads to 80
0:46:11.217055 PROGRESS: === Extracted 5963 precursors and 41892 fragments ===
0:46:11.217411 INFO: === FDR correction performed with classifier version -1 ===
0:46:11.217835 PROGRESS: ============================= Precursor FDR =============================
0:46:11.217920 PROGRESS: Total precursors accumulated: 0
0:46:11.217985 PROGRESS: Target precursors: 0 (0.00%)
0:46:11.218036 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:11.218081 PROGRESS: 
0:46:11.218123 PROGRESS: Precursor Summary:
0:46:11.218227 PROGRESS: 
0:46:11.218287 PROGRESS: Protein Summary:
0:46:11.218358 PROGRESS: =========================================================================
0:46:11.218587 INFO: Target number of precursors not reached yet.
0:46:11.227885 INFO: Starting optimization step 4.
0:46:11.228005 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:46:11.228079 INFO: Using ng extraction backend
0:46:11.228148 PROGRESS: Extracting batch of 6366 precursors
0:46:11.239796 INFO: === Search parameters used ===
0:46:11.239913 INFO: rt_error       : 805.5982666015625
0:46:11.239962 INFO: mobility_error : 0.1
0:46:11.240006 INFO: num_candidates : 1
0:46:11.240049 INFO: ms1_error      : 30
0:46:11.240088 INFO: ms2_error      : 30
0:46:11.240128 INFO: fwhm_rt        : 5
0:46:11.240166 INFO: quant_window   : 3
0:46:11.240215 INFO: ==============================================
0:46:11.312952 INFO: performing precursor FDR with 40 features
0:46:11.313066 INFO: Decoy channel: -1
0:46:11.313095 INFO: Competetive: True
0:46:11.318105 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:11.321764 INFO: Using random state 196698 for train-test-split
0:46:11.357752 INFO: Test AUC: 0.574
0:46:11.357851 INFO: Train AUC: 0.588
0:46:11.357884 INFO: AUC difference: 2.39%
0:46:11.569805 INFO: Resetting torch num_threads to 80
0:46:11.573483 PROGRESS: === Extracted 12323 precursors and 86261 fragments ===
0:46:11.573850 INFO: === FDR correction performed with classifier version -1 ===
0:46:11.574295 PROGRESS: ============================= Precursor FDR =============================
0:46:11.574386 PROGRESS: Total precursors accumulated: 0
0:46:11.574447 PROGRESS: Target precursors: 0 (0.00%)
0:46:11.574502 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:11.574553 PROGRESS: 
0:46:11.574600 PROGRESS: Precursor Summary:
0:46:11.574711 PROGRESS: 
0:46:11.574777 PROGRESS: Protein Summary:
0:46:11.574856 PROGRESS: =========================================================================
0:46:11.575119 INFO: Target number of precursors not reached yet.
0:46:11.589861 INFO: Starting optimization step 5.
0:46:11.590039 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:46:11.590121 INFO: Using ng extraction backend
0:46:11.590187 PROGRESS: Extracting batch of 12747 precursors
0:46:11.612327 INFO: === Search parameters used ===
0:46:11.612476 INFO: rt_error       : 805.5982666015625
0:46:11.612532 INFO: mobility_error : 0.1
0:46:11.612583 INFO: num_candidates : 1
0:46:11.612630 INFO: ms1_error      : 30
0:46:11.612674 INFO: ms2_error      : 30
0:46:11.612718 INFO: fwhm_rt        : 5
0:46:11.612773 INFO: quant_window   : 3
0:46:11.612820 INFO: ==============================================
0:46:11.740083 INFO: performing precursor FDR with 40 features
0:46:11.740204 INFO: Decoy channel: -1
0:46:11.740232 INFO: Competetive: True
0:46:11.749141 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:11.754405 INFO: Using random state 349597 for train-test-split
0:46:12.094398 INFO: Test AUC: 0.809
0:46:12.094520 INFO: Train AUC: 0.808
0:46:12.094553 INFO: AUC difference: 0.16%
0:46:12.320825 INFO: Resetting torch num_threads to 80
0:46:12.326915 PROGRESS: === Extracted 25057 precursors and 176595 fragments ===
0:46:12.327318 INFO: === FDR correction performed with classifier version -1 ===
0:46:12.328259 PROGRESS: ============================= Precursor FDR =============================
0:46:12.328363 PROGRESS: Total precursors accumulated: 4,541
0:46:12.328427 PROGRESS: Target precursors: 4,497 (99.03%)
0:46:12.328481 PROGRESS: Decoy precursors: 44 (0.97%)
0:46:12.328535 PROGRESS: 
0:46:12.328583 PROGRESS: Precursor Summary:
0:46:12.330517 PROGRESS: Channel   0:	 0.050 FDR: 4,497; 0.010 FDR: 4,497; 0.001 FDR: 2,100
0:46:12.330619 PROGRESS: 
0:46:12.330680 PROGRESS: Protein Summary:
0:46:12.333396 PROGRESS: Channel   0:	 0.050 FDR: 2,705; 0.010 FDR: 2,705; 0.001 FDR: 1,412
0:46:12.333501 PROGRESS: =========================================================================
0:46:12.333875 INFO: Target number of precursors reached.
0:46:12.360968 INFO: fragments_df: keeping 5000 of 176595 [sum(precursor_idx_mask)=49355 sum(mass_error_mask)=176595 stop_rank=5000
0:46:12.366937 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:12.972226 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:13.645295 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:46:13.645777 INFO: Using score_cutoff 13.872041530609131 (fac=0.99, q=1)
0:46:13.646111 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:46:13.646196 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:46:13.646256 INFO: Updating optimization_manager: score_cutoff        : 0 -> 13.872041530609131
0:46:13.646317 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:13.647867 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:13.649911 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
0:46:13.650009 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:46:13.650093 INFO: Starting optimization step 6.
0:46:13.650162 PROGRESS: === Extracting elution groups 0 to 600 ===
0:46:13.650231 INFO: Using ng extraction backend
0:46:13.650292 PROGRESS: Extracting batch of 1194 precursors
0:46:13.653588 INFO: === Search parameters used ===
0:46:13.653684 INFO: rt_error       : 805.5982666015625
0:46:13.653742 INFO: mobility_error : 0.1
0:46:13.653791 INFO: num_candidates : 3
0:46:13.653839 INFO: ms1_error      : 30
0:46:13.653884 INFO: ms2_error      : 30
0:46:13.653930 INFO: fwhm_rt        : 3.0
0:46:13.653976 INFO: quant_window   : 3
0:46:13.654019 INFO: ==============================================
0:46:13.702557 INFO: performing precursor FDR with 40 features
0:46:13.702646 INFO: Decoy channel: -1
0:46:13.702674 INFO: Competetive: True
0:46:13.705307 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:13.707095 INFO: Using random state 501489 for train-test-split
0:46:13.718150 INFO: Test AUC: 0.670
0:46:13.718221 INFO: Train AUC: 0.636
0:46:13.718254 INFO: AUC difference: 5.41%
0:46:13.718282 WARNING: AUC difference > 5%. This may indicate overfitting.
0:46:13.928964 INFO: Resetting torch num_threads to 80
0:46:13.930461 PROGRESS: === Extracted 3574 precursors and 21799 fragments ===
0:46:13.930791 INFO: === FDR correction performed with classifier version 5 ===
0:46:13.931232 PROGRESS: ============================= Precursor FDR =============================
0:46:13.931319 PROGRESS: Total precursors accumulated: 116
0:46:13.931383 PROGRESS: Target precursors: 115 (99.14%)
0:46:13.931438 PROGRESS: Decoy precursors: 1 (0.86%)
0:46:13.931490 PROGRESS: 
0:46:13.931537 PROGRESS: Precursor Summary:
0:46:13.932405 PROGRESS: Channel   0:	 0.050 FDR:   115; 0.010 FDR:   115; 0.001 FDR:   102
0:46:13.932496 PROGRESS: 
0:46:13.932558 PROGRESS: Protein Summary:
0:46:13.933555 PROGRESS: Channel   0:	 0.050 FDR:   111; 0.010 FDR:   111; 0.001 FDR:    99
0:46:13.933650 PROGRESS: =========================================================================
0:46:13.934011 INFO: Target number of precursors not reached yet.
0:46:13.938498 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:13.940131 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:13.942699 INFO: === skipping optimization until target number of precursors are found ===
0:46:13.942818 INFO: Starting optimization step 7.
0:46:13.942889 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:46:13.942958 INFO: Using ng extraction backend
0:46:13.943029 PROGRESS: Extracting batch of 1593 precursors
0:46:13.947189 INFO: === Search parameters used ===
0:46:13.947283 INFO: rt_error       : 805.5982666015625
0:46:13.947338 INFO: mobility_error : 0.1
0:46:13.947388 INFO: num_candidates : 3
0:46:13.947434 INFO: ms1_error      : 30
0:46:13.947479 INFO: ms2_error      : 30
0:46:13.947525 INFO: fwhm_rt        : 3.0
0:46:13.947567 INFO: quant_window   : 3
0:46:13.947609 INFO: ==============================================
0:46:13.992332 INFO: performing precursor FDR with 40 features
0:46:13.992425 INFO: Decoy channel: -1
0:46:13.992453 INFO: Competetive: True
0:46:13.996650 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:13.999113 INFO: Using random state 501489 for train-test-split
0:46:14.019383 INFO: Test AUC: 0.641
0:46:14.019469 INFO: Train AUC: 0.657
0:46:14.019503 INFO: AUC difference: 2.33%
0:46:15.866582 INFO: Resetting torch num_threads to 80
0:46:15.869599 PROGRESS: === Extracted 8347 precursors and 51067 fragments ===
0:46:15.869945 INFO: === FDR correction performed with classifier version 5 ===
0:46:15.870435 PROGRESS: ============================= Precursor FDR =============================
0:46:15.870525 PROGRESS: Total precursors accumulated: 372
0:46:15.870583 PROGRESS: Target precursors: 369 (99.19%)
0:46:15.870644 PROGRESS: Decoy precursors: 3 (0.81%)
0:46:15.870691 PROGRESS: 
0:46:15.870735 PROGRESS: Precursor Summary:
0:46:15.871707 PROGRESS: Channel   0:	 0.050 FDR:   369; 0.010 FDR:   369; 0.001 FDR:   272
0:46:15.871801 PROGRESS: 
0:46:15.871855 PROGRESS: Protein Summary:
0:46:15.873012 PROGRESS: Channel   0:	 0.050 FDR:   339; 0.010 FDR:   339; 0.001 FDR:   252
0:46:15.873112 PROGRESS: =========================================================================
0:46:15.873347 INFO: Target number of precursors reached.
0:46:15.879469 INFO: fragments_df: keeping 4685 of 51067 [sum(precursor_idx_mask)=8815 sum(mass_error_mask)=51067 stop_rank=4685
0:46:15.886653 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:16.010416 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:16.637606 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:16.638029 INFO: Using score_cutoff 15.94247903366089 (fac=0.99, q=1)
0:46:16.638317 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:16.638399 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:16.638453 INFO: Updating optimization_manager: score_cutoff        : 13.872041530609131 -> 15.94247903366089
0:46:16.638506 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:16.640863 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:16.645041 INFO: === checking if optimization conditions were reached ===
0:46:16.646654 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:46:16.646755 INFO: Updating optimization_manager: classifier_version  : 5 -> 7
0:46:16.646819 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:46:16.646876 INFO: ==============================================
0:46:16.646938 INFO: Starting optimization step 8.
0:46:16.646994 PROGRESS: === Extracting elution groups 0 to 1400 ===
0:46:16.647061 INFO: Using ng extraction backend
0:46:16.647118 PROGRESS: Extracting batch of 2787 precursors
0:46:23.144972 INFO: === Search parameters used ===
0:46:23.145122 INFO: rt_error       : 805.5982666015625
0:46:23.145180 INFO: mobility_error : 0.1
0:46:23.145232 INFO: num_candidates : 3
0:46:23.145279 INFO: ms1_error      : 30
0:46:23.145327 INFO: ms2_error      : 10.0
0:46:23.145374 INFO: fwhm_rt        : 3.0
0:46:23.145418 INFO: quant_window   : 3
0:46:23.145459 INFO: ==============================================
0:46:23.212336 INFO: performing precursor FDR with 40 features
0:46:23.212445 INFO: Decoy channel: -1
0:46:23.212470 INFO: Competetive: True
0:46:23.215727 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:23.218354 INFO: Using random state 511215 for train-test-split
0:46:23.239816 INFO: Test AUC: 0.648
0:46:23.239898 INFO: Train AUC: 0.683
0:46:23.239928 INFO: AUC difference: 5.20%
0:46:23.239950 WARNING: AUC difference > 5%. This may indicate overfitting.
0:46:23.508628 INFO: Resetting torch num_threads to 80
0:46:23.510619 PROGRESS: === Extracted 8360 precursors and 57232 fragments ===
0:46:23.510985 INFO: === FDR correction performed with classifier version 7 ===
0:46:23.511550 PROGRESS: ============================= Precursor FDR =============================
0:46:23.511641 PROGRESS: Total precursors accumulated: 952
0:46:23.511699 PROGRESS: Target precursors: 943 (99.05%)
0:46:23.511749 PROGRESS: Decoy precursors: 9 (0.95%)
0:46:23.511795 PROGRESS: 
0:46:23.511839 PROGRESS: Precursor Summary:
0:46:23.512964 PROGRESS: Channel   0:	 0.050 FDR:   943; 0.010 FDR:   943; 0.001 FDR:   652
0:46:23.513072 PROGRESS: 
0:46:23.513125 PROGRESS: Protein Summary:
0:46:23.514553 PROGRESS: Channel   0:	 0.050 FDR:   834; 0.010 FDR:   834; 0.001 FDR:   585
0:46:23.514644 PROGRESS: =========================================================================
0:46:23.514952 INFO: Target number of precursors reached.
0:46:23.523520 INFO: fragments_df: keeping 5000 of 57232 [sum(precursor_idx_mask)=22569 sum(mass_error_mask)=57232 stop_rank=5000
0:46:23.528605 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:23.784022 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:24.577402 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:24.577871 INFO: Using score_cutoff 12.512364765930176 (fac=0.99, q=1)
0:46:24.578202 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:24.578290 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:24.578350 INFO: Updating optimization_manager: score_cutoff        : 15.94247903366089 -> 12.512364765930176
0:46:24.578412 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:24.580149 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:24.582599 INFO: === checking if optimization conditions were reached ===
0:46:24.584474 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:46:24.584584 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:46:24.584654 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:46:24.584719 INFO: ==============================================
0:46:24.584795 PROGRESS: Optimization finished for ms2_error.
0:46:24.590098 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:24.591408 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:24.593516 INFO: Starting optimization step 0.
0:46:24.593615 PROGRESS: === Extracting elution groups 0 to 600 ===
0:46:24.593686 INFO: Using ng extraction backend
0:46:24.593742 PROGRESS: Extracting batch of 1194 precursors
0:46:24.597136 INFO: === Search parameters used ===
0:46:24.597235 INFO: rt_error       : 805.5982666015625
0:46:24.597286 INFO: mobility_error : 0.1
0:46:24.597332 INFO: num_candidates : 3
0:46:24.597373 INFO: ms1_error      : 30
0:46:24.597413 INFO: ms2_error      : 10.0
0:46:24.597452 INFO: fwhm_rt        : 3.0
0:46:24.597493 INFO: quant_window   : 3
0:46:24.597531 INFO: ==============================================
0:46:24.743389 INFO: performing precursor FDR with 40 features
0:46:24.743485 INFO: Decoy channel: -1
0:46:24.743511 INFO: Competetive: True
0:46:24.748444 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:24.750331 INFO: Using random state 639339 for train-test-split
0:46:24.761375 INFO: Test AUC: 0.691
0:46:24.761442 INFO: Train AUC: 0.665
0:46:24.761470 INFO: AUC difference: 3.97%
0:46:24.973331 INFO: Resetting torch num_threads to 80
0:46:24.974878 PROGRESS: === Extracted 3581 precursors and 24617 fragments ===
0:46:24.975217 INFO: === FDR correction performed with classifier version 8 ===
0:46:24.975684 PROGRESS: ============================= Precursor FDR =============================
0:46:24.975769 PROGRESS: Total precursors accumulated: 390
0:46:24.975825 PROGRESS: Target precursors: 387 (99.23%)
0:46:24.975873 PROGRESS: Decoy precursors: 3 (0.77%)
0:46:24.975924 PROGRESS: 
0:46:24.975969 PROGRESS: Precursor Summary:
0:46:24.976962 PROGRESS: Channel   0:	 0.050 FDR:   387; 0.010 FDR:   387; 0.001 FDR:   263
0:46:24.977061 PROGRESS: 
0:46:24.977115 PROGRESS: Protein Summary:
0:46:24.978267 PROGRESS: Channel   0:	 0.050 FDR:   367; 0.010 FDR:   367; 0.001 FDR:   252
0:46:24.978357 PROGRESS: =========================================================================
0:46:24.978592 INFO: Target number of precursors reached.
0:46:24.982747 INFO: fragments_df: keeping 4066 of 24617 [sum(precursor_idx_mask)=9262 sum(mass_error_mask)=24617 stop_rank=4066
0:46:24.987576 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:25.121103 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:25.654640 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:25.655050 INFO: Using score_cutoff 12.505400372886657 (fac=0.99, q=1)
0:46:25.655347 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:25.655424 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:25.655478 INFO: Updating optimization_manager: score_cutoff        : 12.512364765930176 -> 12.505400372886657
0:46:25.655539 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:25.657116 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:25.659330 INFO: === checking if optimization conditions were reached ===
0:46:25.659431 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:46:25.660945 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 101.64816695490399
0:46:25.661052 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 101.6482.
0:46:25.661124 INFO: ==============================================
0:46:25.661193 INFO: Starting optimization step 1.
0:46:25.661248 PROGRESS: === Extracting elution groups 0 to 600 ===
0:46:25.661305 INFO: Using ng extraction backend
0:46:25.661358 PROGRESS: Extracting batch of 1194 precursors
0:46:25.664692 INFO: === Search parameters used ===
0:46:25.664783 INFO: rt_error       : 101.64816695490399
0:46:25.664831 INFO: mobility_error : 0.1
0:46:25.664874 INFO: num_candidates : 3
0:46:25.664914 INFO: ms1_error      : 30
0:46:25.664955 INFO: ms2_error      : 10.0
0:46:25.665008 INFO: fwhm_rt        : 3.0
0:46:25.665054 INFO: quant_window   : 3
0:46:25.665092 INFO: ==============================================
0:46:25.712259 INFO: performing precursor FDR with 40 features
0:46:25.712338 INFO: Decoy channel: -1
0:46:25.712364 INFO: Competetive: True
0:46:25.714993 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:25.716840 INFO: Using random state 639339 for train-test-split
0:46:25.728263 INFO: Test AUC: 0.725
0:46:25.728324 INFO: Train AUC: 0.704
0:46:25.728354 INFO: AUC difference: 2.99%
0:46:25.940171 INFO: Resetting torch num_threads to 80
0:46:25.941620 PROGRESS: === Extracted 3577 precursors and 22676 fragments ===
0:46:25.941940 INFO: === FDR correction performed with classifier version 8 ===
0:46:25.942420 PROGRESS: ============================= Precursor FDR =============================
0:46:25.942507 PROGRESS: Total precursors accumulated: 444
0:46:25.942573 PROGRESS: Target precursors: 440 (99.10%)
0:46:25.942625 PROGRESS: Decoy precursors: 4 (0.90%)
0:46:25.942670 PROGRESS: 
0:46:25.942713 PROGRESS: Precursor Summary:
0:46:25.943681 PROGRESS: Channel   0:	 0.050 FDR:   440; 0.010 FDR:   440; 0.001 FDR:   357
0:46:25.943769 PROGRESS: 
0:46:25.943824 PROGRESS: Protein Summary:
0:46:25.945000 PROGRESS: Channel   0:	 0.050 FDR:   415; 0.010 FDR:   415; 0.001 FDR:   338
0:46:25.945091 PROGRESS: =========================================================================
0:46:25.945302 INFO: Target number of precursors reached.
0:46:25.949414 INFO: fragments_df: keeping 4351 of 22676 [sum(precursor_idx_mask)=10020 sum(mass_error_mask)=22676 stop_rank=4351
0:46:25.954200 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:26.106215 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:26.648194 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:26.648628 INFO: Using score_cutoff 11.69725616798401 (fac=0.99, q=1)
0:46:26.648931 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:26.649033 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:26.649108 INFO: Updating optimization_manager: score_cutoff        : 12.505400372886657 -> 11.69725616798401
0:46:26.649181 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:26.650777 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:26.652954 INFO: === checking if optimization conditions were reached ===
0:46:26.653079 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:46:26.654781 INFO: Updating optimization_manager: rt_error            : 101.64816695490399 -> 15.515404947712423
0:46:26.654892 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 15.5154.
0:46:26.654976 INFO: ==============================================
0:46:26.655082 INFO: Starting optimization step 2.
0:46:26.655164 PROGRESS: === Extracting elution groups 0 to 600 ===
0:46:26.655243 INFO: Using ng extraction backend
0:46:26.655317 PROGRESS: Extracting batch of 1194 precursors
0:46:26.658906 INFO: === Search parameters used ===
0:46:26.659019 INFO: rt_error       : 15.515404947712423
0:46:26.659095 INFO: mobility_error : 0.1
0:46:26.659166 INFO: num_candidates : 3
0:46:26.659228 INFO: ms1_error      : 30
0:46:26.659287 INFO: ms2_error      : 10.0
0:46:26.659347 INFO: fwhm_rt        : 3.0
0:46:26.659405 INFO: quant_window   : 3
0:46:26.659466 INFO: ==============================================
0:46:26.697824 INFO: performing precursor FDR with 40 features
0:46:26.697913 INFO: Decoy channel: -1
0:46:26.697939 INFO: Competetive: True
0:46:26.700760 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:26.702586 INFO: Using random state 639339 for train-test-split
0:46:26.715197 INFO: Test AUC: 0.737
0:46:26.715267 INFO: Train AUC: 0.718
0:46:26.715297 INFO: AUC difference: 2.67%
0:46:26.936372 INFO: Resetting torch num_threads to 80
0:46:26.937920 PROGRESS: === Extracted 3308 precursors and 19648 fragments ===
0:46:26.938256 INFO: === FDR correction performed with classifier version 8 ===
0:46:26.938734 PROGRESS: ============================= Precursor FDR =============================
0:46:26.938825 PROGRESS: Total precursors accumulated: 477
0:46:26.938886 PROGRESS: Target precursors: 473 (99.16%)
0:46:26.938937 PROGRESS: Decoy precursors: 4 (0.84%)
0:46:26.938983 PROGRESS: 
0:46:26.939026 PROGRESS: Precursor Summary:
0:46:26.940001 PROGRESS: Channel   0:	 0.050 FDR:   473; 0.010 FDR:   473; 0.001 FDR:   409
0:46:26.940088 PROGRESS: 
0:46:26.940143 PROGRESS: Protein Summary:
0:46:26.941381 PROGRESS: Channel   0:	 0.050 FDR:   444; 0.010 FDR:   444; 0.001 FDR:   388
0:46:26.941475 PROGRESS: =========================================================================
0:46:26.941693 INFO: Target number of precursors reached.
0:46:26.945604 INFO: fragments_df: keeping 4221 of 19648 [sum(precursor_idx_mask)=9459 sum(mass_error_mask)=19648 stop_rank=4221
0:46:26.950420 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:27.081026 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:27.637054 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:27.637480 INFO: Using score_cutoff 11.544943664932251 (fac=0.99, q=1)
0:46:27.637760 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:27.637839 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:27.637893 INFO: Updating optimization_manager: score_cutoff        : 11.69725616798401 -> 11.544943664932251
0:46:27.637945 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:27.639498 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:27.641673 INFO: === checking if optimization conditions were reached ===
0:46:27.641775 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:46:27.643456 INFO: Updating optimization_manager: rt_error            : 15.515404947712423 -> 9.641171035871803
0:46:27.643552 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 9.6412.
0:46:27.643617 INFO: ==============================================
0:46:27.643683 INFO: Starting optimization step 3.
0:46:27.643742 PROGRESS: === Extracting elution groups 0 to 600 ===
0:46:27.643802 INFO: Using ng extraction backend
0:46:27.643855 PROGRESS: Extracting batch of 1194 precursors
0:46:27.647255 INFO: === Search parameters used ===
0:46:27.647357 INFO: rt_error       : 9.641171035871803
0:46:27.647413 INFO: mobility_error : 0.1
0:46:27.647459 INFO: num_candidates : 3
0:46:27.647501 INFO: ms1_error      : 30
0:46:27.647541 INFO: ms2_error      : 10.0
0:46:27.647580 INFO: fwhm_rt        : 3.0
0:46:27.647618 INFO: quant_window   : 3
0:46:27.647657 INFO: ==============================================
0:46:27.682088 INFO: performing precursor FDR with 40 features
0:46:27.682184 INFO: Decoy channel: -1
0:46:27.682210 INFO: Competetive: True
0:46:27.684753 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:27.686491 INFO: Using random state 639339 for train-test-split
0:46:27.698328 INFO: Test AUC: 0.714
0:46:27.698395 INFO: Train AUC: 0.724
0:46:27.698425 INFO: AUC difference: 1.37%
0:46:27.914260 INFO: Resetting torch num_threads to 80
0:46:27.915806 PROGRESS: === Extracted 3306 precursors and 19644 fragments ===
0:46:27.916142 INFO: === FDR correction performed with classifier version 8 ===
0:46:27.916613 PROGRESS: ============================= Precursor FDR =============================
0:46:27.916697 PROGRESS: Total precursors accumulated: 477
0:46:27.916755 PROGRESS: Target precursors: 473 (99.16%)
0:46:27.916804 PROGRESS: Decoy precursors: 4 (0.84%)
0:46:27.916850 PROGRESS: 
0:46:27.916900 PROGRESS: Precursor Summary:
0:46:27.917892 PROGRESS: Channel   0:	 0.050 FDR:   473; 0.010 FDR:   473; 0.001 FDR:   409
0:46:27.917983 PROGRESS: 
0:46:27.918039 PROGRESS: Protein Summary:
0:46:27.919218 PROGRESS: Channel   0:	 0.050 FDR:   444; 0.010 FDR:   444; 0.001 FDR:   388
0:46:27.919307 PROGRESS: =========================================================================
0:46:27.919526 INFO: Target number of precursors reached.
0:46:27.923360 INFO: fragments_df: keeping 4225 of 19644 [sum(precursor_idx_mask)=9466 sum(mass_error_mask)=19644 stop_rank=4225
0:46:27.928292 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:28.063604 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:28.620063 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:28.620509 INFO: Using score_cutoff 11.544943664932251 (fac=0.99, q=1)
0:46:28.620815 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:28.620907 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:28.621192 INFO: Updating optimization_manager: score_cutoff        : 11.544943664932251 -> 11.544943664932251
0:46:28.621275 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:28.622881 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:28.625111 INFO: === checking if optimization conditions were reached ===
0:46:28.625225 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:46:28.626993 INFO: Updating optimization_manager: rt_error            : 9.641171035871803 -> 9.641171035982271
0:46:28.627105 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 9.6412.
0:46:28.627186 INFO: ==============================================
0:46:28.627270 INFO: Starting optimization step 4.
0:46:28.627344 PROGRESS: === Extracting elution groups 0 to 600 ===
0:46:28.627420 INFO: Using ng extraction backend
0:46:28.627493 PROGRESS: Extracting batch of 1194 precursors
0:46:28.630896 INFO: === Search parameters used ===
0:46:28.631006 INFO: rt_error       : 9.641171035982271
0:46:28.631080 INFO: mobility_error : 0.1
0:46:28.631151 INFO: num_candidates : 3
0:46:28.631212 INFO: ms1_error      : 30
0:46:28.631273 INFO: ms2_error      : 10.0
0:46:28.631330 INFO: fwhm_rt        : 3.0
0:46:28.631387 INFO: quant_window   : 3
0:46:28.631443 INFO: ==============================================
0:46:28.665861 INFO: performing precursor FDR with 40 features
0:46:28.665970 INFO: Decoy channel: -1
0:46:28.665996 INFO: Competetive: True
0:46:28.668644 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:28.670382 INFO: Using random state 639339 for train-test-split
0:46:28.682534 INFO: Test AUC: 0.761
0:46:28.682597 INFO: Train AUC: 0.711
0:46:28.682631 INFO: AUC difference: 6.97%
0:46:28.682653 WARNING: AUC difference > 5%. This may indicate overfitting.
0:46:28.895623 INFO: Resetting torch num_threads to 80
0:46:28.897148 PROGRESS: === Extracted 3306 precursors and 19646 fragments ===
0:46:28.897599 INFO: === FDR correction performed with classifier version 8 ===
0:46:28.898069 PROGRESS: ============================= Precursor FDR =============================
0:46:28.898164 PROGRESS: Total precursors accumulated: 477
0:46:28.898223 PROGRESS: Target precursors: 473 (99.16%)
0:46:28.898273 PROGRESS: Decoy precursors: 4 (0.84%)
0:46:28.898319 PROGRESS: 
0:46:28.898362 PROGRESS: Precursor Summary:
0:46:28.899333 PROGRESS: Channel   0:	 0.050 FDR:   473; 0.010 FDR:   473; 0.001 FDR:   409
0:46:28.899425 PROGRESS: 
0:46:28.899480 PROGRESS: Protein Summary:
0:46:28.900655 PROGRESS: Channel   0:	 0.050 FDR:   444; 0.010 FDR:   444; 0.001 FDR:   388
0:46:28.900744 PROGRESS: =========================================================================
0:46:28.900961 INFO: Target number of precursors reached.
0:46:28.904660 INFO: fragments_df: keeping 4230 of 19646 [sum(precursor_idx_mask)=9469 sum(mass_error_mask)=19646 stop_rank=4230
0:46:28.909413 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:29.038737 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:29.594158 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:29.594578 INFO: Using score_cutoff 11.544943664932251 (fac=0.99, q=1)
0:46:29.594868 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:29.594954 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:29.595011 INFO: Updating optimization_manager: score_cutoff        : 11.544943664932251 -> 11.544943664932251
0:46:29.595065 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:29.596619 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:29.598865 INFO: === checking if optimization conditions were reached ===
0:46:29.598963 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:46:29.599833 INFO: Updating optimization_manager: rt_error            : 9.641171035982271 -> 9.641171035871803
0:46:29.599955 INFO: Updating optimization_manager: classifier_version  : 8 -> 12
0:46:29.600048 INFO: Updating optimization_manager: score_cutoff        : 11.544943664932251 -> 11.544943664932251
0:46:29.600134 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:29.600218 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:29.600300 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 9.6412 found after 5 searches.
0:46:29.600360 INFO: ==============================================
0:46:29.600426 PROGRESS: Optimization finished for rt_error.
0:46:29.605000 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:29.606338 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:29.635281 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:46:29.635426 PROGRESS: ==============================================
0:46:29.635504 PROGRESS: ms2_error      : 10.0000
0:46:29.635564 PROGRESS: rt_error       : 9.6412
0:46:29.635614 PROGRESS: ==============================================
0:46:29.636023 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:29.760890 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:30.101633 INFO: Using ng extraction backend
0:46:30.101912 PROGRESS: Extracting batch of 230645 precursors
0:46:30.466868 INFO: === Search parameters used ===
0:46:30.467116 INFO: rt_error       : 9.641171035871803
0:46:30.467175 INFO: mobility_error : 0.1
0:46:30.467224 INFO: num_candidates : 3
0:46:30.467268 INFO: ms1_error      : 30
0:46:30.467311 INFO: ms2_error      : 10.0
0:46:30.467352 INFO: fwhm_rt        : 3.0
0:46:30.467393 INFO: quant_window   : 3
0:46:30.467434 INFO: ==============================================
0:46:30.708740 INFO: Removed 298151 precursors with score below cutoff 11.544943664932251
0:46:31.014824 INFO: performing precursor FDR with 40 features
0:46:31.014942 INFO: Decoy channel: -1
0:46:31.014968 INFO: Competetive: True
0:46:31.043496 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:31.059356 WARNING: FDR calculation for 208961 target and 128582 decoy PSMs
0:46:31.059499 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
0:46:31.138824 INFO: Using random state 253763 for train-test-split
0:46:35.463932 INFO: Test AUC: 0.872
0:46:35.464535 INFO: Train AUC: 0.874
0:46:35.464574 INFO: AUC difference: 0.23%
0:46:35.781853 INFO: Resetting torch num_threads to 80
0:46:36.060881 PROGRESS: ============================= Precursor FDR =============================
0:46:36.061129 PROGRESS: Total precursors accumulated: 106,631
0:46:36.061203 PROGRESS: Target precursors: 105,576 (99.01%)
0:46:36.061258 PROGRESS: Decoy precursors: 1,055 (0.99%)
0:46:36.061306 PROGRESS: 
0:46:36.061361 PROGRESS: Precursor Summary:
0:46:36.087226 PROGRESS: Channel   0:	 0.050 FDR: 105,576; 0.010 FDR: 105,576; 0.001 FDR: 96,755
0:46:36.087464 PROGRESS: 
0:46:36.087526 PROGRESS: Protein Summary:
0:46:36.123755 PROGRESS: Channel   0:	 0.050 FDR: 9,970; 0.010 FDR: 9,970; 0.001 FDR: 9,862
0:46:36.123989 PROGRESS: =========================================================================
0:46:36.125534 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/psm.parquet
0:46:36.306496 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.parquet
0:46:36.591419 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:46:36.686339 PROGRESS: 
0:46:36.686471 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant
0:46:36.686535 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/figures
0:46:36.686680 INFO: Initializing TimingManager
0:46:36.687100 INFO: Initializing RawFileManager
0:46:49.130461 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.
0:46:49.134450 INFO: Determining DIA cycle
0:46:49.150713 INFO: Found cycle with start 0.00 min and length 300.
0:46:49.323918 INFO: RT (min)            : 0.0 - 26.9
0:46:49.324009 INFO: RT duration (sec)   : 1611.2
0:46:49.324038 INFO: RT duration (min)   : 26.9
0:46:49.324062 INFO: Cycle len (scans)   : 300
0:46:49.324086 INFO: Cycle len (sec)     : 1.65
0:46:49.324106 INFO: Number of cycles    : 977
0:46:49.324126 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:46:49.324154 INFO: Creating DIA data object took: 12.636956691741943
0:46:50.008514 INFO: Creating DIA data NG object took: 0.6842391490936279
0:46:50.038738 INFO: Initializing CalibrationManager
0:46:50.039009 INFO: Setting up calibration estimators ..
0:46:50.039068 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:46:50.039133 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
0:46:50.039196 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:46:50.039247 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:46:50.039297 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
0:46:50.039346 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:46:50.039390 INFO: Done setting up calibration estimators.
0:46:50.039566 INFO: Initializing OptimizationManager
0:46:50.039684 INFO: initial parameter: ms1_error = 30
0:46:50.039736 INFO: initial parameter: ms2_error = 30
0:46:50.039783 INFO: initial parameter: rt_error = 805.6002197265625
0:46:50.039826 INFO: initial parameter: mobility_error = 0.1
0:46:50.039873 INFO: initial parameter: num_candidates = 1
0:46:50.039913 INFO: initial parameter: fwhm_rt = 5
0:46:50.039953 INFO: initial parameter: fwhm_mobility = 0.01
0:46:50.039993 INFO: initial parameter: score_cutoff = 0
0:46:50.040032 INFO: initial parameter: classifier_version = -1
0:46:50.040099 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:46:50.040309 INFO: FDRManager: loading saved state not requested, will be initialized.
0:46:50.040340 INFO: Initializing FDRManager
0:46:50.040367 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:46:50.064938 PROGRESS: Initializing spectral library: 115,864 target precursors potentially observable (0 removed)
0:46:50.082042 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:46:50.082373 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
0:46:50.082465 PROGRESS: Starting initial search for precursors.
0:46:50.082540 INFO: Starting optimization step 0.
0:46:50.082597 PROGRESS: === Extracting elution groups 0 to 200 ===
0:46:50.082650 INFO: Using ng extraction backend
0:46:50.082703 PROGRESS: Extracting batch of 397 precursors
0:46:50.084570 INFO: === Search parameters used ===
0:46:50.084657 INFO: rt_error       : 805.6002197265625
0:46:50.084706 INFO: mobility_error : 0.1
0:46:50.084750 INFO: num_candidates : 1
0:46:50.084791 INFO: ms1_error      : 30
0:46:50.084831 INFO: ms2_error      : 30
0:46:50.084869 INFO: fwhm_rt        : 5
0:46:50.084907 INFO: quant_window   : 3
0:46:50.084945 INFO: ==============================================
0:46:50.102737 INFO: performing precursor FDR with 40 features
0:46:50.102801 INFO: Decoy channel: -1
0:46:50.102827 INFO: Competetive: True
0:46:50.103702 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:50.105735 INFO: Using random state 951353 for train-test-split
0:46:50.112474 INFO: Test AUC: 0.618
0:46:50.112529 INFO: Train AUC: 0.553
0:46:50.112559 INFO: AUC difference: 11.79%
0:46:50.112581 WARNING: AUC difference > 5%. This may indicate overfitting.
0:46:50.322592 INFO: Resetting torch num_threads to 80
0:46:50.323898 PROGRESS: === Extracted 396 precursors and 2806 fragments ===
0:46:50.324222 INFO: === FDR correction performed with classifier version -1 ===
0:46:50.324665 PROGRESS: ============================= Precursor FDR =============================
0:46:50.324752 PROGRESS: Total precursors accumulated: 2
0:46:50.324811 PROGRESS: Target precursors: 2 (100.00%)
0:46:50.324860 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:50.324906 PROGRESS: 
0:46:50.324949 PROGRESS: Precursor Summary:
0:46:50.325873 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:46:50.325964 PROGRESS: 
0:46:50.326020 PROGRESS: Protein Summary:
0:46:50.327020 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:46:50.327107 PROGRESS: =========================================================================
0:46:50.327286 INFO: Target number of precursors not reached yet.
0:46:50.330932 INFO: Starting optimization step 1.
0:46:50.331034 PROGRESS: === Extracting elution groups 200 to 600 ===
0:46:50.331107 INFO: Using ng extraction backend
0:46:50.331165 PROGRESS: Extracting batch of 797 precursors
0:46:50.333736 INFO: === Search parameters used ===
0:46:50.333824 INFO: rt_error       : 805.6002197265625
0:46:50.333873 INFO: mobility_error : 0.1
0:46:50.333919 INFO: num_candidates : 1
0:46:50.333960 INFO: ms1_error      : 30
0:46:50.334000 INFO: ms2_error      : 30
0:46:50.334039 INFO: fwhm_rt        : 5
0:46:50.334078 INFO: quant_window   : 3
0:46:50.334117 INFO: ==============================================
0:46:50.357138 INFO: performing precursor FDR with 40 features
0:46:50.357209 INFO: Decoy channel: -1
0:46:50.357235 INFO: Competetive: True
0:46:50.360085 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:50.361629 INFO: Using random state 991889 for train-test-split
0:46:50.369940 INFO: Test AUC: 0.562
0:46:50.369994 INFO: Train AUC: 0.563
0:46:50.370024 INFO: AUC difference: 0.19%
0:46:50.574827 INFO: Resetting torch num_threads to 80
0:46:50.576846 PROGRESS: === Extracted 1192 precursors and 8288 fragments ===
0:46:50.577201 INFO: === FDR correction performed with classifier version -1 ===
0:46:50.577634 PROGRESS: ============================= Precursor FDR =============================
0:46:50.577719 PROGRESS: Total precursors accumulated: 0
0:46:50.577779 PROGRESS: Target precursors: 0 (0.00%)
0:46:50.577830 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:50.577876 PROGRESS: 
0:46:50.577919 PROGRESS: Precursor Summary:
0:46:50.578033 PROGRESS: 
0:46:50.578095 PROGRESS: Protein Summary:
0:46:50.578166 PROGRESS: =========================================================================
0:46:50.578362 INFO: Target number of precursors not reached yet.
0:46:50.583052 INFO: Starting optimization step 2.
0:46:50.583154 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:46:50.583226 INFO: Using ng extraction backend
0:46:50.583286 PROGRESS: Extracting batch of 1593 precursors
0:46:50.587396 INFO: === Search parameters used ===
0:46:50.587488 INFO: rt_error       : 805.6002197265625
0:46:50.587538 INFO: mobility_error : 0.1
0:46:50.587582 INFO: num_candidates : 1
0:46:50.587625 INFO: ms1_error      : 30
0:46:50.587664 INFO: ms2_error      : 30
0:46:50.587705 INFO: fwhm_rt        : 5
0:46:50.587745 INFO: quant_window   : 3
0:46:50.587785 INFO: ==============================================
0:46:50.617633 INFO: performing precursor FDR with 40 features
0:46:50.617705 INFO: Decoy channel: -1
0:46:50.617730 INFO: Competetive: True
0:46:50.620896 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:50.622707 INFO: Using random state 123781 for train-test-split
0:46:50.633684 INFO: Test AUC: 0.582
0:46:50.633742 INFO: Train AUC: 0.565
0:46:50.633770 INFO: AUC difference: 3.14%
0:46:50.837596 INFO: Resetting torch num_threads to 80
0:46:50.839933 PROGRESS: === Extracted 2784 precursors and 19627 fragments ===
0:46:50.840265 INFO: === FDR correction performed with classifier version -1 ===
0:46:50.840690 PROGRESS: ============================= Precursor FDR =============================
0:46:50.840776 PROGRESS: Total precursors accumulated: 0
0:46:50.840841 PROGRESS: Target precursors: 0 (0.00%)
0:46:50.840894 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:50.840940 PROGRESS: 
0:46:50.840987 PROGRESS: Precursor Summary:
0:46:50.841105 PROGRESS: 
0:46:50.841165 PROGRESS: Protein Summary:
0:46:50.841235 PROGRESS: =========================================================================
0:46:50.841438 INFO: Target number of precursors not reached yet.
0:46:50.847796 INFO: Starting optimization step 3.
0:46:50.847909 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:46:50.847979 INFO: Using ng extraction backend
0:46:50.848039 PROGRESS: Extracting batch of 3185 precursors
0:46:50.855090 INFO: === Search parameters used ===
0:46:50.855186 INFO: rt_error       : 805.6002197265625
0:46:50.855235 INFO: mobility_error : 0.1
0:46:50.855279 INFO: num_candidates : 1
0:46:50.855321 INFO: ms1_error      : 30
0:46:50.855361 INFO: ms2_error      : 30
0:46:50.855401 INFO: fwhm_rt        : 5
0:46:50.855439 INFO: quant_window   : 3
0:46:50.855479 INFO: ==============================================
0:46:50.902423 INFO: performing precursor FDR with 40 features
0:46:50.902510 INFO: Decoy channel: -1
0:46:50.902535 INFO: Competetive: True
0:46:50.906487 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:50.908979 INFO: Using random state 215310 for train-test-split
0:46:50.929518 INFO: Test AUC: 0.567
0:46:50.929595 INFO: Train AUC: 0.564
0:46:50.929624 INFO: AUC difference: 0.52%
0:46:51.138398 INFO: Resetting torch num_threads to 80
0:46:51.141300 PROGRESS: === Extracted 5966 precursors and 41749 fragments ===
0:46:51.141640 INFO: === FDR correction performed with classifier version -1 ===
0:46:51.142079 PROGRESS: ============================= Precursor FDR =============================
0:46:51.142172 PROGRESS: Total precursors accumulated: 0
0:46:51.142231 PROGRESS: Target precursors: 0 (0.00%)
0:46:51.142283 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:51.142330 PROGRESS: 
0:46:51.142373 PROGRESS: Precursor Summary:
0:46:51.142477 PROGRESS: 
0:46:51.142539 PROGRESS: Protein Summary:
0:46:51.142611 PROGRESS: =========================================================================
0:46:51.142843 INFO: Target number of precursors not reached yet.
0:46:51.152839 INFO: Starting optimization step 4.
0:46:51.152955 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:46:51.153036 INFO: Using ng extraction backend
0:46:51.153100 PROGRESS: Extracting batch of 6366 precursors
0:46:51.165081 INFO: === Search parameters used ===
0:46:51.165197 INFO: rt_error       : 805.6002197265625
0:46:51.165246 INFO: mobility_error : 0.1
0:46:51.165290 INFO: num_candidates : 1
0:46:51.165332 INFO: ms1_error      : 30
0:46:51.165372 INFO: ms2_error      : 30
0:46:51.165414 INFO: fwhm_rt        : 5
0:46:51.165468 INFO: quant_window   : 3
0:46:51.165511 INFO: ==============================================
0:46:51.235806 INFO: performing precursor FDR with 40 features
0:46:51.235920 INFO: Decoy channel: -1
0:46:51.235946 INFO: Competetive: True
0:46:51.241517 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:51.244763 INFO: Using random state 619155 for train-test-split
0:46:51.280115 INFO: Test AUC: 0.567
0:46:51.280207 INFO: Train AUC: 0.566
0:46:51.280236 INFO: AUC difference: 0.12%
0:46:51.490043 INFO: Resetting torch num_threads to 80
0:46:51.494008 PROGRESS: === Extracted 12326 precursors and 86083 fragments ===
0:46:51.494366 INFO: === FDR correction performed with classifier version -1 ===
0:46:51.494806 PROGRESS: ============================= Precursor FDR =============================
0:46:51.494892 PROGRESS: Total precursors accumulated: 0
0:46:51.494949 PROGRESS: Target precursors: 0 (0.00%)
0:46:51.495000 PROGRESS: Decoy precursors: 0 (0.00%)
0:46:51.495046 PROGRESS: 
0:46:51.495089 PROGRESS: Precursor Summary:
0:46:51.495195 PROGRESS: 
0:46:51.495256 PROGRESS: Protein Summary:
0:46:51.495327 PROGRESS: =========================================================================
0:46:51.495590 INFO: Target number of precursors not reached yet.
0:46:51.510937 INFO: Starting optimization step 5.
0:46:51.511119 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:46:51.511199 INFO: Using ng extraction backend
0:46:51.511261 PROGRESS: Extracting batch of 12747 precursors
0:46:51.533393 INFO: === Search parameters used ===
0:46:51.533540 INFO: rt_error       : 805.6002197265625
0:46:51.533591 INFO: mobility_error : 0.1
0:46:51.533635 INFO: num_candidates : 1
0:46:51.533827 INFO: ms1_error      : 30
0:46:51.533875 INFO: ms2_error      : 30
0:46:51.533916 INFO: fwhm_rt        : 5
0:46:51.533957 INFO: quant_window   : 3
0:46:51.533996 INFO: ==============================================
0:46:51.664813 INFO: performing precursor FDR with 40 features
0:46:51.664924 INFO: Decoy channel: -1
0:46:51.664950 INFO: Competetive: True
0:46:51.674127 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:51.679432 INFO: Using random state 33509 for train-test-split
0:46:51.986228 INFO: Test AUC: 0.807
0:46:51.986340 INFO: Train AUC: 0.812
0:46:51.986370 INFO: AUC difference: 0.58%
0:46:52.209333 INFO: Resetting torch num_threads to 80
0:46:52.215418 PROGRESS: === Extracted 25061 precursors and 175874 fragments ===
0:46:52.215821 INFO: === FDR correction performed with classifier version -1 ===
0:46:52.216792 PROGRESS: ============================= Precursor FDR =============================
0:46:52.216888 PROGRESS: Total precursors accumulated: 4,479
0:46:52.216948 PROGRESS: Target precursors: 4,435 (99.02%)
0:46:52.217007 PROGRESS: Decoy precursors: 44 (0.98%)
0:46:52.217055 PROGRESS: 
0:46:52.217099 PROGRESS: Precursor Summary:
0:46:52.219052 PROGRESS: Channel   0:	 0.050 FDR: 4,435; 0.010 FDR: 4,435; 0.001 FDR: 2,399
0:46:52.219151 PROGRESS: 
0:46:52.219206 PROGRESS: Protein Summary:
0:46:52.221947 PROGRESS: Channel   0:	 0.050 FDR: 2,690; 0.010 FDR: 2,690; 0.001 FDR: 1,592
0:46:52.222052 PROGRESS: =========================================================================
0:46:52.222421 INFO: Target number of precursors reached.
0:46:52.249206 INFO: fragments_df: keeping 5000 of 175874 [sum(precursor_idx_mask)=48874 sum(mass_error_mask)=175874 stop_rank=5000
0:46:52.255132 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:52.852923 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:53.529386 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:46:53.529840 INFO: Using score_cutoff 14.050187790298462 (fac=0.99, q=1)
0:46:53.530157 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:46:53.530237 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:46:53.530290 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.050187790298462
0:46:53.530343 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:53.531891 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:53.533930 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
0:46:53.534029 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:46:53.534105 INFO: Starting optimization step 6.
0:46:53.534165 PROGRESS: === Extracting elution groups 0 to 600 ===
0:46:53.534225 INFO: Using ng extraction backend
0:46:53.534279 PROGRESS: Extracting batch of 1194 precursors
0:46:53.537525 INFO: === Search parameters used ===
0:46:53.537611 INFO: rt_error       : 805.6002197265625
0:46:53.537664 INFO: mobility_error : 0.1
0:46:53.537707 INFO: num_candidates : 3
0:46:53.537748 INFO: ms1_error      : 30
0:46:53.537786 INFO: ms2_error      : 30
0:46:53.537835 INFO: fwhm_rt        : 3.0
0:46:53.537876 INFO: quant_window   : 3
0:46:53.537914 INFO: ==============================================
0:46:53.576171 INFO: performing precursor FDR with 40 features
0:46:53.576261 INFO: Decoy channel: -1
0:46:53.576286 INFO: Competetive: True
0:46:53.578793 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:53.580500 INFO: Using random state 835224 for train-test-split
0:46:53.591924 INFO: Test AUC: 0.677
0:46:53.591986 INFO: Train AUC: 0.629
0:46:53.592016 INFO: AUC difference: 7.57%
0:46:53.592041 WARNING: AUC difference > 5%. This may indicate overfitting.
0:46:53.803541 INFO: Resetting torch num_threads to 80
0:46:53.805034 PROGRESS: === Extracted 3576 precursors and 21762 fragments ===
0:46:53.805362 INFO: === FDR correction performed with classifier version 5 ===
0:46:53.805800 PROGRESS: ============================= Precursor FDR =============================
0:46:53.805887 PROGRESS: Total precursors accumulated: 178
0:46:53.805945 PROGRESS: Target precursors: 177 (99.44%)
0:46:53.805996 PROGRESS: Decoy precursors: 1 (0.56%)
0:46:53.806042 PROGRESS: 
0:46:53.806083 PROGRESS: Precursor Summary:
0:46:53.806958 PROGRESS: Channel   0:	 0.050 FDR:   177; 0.010 FDR:   177; 0.001 FDR:   118
0:46:53.807047 PROGRESS: 
0:46:53.807101 PROGRESS: Protein Summary:
0:46:53.808095 PROGRESS: Channel   0:	 0.050 FDR:   170; 0.010 FDR:   170; 0.001 FDR:   115
0:46:53.808183 PROGRESS: =========================================================================
0:46:53.808542 INFO: Target number of precursors not reached yet.
0:46:53.813165 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:53.814807 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:53.817456 INFO: === skipping optimization until target number of precursors are found ===
0:46:53.817572 INFO: Starting optimization step 7.
0:46:53.817642 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:46:53.817709 INFO: Using ng extraction backend
0:46:53.817767 PROGRESS: Extracting batch of 1593 precursors
0:46:53.821908 INFO: === Search parameters used ===
0:46:53.821995 INFO: rt_error       : 805.6002197265625
0:46:53.822046 INFO: mobility_error : 0.1
0:46:53.822090 INFO: num_candidates : 3
0:46:53.822145 INFO: ms1_error      : 30
0:46:53.822187 INFO: ms2_error      : 30
0:46:53.822230 INFO: fwhm_rt        : 3.0
0:46:53.822269 INFO: quant_window   : 3
0:46:53.822309 INFO: ==============================================
0:46:53.866987 INFO: performing precursor FDR with 40 features
0:46:53.867084 INFO: Decoy channel: -1
0:46:53.867111 INFO: Competetive: True
0:46:53.871310 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:53.873833 INFO: Using random state 835224 for train-test-split
0:46:53.892648 INFO: Test AUC: 0.676
0:46:53.892732 INFO: Train AUC: 0.648
0:46:53.892762 INFO: AUC difference: 4.36%
0:46:54.109715 INFO: Resetting torch num_threads to 80
0:46:54.112458 PROGRESS: === Extracted 8346 precursors and 51056 fragments ===
0:46:54.112794 INFO: === FDR correction performed with classifier version 5 ===
0:46:54.113276 PROGRESS: ============================= Precursor FDR =============================
0:46:54.113368 PROGRESS: Total precursors accumulated: 475
0:46:54.113425 PROGRESS: Target precursors: 471 (99.16%)
0:46:54.113475 PROGRESS: Decoy precursors: 4 (0.84%)
0:46:54.113522 PROGRESS: 
0:46:54.113565 PROGRESS: Precursor Summary:
0:46:54.114504 PROGRESS: Channel   0:	 0.050 FDR:   471; 0.010 FDR:   471; 0.001 FDR:   227
0:46:54.114604 PROGRESS: 
0:46:54.114660 PROGRESS: Protein Summary:
0:46:54.115799 PROGRESS: Channel   0:	 0.050 FDR:   430; 0.010 FDR:   430; 0.001 FDR:   211
0:46:54.115896 PROGRESS: =========================================================================
0:46:54.116116 INFO: Target number of precursors reached.
0:46:54.122306 INFO: fragments_df: keeping 5000 of 51056 [sum(precursor_idx_mask)=10947 sum(mass_error_mask)=51056 stop_rank=5000
0:46:54.127337 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:54.259931 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:54.935057 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:54.935474 INFO: Using score_cutoff 15.525725020408629 (fac=0.99, q=1)
0:46:54.935766 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:54.935846 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:54.935900 INFO: Updating optimization_manager: score_cutoff        : 14.050187790298462 -> 15.525725020408629
0:46:54.935954 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:54.937525 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:54.939584 INFO: === checking if optimization conditions were reached ===
0:46:54.941150 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:46:54.941252 INFO: Updating optimization_manager: classifier_version  : 5 -> 7
0:46:54.941316 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:46:54.941376 INFO: ==============================================
0:46:54.941448 INFO: Starting optimization step 8.
0:46:54.941509 PROGRESS: === Extracting elution groups 0 to 600 ===
0:46:54.941570 INFO: Using ng extraction backend
0:46:54.941626 PROGRESS: Extracting batch of 1194 precursors
0:46:54.944923 INFO: === Search parameters used ===
0:46:54.945017 INFO: rt_error       : 805.6002197265625
0:46:54.945070 INFO: mobility_error : 0.1
0:46:54.945132 INFO: num_candidates : 3
0:46:54.945179 INFO: ms1_error      : 30
0:46:54.945222 INFO: ms2_error      : 10.0
0:46:54.945261 INFO: fwhm_rt        : 3.0
0:46:54.945300 INFO: quant_window   : 3
0:46:54.945339 INFO: ==============================================
0:46:54.981847 INFO: performing precursor FDR with 40 features
0:46:54.981930 INFO: Decoy channel: -1
0:46:54.981956 INFO: Competetive: True
0:46:54.984473 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:54.986199 INFO: Using random state 617623 for train-test-split
0:46:54.997679 INFO: Test AUC: 0.679
0:46:54.997741 INFO: Train AUC: 0.676
0:46:54.997770 INFO: AUC difference: 0.37%
0:46:55.207099 INFO: Resetting torch num_threads to 80
0:46:55.208589 PROGRESS: === Extracted 3577 precursors and 24553 fragments ===
0:46:55.209114 INFO: === FDR correction performed with classifier version 7 ===
0:46:55.209604 PROGRESS: ============================= Precursor FDR =============================
0:46:55.209693 PROGRESS: Total precursors accumulated: 338
0:46:55.209750 PROGRESS: Target precursors: 335 (99.11%)
0:46:55.209800 PROGRESS: Decoy precursors: 3 (0.89%)
0:46:55.209843 PROGRESS: 
0:46:55.209887 PROGRESS: Precursor Summary:
0:46:55.210795 PROGRESS: Channel   0:	 0.050 FDR:   335; 0.010 FDR:   335; 0.001 FDR:   280
0:46:55.210884 PROGRESS: 
0:46:55.210938 PROGRESS: Protein Summary:
0:46:55.212029 PROGRESS: Channel   0:	 0.050 FDR:   318; 0.010 FDR:   318; 0.001 FDR:   265
0:46:55.212120 PROGRESS: =========================================================================
0:46:55.212370 INFO: Target number of precursors reached.
0:46:55.216225 INFO: fragments_df: keeping 3757 of 24553 [sum(precursor_idx_mask)=8136 sum(mass_error_mask)=24553 stop_rank=3757
0:46:55.221779 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:55.319512 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:55.741645 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:55.742056 INFO: Using score_cutoff 13.837716483879088 (fac=0.99, q=1)
0:46:55.742347 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:55.742428 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:55.742483 INFO: Updating optimization_manager: score_cutoff        : 15.525725020408629 -> 13.837716483879088
0:46:55.742536 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:55.744097 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:55.746302 INFO: === checking if optimization conditions were reached ===
0:46:55.747715 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:46:55.747814 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:46:55.747888 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:46:55.747948 INFO: ==============================================
0:46:55.748012 PROGRESS: Optimization finished for ms2_error.
0:46:55.752765 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:55.754089 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:55.756236 INFO: Starting optimization step 0.
0:46:55.756330 PROGRESS: === Extracting elution groups 0 to 600 ===
0:46:55.756403 INFO: Using ng extraction backend
0:46:55.756462 PROGRESS: Extracting batch of 1194 precursors
0:46:55.759765 INFO: === Search parameters used ===
0:46:55.759850 INFO: rt_error       : 805.6002197265625
0:46:55.759899 INFO: mobility_error : 0.1
0:46:55.759945 INFO: num_candidates : 3
0:46:55.759989 INFO: ms1_error      : 30
0:46:55.760030 INFO: ms2_error      : 10.0
0:46:55.760072 INFO: fwhm_rt        : 3.0
0:46:55.760110 INFO: quant_window   : 3
0:46:55.760151 INFO: ==============================================
0:46:55.799144 INFO: performing precursor FDR with 40 features
0:46:55.799227 INFO: Decoy channel: -1
0:46:55.799253 INFO: Competetive: True
0:46:55.801766 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:55.803521 INFO: Using random state 797822 for train-test-split
0:46:55.815063 INFO: Test AUC: 0.689
0:46:55.815127 INFO: Train AUC: 0.673
0:46:55.815156 INFO: AUC difference: 2.35%
0:46:56.026119 INFO: Resetting torch num_threads to 80
0:46:56.027585 PROGRESS: === Extracted 3578 precursors and 24566 fragments ===
0:46:56.027908 INFO: === FDR correction performed with classifier version 8 ===
0:46:56.028349 PROGRESS: ============================= Precursor FDR =============================
0:46:56.028437 PROGRESS: Total precursors accumulated: 329
0:46:56.028502 PROGRESS: Target precursors: 326 (99.09%)
0:46:56.028553 PROGRESS: Decoy precursors: 3 (0.91%)
0:46:56.028599 PROGRESS: 
0:46:56.028644 PROGRESS: Precursor Summary:
0:46:56.029543 PROGRESS: Channel   0:	 0.050 FDR:   326; 0.010 FDR:   326; 0.001 FDR:   280
0:46:56.029637 PROGRESS: 
0:46:56.029691 PROGRESS: Protein Summary:
0:46:56.030798 PROGRESS: Channel   0:	 0.050 FDR:   309; 0.010 FDR:   309; 0.001 FDR:   265
0:46:56.030888 PROGRESS: =========================================================================
0:46:56.031079 INFO: Target number of precursors reached.
0:46:56.034862 INFO: fragments_df: keeping 3679 of 24566 [sum(precursor_idx_mask)=7929 sum(mass_error_mask)=24566 stop_rank=3679
0:46:56.039576 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:56.135769 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:56.549379 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:56.549789 INFO: Using score_cutoff 13.835919063091279 (fac=0.99, q=1)
0:46:56.550078 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:56.550157 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:56.550212 INFO: Updating optimization_manager: score_cutoff        : 13.837716483879088 -> 13.835919063091279
0:46:56.550267 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:56.551823 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:56.553994 INFO: === checking if optimization conditions were reached ===
0:46:56.554100 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:46:56.555555 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 71.19408861489288
0:46:56.555652 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 71.1941.
0:46:56.555719 INFO: ==============================================
0:46:56.555786 INFO: Starting optimization step 1.
0:46:56.555845 PROGRESS: === Extracting elution groups 0 to 600 ===
0:46:56.555905 INFO: Using ng extraction backend
0:46:56.555961 PROGRESS: Extracting batch of 1194 precursors
0:46:56.559269 INFO: === Search parameters used ===
0:46:56.559354 INFO: rt_error       : 71.19408861489288
0:46:56.559406 INFO: mobility_error : 0.1
0:46:56.559454 INFO: num_candidates : 3
0:46:56.559499 INFO: ms1_error      : 30
0:46:56.559539 INFO: ms2_error      : 10.0
0:46:56.559580 INFO: fwhm_rt        : 3.0
0:46:56.559619 INFO: quant_window   : 3
0:46:56.559657 INFO: ==============================================
0:46:56.591749 INFO: performing precursor FDR with 40 features
0:46:56.591820 INFO: Decoy channel: -1
0:46:56.591846 INFO: Competetive: True
0:46:56.594375 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:56.596120 INFO: Using random state 797822 for train-test-split
0:46:56.608338 INFO: Test AUC: 0.677
0:46:56.608401 INFO: Train AUC: 0.706
0:46:56.608430 INFO: AUC difference: 4.09%
0:46:56.820471 INFO: Resetting torch num_threads to 80
0:46:56.821947 PROGRESS: === Extracted 3570 precursors and 21802 fragments ===
0:46:56.822275 INFO: === FDR correction performed with classifier version 8 ===
0:46:56.822740 PROGRESS: ============================= Precursor FDR =============================
0:46:56.822827 PROGRESS: Total precursors accumulated: 451
0:46:56.822883 PROGRESS: Target precursors: 447 (99.11%)
0:46:56.822932 PROGRESS: Decoy precursors: 4 (0.89%)
0:46:56.822974 PROGRESS: 
0:46:56.823017 PROGRESS: Precursor Summary:
0:46:56.823928 PROGRESS: Channel   0:	 0.050 FDR:   447; 0.010 FDR:   447; 0.001 FDR:   289
0:46:56.824016 PROGRESS: 
0:46:56.824068 PROGRESS: Protein Summary:
0:46:56.825206 PROGRESS: Channel   0:	 0.050 FDR:   426; 0.010 FDR:   426; 0.001 FDR:   274
0:46:56.825297 PROGRESS: =========================================================================
0:46:56.825485 INFO: Target number of precursors reached.
0:46:56.829354 INFO: fragments_df: keeping 4372 of 21802 [sum(precursor_idx_mask)=9916 sum(mass_error_mask)=21802 stop_rank=4372
0:46:56.834480 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:56.943230 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:57.453723 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:57.454165 INFO: Using score_cutoff 12.057952333831786 (fac=0.99, q=1)
0:46:57.454482 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:57.454576 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:57.454644 INFO: Updating optimization_manager: score_cutoff        : 13.835919063091279 -> 12.057952333831786
0:46:57.454726 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:57.456325 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:57.458569 INFO: === checking if optimization conditions were reached ===
0:46:57.458677 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:46:57.460346 INFO: Updating optimization_manager: rt_error            : 71.19408861489288 -> 28.13124410353823
0:46:57.460455 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 28.1312.
0:46:57.460536 INFO: ==============================================
0:46:57.460620 INFO: Starting optimization step 2.
0:46:57.460695 PROGRESS: === Extracting elution groups 0 to 600 ===
0:46:57.460771 INFO: Using ng extraction backend
0:46:57.460843 PROGRESS: Extracting batch of 1194 precursors
0:46:57.464214 INFO: === Search parameters used ===
0:46:57.464323 INFO: rt_error       : 28.13124410353823
0:46:57.464391 INFO: mobility_error : 0.1
0:46:57.464454 INFO: num_candidates : 3
0:46:57.464517 INFO: ms1_error      : 30
0:46:57.464579 INFO: ms2_error      : 10.0
0:46:57.464636 INFO: fwhm_rt        : 3.0
0:46:57.464694 INFO: quant_window   : 3
0:46:57.464751 INFO: ==============================================
0:46:57.497511 INFO: performing precursor FDR with 40 features
0:46:57.497583 INFO: Decoy channel: -1
0:46:57.497615 INFO: Competetive: True
0:46:57.500086 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:57.501903 INFO: Using random state 797822 for train-test-split
0:46:57.513519 INFO: Test AUC: 0.681
0:46:57.513584 INFO: Train AUC: 0.722
0:46:57.513622 INFO: AUC difference: 5.56%
0:46:57.513656 WARNING: AUC difference > 5%. This may indicate overfitting.
0:46:57.725807 INFO: Resetting torch num_threads to 80
0:46:57.727314 PROGRESS: === Extracted 3264 precursors and 19268 fragments ===
0:46:57.727691 INFO: === FDR correction performed with classifier version 8 ===
0:46:57.728179 PROGRESS: ============================= Precursor FDR =============================
0:46:57.728280 PROGRESS: Total precursors accumulated: 448
0:46:57.728356 PROGRESS: Target precursors: 444 (99.11%)
0:46:57.728425 PROGRESS: Decoy precursors: 4 (0.89%)
0:46:57.728487 PROGRESS: 
0:46:57.728548 PROGRESS: Precursor Summary:
0:46:57.729557 PROGRESS: Channel   0:	 0.050 FDR:   444; 0.010 FDR:   444; 0.001 FDR:   293
0:46:57.729661 PROGRESS: 
0:46:57.729735 PROGRESS: Protein Summary:
0:46:57.730962 PROGRESS: Channel   0:	 0.050 FDR:   423; 0.010 FDR:   423; 0.001 FDR:   278
0:46:57.731070 PROGRESS: =========================================================================
0:46:57.731301 INFO: Target number of precursors reached.
0:46:57.734958 INFO: fragments_df: keeping 4023 of 19268 [sum(precursor_idx_mask)=8733 sum(mass_error_mask)=19268 stop_rank=4023
0:46:57.740220 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:57.849589 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:58.307681 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:58.308097 INFO: Using score_cutoff 12.044924198341368 (fac=0.99, q=1)
0:46:58.308382 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:58.308462 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:58.308523 INFO: Updating optimization_manager: score_cutoff        : 12.057952333831786 -> 12.044924198341368
0:46:58.308581 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:58.310155 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:58.312254 INFO: === checking if optimization conditions were reached ===
0:46:58.312355 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:46:58.314044 INFO: Updating optimization_manager: rt_error            : 28.13124410353823 -> 18.74321433900978
0:46:58.314145 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 18.7432.
0:46:58.314213 INFO: ==============================================
0:46:58.314282 INFO: Starting optimization step 3.
0:46:58.314344 PROGRESS: === Extracting elution groups 0 to 600 ===
0:46:58.314407 INFO: Using ng extraction backend
0:46:58.314462 PROGRESS: Extracting batch of 1194 precursors
0:46:58.317739 INFO: === Search parameters used ===
0:46:58.317826 INFO: rt_error       : 18.74321433900978
0:46:58.317876 INFO: mobility_error : 0.1
0:46:58.317922 INFO: num_candidates : 3
0:46:58.317962 INFO: ms1_error      : 30
0:46:58.318002 INFO: ms2_error      : 10.0
0:46:58.318042 INFO: fwhm_rt        : 3.0
0:46:58.318083 INFO: quant_window   : 3
0:46:58.318130 INFO: ==============================================
0:46:58.348560 INFO: performing precursor FDR with 40 features
0:46:58.348636 INFO: Decoy channel: -1
0:46:58.348661 INFO: Competetive: True
0:46:58.351069 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:58.352693 INFO: Using random state 797822 for train-test-split
0:46:58.363654 INFO: Test AUC: 0.725
0:46:58.363714 INFO: Train AUC: 0.712
0:46:58.363744 INFO: AUC difference: 1.94%
0:46:58.574138 INFO: Resetting torch num_threads to 80
0:46:58.575576 PROGRESS: === Extracted 3272 precursors and 19290 fragments ===
0:46:58.575899 INFO: === FDR correction performed with classifier version 8 ===
0:46:58.576355 PROGRESS: ============================= Precursor FDR =============================
0:46:58.576442 PROGRESS: Total precursors accumulated: 448
0:46:58.576499 PROGRESS: Target precursors: 444 (99.11%)
0:46:58.576548 PROGRESS: Decoy precursors: 4 (0.89%)
0:46:58.576592 PROGRESS: 
0:46:58.576636 PROGRESS: Precursor Summary:
0:46:58.577572 PROGRESS: Channel   0:	 0.050 FDR:   444; 0.010 FDR:   444; 0.001 FDR:   293
0:46:58.577662 PROGRESS: 
0:46:58.577716 PROGRESS: Protein Summary:
0:46:58.578832 PROGRESS: Channel   0:	 0.050 FDR:   423; 0.010 FDR:   423; 0.001 FDR:   278
0:46:58.578922 PROGRESS: =========================================================================
0:46:58.579109 INFO: Target number of precursors reached.
0:46:58.582690 INFO: fragments_df: keeping 4027 of 19290 [sum(precursor_idx_mask)=8737 sum(mass_error_mask)=19290 stop_rank=4027
0:46:58.587744 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:58.717409 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:59.242620 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:59.243043 INFO: Using score_cutoff 12.044924198341368 (fac=0.99, q=1)
0:46:59.243338 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:59.243418 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:59.243472 INFO: Updating optimization_manager: score_cutoff        : 12.044924198341368 -> 12.044924198341368
0:46:59.243532 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:59.245098 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:59.247287 INFO: === checking if optimization conditions were reached ===
0:46:59.247385 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:46:59.249089 INFO: Updating optimization_manager: rt_error            : 18.74321433900978 -> 18.743214339147443
0:46:59.249190 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 18.7432.
0:46:59.249257 INFO: ==============================================
0:46:59.249328 INFO: Starting optimization step 4.
0:46:59.249393 PROGRESS: === Extracting elution groups 0 to 600 ===
0:46:59.249491 INFO: Using ng extraction backend
0:46:59.249564 PROGRESS: Extracting batch of 1194 precursors
0:46:59.252872 INFO: === Search parameters used ===
0:46:59.252953 INFO: rt_error       : 18.743214339147443
0:46:59.253023 INFO: mobility_error : 0.1
0:46:59.253072 INFO: num_candidates : 3
0:46:59.253113 INFO: ms1_error      : 30
0:46:59.253154 INFO: ms2_error      : 10.0
0:46:59.253200 INFO: fwhm_rt        : 3.0
0:46:59.253240 INFO: quant_window   : 3
0:46:59.253279 INFO: ==============================================
0:46:59.283996 INFO: performing precursor FDR with 40 features
0:46:59.284068 INFO: Decoy channel: -1
0:46:59.284093 INFO: Competetive: True
0:46:59.286860 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:59.288536 INFO: Using random state 797822 for train-test-split
0:46:59.300388 INFO: Test AUC: 0.710
0:46:59.300451 INFO: Train AUC: 0.715
0:46:59.300480 INFO: AUC difference: 0.80%
0:46:59.512772 INFO: Resetting torch num_threads to 80
0:46:59.514230 PROGRESS: === Extracted 3272 precursors and 19293 fragments ===
0:46:59.514560 INFO: === FDR correction performed with classifier version 8 ===
0:46:59.515022 PROGRESS: ============================= Precursor FDR =============================
0:46:59.515109 PROGRESS: Total precursors accumulated: 448
0:46:59.515167 PROGRESS: Target precursors: 444 (99.11%)
0:46:59.515216 PROGRESS: Decoy precursors: 4 (0.89%)
0:46:59.515260 PROGRESS: 
0:46:59.515306 PROGRESS: Precursor Summary:
0:46:59.516245 PROGRESS: Channel   0:	 0.050 FDR:   444; 0.010 FDR:   444; 0.001 FDR:   293
0:46:59.516331 PROGRESS: 
0:46:59.516387 PROGRESS: Protein Summary:
0:46:59.517541 PROGRESS: Channel   0:	 0.050 FDR:   423; 0.010 FDR:   423; 0.001 FDR:   278
0:46:59.517634 PROGRESS: =========================================================================
0:46:59.517825 INFO: Target number of precursors reached.
0:46:59.521391 INFO: fragments_df: keeping 4027 of 19293 [sum(precursor_idx_mask)=8742 sum(mass_error_mask)=19293 stop_rank=4027
0:46:59.526280 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:59.655179 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:00.179196 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:00.179620 INFO: Using score_cutoff 12.044924198341368 (fac=0.99, q=1)
0:47:00.179910 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:00.179992 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:00.180047 INFO: Updating optimization_manager: score_cutoff        : 12.044924198341368 -> 12.044924198341368
0:47:00.180100 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:00.181683 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:00.183856 INFO: === checking if optimization conditions were reached ===
0:47:00.183950 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:47:00.184820 INFO: Updating optimization_manager: rt_error            : 18.743214339147443 -> 18.74321433900978
0:47:00.184944 INFO: Updating optimization_manager: classifier_version  : 8 -> 12
0:47:00.185051 INFO: Updating optimization_manager: score_cutoff        : 12.044924198341368 -> 12.044924198341368
0:47:00.185142 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:00.185226 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:00.185308 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 18.7432 found after 5 searches.
0:47:00.185370 INFO: ==============================================
0:47:00.185439 PROGRESS: Optimization finished for rt_error.
0:47:00.189998 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:00.191332 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:00.218966 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:47:00.219095 PROGRESS: ==============================================
0:47:00.219166 PROGRESS: ms2_error      : 10.0000
0:47:00.219222 PROGRESS: rt_error       : 18.7432
0:47:00.219269 PROGRESS: ==============================================
0:47:00.219711 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:00.343936 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:00.681882 INFO: Using ng extraction backend
0:47:00.682147 PROGRESS: Extracting batch of 230645 precursors
0:47:01.048086 INFO: === Search parameters used ===
0:47:01.048316 INFO: rt_error       : 18.74321433900978
0:47:01.048372 INFO: mobility_error : 0.1
0:47:01.048423 INFO: num_candidates : 3
0:47:01.048466 INFO: ms1_error      : 30
0:47:01.048507 INFO: ms2_error      : 10.0
0:47:01.048549 INFO: fwhm_rt        : 3.0
0:47:01.048588 INFO: quant_window   : 3
0:47:01.048626 INFO: ==============================================
0:47:01.287652 INFO: Removed 318719 precursors with score below cutoff 12.044924198341368
0:47:01.589195 INFO: performing precursor FDR with 40 features
0:47:01.589310 INFO: Decoy channel: -1
0:47:01.589337 INFO: Competetive: True
0:47:01.616146 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:01.631690 WARNING: FDR calculation for 200037 target and 117308 decoy PSMs
0:47:01.631824 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
0:47:01.696296 INFO: Using random state 984935 for train-test-split
0:47:05.933690 INFO: Test AUC: 0.877
0:47:05.933847 INFO: Train AUC: 0.878
0:47:05.933879 INFO: AUC difference: 0.12%
0:47:06.244622 INFO: Resetting torch num_threads to 80
0:47:06.525928 PROGRESS: ============================= Precursor FDR =============================
0:47:06.526185 PROGRESS: Total precursors accumulated: 105,959
0:47:06.526267 PROGRESS: Target precursors: 104,910 (99.01%)
0:47:06.526322 PROGRESS: Decoy precursors: 1,049 (0.99%)
0:47:06.526366 PROGRESS: 
0:47:06.526412 PROGRESS: Precursor Summary:
0:47:06.551220 PROGRESS: Channel   0:	 0.050 FDR: 104,910; 0.010 FDR: 104,910; 0.001 FDR: 95,179
0:47:06.551455 PROGRESS: 
0:47:06.551517 PROGRESS: Protein Summary:
0:47:06.586909 PROGRESS: Channel   0:	 0.050 FDR: 9,969; 0.010 FDR: 9,969; 0.001 FDR: 9,843
0:47:06.587139 PROGRESS: =========================================================================
0:47:06.588883 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/psm.parquet
0:47:23.322933 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.parquet
0:47:23.600668 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:47:23.684935 PROGRESS: 
0:47:23.685078 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant
0:47:23.685145 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/figures
0:47:23.685304 INFO: Initializing TimingManager
0:47:23.685715 INFO: Initializing RawFileManager
0:47:34.414866 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.
0:47:34.418917 INFO: Determining DIA cycle
0:47:34.435202 INFO: Found cycle with start 0.00 min and length 300.
0:47:34.600685 INFO: RT (min)            : 0.0 - 26.9
0:47:34.600779 INFO: RT duration (sec)   : 1611.2
0:47:34.600808 INFO: RT duration (min)   : 26.9
0:47:34.600833 INFO: Cycle len (scans)   : 300
0:47:34.600853 INFO: Cycle len (sec)     : 1.65
0:47:34.600873 INFO: Number of cycles    : 978
0:47:34.600890 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:47:34.600922 INFO: Creating DIA data object took: 10.915111303329468
0:47:35.277303 INFO: Creating DIA data NG object took: 0.6762416362762451
0:47:35.295756 INFO: Initializing CalibrationManager
0:47:35.296032 INFO: Setting up calibration estimators ..
0:47:35.296093 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:47:35.296178 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'}' ..
0:47:35.296264 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:47:35.296313 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:47:35.296367 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}}' ..
0:47:35.296416 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:47:35.296458 INFO: Done setting up calibration estimators.
0:47:35.296635 INFO: Initializing OptimizationManager
0:47:35.296749 INFO: initial parameter: ms1_error = 30
0:47:35.296799 INFO: initial parameter: ms2_error = 30
0:47:35.296843 INFO: initial parameter: rt_error = 805.611083984375
0:47:35.296884 INFO: initial parameter: mobility_error = 0.1
0:47:35.296923 INFO: initial parameter: num_candidates = 1
0:47:35.296963 INFO: initial parameter: fwhm_rt = 5
0:47:35.297015 INFO: initial parameter: fwhm_mobility = 0.01
0:47:35.297059 INFO: initial parameter: score_cutoff = 0
0:47:35.297096 INFO: initial parameter: classifier_version = -1
0:47:35.297162 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:47:35.297403 INFO: FDRManager: loading saved state not requested, will be initialized.
0:47:35.297436 INFO: Initializing FDRManager
0:47:35.297472 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:47:35.321263 PROGRESS: Initializing spectral library: 115,864 target precursors potentially observable (0 removed)
0:47:35.338239 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:47:35.338583 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
0:47:35.338682 PROGRESS: Starting initial search for precursors.
0:47:35.338759 INFO: Starting optimization step 0.
0:47:35.338820 PROGRESS: === Extracting elution groups 0 to 200 ===
0:47:35.338876 INFO: Using ng extraction backend
0:47:35.338933 PROGRESS: Extracting batch of 397 precursors
0:47:35.342896 INFO: === Search parameters used ===
0:47:35.342995 INFO: rt_error       : 805.611083984375
0:47:35.343045 INFO: mobility_error : 0.1
0:47:35.343090 INFO: num_candidates : 1
0:47:35.343131 INFO: ms1_error      : 30
0:47:35.343171 INFO: ms2_error      : 30
0:47:35.343211 INFO: fwhm_rt        : 5
0:47:35.343250 INFO: quant_window   : 3
0:47:35.343288 INFO: ==============================================
0:47:35.360515 INFO: performing precursor FDR with 40 features
0:47:35.360620 INFO: Decoy channel: -1
0:47:35.360645 INFO: Competetive: True
0:47:35.361593 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:35.363695 INFO: Using random state 736536 for train-test-split
0:47:35.370334 INFO: Test AUC: 0.259
0:47:35.370389 INFO: Train AUC: 0.293
0:47:35.370418 INFO: AUC difference: 11.50%
0:47:35.370452 WARNING: AUC difference > 5%. This may indicate overfitting.
0:47:35.579156 INFO: Resetting torch num_threads to 80
0:47:35.580437 PROGRESS: === Extracted 397 precursors and 2702 fragments ===
0:47:35.580763 INFO: === FDR correction performed with classifier version -1 ===
0:47:35.581203 PROGRESS: ============================= Precursor FDR =============================
0:47:35.581290 PROGRESS: Total precursors accumulated: 0
0:47:35.581360 PROGRESS: Target precursors: 0 (0.00%)
0:47:35.581409 PROGRESS: Decoy precursors: 0 (0.00%)
0:47:35.581454 PROGRESS: 
0:47:35.581495 PROGRESS: Precursor Summary:
0:47:35.581600 PROGRESS: 
0:47:35.581660 PROGRESS: Protein Summary:
0:47:35.581728 PROGRESS: =========================================================================
0:47:35.581902 INFO: Target number of precursors not reached yet.
0:47:35.585544 INFO: Starting optimization step 1.
0:47:35.585650 PROGRESS: === Extracting elution groups 200 to 600 ===
0:47:35.585724 INFO: Using ng extraction backend
0:47:35.585787 PROGRESS: Extracting batch of 797 precursors
0:47:35.588400 INFO: === Search parameters used ===
0:47:35.588481 INFO: rt_error       : 805.611083984375
0:47:35.588531 INFO: mobility_error : 0.1
0:47:35.588574 INFO: num_candidates : 1
0:47:35.588615 INFO: ms1_error      : 30
0:47:35.588656 INFO: ms2_error      : 30
0:47:35.588698 INFO: fwhm_rt        : 5
0:47:35.588738 INFO: quant_window   : 3
0:47:35.588777 INFO: ==============================================
0:47:35.613423 INFO: performing precursor FDR with 40 features
0:47:35.613530 INFO: Decoy channel: -1
0:47:35.613556 INFO: Competetive: True
0:47:35.616341 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:35.617828 INFO: Using random state 423760 for train-test-split
0:47:35.625866 INFO: Test AUC: 0.290
0:47:35.625922 INFO: Train AUC: 0.298
0:47:35.625952 INFO: AUC difference: 2.75%
0:47:35.833271 INFO: Resetting torch num_threads to 80
0:47:35.835244 PROGRESS: === Extracted 1192 precursors and 8182 fragments ===
0:47:35.835582 INFO: === FDR correction performed with classifier version -1 ===
0:47:35.836016 PROGRESS: ============================= Precursor FDR =============================
0:47:35.836102 PROGRESS: Total precursors accumulated: 0
0:47:35.836162 PROGRESS: Target precursors: 0 (0.00%)
0:47:35.836213 PROGRESS: Decoy precursors: 0 (0.00%)
0:47:35.836261 PROGRESS: 
0:47:35.836306 PROGRESS: Precursor Summary:
0:47:35.836413 PROGRESS: 
0:47:35.836474 PROGRESS: Protein Summary:
0:47:35.836554 PROGRESS: =========================================================================
0:47:35.836747 INFO: Target number of precursors not reached yet.
0:47:35.841357 INFO: Starting optimization step 2.
0:47:35.841464 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:47:35.841537 INFO: Using ng extraction backend
0:47:35.841596 PROGRESS: Extracting batch of 1593 precursors
0:47:35.845591 INFO: === Search parameters used ===
0:47:35.845692 INFO: rt_error       : 805.611083984375
0:47:35.845744 INFO: mobility_error : 0.1
0:47:35.845791 INFO: num_candidates : 1
0:47:35.845833 INFO: ms1_error      : 30
0:47:35.845878 INFO: ms2_error      : 30
0:47:35.845922 INFO: fwhm_rt        : 5
0:47:35.845963 INFO: quant_window   : 3
0:47:35.846003 INFO: ==============================================
0:47:35.876387 INFO: performing precursor FDR with 40 features
0:47:35.876467 INFO: Decoy channel: -1
0:47:35.876493 INFO: Competetive: True
0:47:35.879550 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:35.881304 INFO: Using random state 966421 for train-test-split
0:47:35.891918 INFO: Test AUC: 0.266
0:47:35.891981 INFO: Train AUC: 0.288
0:47:35.892011 INFO: AUC difference: 7.61%
0:47:35.892032 WARNING: AUC difference > 5%. This may indicate overfitting.
0:47:36.096986 INFO: Resetting torch num_threads to 80
0:47:36.099276 PROGRESS: === Extracted 2783 precursors and 19406 fragments ===
0:47:36.099612 INFO: === FDR correction performed with classifier version -1 ===
0:47:36.100045 PROGRESS: ============================= Precursor FDR =============================
0:47:36.100130 PROGRESS: Total precursors accumulated: 0
0:47:36.100187 PROGRESS: Target precursors: 0 (0.00%)
0:47:36.100237 PROGRESS: Decoy precursors: 0 (0.00%)
0:47:36.100282 PROGRESS: 
0:47:36.100334 PROGRESS: Precursor Summary:
0:47:36.100442 PROGRESS: 
0:47:36.100504 PROGRESS: Protein Summary:
0:47:36.100575 PROGRESS: =========================================================================
0:47:36.100773 INFO: Target number of precursors not reached yet.
0:47:36.107009 INFO: Starting optimization step 3.
0:47:36.107114 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:47:36.107184 INFO: Using ng extraction backend
0:47:36.107241 PROGRESS: Extracting batch of 3185 precursors
0:47:36.114296 INFO: === Search parameters used ===
0:47:36.114398 INFO: rt_error       : 805.611083984375
0:47:36.114454 INFO: mobility_error : 0.1
0:47:36.114499 INFO: num_candidates : 1
0:47:36.114538 INFO: ms1_error      : 30
0:47:36.114577 INFO: ms2_error      : 30
0:47:36.114625 INFO: fwhm_rt        : 5
0:47:36.114664 INFO: quant_window   : 3
0:47:36.114705 INFO: ==============================================
0:47:36.159490 INFO: performing precursor FDR with 40 features
0:47:36.159572 INFO: Decoy channel: -1
0:47:36.159598 INFO: Competetive: True
0:47:36.164202 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:36.166447 INFO: Using random state 570727 for train-test-split
0:47:36.184595 INFO: Test AUC: 0.287
0:47:36.184664 INFO: Train AUC: 0.285
0:47:36.184693 INFO: AUC difference: 0.68%
0:47:36.397313 INFO: Resetting torch num_threads to 80
0:47:36.400325 PROGRESS: === Extracted 5965 precursors and 41691 fragments ===
0:47:36.400660 INFO: === FDR correction performed with classifier version -1 ===
0:47:36.401096 PROGRESS: ============================= Precursor FDR =============================
0:47:36.401184 PROGRESS: Total precursors accumulated: 0
0:47:36.401250 PROGRESS: Target precursors: 0 (0.00%)
0:47:36.401301 PROGRESS: Decoy precursors: 0 (0.00%)
0:47:36.401347 PROGRESS: 
0:47:36.401389 PROGRESS: Precursor Summary:
0:47:36.401494 PROGRESS: 
0:47:36.401553 PROGRESS: Protein Summary:
0:47:36.401622 PROGRESS: =========================================================================
0:47:36.401839 INFO: Target number of precursors not reached yet.
0:47:36.411247 INFO: Starting optimization step 4.
0:47:36.411362 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:47:36.411434 INFO: Using ng extraction backend
0:47:36.411493 PROGRESS: Extracting batch of 6366 precursors
0:47:36.423345 INFO: === Search parameters used ===
0:47:36.423448 INFO: rt_error       : 805.611083984375
0:47:36.423496 INFO: mobility_error : 0.1
0:47:36.423541 INFO: num_candidates : 1
0:47:36.423583 INFO: ms1_error      : 30
0:47:36.423622 INFO: ms2_error      : 30
0:47:36.423662 INFO: fwhm_rt        : 5
0:47:36.423700 INFO: quant_window   : 3
0:47:36.423738 INFO: ==============================================
0:47:36.494454 INFO: performing precursor FDR with 40 features
0:47:36.494563 INFO: Decoy channel: -1
0:47:36.494589 INFO: Competetive: True
0:47:36.499760 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:36.502769 INFO: Using random state 299130 for train-test-split
0:47:36.540592 INFO: Test AUC: 0.282
0:47:36.540677 INFO: Train AUC: 0.292
0:47:36.540708 INFO: AUC difference: 3.52%
0:47:36.753474 INFO: Resetting torch num_threads to 80
0:47:36.757134 PROGRESS: === Extracted 12324 precursors and 86198 fragments ===
0:47:36.757496 INFO: === FDR correction performed with classifier version -1 ===
0:47:36.757931 PROGRESS: ============================= Precursor FDR =============================
0:47:36.758017 PROGRESS: Total precursors accumulated: 0
0:47:36.758076 PROGRESS: Target precursors: 0 (0.00%)
0:47:36.758125 PROGRESS: Decoy precursors: 0 (0.00%)
0:47:36.758169 PROGRESS: 
0:47:36.758212 PROGRESS: Precursor Summary:
0:47:36.758313 PROGRESS: 
0:47:36.758373 PROGRESS: Protein Summary:
0:47:36.758442 PROGRESS: =========================================================================
0:47:36.758702 INFO: Target number of precursors not reached yet.
0:47:36.774066 INFO: Starting optimization step 5.
0:47:36.774238 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:47:36.774316 INFO: Using ng extraction backend
0:47:36.774376 PROGRESS: Extracting batch of 12747 precursors
0:47:36.796574 INFO: === Search parameters used ===
0:47:36.796713 INFO: rt_error       : 805.611083984375
0:47:36.796762 INFO: mobility_error : 0.1
0:47:36.796808 INFO: num_candidates : 1
0:47:36.796850 INFO: ms1_error      : 30
0:47:36.796890 INFO: ms2_error      : 30
0:47:36.796932 INFO: fwhm_rt        : 5
0:47:36.796982 INFO: quant_window   : 3
0:47:36.797035 INFO: ==============================================
0:47:36.923419 INFO: performing precursor FDR with 40 features
0:47:36.923536 INFO: Decoy channel: -1
0:47:36.923561 INFO: Competetive: True
0:47:36.932523 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:36.937687 INFO: Using random state 948994 for train-test-split
0:47:37.177178 INFO: Test AUC: 0.816
0:47:37.177290 INFO: Train AUC: 0.807
0:47:37.177319 INFO: AUC difference: 1.22%
0:47:37.403424 INFO: Resetting torch num_threads to 80
0:47:37.412526 PROGRESS: === Extracted 25060 precursors and 175702 fragments ===
0:47:37.413264 INFO: === FDR correction performed with classifier version -1 ===
0:47:37.414287 PROGRESS: ============================= Precursor FDR =============================
0:47:37.414382 PROGRESS: Total precursors accumulated: 3,481
0:47:37.414443 PROGRESS: Target precursors: 3,447 (99.02%)
0:47:37.414494 PROGRESS: Decoy precursors: 34 (0.98%)
0:47:37.414539 PROGRESS: 
0:47:37.414583 PROGRESS: Precursor Summary:
0:47:37.416342 PROGRESS: Channel   0:	 0.050 FDR: 3,447; 0.010 FDR: 3,447; 0.001 FDR: 1,599
0:47:37.416438 PROGRESS: 
0:47:37.416493 PROGRESS: Protein Summary:
0:47:37.418920 PROGRESS: Channel   0:	 0.050 FDR: 2,144; 0.010 FDR: 2,144; 0.001 FDR: 1,104
0:47:37.419019 PROGRESS: =========================================================================
0:47:37.419551 INFO: Target number of precursors reached.
0:47:37.444687 INFO: fragments_df: keeping 5000 of 175702 [sum(precursor_idx_mask)=38500 sum(mass_error_mask)=175702 stop_rank=5000
0:47:37.454929 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:37.918731 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:38.607284 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:47:38.607899 INFO: Using score_cutoff 14.412561575317381 (fac=0.99, q=1)
0:47:38.608268 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:47:38.608346 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:47:38.608400 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.412561575317381
0:47:38.608454 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:38.611062 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:38.615302 INFO: Updating optimization_manager: classifier_version  : -1 -> 5
0:47:38.615406 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:47:38.615485 INFO: Starting optimization step 6.
0:47:38.615545 PROGRESS: === Extracting elution groups 0 to 1400 ===
0:47:38.615608 INFO: Using ng extraction backend
0:47:38.615666 PROGRESS: Extracting batch of 2787 precursors
0:47:38.622664 INFO: === Search parameters used ===
0:47:38.622772 INFO: rt_error       : 805.611083984375
0:47:38.622824 INFO: mobility_error : 0.1
0:47:38.622870 INFO: num_candidates : 3
0:47:38.622911 INFO: ms1_error      : 30
0:47:38.622950 INFO: ms2_error      : 30
0:47:38.622991 INFO: fwhm_rt        : 3.0
0:47:38.623031 INFO: quant_window   : 3
0:47:38.623069 INFO: ==============================================
0:47:38.689626 INFO: performing precursor FDR with 40 features
0:47:38.689774 INFO: Decoy channel: -1
0:47:38.689801 INFO: Competetive: True
0:47:38.693520 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:38.696265 INFO: Using random state 698635 for train-test-split
0:47:38.715806 INFO: Test AUC: 0.659
0:47:38.715914 INFO: Train AUC: 0.654
0:47:38.715943 INFO: AUC difference: 0.67%
0:47:38.937552 INFO: Resetting torch num_threads to 80
0:47:38.939604 PROGRESS: === Extracted 8348 precursors and 50751 fragments ===
0:47:38.939984 INFO: === FDR correction performed with classifier version 5 ===
0:47:38.940459 PROGRESS: ============================= Precursor FDR =============================
0:47:38.940545 PROGRESS: Total precursors accumulated: 442
0:47:38.940601 PROGRESS: Target precursors: 438 (99.10%)
0:47:38.940652 PROGRESS: Decoy precursors: 4 (0.90%)
0:47:38.940696 PROGRESS: 
0:47:38.940738 PROGRESS: Precursor Summary:
0:47:38.941727 PROGRESS: Channel   0:	 0.050 FDR:   438; 0.010 FDR:   438; 0.001 FDR:   277
0:47:38.941819 PROGRESS: 
0:47:38.941874 PROGRESS: Protein Summary:
0:47:38.943031 PROGRESS: Channel   0:	 0.050 FDR:   398; 0.010 FDR:   398; 0.001 FDR:   254
0:47:38.943123 PROGRESS: =========================================================================
0:47:38.943652 INFO: Target number of precursors reached.
0:47:38.949946 INFO: fragments_df: keeping 5000 of 50751 [sum(precursor_idx_mask)=10137 sum(mass_error_mask)=50751 stop_rank=5000
0:47:38.958477 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:39.088762 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:39.735166 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:39.735719 INFO: Using score_cutoff 15.63824774236679 (fac=0.99, q=1)
0:47:39.736042 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:39.736130 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:39.736186 INFO: Updating optimization_manager: score_cutoff        : 14.412561575317381 -> 15.63824774236679
0:47:39.736239 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:39.738847 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:39.742941 INFO: === checking if optimization conditions were reached ===
0:47:39.744595 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:47:39.744697 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
0:47:39.744764 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:47:39.744826 INFO: ==============================================
0:47:39.744889 INFO: Starting optimization step 7.
0:47:39.744947 PROGRESS: === Extracting elution groups 0 to 1400 ===
0:47:39.745017 INFO: Using ng extraction backend
0:47:39.745078 PROGRESS: Extracting batch of 2787 precursors
0:47:39.752216 INFO: === Search parameters used ===
0:47:39.752331 INFO: rt_error       : 805.611083984375
0:47:39.752383 INFO: mobility_error : 0.1
0:47:39.752431 INFO: num_candidates : 3
0:47:39.752478 INFO: ms1_error      : 30
0:47:39.752520 INFO: ms2_error      : 10.0
0:47:39.752563 INFO: fwhm_rt        : 3.0
0:47:39.752619 INFO: quant_window   : 3
0:47:39.752662 INFO: ==============================================
0:47:39.820137 INFO: performing precursor FDR with 40 features
0:47:39.820291 INFO: Decoy channel: -1
0:47:39.820317 INFO: Competetive: True
0:47:39.823797 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:39.826488 INFO: Using random state 282403 for train-test-split
0:47:39.846308 INFO: Test AUC: 0.661
0:47:39.846424 INFO: Train AUC: 0.688
0:47:39.846453 INFO: AUC difference: 4.01%
0:47:40.066890 INFO: Resetting torch num_threads to 80
0:47:40.069036 PROGRESS: === Extracted 8360 precursors and 56945 fragments ===
0:47:40.069421 INFO: === FDR correction performed with classifier version 6 ===
0:47:40.069957 PROGRESS: ============================= Precursor FDR =============================
0:47:40.070047 PROGRESS: Total precursors accumulated: 839
0:47:40.070106 PROGRESS: Target precursors: 831 (99.05%)
0:47:40.070156 PROGRESS: Decoy precursors: 8 (0.95%)
0:47:40.070205 PROGRESS: 
0:47:40.070250 PROGRESS: Precursor Summary:
0:47:40.071324 PROGRESS: Channel   0:	 0.050 FDR:   831; 0.010 FDR:   831; 0.001 FDR:   615
0:47:40.071417 PROGRESS: 
0:47:40.071472 PROGRESS: Protein Summary:
0:47:40.072867 PROGRESS: Channel   0:	 0.050 FDR:   729; 0.010 FDR:   729; 0.001 FDR:   550
0:47:40.072960 PROGRESS: =========================================================================
0:47:40.073268 INFO: Target number of precursors reached.
0:47:40.081593 INFO: fragments_df: keeping 5000 of 56945 [sum(precursor_idx_mask)=19999 sum(mass_error_mask)=56945 stop_rank=5000
0:47:40.087323 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:40.258711 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:40.941767 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:40.942328 INFO: Using score_cutoff 12.916725179672241 (fac=0.99, q=1)
0:47:40.942664 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:40.942744 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:40.942800 INFO: Updating optimization_manager: score_cutoff        : 15.63824774236679 -> 12.916725179672241
0:47:40.942863 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:40.944630 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:40.946804 INFO: === checking if optimization conditions were reached ===
0:47:40.948410 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:47:40.948509 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:47:40.948575 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:47:40.948632 INFO: ==============================================
0:47:40.948694 PROGRESS: Optimization finished for ms2_error.
0:47:40.954098 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:40.955424 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:40.957577 INFO: Starting optimization step 0.
0:47:40.957677 PROGRESS: === Extracting elution groups 0 to 600 ===
0:47:40.957750 INFO: Using ng extraction backend
0:47:40.957810 PROGRESS: Extracting batch of 1194 precursors
0:47:40.962043 INFO: === Search parameters used ===
0:47:40.962157 INFO: rt_error       : 805.611083984375
0:47:40.962218 INFO: mobility_error : 0.1
0:47:40.962265 INFO: num_candidates : 3
0:47:40.962306 INFO: ms1_error      : 30
0:47:40.962348 INFO: ms2_error      : 10.0
0:47:40.962388 INFO: fwhm_rt        : 3.0
0:47:40.962426 INFO: quant_window   : 3
0:47:40.962464 INFO: ==============================================
0:47:41.001672 INFO: performing precursor FDR with 40 features
0:47:41.001774 INFO: Decoy channel: -1
0:47:41.001801 INFO: Competetive: True
0:47:41.004583 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:41.006492 INFO: Using random state 99247 for train-test-split
0:47:41.017794 INFO: Test AUC: 0.710
0:47:41.017871 INFO: Train AUC: 0.674
0:47:41.017901 INFO: AUC difference: 5.46%
0:47:41.017926 WARNING: AUC difference > 5%. This may indicate overfitting.
0:47:41.230862 INFO: Resetting torch num_threads to 80
0:47:41.232730 PROGRESS: === Extracted 3582 precursors and 24373 fragments ===
0:47:41.233140 INFO: === FDR correction performed with classifier version 7 ===
0:47:41.233634 PROGRESS: ============================= Precursor FDR =============================
0:47:41.233721 PROGRESS: Total precursors accumulated: 310
0:47:41.233778 PROGRESS: Target precursors: 307 (99.03%)
0:47:41.233825 PROGRESS: Decoy precursors: 3 (0.97%)
0:47:41.233869 PROGRESS: 
0:47:41.233911 PROGRESS: Precursor Summary:
0:47:41.234828 PROGRESS: Channel   0:	 0.050 FDR:   307; 0.010 FDR:   307; 0.001 FDR:   238
0:47:41.234917 PROGRESS: 
0:47:41.234971 PROGRESS: Protein Summary:
0:47:41.236063 PROGRESS: Channel   0:	 0.050 FDR:   290; 0.010 FDR:   290; 0.001 FDR:   228
0:47:41.236151 PROGRESS: =========================================================================
0:47:41.236425 INFO: Target number of precursors reached.
0:47:41.240330 INFO: fragments_df: keeping 3479 of 24373 [sum(precursor_idx_mask)=7405 sum(mass_error_mask)=24373 stop_rank=3479
0:47:41.245894 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:41.367233 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:41.824400 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:41.824960 INFO: Using score_cutoff 12.727837750053405 (fac=0.99, q=1)
0:47:41.825299 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:41.825380 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:41.825436 INFO: Updating optimization_manager: score_cutoff        : 12.916725179672241 -> 12.727837750053405
0:47:41.825491 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:41.827295 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:41.829532 INFO: === checking if optimization conditions were reached ===
0:47:41.829652 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:47:41.831176 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 43.111417052220695
0:47:41.831292 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 43.1114.
0:47:41.831361 INFO: ==============================================
0:47:41.831426 INFO: Starting optimization step 1.
0:47:41.831486 PROGRESS: === Extracting elution groups 0 to 600 ===
0:47:41.831548 INFO: Using ng extraction backend
0:47:41.831604 PROGRESS: Extracting batch of 1194 precursors
0:47:41.835871 INFO: === Search parameters used ===
0:47:41.835996 INFO: rt_error       : 43.111417052220695
0:47:41.836051 INFO: mobility_error : 0.1
0:47:41.836097 INFO: num_candidates : 3
0:47:41.836141 INFO: ms1_error      : 30
0:47:41.836184 INFO: ms2_error      : 10.0
0:47:41.836225 INFO: fwhm_rt        : 3.0
0:47:41.836266 INFO: quant_window   : 3
0:47:41.836306 INFO: ==============================================
0:47:41.874930 INFO: performing precursor FDR with 40 features
0:47:41.875028 INFO: Decoy channel: -1
0:47:41.875055 INFO: Competetive: True
0:47:41.877735 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:41.879577 INFO: Using random state 99247 for train-test-split
0:47:41.890924 INFO: Test AUC: 0.765
0:47:41.890997 INFO: Train AUC: 0.712
0:47:41.891026 INFO: AUC difference: 7.41%
0:47:41.891049 WARNING: AUC difference > 5%. This may indicate overfitting.
0:47:42.113169 INFO: Resetting torch num_threads to 80
0:47:42.115006 PROGRESS: === Extracted 3283 precursors and 19283 fragments ===
0:47:42.115397 INFO: === FDR correction performed with classifier version 7 ===
0:47:42.115857 PROGRESS: ============================= Precursor FDR =============================
0:47:42.115944 PROGRESS: Total precursors accumulated: 362
0:47:42.116005 PROGRESS: Target precursors: 359 (99.17%)
0:47:42.116055 PROGRESS: Decoy precursors: 3 (0.83%)
0:47:42.116100 PROGRESS: 
0:47:42.116141 PROGRESS: Precursor Summary:
0:47:42.117139 PROGRESS: Channel   0:	 0.050 FDR:   359; 0.010 FDR:   359; 0.001 FDR:   267
0:47:42.117233 PROGRESS: 
0:47:42.117288 PROGRESS: Protein Summary:
0:47:42.118424 PROGRESS: Channel   0:	 0.050 FDR:   339; 0.010 FDR:   339; 0.001 FDR:   253
0:47:42.118514 PROGRESS: =========================================================================
0:47:42.118754 INFO: Target number of precursors reached.
0:47:42.122341 INFO: fragments_df: keeping 3401 of 19283 [sum(precursor_idx_mask)=7065 sum(mass_error_mask)=19283 stop_rank=3401
0:47:42.127902 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:42.251381 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:42.701517 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:42.702086 INFO: Using score_cutoff 12.364024986076354 (fac=0.99, q=1)
0:47:42.702410 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:42.702490 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:42.702543 INFO: Updating optimization_manager: score_cutoff        : 12.727837750053405 -> 12.364024986076354
0:47:42.702597 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:42.704386 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:42.706592 INFO: === checking if optimization conditions were reached ===
0:47:42.706696 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:47:42.708349 INFO: Updating optimization_manager: rt_error            : 43.111417052220695 -> 12.774709455906361
0:47:42.708452 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 12.7747.
0:47:42.708518 INFO: ==============================================
0:47:42.708584 INFO: Starting optimization step 2.
0:47:42.708643 PROGRESS: === Extracting elution groups 0 to 600 ===
0:47:42.708708 INFO: Using ng extraction backend
0:47:42.708778 PROGRESS: Extracting batch of 1194 precursors
0:47:42.712885 INFO: === Search parameters used ===
0:47:42.712998 INFO: rt_error       : 12.774709455906361
0:47:42.713052 INFO: mobility_error : 0.1
0:47:42.713097 INFO: num_candidates : 3
0:47:42.713146 INFO: ms1_error      : 30
0:47:42.713189 INFO: ms2_error      : 10.0
0:47:42.713228 INFO: fwhm_rt        : 3.0
0:47:42.713267 INFO: quant_window   : 3
0:47:42.713305 INFO: ==============================================
0:47:42.749720 INFO: performing precursor FDR with 40 features
0:47:42.749810 INFO: Decoy channel: -1
0:47:42.749836 INFO: Competetive: True
0:47:42.752548 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:42.754372 INFO: Using random state 99247 for train-test-split
0:47:42.766126 INFO: Test AUC: 0.742
0:47:42.766201 INFO: Train AUC: 0.721
0:47:42.766230 INFO: AUC difference: 2.99%
0:47:42.987940 INFO: Resetting torch num_threads to 80
0:47:42.989761 PROGRESS: === Extracted 3284 precursors and 19300 fragments ===
0:47:42.990144 INFO: === FDR correction performed with classifier version 7 ===
0:47:42.990608 PROGRESS: ============================= Precursor FDR =============================
0:47:42.990693 PROGRESS: Total precursors accumulated: 362
0:47:42.990750 PROGRESS: Target precursors: 359 (99.17%)
0:47:42.990800 PROGRESS: Decoy precursors: 3 (0.83%)
0:47:42.990847 PROGRESS: 
0:47:42.990891 PROGRESS: Precursor Summary:
0:47:42.991838 PROGRESS: Channel   0:	 0.050 FDR:   359; 0.010 FDR:   359; 0.001 FDR:   264
0:47:42.991928 PROGRESS: 
0:47:42.991982 PROGRESS: Protein Summary:
0:47:42.993137 PROGRESS: Channel   0:	 0.050 FDR:   339; 0.010 FDR:   339; 0.001 FDR:   250
0:47:42.993243 PROGRESS: =========================================================================
0:47:42.993475 INFO: Target number of precursors reached.
0:47:42.997118 INFO: fragments_df: keeping 3400 of 19300 [sum(precursor_idx_mask)=7070 sum(mass_error_mask)=19300 stop_rank=3400
0:47:43.002692 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:43.125695 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:45.641254 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:45.641675 INFO: Using score_cutoff 12.364024986076354 (fac=0.99, q=1)
0:47:45.641958 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:45.642037 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:45.642090 INFO: Updating optimization_manager: score_cutoff        : 12.364024986076354 -> 12.364024986076354
0:47:45.642142 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:45.643687 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:45.645864 INFO: === checking if optimization conditions were reached ===
0:47:45.645961 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:47:45.647585 INFO: Updating optimization_manager: rt_error            : 12.774709455906361 -> 12.774709455898018
0:47:45.647685 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 12.7747.
0:47:45.647747 INFO: ==============================================
0:47:45.647812 INFO: Starting optimization step 3.
0:47:45.647876 PROGRESS: === Extracting elution groups 0 to 600 ===
0:47:45.647938 INFO: Using ng extraction backend
0:47:45.647995 PROGRESS: Extracting batch of 1194 precursors
0:47:45.651329 INFO: === Search parameters used ===
0:47:45.651424 INFO: rt_error       : 12.774709455898018
0:47:45.651473 INFO: mobility_error : 0.1
0:47:45.651518 INFO: num_candidates : 3
0:47:45.651559 INFO: ms1_error      : 30
0:47:45.651599 INFO: ms2_error      : 10.0
0:47:45.651639 INFO: fwhm_rt        : 3.0
0:47:45.651677 INFO: quant_window   : 3
0:47:45.651716 INFO: ==============================================
0:47:45.683779 INFO: performing precursor FDR with 40 features
0:47:45.683861 INFO: Decoy channel: -1
0:47:45.683887 INFO: Competetive: True
0:47:45.686403 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:45.688068 INFO: Using random state 99247 for train-test-split
0:47:45.700791 INFO: Test AUC: 0.726
0:47:45.700858 INFO: Train AUC: 0.725
0:47:45.700889 INFO: AUC difference: 0.22%
0:47:45.919482 INFO: Resetting torch num_threads to 80
0:47:45.921000 PROGRESS: === Extracted 3285 precursors and 19310 fragments ===
0:47:45.921330 INFO: === FDR correction performed with classifier version 7 ===
0:47:45.921787 PROGRESS: ============================= Precursor FDR =============================
0:47:45.921873 PROGRESS: Total precursors accumulated: 362
0:47:45.921930 PROGRESS: Target precursors: 359 (99.17%)
0:47:45.921979 PROGRESS: Decoy precursors: 3 (0.83%)
0:47:45.922023 PROGRESS: 
0:47:45.922065 PROGRESS: Precursor Summary:
0:47:45.922984 PROGRESS: Channel   0:	 0.050 FDR:   359; 0.010 FDR:   359; 0.001 FDR:   264
0:47:45.923072 PROGRESS: 
0:47:45.923133 PROGRESS: Protein Summary:
0:47:45.924233 PROGRESS: Channel   0:	 0.050 FDR:   339; 0.010 FDR:   339; 0.001 FDR:   250
0:47:45.924323 PROGRESS: =========================================================================
0:47:45.924520 INFO: Target number of precursors reached.
0:47:45.927984 INFO: fragments_df: keeping 3404 of 19310 [sum(precursor_idx_mask)=7078 sum(mass_error_mask)=19310 stop_rank=3404
0:47:45.932848 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:46.055390 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:46.500163 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:46.500577 INFO: Using score_cutoff 12.364024986076354 (fac=0.99, q=1)
0:47:46.500863 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:46.500943 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:46.501012 INFO: Updating optimization_manager: score_cutoff        : 12.364024986076354 -> 12.364024986076354
0:47:46.501069 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:46.502651 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:46.504781 INFO: === checking if optimization conditions were reached ===
0:47:46.504880 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:47:46.505746 INFO: Updating optimization_manager: rt_error            : 12.774709455898018 -> 12.774709455898018
0:47:46.505874 INFO: Updating optimization_manager: classifier_version  : 7 -> 11
0:47:46.505971 INFO: Updating optimization_manager: score_cutoff        : 12.364024986076354 -> 12.364024986076354
0:47:46.506208 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:46.506296 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:46.506379 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 12.7747 found after 4 searches.
0:47:46.506442 INFO: ==============================================
0:47:46.506506 PROGRESS: Optimization finished for rt_error.
0:47:46.511050 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:46.512374 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:46.539547 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:47:46.539690 PROGRESS: ==============================================
0:47:46.539759 PROGRESS: ms2_error      : 10.0000
0:47:46.539815 PROGRESS: rt_error       : 12.7747
0:47:46.539861 PROGRESS: ==============================================
0:47:46.540256 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:46.664708 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:46.999848 INFO: Using ng extraction backend
0:47:47.000151 PROGRESS: Extracting batch of 230645 precursors
0:47:47.365804 INFO: === Search parameters used ===
0:47:47.366041 INFO: rt_error       : 12.774709455898018
0:47:47.366101 INFO: mobility_error : 0.1
0:47:47.366149 INFO: num_candidates : 3
0:47:47.366205 INFO: ms1_error      : 30
0:47:47.366252 INFO: ms2_error      : 10.0
0:47:47.366299 INFO: fwhm_rt        : 3.0
0:47:47.366340 INFO: quant_window   : 3
0:47:47.366380 INFO: ==============================================
0:47:47.612289 INFO: Removed 331705 precursors with score below cutoff 12.364024986076354
0:47:47.896666 INFO: performing precursor FDR with 40 features
0:47:47.896791 INFO: Decoy channel: -1
0:47:47.896817 INFO: Competetive: True
0:47:47.922558 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:47.937974 WARNING: FDR calculation for 194123 target and 109894 decoy PSMs
0:47:47.938103 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
0:47:48.000726 INFO: Using random state 440306 for train-test-split
0:47:51.954039 INFO: Test AUC: 0.874
0:47:51.954158 INFO: Train AUC: 0.878
0:47:51.954188 INFO: AUC difference: 0.45%
0:47:52.257142 INFO: Resetting torch num_threads to 80
0:47:52.539674 PROGRESS: ============================= Precursor FDR =============================
0:47:52.539915 PROGRESS: Total precursors accumulated: 104,146
0:47:52.539991 PROGRESS: Target precursors: 103,115 (99.01%)
0:47:52.540064 PROGRESS: Decoy precursors: 1,031 (0.99%)
0:47:52.540112 PROGRESS: 
0:47:52.540157 PROGRESS: Precursor Summary:
0:47:52.565511 PROGRESS: Channel   0:	 0.050 FDR: 103,115; 0.010 FDR: 103,115; 0.001 FDR: 92,488
0:47:52.565758 PROGRESS: 
0:47:52.565821 PROGRESS: Protein Summary:
0:47:52.600883 PROGRESS: Channel   0:	 0.050 FDR: 9,957; 0.010 FDR: 9,957; 0.001 FDR: 9,777
0:47:52.601134 PROGRESS: =========================================================================
0:47:52.602870 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/psm.parquet
0:47:52.778779 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.parquet
0:47:53.048198 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:47:53.622300 PROGRESS: Processing search outputs
0:47:53.622410 PROGRESS: Performing protein grouping and FDR
0:47:53.622443 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:47:53.677240 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:47:53.726825 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:47:53.781373 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:47:53.837506 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:47:53.887850 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:47:53.943064 INFO: Building combined output
0:47:53.962595 INFO: Performing protein inference
0:47:54.618460 INFO: Inference strategy: library. Using library grouping for protein inference
0:47:54.621170 INFO: Performing protein FDR
0:47:57.965744 INFO: Normalizing q-values using 9,993 targets and 3,246 decoys
0:47:57.969594 INFO: Test AUC: 1.000
0:47:57.969670 INFO: Train AUC: 1.000
0:47:57.969706 INFO: AUC difference: 0.00%
0:47:58.663089 PROGRESS: ================ Protein FDR =================
0:47:58.663232 PROGRESS: Unique protein groups in output
0:47:58.663262 PROGRESS:   1% protein FDR: 9,988
0:47:58.663282 PROGRESS: 
0:47:58.663300 PROGRESS: Unique precursor in output
0:47:58.663318 PROGRESS:   1% protein FDR: 114,009
0:47:58.663337 PROGRESS: ================================================
0:47:58.731238 PROGRESS: Building search statistics
0:47:58.851396 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
0:47:58.851583 INFO: Initializing OptimizationManager
0:47:58.851802 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
0:47:58.851873 INFO: Initializing CalibrationManager
0:47:58.852094 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
0:47:58.852168 INFO: Initializing RawFileManager
0:47:58.888554 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
0:47:58.888740 INFO: Initializing OptimizationManager
0:47:58.888959 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
0:47:58.889053 INFO: Initializing CalibrationManager
0:47:58.889272 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
0:47:58.889349 INFO: Initializing RawFileManager
0:47:58.926017 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
0:47:58.926200 INFO: Initializing OptimizationManager
0:47:58.926400 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
0:47:58.926479 INFO: Initializing CalibrationManager
0:47:58.926709 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
0:47:58.926789 INFO: Initializing RawFileManager
0:47:58.963416 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
0:47:58.963599 INFO: Initializing OptimizationManager
0:47:58.963794 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
0:47:58.963864 INFO: Initializing CalibrationManager
0:47:58.964077 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
0:47:58.964150 INFO: Initializing RawFileManager
0:47:59.001125 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
0:47:59.001308 INFO: Initializing OptimizationManager
0:47:59.001502 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
0:47:59.001573 INFO: Initializing CalibrationManager
0:47:59.002163 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
0:47:59.002240 INFO: Initializing RawFileManager
0:47:59.040165 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
0:47:59.040351 INFO: Initializing OptimizationManager
0:47:59.040546 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
0:47:59.040617 INFO: Initializing CalibrationManager
0:47:59.040824 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
0:47:59.040903 INFO: Initializing RawFileManager
0:47:59.044036 INFO: Writing stat output to disk
0:47:59.044099 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/stat.tsv to disk
0:47:59.055697 PROGRESS: Building internal statistics
0:47:59.055980 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
0:47:59.056028 INFO: Initializing TimingManager
0:47:59.056385 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
0:47:59.056426 INFO: Initializing TimingManager
0:47:59.056609 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
0:47:59.056647 INFO: Initializing TimingManager
0:47:59.056823 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
0:47:59.056870 INFO: Initializing TimingManager
0:47:59.057050 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
0:47:59.057088 INFO: Initializing TimingManager
0:47:59.057258 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
0:47:59.057292 INFO: Initializing TimingManager
0:47:59.057707 INFO: Writing internal output to disk
0:47:59.057752 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/internal.tsv to disk
0:47:59.058256 PROGRESS: Performing label free quantification
0:47:59.145574 INFO: Accumulating fragment data
0:47:59.145724 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:47:59.211704 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:48:00.587911 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:48:01.961318 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:48:03.369567 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:48:04.807652 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:48:06.484055 PROGRESS: Performing label free quantification on the precursor level
0:48:06.484189 INFO: Filtering fragments by quality
0:48:06.819951 INFO: Performing label-free quantification using directLFQ
0:48:07.899390 INFO: 114009 lfq-groups total
0:48:45.507568 INFO: using 80 processes
0:48:45.805117 INFO: lfq-object 0
0:48:45.917861 INFO: lfq-object 100
0:48:45.947172 INFO: lfq-object 400
0:48:46.025104 INFO: lfq-object 200
0:48:46.060402 INFO: lfq-object 500
0:48:46.078669 INFO: lfq-object 800
0:48:46.105660 INFO: lfq-object 1100
0:48:46.142322 INFO: lfq-object 300
0:48:46.172884 INFO: lfq-object 600
0:48:46.190753 INFO: lfq-object 900
0:48:46.216057 INFO: lfq-object 1200
0:48:46.247845 INFO: lfq-object 1500
0:48:46.272561 INFO: lfq-object 1800
0:48:46.284435 INFO: lfq-object 700
0:48:46.303159 INFO: lfq-object 1000
0:48:46.329324 INFO: lfq-object 1300
0:48:46.357000 INFO: lfq-object 1600
0:48:46.385950 INFO: lfq-object 1900
0:48:46.409950 INFO: lfq-object 2200
0:48:46.441834 INFO: lfq-object 1400
0:48:46.471920 INFO: lfq-object 1700
0:48:46.497115 INFO: lfq-object 2500
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0:50:09.139347 INFO: Writing precursor output to disk
0:50:09.139500 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/precursor.matrix.tsv to disk
0:50:09.742907 PROGRESS: Performing label free quantification on the pg level
0:50:09.743014 INFO: Filtering fragments by quality
0:50:10.151196 INFO: Performing label-free quantification using directLFQ
0:50:10.531473 INFO: 9988 lfq-groups total
0:50:29.167199 INFO: using 80 processes
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0:50:35.589897 INFO: Writing pg output to disk
0:50:35.590183 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/pg.matrix.tsv to disk
0:50:35.888181 INFO: Writing psm output to disk
0:50:35.888353 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark_MBR/precursors.tsv to disk
0:50:47.792104 PROGRESS: Building MBR spectral library
0:50:47.913611 INFO: Running MbrLibraryBuilder
0:50:48.248463 INFO: MBR spectral library contains 114,009 precursors, 9,988 proteins
0:50:48.248629 INFO: Writing MBR spectral library to disk
0:50:49.109093 PROGRESS: =================== Search Finished ===================
0:50:49.150215 WARNING: WARNING: Temp mmap arrays were written to /tmp/temp_mmap_pxw2xfac. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 1,069,847,166,976
