0:00:00.000031 INFO: Moved old log file ./run_output_Astral/alphadia_1.12.1_rs_benchmark/log.txt to run_output_Astral/alphadia_1.12.1_rs_benchmark/log.txt
0:00:00.000167 INFO: Output directory: /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark, cwd: /home/robbe/ProteoBench_diaPASEF.
0:00:00.000203 INFO: User provided config file: config_alphadia112_rs_Astral.yaml.
0:00:00.000231 INFO: User provided config dict: {}.
0:00:00.011385 PROGRESS:           _      _         ___ ___   _   
0:00:00.011451 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.011477 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.011504 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.011529 PROGRESS:            |_|                           
0:00:00.011548 PROGRESS: 
0:00:00.011567 PROGRESS: version: 1.12.1
0:00:00.011595 INFO: hostname: thestral
0:00:00.011649 INFO: date: 2025-10-15 11:40:51
0:00:00.011672 INFO: ================ AlphaX Environment ===============
0:00:00.011695 INFO: alphatims       : 1.0.8
0:00:00.011715 INFO: alpharaw        : 0.4.5
0:00:00.011732 INFO: alphabase       : 1.5.0
0:00:00.011750 INFO: alphapeptdeep   : 1.3.0
0:00:00.011769 INFO: directlfq       : 0.2.19
0:00:00.011786 INFO: ===================================================
0:00:00.011803 INFO: ================= Pip Environment =================
0:00:00.067303 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
0:00:00.068244 INFO: ===================================================
0:00:00.068307 INFO: Running step 'library'
0:00:00.068371 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.079336 INFO: loading additional config provided via CLI
0:00:00.079400 INFO: loading additional config provided via CLI parameters
0:00:00.079782 INFO: Updating config with 'user defined'
0:00:00.079921 INFO: Updating config with 'user defined (cli)'
0:00:00.079958 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default_ng.yaml
0:00:00.080550 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': False, 'reuse_calibration': False, 'reuse_quant': False, 'astral_ms1': False, 'log_level': 'INFO', 'mmap_detector_events': False, 'use_gpu': False, 'save_figures': True, 'save_library': True, 'save_flat_library': False, 'input_library_type': 'base', 'save_mbr_library': True, 'random_state': None}, 'library_loading': {'rt_heuristic': 180}, 'library_prediction': {'enabled': True, 'enzyme': 'trypsin/p', 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M;Acetyl@Protein_N-term', 'max_var_mod_num': 1, 'missed_cleavages': 1, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [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'], 'fasta_paths': ['./ProteoBenchFASTA_DDAQuantification.fasta']}]
0:00:00.080828 INFO: Updating config with 'ng_default'
0:00:00.080865 INFO: Updating config with 'user defined'
0:00:00.080979 INFO: Updating config with 'user defined (cli)'
0:00:00.081017 INFO: ├──version: 1
0:00:00.081043 INFO: ├──workflow_name: None
0:00:00.081063 INFO: ├──output_directory: None
0:00:00.081084 INFO: ├──library_path: None
0:00:00.081104 INFO: ├──raw_paths:
0:00:00.081123 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:00:00.081145 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:00:00.081163 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:00:00.081190 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:00:00.081210 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:00:00.081229 INFO: │   [32;20m- ./Raw_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:00:00.081248 INFO: ├──fasta_paths:
0:00:00.081268 INFO: │   [32;20m- ./ProteoBenchFASTA_DDAQuantification.fasta [user defined (cli), default: None][0m
0:00:00.081289 INFO: ├──quant_directory: None
0:00:00.081309 INFO: ├──general
0:00:00.081331 INFO: │   [32;20m├──thread_count: 80 [user defined, default: 10][0m
0:00:00.081350 INFO: │   ├──transfer_step_enabled: False
0:00:00.081368 INFO: │   ├──mbr_step_enabled: False
0:00:00.081388 INFO: │   ├──reuse_calibration: False
0:00:00.081406 INFO: │   ├──reuse_quant: False
0:00:00.081423 INFO: │   ├──astral_ms1: False
0:00:00.081442 INFO: │   ├──log_level: INFO
0:00:00.081460 INFO: │   ├──mmap_detector_events: False
0:00:00.081484 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:00:00.081505 INFO: │   ├──save_figures: True
0:00:00.081523 INFO: │   ├──save_library: True
0:00:00.081541 INFO: │   ├──save_flat_library: False
0:00:00.081561 INFO: │   ├──input_library_type: base
0:00:00.081579 INFO: │   ├──save_mbr_library: True
0:00:00.081599 INFO: │   └──random_state: None
0:00:00.081619 INFO: ├──library_loading
0:00:00.081637 INFO: │   └──rt_heuristic: 180
0:00:00.081655 INFO: ├──library_prediction
0:00:00.081674 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.081692 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.081712 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.081730 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.081750 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.081769 INFO: │   ├──missed_cleavages: 1
0:00:00.081789 INFO: │   ├──precursor_len:
0:00:00.081808 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.081827 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.081845 INFO: │   ├──precursor_charge:
0:00:00.081865 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.081882 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.081901 INFO: │   ├──precursor_mz:
0:00:00.081919 INFO: │   │   - 400
0:00:00.081936 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
0:00:00.081954 INFO: │   ├──fragment_mz:
0:00:00.081974 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
0:00:00.081991 INFO: │   │   - 2000
0:00:00.082009 INFO: │   ├──nce: 25.0
0:00:00.082026 INFO: │   ├──fragment_types:
0:00:00.082045 INFO: │   │   - b
0:00:00.082062 INFO: │   │   - y
0:00:00.082079 INFO: │   ├──max_fragment_charge: 2
0:00:00.082098 INFO: │   [32;20m├──instrument: Astral [user defined, default: Lumos][0m
0:00:00.082118 INFO: │   ├──peptdeep_model_path: None
0:00:00.082136 INFO: │   └──peptdeep_model_type: generic
0:00:00.082155 INFO: ├──custom_modifications:
0:00:00.082173 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.082191 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.082210 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.082228 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.082247 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.082264 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.082283 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.082301 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.082324 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.082343 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.082361 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.082378 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.082398 INFO: │   ├──name: Label:13C(12)@K
0:00:00.082417 INFO: │   └──composition: C(12)
0:00:00.082434 INFO: ├──search
0:00:00.082453 INFO: │   [32;20m├──extraction_backend: ng [user defined, default: classic][0m
0:00:00.082471 INFO: │   ├──target_ms1_tolerance: 5
0:00:00.082488 INFO: │   ├──target_ms2_tolerance: 10
0:00:00.082508 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.082526 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.082546 INFO: │   ├──quant_window: 3
0:00:00.082563 INFO: │   ├──target_num_candidates: 3
0:00:00.082582 INFO: │   ├──channel_filter: 
0:00:00.082599 INFO: │   ├──exclude_shared_ions: True
0:00:00.082618 INFO: │   ├──compete_for_fragments: True
0:00:00.082636 INFO: │   ├──quant_all: True
0:00:00.082653 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.082671 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.082689 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.082706 INFO: │   ├──experimental_xic: True
0:00:00.082724 INFO: │   └──optimized_peak_group_score: False
0:00:00.082742 INFO: ├──calibration
0:00:00.082762 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
0:00:00.082781 INFO: │   ├──optimization_lock_target: 200
0:00:00.082801 INFO: │   ├──max_steps: 20
0:00:00.082820 INFO: │   ├──min_steps: 2
0:00:00.082838 INFO: │   ├──max_skips: 1
0:00:00.082855 INFO: │   ├──max_fragments: 5000
0:00:00.082875 INFO: │   └──min_correlation: 0.7
0:00:00.082893 INFO: ├──search_initial
0:00:00.082913 INFO: │   ├──initial_num_candidates: 1
0:00:00.082932 INFO: │   ├──initial_ms1_tolerance: 30
0:00:00.082951 INFO: │   ├──initial_ms2_tolerance: 30
0:00:00.082969 INFO: │   ├──initial_mobility_tolerance: 0.1
0:00:00.082987 INFO: │   └──initial_rt_tolerance: 0.5
0:00:00.083005 INFO: ├──selection_config
0:00:00.083024 INFO: │   ├──peak_len_rt: 10.0
0:00:00.083042 INFO: │   ├──sigma_scale_rt: 0.5
0:00:00.083062 INFO: │   ├──peak_len_mobility: 0.01
0:00:00.083080 INFO: │   ├──sigma_scale_mobility: 1.0
0:00:00.083098 INFO: │   ├──top_k_precursors: 3
0:00:00.083117 INFO: │   ├──kernel_size: 30
0:00:00.083135 INFO: │   ├──f_mobility: 1.0
0:00:00.083152 INFO: │   ├──f_rt: 0.99
0:00:00.083172 INFO: │   ├──center_fraction: 0.5
0:00:00.083190 INFO: │   ├──min_size_mobility: 8
0:00:00.083207 INFO: │   ├──min_size_rt: 3
0:00:00.083224 INFO: │   ├──max_size_mobility: 20
0:00:00.083242 INFO: │   ├──max_size_rt: 15
0:00:00.083260 INFO: │   ├──group_channels: False
0:00:00.083277 INFO: │   ├──use_weighted_score: True
0:00:00.083295 INFO: │   ├──join_close_candidates: False
0:00:00.083313 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:00:00.083332 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:00:00.083350 INFO: ├──scoring_config
0:00:00.083369 INFO: │   ├──score_grouped: False
0:00:00.083387 INFO: │   ├──top_k_isotopes: 3
0:00:00.083405 INFO: │   ├──reference_channel: -1
0:00:00.083423 INFO: │   ├──precursor_mz_tolerance: 10
0:00:00.083441 INFO: │   └──fragment_mz_tolerance: 15
0:00:00.083457 INFO: ├──library_multiplexing
0:00:00.083476 INFO: │   ├──enabled: False
0:00:00.083493 INFO: │   ├──input_channel: 0
0:00:00.083510 INFO: │   └──multiplex_mapping:
0:00:00.083527 INFO: ├──multiplexing
0:00:00.083546 INFO: │   ├──enabled: False
0:00:00.083565 INFO: │   ├──target_channels: 4,8
0:00:00.083587 INFO: │   ├──decoy_channel: 12
0:00:00.083605 INFO: │   ├──reference_channel: 0
0:00:00.083623 INFO: │   └──competetive_scoring: True
0:00:00.083641 INFO: ├──fdr
0:00:00.083661 INFO: │   ├──fdr: 0.01
0:00:00.083678 INFO: │   ├──group_level: proteins
0:00:00.083695 INFO: │   ├──inference_strategy: heuristic
0:00:00.083714 INFO: │   ├──competetive_scoring: True
0:00:00.083732 INFO: │   ├──keep_decoys: False
0:00:00.083750 INFO: │   ├──channel_wise_fdr: False
0:00:00.083767 INFO: │   ├──enable_two_step_classifier: False
0:00:00.083785 INFO: │   ├──two_step_classifier_max_iterations: 5
0:00:00.083802 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:00:00.083819 INFO: ├──search_output
0:00:00.083838 INFO: │   ├──file_format: tsv
0:00:00.083855 INFO: │   ├──peptide_level_lfq: False
0:00:00.083873 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:00:00.083892 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.083910 INFO: │   ├──min_k_fragments: 12
0:00:00.083927 INFO: │   ├──min_correlation: 0.9
0:00:00.083944 INFO: │   ├──num_samples_quadratic: 50
0:00:00.083961 INFO: │   ├──min_nonnan: 3
0:00:00.083979 INFO: │   └──normalize_lfq: True
0:00:00.083997 INFO: ├──optimization
0:00:00.084016 INFO: │   ├──order_of_optimization: None
0:00:00.084034 INFO: │   ├──ms2_error
0:00:00.084052 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.084070 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.084089 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.084107 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.084125 INFO: │   │   ├──try_narrower_values: True
0:00:00.084144 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.084161 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.084179 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.084198 INFO: │   ├──ms1_error
0:00:00.084215 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.084233 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.084250 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.084269 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.084288 INFO: │   │   ├──try_narrower_values: False
0:00:00.084306 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.084324 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.084341 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.084359 INFO: │   ├──mobility_error
0:00:00.084379 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.084397 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.084414 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.084432 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.084450 INFO: │   │   ├──try_narrower_values: False
0:00:00.084467 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.084483 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.084503 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.084520 INFO: │   └──rt_error
0:00:00.084537 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.084555 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.084574 INFO: │       ├──automatic_update_percentile_range: 0.99
0:00:00.084590 INFO: │       ├──automatic_update_factor: 1.1
0:00:00.084607 INFO: │       ├──try_narrower_values: True
0:00:00.084626 INFO: │       ├──maximal_decrease: 0.2
0:00:00.084643 INFO: │       ├──favour_narrower_optimum: True
0:00:00.084660 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:00:00.084678 INFO: ├──optimization_manager
0:00:00.084699 INFO: │   ├──fwhm_rt: 5
0:00:00.084717 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.084734 INFO: │   └──score_cutoff: 0
0:00:00.084752 INFO: ├──transfer_library
0:00:00.084770 INFO: │   ├──enabled: False
0:00:00.084787 INFO: │   ├──fragment_types:
0:00:00.084815 INFO: │   │   - b
0:00:00.084834 INFO: │   │   - y
0:00:00.084851 INFO: │   ├──max_charge: 2
0:00:00.084868 INFO: │   ├──top_k_samples: 3
0:00:00.084886 INFO: │   ├──norm_delta_max: True
0:00:00.084905 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.084923 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.084941 INFO: └──transfer_learning
0:00:00.084959 INFO:     ├──enabled: False
0:00:00.084976 INFO:     ├──batch_size: 2000
0:00:00.084994 INFO:     ├──max_lr: 0.0001
0:00:00.085011 INFO:     ├──train_fraction: 0.7
0:00:00.085028 INFO:     ├──validation_fraction: 0.2
0:00:00.085046 INFO:     ├──test_fraction: 0.1
0:00:00.085063 INFO:     ├──test_interval: 1
0:00:00.085080 INFO:     ├──lr_patience: 3
0:00:00.085099 INFO:     ├──epochs: 51
0:00:00.085118 INFO:     ├──warmup_epochs: 5
0:00:00.085135 INFO:     ├──nce: 25
0:00:00.085153 INFO:     [32;20m└──instrument: Astral [user defined, default: Lumos][0m
0:00:00.089717 INFO: Moved existing config file run_output_Astral/alphadia_1.12.1_rs_benchmark/frozen_config.yaml to run_output_Astral/alphadia_1.12.1_rs_benchmark/frozen_config.yaml
0:00:00.089867 INFO: Registering 7 custom modifications
0:00:00.116647 INFO: Searching 6 files:
0:00:00.116727 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:00:00.116752 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:00:00.116772 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:00:00.116790 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:00:00.116812 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:00:00.116830 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:00:00.116847 INFO: Using 1 fasta files:
0:00:00.116865 INFO:   ./ProteoBenchFASTA_DDAQuantification.fasta
0:00:00.116886 INFO: Using library: None
0:00:00.116907 INFO: Saving output to: run_output_Astral/alphadia_1.12.1_rs_benchmark
0:00:00.116932 PROGRESS: Loading spectral library
0:00:00.116955 PROGRESS: No library provided. Building library from fasta files.
0:00:00.116983 INFO: Running FastaDigest
0:00:00.988010 INFO: Digesting fasta file
0:00:07.297216 INFO: Adding modifications
0:01:44.598818 INFO: Removing non-canonical amino acids
0:01:50.955997 INFO: Fasta library contains 6,124,046 precursors
0:01:50.956177 PROGRESS: Predicting library properties.
0:01:50.956250 INFO: Running PeptDeepPrediction
0:01:50.956331 INFO: Device set to cpu
0:01:51.897415 INFO: Loading PeptDeep models of type generic
0:01:52.663962 INFO: Predicting RT, MS2 and mobility
0:01:52.664150 INFO: Using multiprocessing with 80 processes ...
0:01:53.094488 INFO: Predicting rt,ms2,mobility ...
0:08:55.665826 INFO: Adding fragment mz information
0:08:56.028362 INFO: Adding fragment intensity information
0:08:56.385191 INFO: Adding precursor information
0:08:56.995160 INFO: Running PrecursorInitializer
0:08:57.021752 INFO: Running AnnotateFasta
0:08:57.175584 INFO: Dropping decoys from input library before annotation
0:09:25.169310 INFO: Running IsotopeGenerator
0:09:44.124698 INFO: Running RTNormalization
0:09:44.125271 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:09:44.125382 INFO: Saving library to run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf
0:10:21.475035 INFO: Running DecoyGenerator
0:12:28.574897 INFO: Running FlattenLibrary
0:13:05.053245 INFO: Running InitFlatColumns
0:13:05.355080 INFO: Running LogFlatLibraryStats
0:13:05.355226 INFO: ============ Library Stats ============
0:13:05.355264 INFO: Number of precursors: 12,218,312
0:13:07.260486 INFO: 	thereof targets:6,124,046
0:13:07.260625 INFO: 	thereof decoys: 6,094,266
0:13:07.355689 INFO: Number of elution groups: 6,124,046
0:13:07.355828 INFO: 	average size: 2.00
0:13:07.724158 INFO: Number of proteins: 117,993
0:13:07.753897 INFO: Number of channels: 1 ([0])
0:13:07.754063 INFO: Isotopes Distribution for 4 isotopes
0:13:07.754092 INFO: =======================================
0:13:07.765082 PROGRESS: Starting Search Workflows
0:13:07.765252 PROGRESS: 
0:13:07.765328 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark/quant
0:13:07.765408 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/figures
0:13:07.765631 INFO: Initializing TimingManager
0:13:07.766611 INFO: Initializing RawFileManager
0:13:19.797257 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.
0:13:19.801962 INFO: Determining DIA cycle
0:13:20.215096 INFO: Found cycle with start 0.00 min and length 300.
0:13:20.372825 INFO: RT (min)            : 0.0 - 26.9
0:13:20.372916 INFO: RT duration (sec)   : 1611.2
0:13:20.372949 INFO: RT duration (min)   : 26.9
0:13:20.372974 INFO: Cycle len (scans)   : 300
0:13:20.372994 INFO: Cycle len (sec)     : 1.65
0:13:20.373013 INFO: Number of cycles    : 977
0:13:20.373033 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:13:20.373078 INFO: Creating DIA data object took: 12.60636830329895
0:13:21.195257 INFO: Creating DIA data NG object took: 0.8220484256744385
0:13:22.901238 INFO: Initializing CalibrationManager
0:13:22.901661 INFO: Setting up calibration estimators ..
0:13:22.901733 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:13:22.901836 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'}' ..
0:13:22.901964 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:13:22.902021 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:13:22.902078 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}}' ..
0:13:22.902134 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:13:22.902178 INFO: Done setting up calibration estimators.
0:13:22.902879 INFO: Initializing OptimizationManager
0:13:22.903059 INFO: initial parameter: ms1_error = 30
0:13:22.903114 INFO: initial parameter: ms2_error = 30
0:13:22.903163 INFO: initial parameter: rt_error = 805.5992431640625
0:13:22.903210 INFO: initial parameter: mobility_error = 0.1
0:13:22.903251 INFO: initial parameter: num_candidates = 1
0:13:22.903290 INFO: initial parameter: fwhm_rt = 5
0:13:22.903329 INFO: initial parameter: fwhm_mobility = 0.01
0:13:22.903370 INFO: initial parameter: score_cutoff = 0
0:13:22.903410 INFO: initial parameter: classifier_version = -1
0:13:22.903488 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:13:22.903862 INFO: FDRManager: loading saved state not requested, will be initialized.
0:13:22.903903 INFO: Initializing FDRManager
0:13:22.903944 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:13:24.360651 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:13:25.856285 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:13:25.856707 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
0:13:25.856837 PROGRESS: Starting initial search for precursors.
0:13:25.856929 INFO: Starting optimization step 0.
0:13:25.856991 PROGRESS: === Extracting elution groups 0 to 200 ===
0:13:25.857061 INFO: Using ng extraction backend
0:13:25.857129 PROGRESS: Extracting batch of 396 precursors
0:13:25.858950 INFO: === Search parameters used ===
0:13:25.859043 INFO: rt_error       : 805.5992431640625
0:13:25.859090 INFO: mobility_error : 0.1
0:13:25.859131 INFO: num_candidates : 1
0:13:25.859172 INFO: ms1_error      : 30
0:13:25.859209 INFO: ms2_error      : 30
0:13:25.859247 INFO: fwhm_rt        : 5
0:13:25.859285 INFO: quant_window   : 3
0:13:25.859324 INFO: ==============================================
0:13:25.883384 INFO: performing precursor FDR with 40 features
0:13:25.883472 INFO: Decoy channel: -1
0:13:25.883497 INFO: Competetive: True
0:13:25.884396 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:25.888106 INFO: Using random state 132481 for train-test-split
0:13:26.612513 INFO: Test AUC: 0.526
0:13:26.612594 INFO: Train AUC: 0.552
0:13:26.612624 INFO: AUC difference: 4.71%
0:13:26.892566 INFO: Resetting torch num_threads to 80
0:13:26.893863 PROGRESS: === Extracted 394 precursors and 1879 fragments ===
0:13:26.894198 INFO: === FDR correction performed with classifier version -1 ===
0:13:26.894618 PROGRESS: ============================= Precursor FDR =============================
0:13:26.894699 PROGRESS: Total precursors accumulated: 0
0:13:26.894756 PROGRESS: Target precursors: 0 (0.00%)
0:13:26.894804 PROGRESS: Decoy precursors: 0 (0.00%)
0:13:26.894849 PROGRESS: 
0:13:26.894893 PROGRESS: Precursor Summary:
0:13:26.894997 PROGRESS: 
0:13:26.895058 PROGRESS: Protein Summary:
0:13:26.895128 PROGRESS: =========================================================================
0:13:26.895279 INFO: Target number of precursors not reached yet.
0:13:26.959930 INFO: Starting optimization step 1.
0:13:26.960137 PROGRESS: === Extracting elution groups 200 to 600 ===
0:13:26.960221 INFO: Using ng extraction backend
0:13:26.960282 PROGRESS: Extracting batch of 786 precursors
0:13:26.962672 INFO: === Search parameters used ===
0:13:26.962760 INFO: rt_error       : 805.5992431640625
0:13:26.962808 INFO: mobility_error : 0.1
0:13:26.962849 INFO: num_candidates : 1
0:13:26.962890 INFO: ms1_error      : 30
0:13:26.962929 INFO: ms2_error      : 30
0:13:26.962968 INFO: fwhm_rt        : 5
0:13:26.963010 INFO: quant_window   : 3
0:13:26.963048 INFO: ==============================================
0:13:26.988446 INFO: performing precursor FDR with 40 features
0:13:26.988542 INFO: Decoy channel: -1
0:13:26.988569 INFO: Competetive: True
0:13:26.991531 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:26.993195 INFO: Using random state 598132 for train-test-split
0:13:27.001710 INFO: Test AUC: 0.608
0:13:27.001770 INFO: Train AUC: 0.519
0:13:27.001799 INFO: AUC difference: 17.06%
0:13:27.001822 WARNING: AUC difference > 5%. This may indicate overfitting.
0:13:27.482243 INFO: Resetting torch num_threads to 80
0:13:27.484247 PROGRESS: === Extracted 1169 precursors and 5549 fragments ===
0:13:27.484571 INFO: === FDR correction performed with classifier version -1 ===
0:13:27.485021 PROGRESS: ============================= Precursor FDR =============================
0:13:27.485118 PROGRESS: Total precursors accumulated: 1
0:13:27.485175 PROGRESS: Target precursors: 1 (100.00%)
0:13:27.485223 PROGRESS: Decoy precursors: 0 (0.00%)
0:13:27.485265 PROGRESS: 
0:13:27.485307 PROGRESS: Precursor Summary:
0:13:27.486220 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:13:27.486304 PROGRESS: 
0:13:27.486371 PROGRESS: Protein Summary:
0:13:27.487359 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:13:27.487442 PROGRESS: =========================================================================
0:13:27.487619 INFO: Target number of precursors not reached yet.
0:13:27.554256 INFO: Starting optimization step 2.
0:13:27.554448 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:13:27.554529 INFO: Using ng extraction backend
0:13:27.554590 PROGRESS: Extracting batch of 1592 precursors
0:13:27.558464 INFO: === Search parameters used ===
0:13:27.558570 INFO: rt_error       : 805.5992431640625
0:13:27.558619 INFO: mobility_error : 0.1
0:13:27.558662 INFO: num_candidates : 1
0:13:27.558703 INFO: ms1_error      : 30
0:13:27.558743 INFO: ms2_error      : 30
0:13:27.558780 INFO: fwhm_rt        : 5
0:13:27.558820 INFO: quant_window   : 3
0:13:27.558856 INFO: ==============================================
0:13:27.592478 INFO: performing precursor FDR with 40 features
0:13:27.592549 INFO: Decoy channel: -1
0:13:27.592575 INFO: Competetive: True
0:13:27.596064 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:27.598121 INFO: Using random state 484275 for train-test-split
0:13:27.610930 INFO: Test AUC: 0.509
0:13:27.610990 INFO: Train AUC: 0.530
0:13:27.611019 INFO: AUC difference: 3.94%
0:13:27.818829 INFO: Resetting torch num_threads to 80
0:13:27.821243 PROGRESS: === Extracted 2751 precursors and 13122 fragments ===
0:13:27.821584 INFO: === FDR correction performed with classifier version -1 ===
0:13:27.822001 PROGRESS: ============================= Precursor FDR =============================
0:13:27.822083 PROGRESS: Total precursors accumulated: 0
0:13:27.822145 PROGRESS: Target precursors: 0 (0.00%)
0:13:27.822195 PROGRESS: Decoy precursors: 0 (0.00%)
0:13:27.822238 PROGRESS: 
0:13:27.822281 PROGRESS: Precursor Summary:
0:13:27.822381 PROGRESS: 
0:13:27.822439 PROGRESS: Protein Summary:
0:13:27.822508 PROGRESS: =========================================================================
0:13:27.822692 INFO: Target number of precursors not reached yet.
0:13:27.893266 INFO: Starting optimization step 3.
0:13:27.893467 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:13:27.893546 INFO: Using ng extraction backend
0:13:27.893610 PROGRESS: Extracting batch of 3177 precursors
0:13:27.900213 INFO: === Search parameters used ===
0:13:27.900321 INFO: rt_error       : 805.5992431640625
0:13:27.900374 INFO: mobility_error : 0.1
0:13:27.900416 INFO: num_candidates : 1
0:13:27.900460 INFO: ms1_error      : 30
0:13:27.900501 INFO: ms2_error      : 30
0:13:27.900540 INFO: fwhm_rt        : 5
0:13:27.900578 INFO: quant_window   : 3
0:13:27.900616 INFO: ==============================================
0:13:27.948210 INFO: performing precursor FDR with 40 features
0:13:27.948291 INFO: Decoy channel: -1
0:13:27.948316 INFO: Competetive: True
0:13:27.952755 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:27.955922 INFO: Using random state 386875 for train-test-split
0:13:27.977940 INFO: Test AUC: 0.543
0:13:27.978005 INFO: Train AUC: 0.520
0:13:27.978034 INFO: AUC difference: 4.34%
0:13:28.191664 INFO: Resetting torch num_threads to 80
0:13:28.195464 PROGRESS: === Extracted 5904 precursors and 28052 fragments ===
0:13:28.195800 INFO: === FDR correction performed with classifier version -1 ===
0:13:28.196236 PROGRESS: ============================= Precursor FDR =============================
0:13:28.196318 PROGRESS: Total precursors accumulated: 0
0:13:28.196374 PROGRESS: Target precursors: 0 (0.00%)
0:13:28.196423 PROGRESS: Decoy precursors: 0 (0.00%)
0:13:28.196469 PROGRESS: 
0:13:28.196512 PROGRESS: Precursor Summary:
0:13:28.196614 PROGRESS: 
0:13:28.196672 PROGRESS: Protein Summary:
0:13:28.196741 PROGRESS: =========================================================================
0:13:28.196968 INFO: Target number of precursors not reached yet.
0:13:28.274858 INFO: Starting optimization step 4.
0:13:28.275068 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:13:28.275148 INFO: Using ng extraction backend
0:13:28.275215 PROGRESS: Extracting batch of 6340 precursors
0:13:28.287628 INFO: === Search parameters used ===
0:13:28.287765 INFO: rt_error       : 805.5992431640625
0:13:28.287814 INFO: mobility_error : 0.1
0:13:28.287858 INFO: num_candidates : 1
0:13:28.287898 INFO: ms1_error      : 30
0:13:28.287936 INFO: ms2_error      : 30
0:13:28.287972 INFO: fwhm_rt        : 5
0:13:28.288021 INFO: quant_window   : 3
0:13:28.288059 INFO: ==============================================
0:13:28.364486 INFO: performing precursor FDR with 40 features
0:13:28.364595 INFO: Decoy channel: -1
0:13:28.364620 INFO: Competetive: True
0:13:28.371689 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:28.375501 INFO: Using random state 654498 for train-test-split
0:13:28.418876 INFO: Test AUC: 0.507
0:13:28.418966 INFO: Train AUC: 0.527
0:13:28.418995 INFO: AUC difference: 3.90%
0:13:28.636379 INFO: Resetting torch num_threads to 80
0:13:28.640431 PROGRESS: === Extracted 12173 precursors and 57356 fragments ===
0:13:28.640770 INFO: === FDR correction performed with classifier version -1 ===
0:13:28.641204 PROGRESS: ============================= Precursor FDR =============================
0:13:28.641285 PROGRESS: Total precursors accumulated: 0
0:13:28.641340 PROGRESS: Target precursors: 0 (0.00%)
0:13:28.641387 PROGRESS: Decoy precursors: 0 (0.00%)
0:13:28.641429 PROGRESS: 
0:13:28.641470 PROGRESS: Precursor Summary:
0:13:28.641570 PROGRESS: 
0:13:28.641629 PROGRESS: Protein Summary:
0:13:28.641696 PROGRESS: =========================================================================
0:13:28.641964 INFO: Target number of precursors not reached yet.
0:13:28.731756 INFO: Starting optimization step 5.
0:13:28.731970 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:13:28.732051 INFO: Using ng extraction backend
0:13:28.732117 PROGRESS: Extracting batch of 12663 precursors
0:13:28.755285 INFO: === Search parameters used ===
0:13:28.755458 INFO: rt_error       : 805.5992431640625
0:13:28.755509 INFO: mobility_error : 0.1
0:13:28.755553 INFO: num_candidates : 1
0:13:28.755611 INFO: ms1_error      : 30
0:13:28.755655 INFO: ms2_error      : 30
0:13:28.755693 INFO: fwhm_rt        : 5
0:13:28.755732 INFO: quant_window   : 3
0:13:28.755768 INFO: ==============================================
0:13:28.878497 INFO: performing precursor FDR with 40 features
0:13:28.878607 INFO: Decoy channel: -1
0:13:28.878632 INFO: Competetive: True
0:13:28.889705 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:28.897522 INFO: Using random state 985564 for train-test-split
0:13:29.153841 INFO: Test AUC: 0.543
0:13:29.153952 INFO: Train AUC: 0.535
0:13:29.153981 INFO: AUC difference: 1.66%
0:13:29.368910 INFO: Resetting torch num_threads to 80
0:13:29.375048 PROGRESS: === Extracted 24702 precursors and 116046 fragments ===
0:13:29.375462 INFO: === FDR correction performed with classifier version -1 ===
0:13:29.375946 PROGRESS: ============================= Precursor FDR =============================
0:13:29.376030 PROGRESS: Total precursors accumulated: 26
0:13:29.376086 PROGRESS: Target precursors: 26 (100.00%)
0:13:29.376134 PROGRESS: Decoy precursors: 0 (0.00%)
0:13:29.376177 PROGRESS: 
0:13:29.376218 PROGRESS: Precursor Summary:
0:13:29.377205 PROGRESS: Channel   0:	 0.050 FDR:    26; 0.010 FDR:    26; 0.001 FDR:    26
0:13:29.377292 PROGRESS: 
0:13:29.377346 PROGRESS: Protein Summary:
0:13:29.378359 PROGRESS: Channel   0:	 0.050 FDR:    26; 0.010 FDR:    26; 0.001 FDR:    26
0:13:29.378442 PROGRESS: =========================================================================
0:13:29.378870 INFO: Target number of precursors not reached yet.
0:13:29.486705 INFO: Starting optimization step 6.
0:13:29.486924 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:13:29.487018 INFO: Using ng extraction backend
0:13:29.487081 PROGRESS: Extracting batch of 25339 precursors
0:13:29.531950 INFO: === Search parameters used ===
0:13:29.532149 INFO: rt_error       : 805.5992431640625
0:13:29.532198 INFO: mobility_error : 0.1
0:13:29.532241 INFO: num_candidates : 1
0:13:29.532281 INFO: ms1_error      : 30
0:13:29.532320 INFO: ms2_error      : 30
0:13:29.532359 INFO: fwhm_rt        : 5
0:13:29.532396 INFO: quant_window   : 3
0:13:29.532433 INFO: ==============================================
0:13:29.733150 INFO: performing precursor FDR with 40 features
0:13:29.734056 INFO: Decoy channel: -1
0:13:29.734098 INFO: Competetive: True
0:13:29.755438 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:29.767768 INFO: Using random state 527369 for train-test-split
0:13:30.393659 INFO: Test AUC: 0.561
0:13:30.393769 INFO: Train AUC: 0.577
0:13:30.393806 INFO: AUC difference: 2.80%
0:13:30.620543 INFO: Resetting torch num_threads to 80
0:13:30.630828 PROGRESS: === Extracted 49766 precursors and 233332 fragments ===
0:13:30.631293 INFO: === FDR correction performed with classifier version -1 ===
0:13:30.631811 PROGRESS: ============================= Precursor FDR =============================
0:13:30.631894 PROGRESS: Total precursors accumulated: 17
0:13:30.631950 PROGRESS: Target precursors: 17 (100.00%)
0:13:30.631997 PROGRESS: Decoy precursors: 0 (0.00%)
0:13:30.632040 PROGRESS: 
0:13:30.632082 PROGRESS: Precursor Summary:
0:13:30.632996 PROGRESS: Channel   0:	 0.050 FDR:    17; 0.010 FDR:    17; 0.001 FDR:    17
0:13:30.633092 PROGRESS: 
0:13:30.633144 PROGRESS: Protein Summary:
0:13:30.634168 PROGRESS: Channel   0:	 0.050 FDR:    16; 0.010 FDR:    16; 0.001 FDR:    16
0:13:30.634254 PROGRESS: =========================================================================
0:13:30.634941 INFO: Target number of precursors not reached yet.
0:13:30.774941 INFO: Starting optimization step 7.
0:13:30.775170 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:13:30.775252 INFO: Using ng extraction backend
0:13:30.775316 PROGRESS: Extracting batch of 50691 precursors
0:13:30.863426 INFO: === Search parameters used ===
0:13:30.863648 INFO: rt_error       : 805.5992431640625
0:13:30.863699 INFO: mobility_error : 0.1
0:13:30.863743 INFO: num_candidates : 1
0:13:30.863784 INFO: ms1_error      : 30
0:13:30.863823 INFO: ms2_error      : 30
0:13:30.863861 INFO: fwhm_rt        : 5
0:13:30.863898 INFO: quant_window   : 3
0:13:30.863934 INFO: ==============================================
0:13:31.220142 INFO: performing precursor FDR with 40 features
0:13:31.220251 INFO: Decoy channel: -1
0:13:31.220278 INFO: Competetive: True
0:13:31.264598 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:31.290715 INFO: Using random state 169006 for train-test-split
0:13:32.739091 INFO: Test AUC: 0.577
0:13:32.739205 INFO: Train AUC: 0.601
0:13:32.739235 INFO: AUC difference: 4.00%
0:13:32.990696 INFO: Resetting torch num_threads to 80
0:13:33.021685 PROGRESS: === Extracted 99917 precursors and 469358 fragments ===
0:13:33.022248 INFO: === FDR correction performed with classifier version -1 ===
0:13:33.022822 PROGRESS: ============================= Precursor FDR =============================
0:13:33.022914 PROGRESS: Total precursors accumulated: 305
0:13:33.022970 PROGRESS: Target precursors: 302 (99.02%)
0:13:33.023027 PROGRESS: Decoy precursors: 3 (0.98%)
0:13:33.023069 PROGRESS: 
0:13:33.023109 PROGRESS: Precursor Summary:
0:13:33.024052 PROGRESS: Channel   0:	 0.050 FDR:   302; 0.010 FDR:   302; 0.001 FDR:   242
0:13:33.024139 PROGRESS: 
0:13:33.024191 PROGRESS: Protein Summary:
0:13:33.025327 PROGRESS: Channel   0:	 0.050 FDR:   290; 0.010 FDR:   290; 0.001 FDR:   234
0:13:33.025417 PROGRESS: =========================================================================
0:13:33.027174 INFO: Target number of precursors reached.
0:13:33.061685 INFO: fragments_df: keeping 2470 of 469358 [sum(precursor_idx_mask)=3149 sum(mass_error_mask)=469358 stop_rank=2470
0:13:33.298866 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:13:33.445374 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:13:33.778046 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:13:33.778466 INFO: Using score_cutoff 11.16677600669861 (fac=0.99, q=1)
0:13:33.778829 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:13:33.778907 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:13:33.778959 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.16677600669861
0:13:33.779020 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:33.844860 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:33.998168 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:13:33.999098 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:13:33.999210 INFO: Starting optimization step 8.
0:13:33.999286 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:13:33.999362 INFO: Using ng extraction backend
0:13:33.999430 PROGRESS: Extracting batch of 100984 precursors
0:13:34.176605 INFO: === Search parameters used ===
0:13:34.176910 INFO: rt_error       : 805.5992431640625
0:13:34.176968 INFO: mobility_error : 0.1
0:13:34.177011 INFO: num_candidates : 3
0:13:34.177052 INFO: ms1_error      : 30
0:13:34.177091 INFO: ms2_error      : 30
0:13:34.177130 INFO: fwhm_rt        : 3.0
0:13:34.177168 INFO: quant_window   : 3
0:13:34.177207 INFO: ==============================================
0:13:35.495935 INFO: performing precursor FDR with 40 features
0:13:35.496122 INFO: Decoy channel: -1
0:13:35.496153 INFO: Competetive: True
0:13:35.582936 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:35.694767 INFO: Using random state 651705 for train-test-split
0:13:40.302929 INFO: Test AUC: 0.590
0:13:40.303047 INFO: Train AUC: 0.604
0:13:40.303081 INFO: AUC difference: 2.29%
0:13:40.623070 INFO: Resetting torch num_threads to 80
0:13:40.634634 PROGRESS: === Extracted 299716 precursors and 1377945 fragments ===
0:13:40.635059 INFO: === FDR correction performed with classifier version 7 ===
0:13:40.635512 PROGRESS: ============================= Precursor FDR =============================
0:13:40.635601 PROGRESS: Total precursors accumulated: 219
0:13:40.635662 PROGRESS: Target precursors: 217 (99.09%)
0:13:40.635713 PROGRESS: Decoy precursors: 2 (0.91%)
0:13:40.635759 PROGRESS: 
0:13:40.635803 PROGRESS: Precursor Summary:
0:13:40.636669 PROGRESS: Channel   0:	 0.050 FDR:   217; 0.010 FDR:   217; 0.001 FDR:     1
0:13:40.636754 PROGRESS: 
0:13:40.636815 PROGRESS: Protein Summary:
0:13:40.637822 PROGRESS: Channel   0:	 0.050 FDR:   209; 0.010 FDR:   209; 0.001 FDR:     1
0:13:40.637908 PROGRESS: =========================================================================
0:13:40.643300 INFO: Target number of precursors reached.
0:13:40.731644 INFO: fragments_df: keeping 2780 of 1377945 [sum(precursor_idx_mask)=5119 sum(mass_error_mask)=1377945 stop_rank=2780
0:13:41.014778 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:13:41.122980 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:13:41.488483 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:13:41.488887 INFO: Using score_cutoff 13.719872876358034 (fac=0.99, q=1)
0:13:41.489187 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:41.489263 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:41.489315 INFO: Updating optimization_manager: score_cutoff        : 11.16677600669861 -> 13.719872876358034
0:13:41.489373 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:41.551864 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:41.698524 INFO: === checking if optimization conditions were reached ===
0:13:41.700613 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:13:41.700732 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:13:41.700833 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:13:41.700910 INFO: ==============================================
0:13:41.700990 INFO: Starting optimization step 9.
0:13:41.701057 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:13:41.701138 INFO: Using ng extraction backend
0:13:41.701213 PROGRESS: Extracting batch of 100984 precursors
0:13:41.875290 INFO: === Search parameters used ===
0:13:41.875529 INFO: rt_error       : 805.5992431640625
0:13:41.875580 INFO: mobility_error : 0.1
0:13:41.875623 INFO: num_candidates : 3
0:13:41.875662 INFO: ms1_error      : 30
0:13:41.875700 INFO: ms2_error      : 10.0
0:13:41.875737 INFO: fwhm_rt        : 3.0
0:13:41.875774 INFO: quant_window   : 3
0:13:41.875810 INFO: ==============================================
0:13:43.082981 INFO: performing precursor FDR with 40 features
0:13:43.083091 INFO: Decoy channel: -1
0:13:43.083118 INFO: Competetive: True
0:13:43.160212 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:43.263993 INFO: Using random state 669957 for train-test-split
0:13:47.313838 INFO: Test AUC: 0.597
0:13:47.313952 INFO: Train AUC: 0.608
0:13:47.313982 INFO: AUC difference: 1.78%
0:13:48.006024 INFO: Resetting torch num_threads to 80
0:13:48.023403 PROGRESS: === Extracted 302185 precursors and 1612304 fragments ===
0:13:48.023828 INFO: === FDR correction performed with classifier version 8 ===
0:13:48.024353 PROGRESS: ============================= Precursor FDR =============================
0:13:48.024436 PROGRESS: Total precursors accumulated: 557
0:13:48.024492 PROGRESS: Target precursors: 552 (99.10%)
0:13:48.024542 PROGRESS: Decoy precursors: 5 (0.90%)
0:13:48.024595 PROGRESS: 
0:13:48.024638 PROGRESS: Precursor Summary:
0:13:48.025695 PROGRESS: Channel   0:	 0.050 FDR:   552; 0.010 FDR:   552; 0.001 FDR:   464
0:13:48.025781 PROGRESS: 
0:13:48.025833 PROGRESS: Protein Summary:
0:13:48.027044 PROGRESS: Channel   0:	 0.050 FDR:   518; 0.010 FDR:   518; 0.001 FDR:   437
0:13:48.027128 PROGRESS: =========================================================================
0:13:48.032990 INFO: Target number of precursors reached.
0:13:48.144002 INFO: fragments_df: keeping 5000 of 1612304 [sum(precursor_idx_mask)=12803 sum(mass_error_mask)=1612304 stop_rank=5000
0:13:48.340298 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:13:48.479781 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:13:49.160024 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:13:49.160434 INFO: Using score_cutoff 8.387417001914978 (fac=0.99, q=1)
0:13:49.160758 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:49.160841 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:49.160898 INFO: Updating optimization_manager: score_cutoff        : 13.719872876358034 -> 8.387417001914978
0:13:49.160958 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:49.191932 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:49.259813 INFO: === checking if optimization conditions were reached ===
0:13:49.262198 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:13:49.262335 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:13:49.262414 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:13:49.262483 INFO: ==============================================
0:13:49.262560 PROGRESS: Optimization finished for ms2_error.
0:13:49.417546 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:49.448416 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:49.512934 INFO: Starting optimization step 0.
0:13:49.513207 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:13:49.513325 INFO: Using ng extraction backend
0:13:49.513425 PROGRESS: Extracting batch of 50293 precursors
0:13:49.605487 INFO: === Search parameters used ===
0:13:49.605738 INFO: rt_error       : 805.5992431640625
0:13:49.605790 INFO: mobility_error : 0.1
0:13:49.605833 INFO: num_candidates : 3
0:13:49.605873 INFO: ms1_error      : 30
0:13:49.605911 INFO: ms2_error      : 10.0
0:13:49.605948 INFO: fwhm_rt        : 3.0
0:13:49.605985 INFO: quant_window   : 3
0:13:49.606020 INFO: ==============================================
0:13:50.272120 INFO: performing precursor FDR with 40 features
0:13:50.272239 INFO: Decoy channel: -1
0:13:50.272264 INFO: Competetive: True
0:13:50.313335 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:50.349232 INFO: Using random state 519797 for train-test-split
0:13:52.286602 INFO: Test AUC: 0.606
0:13:52.286719 INFO: Train AUC: 0.618
0:13:52.286749 INFO: AUC difference: 2.01%
0:13:52.548917 INFO: Resetting torch num_threads to 80
0:13:52.555795 PROGRESS: === Extracted 150483 precursors and 802970 fragments ===
0:13:52.556166 INFO: === FDR correction performed with classifier version 9 ===
0:13:52.556620 PROGRESS: ============================= Precursor FDR =============================
0:13:52.556700 PROGRESS: Total precursors accumulated: 323
0:13:52.556754 PROGRESS: Target precursors: 320 (99.07%)
0:13:52.556800 PROGRESS: Decoy precursors: 3 (0.93%)
0:13:52.556852 PROGRESS: 
0:13:52.556893 PROGRESS: Precursor Summary:
0:13:52.557788 PROGRESS: Channel   0:	 0.050 FDR:   320; 0.010 FDR:   320; 0.001 FDR:   253
0:13:52.557869 PROGRESS: 
0:13:52.557921 PROGRESS: Protein Summary:
0:13:52.558998 PROGRESS: Channel   0:	 0.050 FDR:   311; 0.010 FDR:   311; 0.001 FDR:   244
0:13:52.559080 PROGRESS: =========================================================================
0:13:52.561286 INFO: Target number of precursors reached.
0:13:52.615540 INFO: fragments_df: keeping 3229 of 802970 [sum(precursor_idx_mask)=7124 sum(mass_error_mask)=802970 stop_rank=3229
0:13:52.795747 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:13:52.911294 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:13:53.334823 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:13:53.335227 INFO: Using score_cutoff 6.594340767002105 (fac=0.99, q=1)
0:13:53.335518 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:53.335596 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:53.335652 INFO: Updating optimization_manager: score_cutoff        : 8.387417001914978 -> 6.594340767002105
0:13:53.335717 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:53.368395 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:53.437277 INFO: === checking if optimization conditions were reached ===
0:13:53.437536 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:13:53.440051 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 418.063278519085
0:13:53.440163 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 418.0633.
0:13:53.440236 INFO: ==============================================
0:13:53.440311 INFO: Starting optimization step 1.
0:13:53.440375 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:13:53.440444 INFO: Using ng extraction backend
0:13:53.440506 PROGRESS: Extracting batch of 50293 precursors
0:13:53.530233 INFO: === Search parameters used ===
0:13:53.530469 INFO: rt_error       : 418.063278519085
0:13:53.530522 INFO: mobility_error : 0.1
0:13:53.530570 INFO: num_candidates : 3
0:13:53.530612 INFO: ms1_error      : 30
0:13:53.530650 INFO: ms2_error      : 10.0
0:13:53.530688 INFO: fwhm_rt        : 3.0
0:13:53.530725 INFO: quant_window   : 3
0:13:53.530763 INFO: ==============================================
0:13:54.153800 INFO: performing precursor FDR with 40 features
0:13:54.153902 INFO: Decoy channel: -1
0:13:54.153927 INFO: Competetive: True
0:13:54.194290 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:54.231076 INFO: Using random state 519797 for train-test-split
0:13:56.266838 INFO: Test AUC: 0.592
0:13:56.266951 INFO: Train AUC: 0.618
0:13:56.266980 INFO: AUC difference: 4.25%
0:13:56.530640 INFO: Resetting torch num_threads to 80
0:13:56.536977 PROGRESS: === Extracted 150497 precursors and 796455 fragments ===
0:13:56.537314 INFO: === FDR correction performed with classifier version 9 ===
0:13:56.537735 PROGRESS: ============================= Precursor FDR =============================
0:13:56.537814 PROGRESS: Total precursors accumulated: 236
0:13:56.537867 PROGRESS: Target precursors: 234 (99.15%)
0:13:56.537913 PROGRESS: Decoy precursors: 2 (0.85%)
0:13:56.537955 PROGRESS: 
0:13:56.537995 PROGRESS: Precursor Summary:
0:13:56.538839 PROGRESS: Channel   0:	 0.050 FDR:   234; 0.010 FDR:   234; 0.001 FDR:   149
0:13:56.538921 PROGRESS: 
0:13:56.538971 PROGRESS: Protein Summary:
0:13:56.539957 PROGRESS: Channel   0:	 0.050 FDR:   226; 0.010 FDR:   226; 0.001 FDR:   145
0:13:56.540042 PROGRESS: =========================================================================
0:13:56.542165 INFO: Target number of precursors reached.
0:13:56.595561 INFO: fragments_df: keeping 2718 of 796455 [sum(precursor_idx_mask)=5654 sum(mass_error_mask)=796455 stop_rank=2718
0:13:56.728984 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:13:56.836102 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:13:57.235361 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:13:57.235745 INFO: Using score_cutoff 13.268178040409088 (fac=0.99, q=1)
0:13:57.236016 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:13:57.236088 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:13:57.236145 INFO: Updating optimization_manager: score_cutoff        : 6.594340767002105 -> 13.268178040409088
0:13:57.236198 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:13:57.267571 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:13:57.354280 INFO: === checking if optimization conditions were reached ===
0:13:57.354536 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:13:57.356686 INFO: Updating optimization_manager: rt_error            : 418.063278519085 -> 101.00971599685883
0:13:57.356797 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 101.0097.
0:13:57.356913 INFO: ==============================================
0:13:57.357007 INFO: Starting optimization step 2.
0:13:57.357087 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:13:57.357172 INFO: Using ng extraction backend
0:13:57.357250 PROGRESS: Extracting batch of 50293 precursors
0:13:57.446419 INFO: === Search parameters used ===
0:13:57.446658 INFO: rt_error       : 101.00971599685883
0:13:57.446710 INFO: mobility_error : 0.1
0:13:57.446753 INFO: num_candidates : 3
0:13:57.446793 INFO: ms1_error      : 30
0:13:57.446831 INFO: ms2_error      : 10.0
0:13:57.446870 INFO: fwhm_rt        : 3.0
0:13:57.446907 INFO: quant_window   : 3
0:13:57.446955 INFO: ==============================================
0:13:58.031030 INFO: performing precursor FDR with 40 features
0:13:58.031157 INFO: Decoy channel: -1
0:13:58.031187 INFO: Competetive: True
0:13:58.077218 INFO: Setting torch num_threads to 2 for FDR classification task
0:13:58.113504 INFO: Using random state 519797 for train-test-split
0:13:59.803051 INFO: Test AUC: 0.590
0:13:59.803162 INFO: Train AUC: 0.609
0:13:59.803192 INFO: AUC difference: 3.08%
0:14:00.057124 INFO: Resetting torch num_threads to 80
0:14:00.064839 PROGRESS: === Extracted 146939 precursors and 591386 fragments ===
0:14:00.065185 INFO: === FDR correction performed with classifier version 9 ===
0:14:00.065631 PROGRESS: ============================= Precursor FDR =============================
0:14:00.065712 PROGRESS: Total precursors accumulated: 267
0:14:00.065768 PROGRESS: Target precursors: 265 (99.25%)
0:14:00.065816 PROGRESS: Decoy precursors: 2 (0.75%)
0:14:00.065859 PROGRESS: 
0:14:00.065901 PROGRESS: Precursor Summary:
0:14:00.066766 PROGRESS: Channel   0:	 0.050 FDR:   265; 0.010 FDR:   265; 0.001 FDR:   242
0:14:00.066848 PROGRESS: 
0:14:00.066900 PROGRESS: Protein Summary:
0:14:00.067917 PROGRESS: Channel   0:	 0.050 FDR:   256; 0.010 FDR:   256; 0.001 FDR:   234
0:14:00.068000 PROGRESS: =========================================================================
0:14:00.070163 INFO: Target number of precursors reached.
0:14:00.110854 INFO: fragments_df: keeping 2906 of 591386 [sum(precursor_idx_mask)=6132 sum(mass_error_mask)=591386 stop_rank=2906
0:14:00.272360 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:14:00.393982 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:14:00.777768 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:14:00.778180 INFO: Using score_cutoff 12.85886302871704 (fac=0.99, q=1)
0:14:00.778473 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:14:00.778547 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:14:00.778606 INFO: Updating optimization_manager: score_cutoff        : 13.268178040409088 -> 12.85886302871704
0:14:00.778662 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:00.809905 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:00.874496 INFO: === checking if optimization conditions were reached ===
0:14:00.874738 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:14:00.877019 INFO: Updating optimization_manager: rt_error            : 101.00971599685883 -> 82.47488860483814
0:14:00.877129 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 82.4749.
0:14:00.877203 INFO: ==============================================
0:14:00.877282 INFO: Starting optimization step 3.
0:14:00.877347 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:14:00.877416 INFO: Using ng extraction backend
0:14:00.877479 PROGRESS: Extracting batch of 50293 precursors
0:14:00.967595 INFO: === Search parameters used ===
0:14:00.967818 INFO: rt_error       : 82.47488860483814
0:14:00.967871 INFO: mobility_error : 0.1
0:14:00.967914 INFO: num_candidates : 3
0:14:00.967955 INFO: ms1_error      : 30
0:14:00.967995 INFO: ms2_error      : 10.0
0:14:00.968045 INFO: fwhm_rt        : 3.0
0:14:00.968084 INFO: quant_window   : 3
0:14:00.968123 INFO: ==============================================
0:14:01.646002 INFO: performing precursor FDR with 40 features
0:14:01.646117 INFO: Decoy channel: -1
0:14:01.646143 INFO: Competetive: True
0:14:01.686198 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:01.721607 INFO: Using random state 519797 for train-test-split
0:14:03.605270 INFO: Test AUC: 0.584
0:14:03.605479 INFO: Train AUC: 0.611
0:14:03.605512 INFO: AUC difference: 4.41%
0:14:03.867833 INFO: Resetting torch num_threads to 80
0:14:03.875905 PROGRESS: === Extracted 145492 precursors and 562202 fragments ===
0:14:03.877403 INFO: === FDR correction performed with classifier version 9 ===
0:14:03.877869 PROGRESS: ============================= Precursor FDR =============================
0:14:03.877952 PROGRESS: Total precursors accumulated: 338
0:14:03.878007 PROGRESS: Target precursors: 335 (99.11%)
0:14:03.878054 PROGRESS: Decoy precursors: 3 (0.89%)
0:14:03.878099 PROGRESS: 
0:14:03.878142 PROGRESS: Precursor Summary:
0:14:03.879038 PROGRESS: Channel   0:	 0.050 FDR:   335; 0.010 FDR:   335; 0.001 FDR:   269
0:14:03.879121 PROGRESS: 
0:14:03.879173 PROGRESS: Protein Summary:
0:14:03.880252 PROGRESS: Channel   0:	 0.050 FDR:   322; 0.010 FDR:   322; 0.001 FDR:   259
0:14:03.880335 PROGRESS: =========================================================================
0:14:03.883089 INFO: Target number of precursors reached.
0:14:03.922791 INFO: fragments_df: keeping 3314 of 562202 [sum(precursor_idx_mask)=7306 sum(mass_error_mask)=562202 stop_rank=3314
0:14:04.084443 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:14:04.358791 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:14:04.903832 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:14:04.904237 INFO: Using score_cutoff 7.63570893201828 (fac=0.99, q=1)
0:14:04.904534 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:14:04.904610 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:14:04.904660 INFO: Updating optimization_manager: score_cutoff        : 12.85886302871704 -> 7.63570893201828
0:14:04.904718 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:04.935393 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:05.050763 INFO: === checking if optimization conditions were reached ===
0:14:05.051038 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:14:05.053458 INFO: Updating optimization_manager: rt_error            : 82.47488860483814 -> 65.51703204654656
0:14:05.053575 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 65.5170.
0:14:05.053671 INFO: ==============================================
0:14:05.053756 INFO: Starting optimization step 4.
0:14:05.053821 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:14:05.053913 INFO: Using ng extraction backend
0:14:05.053993 PROGRESS: Extracting batch of 50293 precursors
0:14:05.145821 INFO: === Search parameters used ===
0:14:05.146066 INFO: rt_error       : 65.51703204654656
0:14:05.146120 INFO: mobility_error : 0.1
0:14:05.146164 INFO: num_candidates : 3
0:14:05.146221 INFO: ms1_error      : 30
0:14:05.146263 INFO: ms2_error      : 10.0
0:14:05.146305 INFO: fwhm_rt        : 3.0
0:14:05.146343 INFO: quant_window   : 3
0:14:05.146381 INFO: ==============================================
0:14:05.725344 INFO: performing precursor FDR with 40 features
0:14:05.725458 INFO: Decoy channel: -1
0:14:05.725485 INFO: Competetive: True
0:14:05.766879 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:05.806299 INFO: Using random state 519797 for train-test-split
0:14:07.537029 INFO: Test AUC: 0.593
0:14:07.537140 INFO: Train AUC: 0.609
0:14:07.537169 INFO: AUC difference: 2.63%
0:14:07.787990 INFO: Resetting torch num_threads to 80
0:14:07.794651 PROGRESS: === Extracted 143321 precursors and 532189 fragments ===
0:14:07.794976 INFO: === FDR correction performed with classifier version 9 ===
0:14:07.795420 PROGRESS: ============================= Precursor FDR =============================
0:14:07.795500 PROGRESS: Total precursors accumulated: 316
0:14:07.795553 PROGRESS: Target precursors: 313 (99.05%)
0:14:07.795600 PROGRESS: Decoy precursors: 3 (0.95%)
0:14:07.795642 PROGRESS: 
0:14:07.795682 PROGRESS: Precursor Summary:
0:14:07.796562 PROGRESS: Channel   0:	 0.050 FDR:   313; 0.010 FDR:   313; 0.001 FDR:   268
0:14:07.796648 PROGRESS: 
0:14:07.796699 PROGRESS: Protein Summary:
0:14:07.797770 PROGRESS: Channel   0:	 0.050 FDR:   303; 0.010 FDR:   303; 0.001 FDR:   260
0:14:07.797857 PROGRESS: =========================================================================
0:14:07.799894 INFO: Target number of precursors reached.
0:14:07.835013 INFO: fragments_df: keeping 3173 of 532189 [sum(precursor_idx_mask)=6820 sum(mass_error_mask)=532189 stop_rank=3173
0:14:07.968096 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:14:08.070960 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:14:08.501225 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:14:08.501612 INFO: Using score_cutoff 12.17331665496826 (fac=0.99, q=1)
0:14:08.501884 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:14:08.501961 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:14:08.502013 INFO: Updating optimization_manager: score_cutoff        : 7.63570893201828 -> 12.17331665496826
0:14:08.502062 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:08.533651 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:08.601876 INFO: === checking if optimization conditions were reached ===
0:14:08.602128 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:14:08.604382 INFO: Updating optimization_manager: rt_error            : 65.51703204654656 -> 51.266015041268474
0:14:08.604489 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 51.2660.
0:14:08.604563 INFO: ==============================================
0:14:08.604640 INFO: Starting optimization step 5.
0:14:08.604705 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:14:08.604774 INFO: Using ng extraction backend
0:14:08.604853 PROGRESS: Extracting batch of 50293 precursors
0:14:08.692433 INFO: === Search parameters used ===
0:14:08.692698 INFO: rt_error       : 51.266015041268474
0:14:08.692769 INFO: mobility_error : 0.1
0:14:08.692826 INFO: num_candidates : 3
0:14:08.692875 INFO: ms1_error      : 30
0:14:08.692917 INFO: ms2_error      : 10.0
0:14:08.692958 INFO: fwhm_rt        : 3.0
0:14:08.693003 INFO: quant_window   : 3
0:14:08.693041 INFO: ==============================================
0:14:09.237494 INFO: performing precursor FDR with 40 features
0:14:09.237620 INFO: Decoy channel: -1
0:14:09.237647 INFO: Competetive: True
0:14:09.275703 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:09.307933 INFO: Using random state 519797 for train-test-split
0:14:11.151694 INFO: Test AUC: 0.595
0:14:11.151811 INFO: Train AUC: 0.612
0:14:11.151843 INFO: AUC difference: 2.73%
0:14:11.409605 INFO: Resetting torch num_threads to 80
0:14:11.416457 PROGRESS: === Extracted 135261 precursors and 482924 fragments ===
0:14:11.416822 INFO: === FDR correction performed with classifier version 9 ===
0:14:11.417265 PROGRESS: ============================= Precursor FDR =============================
0:14:11.417348 PROGRESS: Total precursors accumulated: 247
0:14:11.417404 PROGRESS: Target precursors: 245 (99.19%)
0:14:11.417452 PROGRESS: Decoy precursors: 2 (0.81%)
0:14:11.417496 PROGRESS: 
0:14:11.417538 PROGRESS: Precursor Summary:
0:14:11.418386 PROGRESS: Channel   0:	 0.050 FDR:   245; 0.010 FDR:   245; 0.001 FDR:   202
0:14:11.418468 PROGRESS: 
0:14:11.418520 PROGRESS: Protein Summary:
0:14:11.419513 PROGRESS: Channel   0:	 0.050 FDR:   237; 0.010 FDR:   237; 0.001 FDR:   195
0:14:11.419595 PROGRESS: =========================================================================
0:14:11.421981 INFO: Target number of precursors reached.
0:14:11.455692 INFO: fragments_df: keeping 2432 of 482924 [sum(precursor_idx_mask)=5042 sum(mass_error_mask)=482924 stop_rank=2432
0:14:11.641047 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:14:11.908408 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:14:12.284267 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:14:12.284662 INFO: Using score_cutoff 12.81349306411743 (fac=0.99, q=1)
0:14:12.284943 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:14:12.285019 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:14:12.285072 INFO: Updating optimization_manager: score_cutoff        : 12.17331665496826 -> 12.81349306411743
0:14:12.285124 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:12.317698 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:12.383695 INFO: === checking if optimization conditions were reached ===
0:14:12.383947 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:14:12.385255 INFO: Updating optimization_manager: rt_error            : 51.266015041268474 -> 65.51703204654656
0:14:12.385396 INFO: Updating optimization_manager: classifier_version  : 9 -> 14
0:14:12.385501 INFO: Updating optimization_manager: score_cutoff        : 12.81349306411743 -> 12.17331665496826
0:14:12.385601 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:14:12.385698 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:14:12.385790 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 65.5170 found after 6 searches.
0:14:12.385859 INFO: ==============================================
0:14:12.385948 PROGRESS: Optimization finished for rt_error.
0:14:12.533052 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:12.565923 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:12.664086 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:14:12.664308 PROGRESS: ==============================================
0:14:12.664392 PROGRESS: ms2_error      : 10.0000
0:14:12.664457 PROGRESS: rt_error       : 65.5170
0:14:12.664512 PROGRESS: ==============================================
0:14:12.665149 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:14:20.724483 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:14:38.264546 INFO: Using ng extraction backend
0:14:38.265285 PROGRESS: Extracting batch of 12001526 precursors
0:14:54.073878 INFO: === Search parameters used ===
0:14:54.074207 INFO: rt_error       : 65.51703204654656
0:14:54.074277 INFO: mobility_error : 0.1
0:14:54.074327 INFO: num_candidates : 3
0:14:54.074370 INFO: ms1_error      : 30
0:14:54.074410 INFO: ms2_error      : 10.0
0:14:54.074451 INFO: fwhm_rt        : 3.0
0:14:54.074491 INFO: quant_window   : 3
0:14:54.074532 INFO: ==============================================
0:15:35.706190 INFO: Removed 26561819 precursors with score below cutoff 12.17331665496826
0:15:45.733367 INFO: performing precursor FDR with 40 features
0:15:45.733485 INFO: Decoy channel: -1
0:15:45.733514 INFO: Competetive: True
0:15:46.625825 INFO: Setting torch num_threads to 2 for FDR classification task
0:15:49.964135 INFO: Using random state 540658 for train-test-split
0:17:51.059876 INFO: Test AUC: 0.626
0:17:51.060123 INFO: Train AUC: 0.628
0:17:51.060159 INFO: AUC difference: 0.34%
0:17:53.835825 INFO: Resetting torch num_threads to 80
0:17:55.665816 PROGRESS: ============================= Precursor FDR =============================
0:17:55.666078 PROGRESS: Total precursors accumulated: 83,024
0:17:55.666141 PROGRESS: Target precursors: 82,202 (99.01%)
0:17:55.666191 PROGRESS: Decoy precursors: 822 (0.99%)
0:17:55.666237 PROGRESS: 
0:17:55.666280 PROGRESS: Precursor Summary:
0:17:55.693332 PROGRESS: Channel   0:	 0.050 FDR: 82,202; 0.010 FDR: 82,202; 0.001 FDR: 54,306
0:17:55.693553 PROGRESS: 
0:17:55.693612 PROGRESS: Protein Summary:
0:17:55.734495 PROGRESS: Channel   0:	 0.050 FDR: 13,314; 0.010 FDR: 13,314; 0.001 FDR: 9,388
0:17:55.734714 PROGRESS: =========================================================================
0:17:55.788420 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/psm.parquet
0:17:55.976193 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.parquet
0:17:56.205359 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:17:56.708209 PROGRESS: 
0:17:56.708360 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark/quant
0:17:56.708432 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/figures
0:17:56.708603 INFO: Initializing TimingManager
0:17:56.709116 INFO: Initializing RawFileManager
0:18:06.719584 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.
0:18:06.723557 INFO: Determining DIA cycle
0:18:06.739868 INFO: Found cycle with start 0.00 min and length 300.
0:18:06.905654 INFO: RT (min)            : 0.0 - 26.9
0:18:06.905745 INFO: RT duration (sec)   : 1611.2
0:18:06.905773 INFO: RT duration (min)   : 26.9
0:18:06.905799 INFO: Cycle len (scans)   : 300
0:18:06.905819 INFO: Cycle len (sec)     : 1.65
0:18:06.905840 INFO: Number of cycles    : 978
0:18:06.905860 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:18:06.905887 INFO: Creating DIA data object took: 10.196667671203613
0:18:07.554698 INFO: Creating DIA data NG object took: 0.6487047672271729
0:18:08.807336 INFO: Initializing CalibrationManager
0:18:08.807593 INFO: Setting up calibration estimators ..
0:18:08.807650 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:18:08.807726 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'}' ..
0:18:08.807820 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:18:08.807871 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:18:08.807926 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}}' ..
0:18:08.807993 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:18:08.808041 INFO: Done setting up calibration estimators.
0:18:08.808221 INFO: Initializing OptimizationManager
0:18:08.808370 INFO: initial parameter: ms1_error = 30
0:18:08.808422 INFO: initial parameter: ms2_error = 30
0:18:08.808466 INFO: initial parameter: rt_error = 805.6019897460938
0:18:08.808510 INFO: initial parameter: mobility_error = 0.1
0:18:08.808549 INFO: initial parameter: num_candidates = 1
0:18:08.808590 INFO: initial parameter: fwhm_rt = 5
0:18:08.808629 INFO: initial parameter: fwhm_mobility = 0.01
0:18:08.808669 INFO: initial parameter: score_cutoff = 0
0:18:08.808706 INFO: initial parameter: classifier_version = -1
0:18:08.808770 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:18:08.809007 INFO: FDRManager: loading saved state not requested, will be initialized.
0:18:08.809044 INFO: Initializing FDRManager
0:18:08.809080 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:18:10.228182 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:18:11.098196 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:18:11.098593 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
0:18:11.098726 PROGRESS: Starting initial search for precursors.
0:18:11.098813 INFO: Starting optimization step 0.
0:18:11.098905 PROGRESS: === Extracting elution groups 0 to 200 ===
0:18:11.098970 INFO: Using ng extraction backend
0:18:11.099031 PROGRESS: Extracting batch of 396 precursors
0:18:11.101003 INFO: === Search parameters used ===
0:18:11.101097 INFO: rt_error       : 805.6019897460938
0:18:11.101149 INFO: mobility_error : 0.1
0:18:11.101194 INFO: num_candidates : 1
0:18:11.101239 INFO: ms1_error      : 30
0:18:11.101279 INFO: ms2_error      : 30
0:18:11.101319 INFO: fwhm_rt        : 5
0:18:11.101359 INFO: quant_window   : 3
0:18:11.101398 INFO: ==============================================
0:18:11.118079 INFO: performing precursor FDR with 40 features
0:18:11.118179 INFO: Decoy channel: -1
0:18:11.118207 INFO: Competetive: True
0:18:11.119081 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:11.121160 INFO: Using random state 972839 for train-test-split
0:18:11.127789 INFO: Test AUC: 0.524
0:18:11.127844 INFO: Train AUC: 0.467
0:18:11.127873 INFO: AUC difference: 12.05%
0:18:11.127897 WARNING: AUC difference > 5%. This may indicate overfitting.
0:18:11.779582 INFO: Resetting torch num_threads to 80
0:18:11.780828 PROGRESS: === Extracted 391 precursors and 1831 fragments ===
0:18:11.781166 INFO: === FDR correction performed with classifier version -1 ===
0:18:11.781576 PROGRESS: ============================= Precursor FDR =============================
0:18:11.781661 PROGRESS: Total precursors accumulated: 0
0:18:11.781717 PROGRESS: Target precursors: 0 (0.00%)
0:18:11.781766 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:11.781812 PROGRESS: 
0:18:11.781855 PROGRESS: Precursor Summary:
0:18:11.781958 PROGRESS: 
0:18:11.782017 PROGRESS: Protein Summary:
0:18:11.782088 PROGRESS: =========================================================================
0:18:11.782237 INFO: Target number of precursors not reached yet.
0:18:11.846501 INFO: Starting optimization step 1.
0:18:11.846705 PROGRESS: === Extracting elution groups 200 to 600 ===
0:18:11.846785 INFO: Using ng extraction backend
0:18:11.846845 PROGRESS: Extracting batch of 786 precursors
0:18:11.849470 INFO: === Search parameters used ===
0:18:11.849576 INFO: rt_error       : 805.6019897460938
0:18:11.849626 INFO: mobility_error : 0.1
0:18:11.849673 INFO: num_candidates : 1
0:18:11.849714 INFO: ms1_error      : 30
0:18:11.849753 INFO: ms2_error      : 30
0:18:11.849794 INFO: fwhm_rt        : 5
0:18:11.849831 INFO: quant_window   : 3
0:18:11.849880 INFO: ==============================================
0:18:11.871895 INFO: performing precursor FDR with 40 features
0:18:11.871994 INFO: Decoy channel: -1
0:18:11.872022 INFO: Competetive: True
0:18:11.874801 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:11.876279 INFO: Using random state 445866 for train-test-split
0:18:11.884139 INFO: Test AUC: 0.494
0:18:11.884194 INFO: Train AUC: 0.496
0:18:11.884224 INFO: AUC difference: 0.43%
0:18:12.090288 INFO: Resetting torch num_threads to 80
0:18:12.092266 PROGRESS: === Extracted 1172 precursors and 5506 fragments ===
0:18:12.092596 INFO: === FDR correction performed with classifier version -1 ===
0:18:12.093044 PROGRESS: ============================= Precursor FDR =============================
0:18:12.093135 PROGRESS: Total precursors accumulated: 1
0:18:12.093192 PROGRESS: Target precursors: 1 (100.00%)
0:18:12.093240 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:12.093282 PROGRESS: 
0:18:12.093326 PROGRESS: Precursor Summary:
0:18:12.094206 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:18:12.094291 PROGRESS: 
0:18:12.094361 PROGRESS: Protein Summary:
0:18:12.095334 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:18:12.095421 PROGRESS: =========================================================================
0:18:12.095600 INFO: Target number of precursors not reached yet.
0:18:12.162473 INFO: Starting optimization step 2.
0:18:12.162669 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:18:12.162749 INFO: Using ng extraction backend
0:18:12.162809 PROGRESS: Extracting batch of 1592 precursors
0:18:12.166958 INFO: === Search parameters used ===
0:18:12.167068 INFO: rt_error       : 805.6019897460938
0:18:12.167119 INFO: mobility_error : 0.1
0:18:12.167162 INFO: num_candidates : 1
0:18:12.167205 INFO: ms1_error      : 30
0:18:12.167245 INFO: ms2_error      : 30
0:18:12.167284 INFO: fwhm_rt        : 5
0:18:12.167325 INFO: quant_window   : 3
0:18:12.167364 INFO: ==============================================
0:18:12.197397 INFO: performing precursor FDR with 40 features
0:18:12.197471 INFO: Decoy channel: -1
0:18:12.197497 INFO: Competetive: True
0:18:12.200685 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:12.202536 INFO: Using random state 595720 for train-test-split
0:18:12.213924 INFO: Test AUC: 0.492
0:18:12.213985 INFO: Train AUC: 0.514
0:18:12.214015 INFO: AUC difference: 4.15%
0:18:12.424326 INFO: Resetting torch num_threads to 80
0:18:12.426745 PROGRESS: === Extracted 2752 precursors and 12933 fragments ===
0:18:12.427073 INFO: === FDR correction performed with classifier version -1 ===
0:18:12.427510 PROGRESS: ============================= Precursor FDR =============================
0:18:12.427597 PROGRESS: Total precursors accumulated: 1
0:18:12.427662 PROGRESS: Target precursors: 1 (100.00%)
0:18:12.427712 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:12.427758 PROGRESS: 
0:18:12.427799 PROGRESS: Precursor Summary:
0:18:12.428674 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:18:12.428760 PROGRESS: 
0:18:12.428820 PROGRESS: Protein Summary:
0:18:12.429790 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:18:12.429877 PROGRESS: =========================================================================
0:18:12.430077 INFO: Target number of precursors not reached yet.
0:18:12.498991 INFO: Starting optimization step 3.
0:18:12.499198 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:18:12.499276 INFO: Using ng extraction backend
0:18:12.499337 PROGRESS: Extracting batch of 3177 precursors
0:18:12.506165 INFO: === Search parameters used ===
0:18:12.506286 INFO: rt_error       : 805.6019897460938
0:18:12.506334 INFO: mobility_error : 0.1
0:18:12.506378 INFO: num_candidates : 1
0:18:12.506418 INFO: ms1_error      : 30
0:18:12.506456 INFO: ms2_error      : 30
0:18:12.506497 INFO: fwhm_rt        : 5
0:18:12.506534 INFO: quant_window   : 3
0:18:12.506587 INFO: ==============================================
0:18:12.550934 INFO: performing precursor FDR with 40 features
0:18:12.551017 INFO: Decoy channel: -1
0:18:12.551042 INFO: Competetive: True
0:18:12.555075 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:12.557380 INFO: Using random state 262578 for train-test-split
0:18:12.576757 INFO: Test AUC: 0.491
0:18:12.576835 INFO: Train AUC: 0.505
0:18:12.576865 INFO: AUC difference: 2.73%
0:18:12.785476 INFO: Resetting torch num_threads to 80
0:18:12.788552 PROGRESS: === Extracted 5885 precursors and 27703 fragments ===
0:18:12.788897 INFO: === FDR correction performed with classifier version -1 ===
0:18:12.789310 PROGRESS: ============================= Precursor FDR =============================
0:18:12.789394 PROGRESS: Total precursors accumulated: 0
0:18:12.789451 PROGRESS: Target precursors: 0 (0.00%)
0:18:12.789498 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:12.789541 PROGRESS: 
0:18:12.789582 PROGRESS: Precursor Summary:
0:18:12.789685 PROGRESS: 
0:18:12.789747 PROGRESS: Protein Summary:
0:18:12.789817 PROGRESS: =========================================================================
0:18:12.790037 INFO: Target number of precursors not reached yet.
0:18:12.863014 INFO: Starting optimization step 4.
0:18:12.863217 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:18:12.863312 INFO: Using ng extraction backend
0:18:12.863371 PROGRESS: Extracting batch of 6340 precursors
0:18:12.875742 INFO: === Search parameters used ===
0:18:12.875876 INFO: rt_error       : 805.6019897460938
0:18:12.875925 INFO: mobility_error : 0.1
0:18:12.875970 INFO: num_candidates : 1
0:18:12.876011 INFO: ms1_error      : 30
0:18:12.876061 INFO: ms2_error      : 30
0:18:12.876104 INFO: fwhm_rt        : 5
0:18:12.876142 INFO: quant_window   : 3
0:18:12.876181 INFO: ==============================================
0:18:12.948739 INFO: performing precursor FDR with 40 features
0:18:12.948864 INFO: Decoy channel: -1
0:18:12.948895 INFO: Competetive: True
0:18:12.955437 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:12.959163 INFO: Using random state 680466 for train-test-split
0:18:12.996902 INFO: Test AUC: 0.494
0:18:12.996994 INFO: Train AUC: 0.510
0:18:12.997024 INFO: AUC difference: 3.00%
0:18:13.212291 INFO: Resetting torch num_threads to 80
0:18:13.216361 PROGRESS: === Extracted 12138 precursors and 56682 fragments ===
0:18:13.216707 INFO: === FDR correction performed with classifier version -1 ===
0:18:13.217135 PROGRESS: ============================= Precursor FDR =============================
0:18:13.217223 PROGRESS: Total precursors accumulated: 0
0:18:13.217280 PROGRESS: Target precursors: 0 (0.00%)
0:18:13.217327 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:13.217371 PROGRESS: 
0:18:13.217413 PROGRESS: Precursor Summary:
0:18:13.217515 PROGRESS: 
0:18:13.217575 PROGRESS: Protein Summary:
0:18:13.217644 PROGRESS: =========================================================================
0:18:13.217927 INFO: Target number of precursors not reached yet.
0:18:13.299542 INFO: Starting optimization step 5.
0:18:13.299767 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:18:13.299846 INFO: Using ng extraction backend
0:18:13.299911 PROGRESS: Extracting batch of 12663 precursors
0:18:13.322819 INFO: === Search parameters used ===
0:18:13.322993 INFO: rt_error       : 805.6019897460938
0:18:13.323043 INFO: mobility_error : 0.1
0:18:13.323088 INFO: num_candidates : 1
0:18:13.323132 INFO: ms1_error      : 30
0:18:13.323172 INFO: ms2_error      : 30
0:18:13.323211 INFO: fwhm_rt        : 5
0:18:13.323250 INFO: quant_window   : 3
0:18:13.323286 INFO: ==============================================
0:18:13.448319 INFO: performing precursor FDR with 40 features
0:18:13.448430 INFO: Decoy channel: -1
0:18:13.448455 INFO: Competetive: True
0:18:13.458578 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:13.464142 INFO: Using random state 148983 for train-test-split
0:18:13.702783 INFO: Test AUC: 0.508
0:18:13.702879 INFO: Train AUC: 0.504
0:18:13.702921 INFO: AUC difference: 0.80%
0:18:13.916468 INFO: Resetting torch num_threads to 80
0:18:13.923163 PROGRESS: === Extracted 24633 precursors and 115281 fragments ===
0:18:13.923595 INFO: === FDR correction performed with classifier version -1 ===
0:18:13.924041 PROGRESS: ============================= Precursor FDR =============================
0:18:13.924128 PROGRESS: Total precursors accumulated: 0
0:18:13.924185 PROGRESS: Target precursors: 0 (0.00%)
0:18:13.924234 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:13.924279 PROGRESS: 
0:18:13.924321 PROGRESS: Precursor Summary:
0:18:13.924429 PROGRESS: 
0:18:13.924490 PROGRESS: Protein Summary:
0:18:13.924564 PROGRESS: =========================================================================
0:18:13.924979 INFO: Target number of precursors not reached yet.
0:18:14.022306 INFO: Starting optimization step 6.
0:18:14.022538 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:18:14.022634 INFO: Using ng extraction backend
0:18:14.022697 PROGRESS: Extracting batch of 25339 precursors
0:18:14.067062 INFO: === Search parameters used ===
0:18:14.067258 INFO: rt_error       : 805.6019897460938
0:18:14.067308 INFO: mobility_error : 0.1
0:18:14.067351 INFO: num_candidates : 1
0:18:14.067391 INFO: ms1_error      : 30
0:18:14.067429 INFO: ms2_error      : 30
0:18:14.067469 INFO: fwhm_rt        : 5
0:18:14.067507 INFO: quant_window   : 3
0:18:14.067546 INFO: ==============================================
0:18:14.281009 INFO: performing precursor FDR with 40 features
0:18:14.281118 INFO: Decoy channel: -1
0:18:14.281144 INFO: Competetive: True
0:18:14.299417 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:14.311041 INFO: Using random state 37300 for train-test-split
0:18:14.904605 INFO: Test AUC: 0.548
0:18:14.904718 INFO: Train AUC: 0.560
0:18:14.904747 INFO: AUC difference: 2.23%
0:18:15.131969 INFO: Resetting torch num_threads to 80
0:18:15.141461 PROGRESS: === Extracted 49665 precursors and 231545 fragments ===
0:18:15.141972 INFO: === FDR correction performed with classifier version -1 ===
0:18:15.142498 PROGRESS: ============================= Precursor FDR =============================
0:18:15.142586 PROGRESS: Total precursors accumulated: 1
0:18:15.142643 PROGRESS: Target precursors: 1 (100.00%)
0:18:15.142691 PROGRESS: Decoy precursors: 0 (0.00%)
0:18:15.142735 PROGRESS: 
0:18:15.142777 PROGRESS: Precursor Summary:
0:18:15.143676 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:18:15.143762 PROGRESS: 
0:18:15.143815 PROGRESS: Protein Summary:
0:18:15.144974 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:18:15.145063 PROGRESS: =========================================================================
0:18:15.145866 INFO: Target number of precursors not reached yet.
0:18:15.276693 INFO: Starting optimization step 7.
0:18:15.276929 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:18:15.277014 INFO: Using ng extraction backend
0:18:15.277095 PROGRESS: Extracting batch of 50691 precursors
0:18:15.364798 INFO: === Search parameters used ===
0:18:15.365056 INFO: rt_error       : 805.6019897460938
0:18:15.365117 INFO: mobility_error : 0.1
0:18:15.365164 INFO: num_candidates : 1
0:18:15.365208 INFO: ms1_error      : 30
0:18:15.365249 INFO: ms2_error      : 30
0:18:15.365289 INFO: fwhm_rt        : 5
0:18:15.365330 INFO: quant_window   : 3
0:18:15.365370 INFO: ==============================================
0:18:15.712862 INFO: performing precursor FDR with 40 features
0:18:15.712978 INFO: Decoy channel: -1
0:18:15.713005 INFO: Competetive: True
0:18:15.751714 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:15.778508 INFO: Using random state 604484 for train-test-split
0:18:17.241533 INFO: Test AUC: 0.584
0:18:17.241648 INFO: Train AUC: 0.594
0:18:17.241677 INFO: AUC difference: 1.71%
0:18:17.486909 INFO: Resetting torch num_threads to 80
0:18:17.506501 PROGRESS: === Extracted 99812 precursors and 465578 fragments ===
0:18:17.507062 INFO: === FDR correction performed with classifier version -1 ===
0:18:17.507612 PROGRESS: ============================= Precursor FDR =============================
0:18:17.507700 PROGRESS: Total precursors accumulated: 272
0:18:17.507756 PROGRESS: Target precursors: 270 (99.26%)
0:18:17.507813 PROGRESS: Decoy precursors: 2 (0.74%)
0:18:17.507858 PROGRESS: 
0:18:17.507902 PROGRESS: Precursor Summary:
0:18:17.508820 PROGRESS: Channel   0:	 0.050 FDR:   270; 0.010 FDR:   270; 0.001 FDR:   115
0:18:17.508914 PROGRESS: 
0:18:17.508968 PROGRESS: Protein Summary:
0:18:17.509997 PROGRESS: Channel   0:	 0.050 FDR:   256; 0.010 FDR:   256; 0.001 FDR:   112
0:18:17.510087 PROGRESS: =========================================================================
0:18:17.511729 INFO: Target number of precursors reached.
0:18:17.546142 INFO: fragments_df: keeping 2337 of 465578 [sum(precursor_idx_mask)=2899 sum(mass_error_mask)=465578 stop_rank=2337
0:18:17.751031 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:17.876725 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:18.183390 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:18:18.183788 INFO: Using score_cutoff 13.246682397651673 (fac=0.99, q=1)
0:18:18.184070 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:18:18.184149 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:18:18.184202 INFO: Updating optimization_manager: score_cutoff        : 0 -> 13.246682397651673
0:18:18.184255 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:18.252128 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:18.404074 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:18:18.405097 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:18:18.405222 INFO: Starting optimization step 8.
0:18:18.405302 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:18:18.405380 INFO: Using ng extraction backend
0:18:18.405449 PROGRESS: Extracting batch of 100984 precursors
0:18:18.581344 INFO: === Search parameters used ===
0:18:18.581592 INFO: rt_error       : 805.6019897460938
0:18:18.581647 INFO: mobility_error : 0.1
0:18:18.581693 INFO: num_candidates : 3
0:18:18.581734 INFO: ms1_error      : 30
0:18:18.581773 INFO: ms2_error      : 30
0:18:18.581812 INFO: fwhm_rt        : 3.0
0:18:18.581850 INFO: quant_window   : 3
0:18:18.581891 INFO: ==============================================
0:18:19.892316 INFO: performing precursor FDR with 40 features
0:18:19.892429 INFO: Decoy channel: -1
0:18:19.892456 INFO: Competetive: True
0:18:19.981952 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:20.083074 INFO: Using random state 397149 for train-test-split
0:18:24.191647 INFO: Test AUC: 0.592
0:18:24.191876 INFO: Train AUC: 0.606
0:18:24.191910 INFO: AUC difference: 2.31%
0:18:24.504008 INFO: Resetting torch num_threads to 80
0:18:24.519364 PROGRESS: === Extracted 299631 precursors and 1368190 fragments ===
0:18:24.519814 INFO: === FDR correction performed with classifier version 7 ===
0:18:24.520273 PROGRESS: ============================= Precursor FDR =============================
0:18:24.520362 PROGRESS: Total precursors accumulated: 308
0:18:24.520420 PROGRESS: Target precursors: 305 (99.03%)
0:18:24.520469 PROGRESS: Decoy precursors: 3 (0.97%)
0:18:24.520518 PROGRESS: 
0:18:24.520572 PROGRESS: Precursor Summary:
0:18:24.521489 PROGRESS: Channel   0:	 0.050 FDR:   305; 0.010 FDR:   305; 0.001 FDR:   150
0:18:24.521580 PROGRESS: 
0:18:24.521634 PROGRESS: Protein Summary:
0:18:24.522694 PROGRESS: Channel   0:	 0.050 FDR:   289; 0.010 FDR:   289; 0.001 FDR:   143
0:18:24.522782 PROGRESS: =========================================================================
0:18:24.528737 INFO: Target number of precursors reached.
0:18:24.619314 INFO: fragments_df: keeping 3652 of 1368190 [sum(precursor_idx_mask)=6940 sum(mass_error_mask)=1368190 stop_rank=3652
0:18:24.897260 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:25.045059 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:25.521290 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:25.521695 INFO: Using score_cutoff 14.636674305725098 (fac=0.99, q=1)
0:18:25.521993 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:25.522072 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:25.522126 INFO: Updating optimization_manager: score_cutoff        : 13.246682397651673 -> 14.636674305725098
0:18:25.522184 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:25.590071 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:25.747591 INFO: === checking if optimization conditions were reached ===
0:18:25.799200 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:18:25.835558 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:18:25.835874 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:18:25.836141 INFO: ==============================================
0:18:25.836435 INFO: Starting optimization step 9.
0:18:25.836688 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:18:25.836980 INFO: Using ng extraction backend
0:18:25.838163 PROGRESS: Extracting batch of 100984 precursors
0:18:26.019429 INFO: === Search parameters used ===
0:18:26.019701 INFO: rt_error       : 805.6019897460938
0:18:26.019779 INFO: mobility_error : 0.1
0:18:26.019843 INFO: num_candidates : 3
0:18:26.019901 INFO: ms1_error      : 30
0:18:26.019957 INFO: ms2_error      : 10.0
0:18:26.020008 INFO: fwhm_rt        : 3.0
0:18:26.020057 INFO: quant_window   : 3
0:18:26.020105 INFO: ==============================================
0:18:27.417912 INFO: performing precursor FDR with 40 features
0:18:27.418028 INFO: Decoy channel: -1
0:18:27.418055 INFO: Competetive: True
0:18:27.497161 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:27.601895 INFO: Using random state 806613 for train-test-split
0:18:31.626945 INFO: Test AUC: 0.597
0:18:31.627067 INFO: Train AUC: 0.610
0:18:31.627099 INFO: AUC difference: 2.07%
0:18:31.933775 INFO: Resetting torch num_threads to 80
0:18:31.946186 PROGRESS: === Extracted 302148 precursors and 1604368 fragments ===
0:18:31.946563 INFO: === FDR correction performed with classifier version 8 ===
0:18:31.947053 PROGRESS: ============================= Precursor FDR =============================
0:18:31.947138 PROGRESS: Total precursors accumulated: 615
0:18:31.947195 PROGRESS: Target precursors: 609 (99.02%)
0:18:31.947245 PROGRESS: Decoy precursors: 6 (0.98%)
0:18:31.947299 PROGRESS: 
0:18:31.947341 PROGRESS: Precursor Summary:
0:18:31.948285 PROGRESS: Channel   0:	 0.050 FDR:   609; 0.010 FDR:   609; 0.001 FDR:   214
0:18:31.948371 PROGRESS: 
0:18:31.948422 PROGRESS: Protein Summary:
0:18:31.949599 PROGRESS: Channel   0:	 0.050 FDR:   565; 0.010 FDR:   565; 0.001 FDR:   203
0:18:31.949695 PROGRESS: =========================================================================
0:18:31.954883 INFO: Target number of precursors reached.
0:18:32.061941 INFO: fragments_df: keeping 5000 of 1604368 [sum(precursor_idx_mask)=14385 sum(mass_error_mask)=1604368 stop_rank=5000
0:18:32.207266 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:32.350503 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:33.028641 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:33.029047 INFO: Using score_cutoff 11.549243380737304 (fac=0.99, q=1)
0:18:33.029328 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:33.029406 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:33.029459 INFO: Updating optimization_manager: score_cutoff        : 14.636674305725098 -> 11.549243380737304
0:18:33.029510 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:33.059707 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:33.124028 INFO: === checking if optimization conditions were reached ===
0:18:33.126421 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:18:33.126545 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:18:33.126620 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:18:33.126686 INFO: ==============================================
0:18:33.126760 PROGRESS: Optimization finished for ms2_error.
0:18:33.272121 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:33.306080 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:33.369831 INFO: Starting optimization step 0.
0:18:33.370084 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:18:33.370177 INFO: Using ng extraction backend
0:18:33.370251 PROGRESS: Extracting batch of 50293 precursors
0:18:33.460986 INFO: === Search parameters used ===
0:18:33.461236 INFO: rt_error       : 805.6019897460938
0:18:33.461290 INFO: mobility_error : 0.1
0:18:33.461336 INFO: num_candidates : 3
0:18:33.461381 INFO: ms1_error      : 30
0:18:33.461422 INFO: ms2_error      : 10.0
0:18:33.461463 INFO: fwhm_rt        : 3.0
0:18:33.461502 INFO: quant_window   : 3
0:18:33.461540 INFO: ==============================================
0:18:34.115356 INFO: performing precursor FDR with 40 features
0:18:34.115481 INFO: Decoy channel: -1
0:18:34.115508 INFO: Competetive: True
0:18:34.156115 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:34.194312 INFO: Using random state 598898 for train-test-split
0:18:36.207302 INFO: Test AUC: 0.597
0:18:36.207418 INFO: Train AUC: 0.620
0:18:36.207448 INFO: AUC difference: 3.72%
0:18:36.465232 INFO: Resetting torch num_threads to 80
0:18:36.471631 PROGRESS: === Extracted 150469 precursors and 799147 fragments ===
0:18:36.471969 INFO: === FDR correction performed with classifier version 9 ===
0:18:36.472414 PROGRESS: ============================= Precursor FDR =============================
0:18:36.472521 PROGRESS: Total precursors accumulated: 248
0:18:36.472578 PROGRESS: Target precursors: 246 (99.19%)
0:18:36.472626 PROGRESS: Decoy precursors: 2 (0.81%)
0:18:36.472671 PROGRESS: 
0:18:36.472713 PROGRESS: Precursor Summary:
0:18:36.473581 PROGRESS: Channel   0:	 0.050 FDR:   246; 0.010 FDR:   246; 0.001 FDR:   134
0:18:36.473670 PROGRESS: 
0:18:36.473723 PROGRESS: Protein Summary:
0:18:36.474725 PROGRESS: Channel   0:	 0.050 FDR:   239; 0.010 FDR:   239; 0.001 FDR:   131
0:18:36.474810 PROGRESS: =========================================================================
0:18:36.476960 INFO: Target number of precursors reached.
0:18:36.530105 INFO: fragments_df: keeping 2827 of 799147 [sum(precursor_idx_mask)=5902 sum(mass_error_mask)=799147 stop_rank=2827
0:18:36.663392 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:36.778593 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:37.151830 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:37.152224 INFO: Using score_cutoff 12.59899937725067 (fac=0.99, q=1)
0:18:37.152497 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:37.152574 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:37.152626 INFO: Updating optimization_manager: score_cutoff        : 11.549243380737304 -> 12.59899937725067
0:18:37.152684 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:37.182780 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:37.246706 INFO: === checking if optimization conditions were reached ===
0:18:37.246984 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:18:37.249027 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 105.42518929308291
0:18:37.249146 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 105.4252.
0:18:37.249222 INFO: ==============================================
0:18:37.249299 INFO: Starting optimization step 1.
0:18:37.249363 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:18:37.249432 INFO: Using ng extraction backend
0:18:37.249513 PROGRESS: Extracting batch of 50293 precursors
0:18:37.339160 INFO: === Search parameters used ===
0:18:37.339418 INFO: rt_error       : 105.42518929308291
0:18:37.339472 INFO: mobility_error : 0.1
0:18:37.339516 INFO: num_candidates : 3
0:18:37.339559 INFO: ms1_error      : 30
0:18:37.339599 INFO: ms2_error      : 10.0
0:18:37.339638 INFO: fwhm_rt        : 3.0
0:18:37.339675 INFO: quant_window   : 3
0:18:37.339712 INFO: ==============================================
0:18:38.021248 INFO: performing precursor FDR with 40 features
0:18:38.021359 INFO: Decoy channel: -1
0:18:38.021387 INFO: Competetive: True
0:18:38.061651 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:38.097156 INFO: Using random state 598898 for train-test-split
0:18:40.088262 INFO: Test AUC: 0.596
0:18:40.088374 INFO: Train AUC: 0.609
0:18:40.088405 INFO: AUC difference: 2.01%
0:18:40.875508 INFO: Resetting torch num_threads to 80
0:18:40.882181 PROGRESS: === Extracted 147105 precursors and 598825 fragments ===
0:18:40.882515 INFO: === FDR correction performed with classifier version 9 ===
0:18:40.882970 PROGRESS: ============================= Precursor FDR =============================
0:18:40.883053 PROGRESS: Total precursors accumulated: 308
0:18:40.883108 PROGRESS: Target precursors: 305 (99.03%)
0:18:40.883157 PROGRESS: Decoy precursors: 3 (0.97%)
0:18:40.883199 PROGRESS: 
0:18:40.883240 PROGRESS: Precursor Summary:
0:18:40.884134 PROGRESS: Channel   0:	 0.050 FDR:   305; 0.010 FDR:   305; 0.001 FDR:   179
0:18:40.884222 PROGRESS: 
0:18:40.884278 PROGRESS: Protein Summary:
0:18:40.885324 PROGRESS: Channel   0:	 0.050 FDR:   294; 0.010 FDR:   294; 0.001 FDR:   175
0:18:40.885413 PROGRESS: =========================================================================
0:18:40.887568 INFO: Target number of precursors reached.
0:18:40.928610 INFO: fragments_df: keeping 3254 of 598825 [sum(precursor_idx_mask)=6942 sum(mass_error_mask)=598825 stop_rank=3254
0:18:41.063701 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:41.184129 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:41.611954 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:41.612343 INFO: Using score_cutoff 12.188660250091553 (fac=0.99, q=1)
0:18:41.612613 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:41.612848 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:41.612911 INFO: Updating optimization_manager: score_cutoff        : 12.59899937725067 -> 12.188660250091553
0:18:41.612965 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:41.643586 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:41.710216 INFO: === checking if optimization conditions were reached ===
0:18:41.710484 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:18:41.712634 INFO: Updating optimization_manager: rt_error            : 105.42518929308291 -> 74.86999397936984
0:18:41.712750 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 74.8700.
0:18:41.712838 INFO: ==============================================
0:18:41.712918 INFO: Starting optimization step 2.
0:18:41.712983 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:18:41.713053 INFO: Using ng extraction backend
0:18:41.713120 PROGRESS: Extracting batch of 50293 precursors
0:18:41.802498 INFO: === Search parameters used ===
0:18:41.802751 INFO: rt_error       : 74.86999397936984
0:18:41.802806 INFO: mobility_error : 0.1
0:18:41.802852 INFO: num_candidates : 3
0:18:41.802894 INFO: ms1_error      : 30
0:18:41.802934 INFO: ms2_error      : 10.0
0:18:41.802974 INFO: fwhm_rt        : 3.0
0:18:41.803025 INFO: quant_window   : 3
0:18:41.803066 INFO: ==============================================
0:18:42.372235 INFO: performing precursor FDR with 40 features
0:18:42.372347 INFO: Decoy channel: -1
0:18:42.372374 INFO: Competetive: True
0:18:42.411409 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:42.445147 INFO: Using random state 598898 for train-test-split
0:18:44.393022 INFO: Test AUC: 0.595
0:18:44.393138 INFO: Train AUC: 0.611
0:18:44.393168 INFO: AUC difference: 2.67%
0:18:44.645231 INFO: Resetting torch num_threads to 80
0:18:44.651431 PROGRESS: === Extracted 145222 precursors and 557968 fragments ===
0:18:44.651769 INFO: === FDR correction performed with classifier version 9 ===
0:18:44.652225 PROGRESS: ============================= Precursor FDR =============================
0:18:44.652311 PROGRESS: Total precursors accumulated: 424
0:18:44.652367 PROGRESS: Target precursors: 420 (99.06%)
0:18:44.652415 PROGRESS: Decoy precursors: 4 (0.94%)
0:18:44.652459 PROGRESS: 
0:18:44.652502 PROGRESS: Precursor Summary:
0:18:44.653444 PROGRESS: Channel   0:	 0.050 FDR:   420; 0.010 FDR:   420; 0.001 FDR:   286
0:18:44.653536 PROGRESS: 
0:18:44.653591 PROGRESS: Protein Summary:
0:18:44.654701 PROGRESS: Channel   0:	 0.050 FDR:   408; 0.010 FDR:   408; 0.001 FDR:   278
0:18:44.654789 PROGRESS: =========================================================================
0:18:44.656876 INFO: Target number of precursors reached.
0:18:44.710749 INFO: fragments_df: keeping 3979 of 557968 [sum(precursor_idx_mask)=9168 sum(mass_error_mask)=557968 stop_rank=3979
0:18:44.878769 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:45.006224 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:45.529774 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:45.530166 INFO: Using score_cutoff 11.363176108932494 (fac=0.99, q=1)
0:18:45.530448 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:45.530526 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:45.530580 INFO: Updating optimization_manager: score_cutoff        : 12.188660250091553 -> 11.363176108932494
0:18:45.530632 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:45.546332 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:45.579796 INFO: === checking if optimization conditions were reached ===
0:18:45.580031 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:18:45.582312 INFO: Updating optimization_manager: rt_error            : 74.86999397936984 -> 58.1180623331877
0:18:45.582436 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 58.1181.
0:18:45.582512 INFO: ==============================================
0:18:45.582590 INFO: Starting optimization step 3.
0:18:45.582658 PROGRESS: === Extracting elution groups 0 to 12600 ===
0:18:45.582727 INFO: Using ng extraction backend
0:18:45.582791 PROGRESS: Extracting batch of 24954 precursors
0:18:45.628621 INFO: === Search parameters used ===
0:18:45.628878 INFO: rt_error       : 58.1180623331877
0:18:45.628943 INFO: mobility_error : 0.1
0:18:45.628997 INFO: num_candidates : 3
0:18:45.629050 INFO: ms1_error      : 30
0:18:45.629100 INFO: ms2_error      : 10.0
0:18:45.629164 INFO: fwhm_rt        : 3.0
0:18:45.629215 INFO: quant_window   : 3
0:18:45.629264 INFO: ==============================================
0:18:45.948609 INFO: performing precursor FDR with 40 features
0:18:45.948720 INFO: Decoy channel: -1
0:18:45.948747 INFO: Competetive: True
0:18:45.966294 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:45.981201 INFO: Using random state 598898 for train-test-split
0:18:46.834325 INFO: Test AUC: 0.594
0:18:46.834439 INFO: Train AUC: 0.616
0:18:46.834468 INFO: AUC difference: 3.54%
0:18:47.069044 INFO: Resetting torch num_threads to 80
0:18:47.072941 PROGRESS: === Extracted 70551 precursors and 262386 fragments ===
0:18:47.073262 INFO: === FDR correction performed with classifier version 9 ===
0:18:47.073686 PROGRESS: ============================= Precursor FDR =============================
0:18:47.073769 PROGRESS: Total precursors accumulated: 209
0:18:47.073826 PROGRESS: Target precursors: 207 (99.04%)
0:18:47.073876 PROGRESS: Decoy precursors: 2 (0.96%)
0:18:47.073933 PROGRESS: 
0:18:47.073978 PROGRESS: Precursor Summary:
0:18:47.074823 PROGRESS: Channel   0:	 0.050 FDR:   207; 0.010 FDR:   207; 0.001 FDR:   183
0:18:47.074910 PROGRESS: 
0:18:47.074965 PROGRESS: Protein Summary:
0:18:47.075962 PROGRESS: Channel   0:	 0.050 FDR:   204; 0.010 FDR:   204; 0.001 FDR:   180
0:18:47.076047 PROGRESS: =========================================================================
0:18:47.077117 INFO: Target number of precursors reached.
0:18:47.095841 INFO: fragments_df: keeping 1894 of 262386 [sum(precursor_idx_mask)=4203 sum(mass_error_mask)=262386 stop_rank=1894
0:18:47.259775 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:47.378020 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:47.630800 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:47.631193 INFO: Using score_cutoff 7.063193367862701 (fac=0.99, q=1)
0:18:47.631465 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:47.631542 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:47.631594 INFO: Updating optimization_manager: score_cutoff        : 11.363176108932494 -> 7.063193367862701
0:18:47.631646 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:47.647819 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:47.681777 INFO: === checking if optimization conditions were reached ===
0:18:47.681968 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:18:47.683967 INFO: Updating optimization_manager: rt_error            : 58.1180623331877 -> 41.785092348167105
0:18:47.684077 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 41.7851.
0:18:47.684151 INFO: ==============================================
0:18:47.684228 INFO: Starting optimization step 4.
0:18:47.684291 PROGRESS: === Extracting elution groups 0 to 12600 ===
0:18:47.684360 INFO: Using ng extraction backend
0:18:47.684423 PROGRESS: Extracting batch of 24954 precursors
0:18:47.729859 INFO: === Search parameters used ===
0:18:47.730263 INFO: rt_error       : 41.785092348167105
0:18:47.730339 INFO: mobility_error : 0.1
0:18:47.730404 INFO: num_candidates : 3
0:18:47.730473 INFO: ms1_error      : 30
0:18:47.730525 INFO: ms2_error      : 10.0
0:18:47.730575 INFO: fwhm_rt        : 3.0
0:18:47.730622 INFO: quant_window   : 3
0:18:47.730669 INFO: ==============================================
0:18:48.049788 INFO: performing precursor FDR with 40 features
0:18:48.049896 INFO: Decoy channel: -1
0:18:48.049924 INFO: Competetive: True
0:18:48.067037 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:48.081290 INFO: Using random state 598898 for train-test-split
0:18:48.853440 INFO: Test AUC: 0.586
0:18:48.853554 INFO: Train AUC: 0.616
0:18:48.853585 INFO: AUC difference: 4.81%
0:18:49.086539 INFO: Resetting torch num_threads to 80
0:18:49.090611 PROGRESS: === Extracted 66522 precursors and 242430 fragments ===
0:18:49.090930 INFO: === FDR correction performed with classifier version 9 ===
0:18:49.091343 PROGRESS: ============================= Precursor FDR =============================
0:18:49.091430 PROGRESS: Total precursors accumulated: 166
0:18:49.091487 PROGRESS: Target precursors: 165 (99.40%)
0:18:49.091536 PROGRESS: Decoy precursors: 1 (0.60%)
0:18:49.091579 PROGRESS: 
0:18:49.091622 PROGRESS: Precursor Summary:
0:18:49.092448 PROGRESS: Channel   0:	 0.050 FDR:   165; 0.010 FDR:   165; 0.001 FDR:   137
0:18:49.092535 PROGRESS: 
0:18:49.092590 PROGRESS: Protein Summary:
0:18:49.093562 PROGRESS: Channel   0:	 0.050 FDR:   162; 0.010 FDR:   162; 0.001 FDR:   134
0:18:49.093650 PROGRESS: =========================================================================
0:18:49.094650 INFO: Target number of precursors not reached yet.
0:18:49.192311 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:49.208924 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:49.243123 INFO: === skipping optimization until target number of precursors are found ===
0:18:49.243338 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
0:18:49.243436 INFO: Starting optimization step 5.
0:18:49.243508 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:18:49.243584 INFO: Using ng extraction backend
0:18:49.243651 PROGRESS: Extracting batch of 25339 precursors
0:18:49.289950 INFO: === Search parameters used ===
0:18:49.290199 INFO: rt_error       : 41.785092348167105
0:18:49.290262 INFO: mobility_error : 0.1
0:18:49.290318 INFO: num_candidates : 3
0:18:49.290371 INFO: ms1_error      : 30
0:18:49.290421 INFO: ms2_error      : 10.0
0:18:49.290471 INFO: fwhm_rt        : 3.0
0:18:49.290520 INFO: quant_window   : 3
0:18:49.290569 INFO: ==============================================
0:18:49.622172 INFO: performing precursor FDR with 40 features
0:18:49.622281 INFO: Decoy channel: -1
0:18:49.622308 INFO: Competetive: True
0:18:49.667159 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:49.698906 INFO: Using random state 598898 for train-test-split
0:18:51.625869 INFO: Test AUC: 0.597
0:18:51.625983 INFO: Train AUC: 0.614
0:18:51.626013 INFO: AUC difference: 2.76%
0:18:51.876386 INFO: Resetting torch num_threads to 80
0:18:51.894701 PROGRESS: === Extracted 133966 precursors and 486500 fragments ===
0:18:51.895243 INFO: === FDR correction performed with classifier version 9 ===
0:18:51.895784 PROGRESS: ============================= Precursor FDR =============================
0:18:51.895872 PROGRESS: Total precursors accumulated: 345
0:18:51.895930 PROGRESS: Target precursors: 342 (99.13%)
0:18:51.895979 PROGRESS: Decoy precursors: 3 (0.87%)
0:18:51.896034 PROGRESS: 
0:18:51.896080 PROGRESS: Precursor Summary:
0:18:51.897018 PROGRESS: Channel   0:	 0.050 FDR:   342; 0.010 FDR:   342; 0.001 FDR:   311
0:18:51.897106 PROGRESS: 
0:18:51.897161 PROGRESS: Protein Summary:
0:18:51.898272 PROGRESS: Channel   0:	 0.050 FDR:   332; 0.010 FDR:   332; 0.001 FDR:   303
0:18:51.898363 PROGRESS: =========================================================================
0:18:51.900158 INFO: Target number of precursors reached.
0:18:51.936492 INFO: fragments_df: keeping 3131 of 486500 [sum(precursor_idx_mask)=6700 sum(mass_error_mask)=486500 stop_rank=3131
0:18:52.069817 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:52.195281 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:52.604142 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:52.604537 INFO: Using score_cutoff 11.175574802398682 (fac=0.99, q=1)
0:18:52.604823 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:52.604923 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:52.604981 INFO: Updating optimization_manager: score_cutoff        : 7.063193367862701 -> 11.175574802398682
0:18:52.605037 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:52.636431 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:52.703503 INFO: === checking if optimization conditions were reached ===
0:18:52.703756 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:18:52.706036 INFO: Updating optimization_manager: rt_error            : 41.785092348167105 -> 34.55962002589339
0:18:52.706150 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 34.5596.
0:18:52.706226 INFO: ==============================================
0:18:52.706304 INFO: Starting optimization step 6.
0:18:52.706368 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:18:52.706437 INFO: Using ng extraction backend
0:18:52.706503 PROGRESS: Extracting batch of 50293 precursors
0:18:52.795911 INFO: === Search parameters used ===
0:18:52.796166 INFO: rt_error       : 34.55962002589339
0:18:52.796224 INFO: mobility_error : 0.1
0:18:52.796271 INFO: num_candidates : 3
0:18:52.796314 INFO: ms1_error      : 30
0:18:52.796822 INFO: ms2_error      : 10.0
0:18:52.796872 INFO: fwhm_rt        : 3.0
0:18:52.796913 INFO: quant_window   : 3
0:18:52.796953 INFO: ==============================================
0:18:53.339872 INFO: performing precursor FDR with 40 features
0:18:53.339978 INFO: Decoy channel: -1
0:18:53.340005 INFO: Competetive: True
0:18:53.378319 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:53.411677 INFO: Using random state 598898 for train-test-split
0:18:55.247151 INFO: Test AUC: 0.595
0:18:55.247261 INFO: Train AUC: 0.613
0:18:55.247292 INFO: AUC difference: 2.82%
0:18:55.503590 INFO: Resetting torch num_threads to 80
0:18:55.510193 PROGRESS: === Extracted 134145 precursors and 488285 fragments ===
0:18:55.510522 INFO: === FDR correction performed with classifier version 9 ===
0:18:55.510972 PROGRESS: ============================= Precursor FDR =============================
0:18:55.511060 PROGRESS: Total precursors accumulated: 349
0:18:55.511125 PROGRESS: Target precursors: 346 (99.14%)
0:18:55.511178 PROGRESS: Decoy precursors: 3 (0.86%)
0:18:55.511222 PROGRESS: 
0:18:55.511266 PROGRESS: Precursor Summary:
0:18:55.512156 PROGRESS: Channel   0:	 0.050 FDR:   346; 0.010 FDR:   346; 0.001 FDR:   266
0:18:55.512243 PROGRESS: 
0:18:55.512297 PROGRESS: Protein Summary:
0:18:55.513394 PROGRESS: Channel   0:	 0.050 FDR:   336; 0.010 FDR:   336; 0.001 FDR:   260
0:18:55.513485 PROGRESS: =========================================================================
0:18:55.515450 INFO: Target number of precursors reached.
0:18:55.549156 INFO: fragments_df: keeping 3140 of 488285 [sum(precursor_idx_mask)=6690 sum(mass_error_mask)=488285 stop_rank=3140
0:18:55.681199 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:55.806595 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:56.217301 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:56.217691 INFO: Using score_cutoff 9.69521160364151 (fac=0.99, q=1)
0:18:56.217967 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:56.218045 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:56.218099 INFO: Updating optimization_manager: score_cutoff        : 11.175574802398682 -> 9.69521160364151
0:18:56.218151 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:56.249146 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:56.316621 INFO: === checking if optimization conditions were reached ===
0:18:56.316889 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:18:56.319153 INFO: Updating optimization_manager: rt_error            : 34.55962002589339 -> 32.871529035771516
0:18:56.319271 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 32.8715.
0:18:56.319347 INFO: ==============================================
0:18:56.319425 INFO: Starting optimization step 7.
0:18:56.319491 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:18:56.319558 INFO: Using ng extraction backend
0:18:56.319624 PROGRESS: Extracting batch of 50293 precursors
0:18:56.408814 INFO: === Search parameters used ===
0:18:56.409071 INFO: rt_error       : 32.871529035771516
0:18:56.409131 INFO: mobility_error : 0.1
0:18:56.409177 INFO: num_candidates : 3
0:18:56.409220 INFO: ms1_error      : 30
0:18:56.409262 INFO: ms2_error      : 10.0
0:18:56.409303 INFO: fwhm_rt        : 3.0
0:18:56.409349 INFO: quant_window   : 3
0:18:56.409391 INFO: ==============================================
0:18:56.948799 INFO: performing precursor FDR with 40 features
0:18:56.948932 INFO: Decoy channel: -1
0:18:56.948959 INFO: Competetive: True
0:18:56.986431 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:57.018693 INFO: Using random state 598898 for train-test-split
0:18:58.796196 INFO: Test AUC: 0.592
0:18:58.796310 INFO: Train AUC: 0.613
0:18:58.796340 INFO: AUC difference: 3.51%
0:18:59.052892 INFO: Resetting torch num_threads to 80
0:18:59.059406 PROGRESS: === Extracted 134156 precursors and 488213 fragments ===
0:18:59.059752 INFO: === FDR correction performed with classifier version 9 ===
0:18:59.060204 PROGRESS: ============================= Precursor FDR =============================
0:18:59.060296 PROGRESS: Total precursors accumulated: 334
0:18:59.060356 PROGRESS: Target precursors: 331 (99.10%)
0:18:59.060408 PROGRESS: Decoy precursors: 3 (0.90%)
0:18:59.060452 PROGRESS: 
0:18:59.060493 PROGRESS: Precursor Summary:
0:18:59.061386 PROGRESS: Channel   0:	 0.050 FDR:   331; 0.010 FDR:   331; 0.001 FDR:   238
0:18:59.061474 PROGRESS: 
0:18:59.061528 PROGRESS: Protein Summary:
0:18:59.062581 PROGRESS: Channel   0:	 0.050 FDR:   323; 0.010 FDR:   323; 0.001 FDR:   233
0:18:59.062668 PROGRESS: =========================================================================
0:18:59.064630 INFO: Target number of precursors reached.
0:18:59.098752 INFO: fragments_df: keeping 3085 of 488213 [sum(precursor_idx_mask)=6472 sum(mass_error_mask)=488213 stop_rank=3085
0:18:59.231786 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:59.356345 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:59.760091 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:59.760486 INFO: Using score_cutoff 11.168662204742432 (fac=0.99, q=1)
0:18:59.760756 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:59.760842 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:59.760897 INFO: Updating optimization_manager: score_cutoff        : 9.69521160364151 -> 11.168662204742432
0:18:59.760949 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:59.792374 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:59.858844 INFO: === checking if optimization conditions were reached ===
0:18:59.859107 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:18:59.860326 INFO: Updating optimization_manager: rt_error            : 32.871529035771516 -> 58.1180623331877
0:18:59.860466 INFO: Updating optimization_manager: classifier_version  : 9 -> 13
0:18:59.860571 INFO: Updating optimization_manager: score_cutoff        : 11.168662204742432 -> 7.063193367862701
0:18:59.860667 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:59.860759 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:59.860870 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 58.1181 found after 7 searches.
0:18:59.860945 INFO: ==============================================
0:18:59.861021 PROGRESS: Optimization finished for rt_error.
0:19:00.035087 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:00.051330 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:00.114634 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:19:00.114849 PROGRESS: ==============================================
0:19:00.114926 PROGRESS: ms2_error      : 10.0000
0:19:00.114987 PROGRESS: rt_error       : 58.1181
0:19:00.115041 PROGRESS: ==============================================
0:19:00.115585 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:07.986135 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:25.797189 INFO: Using ng extraction backend
0:19:25.797766 PROGRESS: Extracting batch of 12001526 precursors
0:19:41.678921 INFO: === Search parameters used ===
0:19:41.679173 INFO: rt_error       : 58.1180623331877
0:19:41.679238 INFO: mobility_error : 0.1
0:19:41.679288 INFO: num_candidates : 3
0:19:41.679334 INFO: ms1_error      : 30
0:19:41.679378 INFO: ms2_error      : 10.0
0:19:41.679421 INFO: fwhm_rt        : 3.0
0:19:41.679463 INFO: quant_window   : 3
0:19:41.679505 INFO: ==============================================
0:20:04.835501 INFO: Removed 14963994 precursors with score below cutoff 7.063193367862701
0:20:22.303169 INFO: performing precursor FDR with 40 features
0:20:22.303284 INFO: Decoy channel: -1
0:20:22.303331 INFO: Competetive: True
0:20:24.457062 INFO: Setting torch num_threads to 2 for FDR classification task
0:20:33.024047 INFO: Using random state 441458 for train-test-split
0:25:51.432827 INFO: Test AUC: 0.620
0:25:51.433239 INFO: Train AUC: 0.621
0:25:51.433280 INFO: AUC difference: 0.14%
0:25:56.384995 INFO: Resetting torch num_threads to 80
0:25:58.312498 PROGRESS: ============================= Precursor FDR =============================
0:25:58.312764 PROGRESS: Total precursors accumulated: 78,551
0:25:58.312842 PROGRESS: Target precursors: 77,774 (99.01%)
0:25:58.312896 PROGRESS: Decoy precursors: 777 (0.99%)
0:25:58.312943 PROGRESS: 
0:25:58.312986 PROGRESS: Precursor Summary:
0:25:58.338064 PROGRESS: Channel   0:	 0.050 FDR: 77,774; 0.010 FDR: 77,774; 0.001 FDR: 51,542
0:25:58.338290 PROGRESS: 
0:25:58.338360 PROGRESS: Protein Summary:
0:25:58.379575 PROGRESS: Channel   0:	 0.050 FDR: 12,487; 0.010 FDR: 12,487; 0.001 FDR: 9,072
0:25:58.379793 PROGRESS: =========================================================================
0:25:58.505223 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/psm.parquet
0:25:58.667004 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.parquet
0:25:58.887211 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:25:59.468023 PROGRESS: 
0:25:59.468168 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark/quant
0:25:59.468241 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/figures
0:25:59.468403 INFO: Initializing TimingManager
0:25:59.468833 INFO: Initializing RawFileManager
0:26:10.055374 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:26:10.059343 INFO: Determining DIA cycle
0:26:10.075623 INFO: Found cycle with start 0.00 min and length 300.
0:26:10.239671 INFO: RT (min)            : 0.0 - 26.9
0:26:10.239762 INFO: RT duration (sec)   : 1611.2
0:26:10.239790 INFO: RT duration (min)   : 26.9
0:26:10.239812 INFO: Cycle len (scans)   : 300
0:26:10.239831 INFO: Cycle len (sec)     : 1.65
0:26:10.239849 INFO: Number of cycles    : 977
0:26:10.239867 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:26:10.239892 INFO: Creating DIA data object took: 10.770965337753296
0:26:10.932004 INFO: Creating DIA data NG object took: 0.6920034885406494
0:26:12.206401 INFO: Initializing CalibrationManager
0:26:12.206662 INFO: Setting up calibration estimators ..
0:26:12.206722 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:26:12.206794 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
0:26:12.206889 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:26:12.206938 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:26:12.206990 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
0:26:12.207041 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:26:12.207085 INFO: Done setting up calibration estimators.
0:26:12.207273 INFO: Initializing OptimizationManager
0:26:12.207421 INFO: initial parameter: ms1_error = 30
0:26:12.207472 INFO: initial parameter: ms2_error = 30
0:26:12.207518 INFO: initial parameter: rt_error = 805.6004638671875
0:26:12.207559 INFO: initial parameter: mobility_error = 0.1
0:26:12.207600 INFO: initial parameter: num_candidates = 1
0:26:12.207646 INFO: initial parameter: fwhm_rt = 5
0:26:12.207687 INFO: initial parameter: fwhm_mobility = 0.01
0:26:12.207726 INFO: initial parameter: score_cutoff = 0
0:26:12.207764 INFO: initial parameter: classifier_version = -1
0:26:12.207828 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:26:12.208049 INFO: FDRManager: loading saved state not requested, will be initialized.
0:26:12.208081 INFO: Initializing FDRManager
0:26:12.208117 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:26:13.627453 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:26:14.496361 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:26:14.496740 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
0:26:14.496861 PROGRESS: Starting initial search for precursors.
0:26:14.496942 INFO: Starting optimization step 0.
0:26:14.497004 PROGRESS: === Extracting elution groups 0 to 200 ===
0:26:14.497064 INFO: Using ng extraction backend
0:26:14.497124 PROGRESS: Extracting batch of 396 precursors
0:26:14.498979 INFO: === Search parameters used ===
0:26:14.499069 INFO: rt_error       : 805.6004638671875
0:26:14.499120 INFO: mobility_error : 0.1
0:26:14.499165 INFO: num_candidates : 1
0:26:14.499207 INFO: ms1_error      : 30
0:26:14.499246 INFO: ms2_error      : 30
0:26:14.499288 INFO: fwhm_rt        : 5
0:26:14.499330 INFO: quant_window   : 3
0:26:14.499370 INFO: ==============================================
0:26:14.525205 INFO: performing precursor FDR with 40 features
0:26:14.525306 INFO: Decoy channel: -1
0:26:14.525333 INFO: Competetive: True
0:26:14.526246 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:14.528264 INFO: Using random state 295903 for train-test-split
0:26:14.534655 INFO: Test AUC: 0.543
0:26:14.534710 INFO: Train AUC: 0.501
0:26:14.534738 INFO: AUC difference: 8.46%
0:26:14.534761 WARNING: AUC difference > 5%. This may indicate overfitting.
0:26:14.740490 INFO: Resetting torch num_threads to 80
0:26:14.741747 PROGRESS: === Extracted 393 precursors and 1883 fragments ===
0:26:14.742065 INFO: === FDR correction performed with classifier version -1 ===
0:26:14.742485 PROGRESS: ============================= Precursor FDR =============================
0:26:14.742570 PROGRESS: Total precursors accumulated: 0
0:26:14.742627 PROGRESS: Target precursors: 0 (0.00%)
0:26:14.742676 PROGRESS: Decoy precursors: 0 (0.00%)
0:26:14.742719 PROGRESS: 
0:26:14.742762 PROGRESS: Precursor Summary:
0:26:14.742864 PROGRESS: 
0:26:14.742923 PROGRESS: Protein Summary:
0:26:14.742993 PROGRESS: =========================================================================
0:26:14.743152 INFO: Target number of precursors not reached yet.
0:26:14.807247 INFO: Starting optimization step 1.
0:26:14.807459 PROGRESS: === Extracting elution groups 200 to 600 ===
0:26:14.807536 INFO: Using ng extraction backend
0:26:14.807596 PROGRESS: Extracting batch of 786 precursors
0:26:14.810276 INFO: === Search parameters used ===
0:26:14.810374 INFO: rt_error       : 805.6004638671875
0:26:14.810428 INFO: mobility_error : 0.1
0:26:14.810474 INFO: num_candidates : 1
0:26:14.810514 INFO: ms1_error      : 30
0:26:14.810554 INFO: ms2_error      : 30
0:26:14.810594 INFO: fwhm_rt        : 5
0:26:14.810632 INFO: quant_window   : 3
0:26:14.810671 INFO: ==============================================
0:26:14.849070 INFO: performing precursor FDR with 40 features
0:26:14.849169 INFO: Decoy channel: -1
0:26:14.849196 INFO: Competetive: True
0:26:14.851944 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:14.853394 INFO: Using random state 886099 for train-test-split
0:26:14.861517 INFO: Test AUC: 0.478
0:26:14.861570 INFO: Train AUC: 0.509
0:26:14.861598 INFO: AUC difference: 6.20%
0:26:14.861622 WARNING: AUC difference > 5%. This may indicate overfitting.
0:26:15.070835 INFO: Resetting torch num_threads to 80
0:26:15.072834 PROGRESS: === Extracted 1169 precursors and 5518 fragments ===
0:26:15.073158 INFO: === FDR correction performed with classifier version -1 ===
0:26:15.073576 PROGRESS: ============================= Precursor FDR =============================
0:26:15.073661 PROGRESS: Total precursors accumulated: 0
0:26:15.073718 PROGRESS: Target precursors: 0 (0.00%)
0:26:15.073766 PROGRESS: Decoy precursors: 0 (0.00%)
0:26:15.073810 PROGRESS: 
0:26:15.073853 PROGRESS: Precursor Summary:
0:26:15.073958 PROGRESS: 
0:26:15.074019 PROGRESS: Protein Summary:
0:26:15.074098 PROGRESS: =========================================================================
0:26:15.074296 INFO: Target number of precursors not reached yet.
0:26:15.140857 INFO: Starting optimization step 2.
0:26:15.141046 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:26:15.141125 INFO: Using ng extraction backend
0:26:15.141187 PROGRESS: Extracting batch of 1592 precursors
0:26:15.145239 INFO: === Search parameters used ===
0:26:15.145352 INFO: rt_error       : 805.6004638671875
0:26:15.145401 INFO: mobility_error : 0.1
0:26:15.145447 INFO: num_candidates : 1
0:26:15.145489 INFO: ms1_error      : 30
0:26:15.145528 INFO: ms2_error      : 30
0:26:15.145569 INFO: fwhm_rt        : 5
0:26:15.145609 INFO: quant_window   : 3
0:26:15.145648 INFO: ==============================================
0:26:15.177809 INFO: performing precursor FDR with 40 features
0:26:15.177882 INFO: Decoy channel: -1
0:26:15.177909 INFO: Competetive: True
0:26:15.181100 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:15.182796 INFO: Using random state 535630 for train-test-split
0:26:15.194383 INFO: Test AUC: 0.488
0:26:15.194437 INFO: Train AUC: 0.506
0:26:15.194466 INFO: AUC difference: 3.55%
0:26:15.398562 INFO: Resetting torch num_threads to 80
0:26:15.400979 PROGRESS: === Extracted 2751 precursors and 13057 fragments ===
0:26:15.401304 INFO: === FDR correction performed with classifier version -1 ===
0:26:15.401719 PROGRESS: ============================= Precursor FDR =============================
0:26:15.401802 PROGRESS: Total precursors accumulated: 0
0:26:15.401858 PROGRESS: Target precursors: 0 (0.00%)
0:26:15.401909 PROGRESS: Decoy precursors: 0 (0.00%)
0:26:15.401955 PROGRESS: 
0:26:15.402004 PROGRESS: Precursor Summary:
0:26:15.402111 PROGRESS: 
0:26:15.402171 PROGRESS: Protein Summary:
0:26:15.402241 PROGRESS: =========================================================================
0:26:15.402447 INFO: Target number of precursors not reached yet.
0:26:15.471443 INFO: Starting optimization step 3.
0:26:15.471640 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:26:15.471718 INFO: Using ng extraction backend
0:26:15.471778 PROGRESS: Extracting batch of 3177 precursors
0:26:15.478611 INFO: === Search parameters used ===
0:26:15.478728 INFO: rt_error       : 805.6004638671875
0:26:15.478777 INFO: mobility_error : 0.1
0:26:15.478822 INFO: num_candidates : 1
0:26:15.478864 INFO: ms1_error      : 30
0:26:15.478905 INFO: ms2_error      : 30
0:26:15.478947 INFO: fwhm_rt        : 5
0:26:15.478985 INFO: quant_window   : 3
0:26:15.479023 INFO: ==============================================
0:26:15.524207 INFO: performing precursor FDR with 40 features
0:26:15.524295 INFO: Decoy channel: -1
0:26:15.524321 INFO: Competetive: True
0:26:15.529383 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:15.531736 INFO: Using random state 7145 for train-test-split
0:26:15.551164 INFO: Test AUC: 0.488
0:26:15.551235 INFO: Train AUC: 0.511
0:26:15.551264 INFO: AUC difference: 4.48%
0:26:16.383821 INFO: Resetting torch num_threads to 80
0:26:16.387118 PROGRESS: === Extracted 5894 precursors and 27935 fragments ===
0:26:16.387472 INFO: === FDR correction performed with classifier version -1 ===
0:26:16.387894 PROGRESS: ============================= Precursor FDR =============================
0:26:16.387978 PROGRESS: Total precursors accumulated: 0
0:26:16.388041 PROGRESS: Target precursors: 0 (0.00%)
0:26:16.388094 PROGRESS: Decoy precursors: 0 (0.00%)
0:26:16.388147 PROGRESS: 
0:26:16.388190 PROGRESS: Precursor Summary:
0:26:16.388293 PROGRESS: 
0:26:16.388351 PROGRESS: Protein Summary:
0:26:16.388421 PROGRESS: =========================================================================
0:26:16.388653 INFO: Target number of precursors not reached yet.
0:26:16.461984 INFO: Starting optimization step 4.
0:26:16.462195 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:26:16.462274 INFO: Using ng extraction backend
0:26:16.462337 PROGRESS: Extracting batch of 6340 precursors
0:26:16.474592 INFO: === Search parameters used ===
0:26:16.474728 INFO: rt_error       : 805.6004638671875
0:26:16.474777 INFO: mobility_error : 0.1
0:26:16.474822 INFO: num_candidates : 1
0:26:16.474863 INFO: ms1_error      : 30
0:26:16.474904 INFO: ms2_error      : 30
0:26:16.474943 INFO: fwhm_rt        : 5
0:26:16.474983 INFO: quant_window   : 3
0:26:16.475021 INFO: ==============================================
0:26:16.557642 INFO: performing precursor FDR with 40 features
0:26:16.557744 INFO: Decoy channel: -1
0:26:16.557770 INFO: Competetive: True
0:26:16.563522 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:16.567003 INFO: Using random state 382670 for train-test-split
0:26:16.603332 INFO: Test AUC: 0.524
0:26:16.603425 INFO: Train AUC: 0.502
0:26:16.603455 INFO: AUC difference: 4.57%
0:26:16.815042 INFO: Resetting torch num_threads to 80
0:26:16.819432 PROGRESS: === Extracted 12164 precursors and 57205 fragments ===
0:26:16.819793 INFO: === FDR correction performed with classifier version -1 ===
0:26:16.820220 PROGRESS: ============================= Precursor FDR =============================
0:26:16.820305 PROGRESS: Total precursors accumulated: 0
0:26:16.820361 PROGRESS: Target precursors: 0 (0.00%)
0:26:16.820410 PROGRESS: Decoy precursors: 0 (0.00%)
0:26:16.820455 PROGRESS: 
0:26:16.820498 PROGRESS: Precursor Summary:
0:26:16.820602 PROGRESS: 
0:26:16.820661 PROGRESS: Protein Summary:
0:26:16.820729 PROGRESS: =========================================================================
0:26:16.821020 INFO: Target number of precursors not reached yet.
0:26:16.902125 INFO: Starting optimization step 5.
0:26:16.902343 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:26:16.902423 INFO: Using ng extraction backend
0:26:16.902483 PROGRESS: Extracting batch of 12663 precursors
0:26:16.925330 INFO: === Search parameters used ===
0:26:16.925498 INFO: rt_error       : 805.6004638671875
0:26:16.925547 INFO: mobility_error : 0.1
0:26:16.925592 INFO: num_candidates : 1
0:26:16.925631 INFO: ms1_error      : 30
0:26:16.925672 INFO: ms2_error      : 30
0:26:16.925710 INFO: fwhm_rt        : 5
0:26:16.925761 INFO: quant_window   : 3
0:26:16.925802 INFO: ==============================================
0:26:17.052981 INFO: performing precursor FDR with 40 features
0:26:17.053099 INFO: Decoy channel: -1
0:26:17.053125 INFO: Competetive: True
0:26:17.062605 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:17.068066 INFO: Using random state 505810 for train-test-split
0:26:17.310473 INFO: Test AUC: 0.508
0:26:17.310573 INFO: Train AUC: 0.515
0:26:17.310603 INFO: AUC difference: 1.44%
0:26:17.538250 INFO: Resetting torch num_threads to 80
0:26:17.544221 PROGRESS: === Extracted 24689 precursors and 116108 fragments ===
0:26:17.544663 INFO: === FDR correction performed with classifier version -1 ===
0:26:17.545128 PROGRESS: ============================= Precursor FDR =============================
0:26:17.545217 PROGRESS: Total precursors accumulated: 0
0:26:17.545275 PROGRESS: Target precursors: 0 (0.00%)
0:26:17.545324 PROGRESS: Decoy precursors: 0 (0.00%)
0:26:17.545369 PROGRESS: 
0:26:17.545413 PROGRESS: Precursor Summary:
0:26:17.545519 PROGRESS: 
0:26:17.545579 PROGRESS: Protein Summary:
0:26:17.545649 PROGRESS: =========================================================================
0:26:17.546047 INFO: Target number of precursors not reached yet.
0:26:17.644475 INFO: Starting optimization step 6.
0:26:17.644709 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:26:17.644840 INFO: Using ng extraction backend
0:26:17.644918 PROGRESS: Extracting batch of 25339 precursors
0:26:17.689137 INFO: === Search parameters used ===
0:26:17.689322 INFO: rt_error       : 805.6004638671875
0:26:17.689374 INFO: mobility_error : 0.1
0:26:17.689432 INFO: num_candidates : 1
0:26:17.689478 INFO: ms1_error      : 30
0:26:17.689522 INFO: ms2_error      : 30
0:26:17.689561 INFO: fwhm_rt        : 5
0:26:17.689601 INFO: quant_window   : 3
0:26:17.689640 INFO: ==============================================
0:26:17.889215 INFO: performing precursor FDR with 40 features
0:26:17.889333 INFO: Decoy channel: -1
0:26:17.889359 INFO: Competetive: True
0:26:17.907887 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:17.919430 INFO: Using random state 831315 for train-test-split
0:26:18.561583 INFO: Test AUC: 0.538
0:26:18.561695 INFO: Train AUC: 0.544
0:26:18.561725 INFO: AUC difference: 0.95%
0:26:18.789517 INFO: Resetting torch num_threads to 80
0:26:18.799196 PROGRESS: === Extracted 49754 precursors and 233575 fragments ===
0:26:18.799680 INFO: === FDR correction performed with classifier version -1 ===
0:26:18.800203 PROGRESS: ============================= Precursor FDR =============================
0:26:18.800293 PROGRESS: Total precursors accumulated: 92
0:26:18.800354 PROGRESS: Target precursors: 92 (100.00%)
0:26:18.800405 PROGRESS: Decoy precursors: 0 (0.00%)
0:26:18.800452 PROGRESS: 
0:26:18.800493 PROGRESS: Precursor Summary:
0:26:18.801410 PROGRESS: Channel   0:	 0.050 FDR:    92; 0.010 FDR:    92; 0.001 FDR:    92
0:26:18.801500 PROGRESS: 
0:26:18.801555 PROGRESS: Protein Summary:
0:26:18.802581 PROGRESS: Channel   0:	 0.050 FDR:    91; 0.010 FDR:    91; 0.001 FDR:    91
0:26:18.802668 PROGRESS: =========================================================================
0:26:18.803360 INFO: Target number of precursors not reached yet.
0:26:18.934135 INFO: Starting optimization step 7.
0:26:18.934370 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:26:18.934464 INFO: Using ng extraction backend
0:26:18.934528 PROGRESS: Extracting batch of 50691 precursors
0:26:19.022166 INFO: === Search parameters used ===
0:26:19.022418 INFO: rt_error       : 805.6004638671875
0:26:19.022472 INFO: mobility_error : 0.1
0:26:19.022519 INFO: num_candidates : 1
0:26:19.022561 INFO: ms1_error      : 30
0:26:19.022604 INFO: ms2_error      : 30
0:26:19.022645 INFO: fwhm_rt        : 5
0:26:19.022685 INFO: quant_window   : 3
0:26:19.022724 INFO: ==============================================
0:26:19.376525 INFO: performing precursor FDR with 40 features
0:26:19.376635 INFO: Decoy channel: -1
0:26:19.376662 INFO: Competetive: True
0:26:19.416800 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:19.442815 INFO: Using random state 15915 for train-test-split
0:26:20.720307 INFO: Test AUC: 0.571
0:26:20.720415 INFO: Train AUC: 0.579
0:26:20.720444 INFO: AUC difference: 1.34%
0:26:20.962004 INFO: Resetting torch num_threads to 80
0:26:20.980821 PROGRESS: === Extracted 99883 precursors and 469354 fragments ===
0:26:20.981373 INFO: === FDR correction performed with classifier version -1 ===
0:26:20.981898 PROGRESS: ============================= Precursor FDR =============================
0:26:20.981984 PROGRESS: Total precursors accumulated: 218
0:26:20.982041 PROGRESS: Target precursors: 216 (99.08%)
0:26:20.982091 PROGRESS: Decoy precursors: 2 (0.92%)
0:26:20.982134 PROGRESS: 
0:26:20.982177 PROGRESS: Precursor Summary:
0:26:20.983040 PROGRESS: Channel   0:	 0.050 FDR:   216; 0.010 FDR:   216; 0.001 FDR:     0
0:26:20.983127 PROGRESS: 
0:26:20.983196 PROGRESS: Protein Summary:
0:26:20.984181 PROGRESS: Channel   0:	 0.050 FDR:   204; 0.010 FDR:   204; 0.001 FDR:     0
0:26:20.984267 PROGRESS: =========================================================================
0:26:20.985976 INFO: Target number of precursors reached.
0:26:21.020672 INFO: fragments_df: keeping 1961 of 469354 [sum(precursor_idx_mask)=2419 sum(mass_error_mask)=469354 stop_rank=1961
0:26:21.222936 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:26:21.402214 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:26:21.673723 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:26:21.674135 INFO: Using score_cutoff 14.025680329799652 (fac=0.99, q=1)
0:26:21.674422 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:26:21.674507 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:26:21.674566 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.025680329799652
0:26:21.674625 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:21.744903 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:21.926363 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:26:21.926671 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:26:21.926789 INFO: Starting optimization step 8.
0:26:21.926877 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:26:21.926969 INFO: Using ng extraction backend
0:26:21.927055 PROGRESS: Extracting batch of 100984 precursors
0:26:22.101546 INFO: === Search parameters used ===
0:26:22.101808 INFO: rt_error       : 805.6004638671875
0:26:22.101863 INFO: mobility_error : 0.1
0:26:22.101909 INFO: num_candidates : 3
0:26:22.101952 INFO: ms1_error      : 30
0:26:22.101991 INFO: ms2_error      : 30
0:26:22.102032 INFO: fwhm_rt        : 3.0
0:26:22.102074 INFO: quant_window   : 3
0:26:22.102113 INFO: ==============================================
0:26:23.362279 INFO: performing precursor FDR with 40 features
0:26:23.362391 INFO: Decoy channel: -1
0:26:23.362418 INFO: Competetive: True
0:26:23.439805 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:23.542887 INFO: Using random state 236211 for train-test-split
0:26:27.355741 INFO: Test AUC: 0.592
0:26:27.355865 INFO: Train AUC: 0.600
0:26:27.355895 INFO: AUC difference: 1.48%
0:26:27.657451 INFO: Resetting torch num_threads to 80
0:26:27.670256 PROGRESS: === Extracted 299671 precursors and 1374052 fragments ===
0:26:27.670638 INFO: === FDR correction performed with classifier version 7 ===
0:26:27.671070 PROGRESS: ============================= Precursor FDR =============================
0:26:27.671156 PROGRESS: Total precursors accumulated: 180
0:26:27.671213 PROGRESS: Target precursors: 179 (99.44%)
0:26:27.671263 PROGRESS: Decoy precursors: 1 (0.56%)
0:26:27.671306 PROGRESS: 
0:26:27.671347 PROGRESS: Precursor Summary:
0:26:27.672185 PROGRESS: Channel   0:	 0.050 FDR:   179; 0.010 FDR:   179; 0.001 FDR:    43
0:26:27.672276 PROGRESS: 
0:26:27.672328 PROGRESS: Protein Summary:
0:26:27.673325 PROGRESS: Channel   0:	 0.050 FDR:   169; 0.010 FDR:   169; 0.001 FDR:    43
0:26:27.673425 PROGRESS: =========================================================================
0:26:27.678630 INFO: Target number of precursors not reached yet.
0:26:27.878961 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:27.951105 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:28.100720 INFO: === skipping optimization until target number of precursors are found ===
0:26:28.101284 INFO: Starting optimization step 9.
0:26:28.101389 PROGRESS: === Extracting elution groups 51000 to 102200 ===
0:26:28.101490 INFO: Using ng extraction backend
0:26:28.101575 PROGRESS: Extracting batch of 101368 precursors
0:26:28.276670 INFO: === Search parameters used ===
0:26:28.276941 INFO: rt_error       : 805.6004638671875
0:26:28.277003 INFO: mobility_error : 0.1
0:26:28.277051 INFO: num_candidates : 3
0:26:28.277092 INFO: ms1_error      : 30
0:26:28.277134 INFO: ms2_error      : 30
0:26:28.277174 INFO: fwhm_rt        : 3.0
0:26:28.277213 INFO: quant_window   : 3
0:26:28.277251 INFO: ==============================================
0:26:29.622394 INFO: performing precursor FDR with 40 features
0:26:29.622510 INFO: Decoy channel: -1
0:26:29.622536 INFO: Competetive: True
0:26:29.878947 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:30.124287 INFO: Using random state 236211 for train-test-split
0:26:39.358303 INFO: Test AUC: 0.595
0:26:39.358432 INFO: Train AUC: 0.602
0:26:39.358463 INFO: AUC difference: 1.16%
0:26:39.762112 INFO: Resetting torch num_threads to 80
0:26:39.855349 PROGRESS: === Extracted 600373 precursors and 2747685 fragments ===
0:26:39.855929 INFO: === FDR correction performed with classifier version 7 ===
0:26:39.856553 PROGRESS: ============================= Precursor FDR =============================
0:26:39.856654 PROGRESS: Total precursors accumulated: 463
0:26:39.856714 PROGRESS: Target precursors: 459 (99.14%)
0:26:39.856765 PROGRESS: Decoy precursors: 4 (0.86%)
0:26:39.856820 PROGRESS: 
0:26:39.856869 PROGRESS: Precursor Summary:
0:26:39.857827 PROGRESS: Channel   0:	 0.050 FDR:   459; 0.010 FDR:   459; 0.001 FDR:   218
0:26:39.857915 PROGRESS: 
0:26:39.857970 PROGRESS: Protein Summary:
0:26:39.859114 PROGRESS: Channel   0:	 0.050 FDR:   421; 0.010 FDR:   421; 0.001 FDR:   205
0:26:39.859202 PROGRESS: =========================================================================
0:26:39.867874 INFO: Target number of precursors reached.
0:26:40.058969 INFO: fragments_df: keeping 5000 of 2747685 [sum(precursor_idx_mask)=10567 sum(mass_error_mask)=2747685 stop_rank=5000
0:26:40.274461 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:26:40.429453 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:26:41.115376 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:26:41.115781 INFO: Using score_cutoff 12.875234506416321 (fac=0.99, q=1)
0:26:41.116060 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:26:41.116140 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:26:41.116195 INFO: Updating optimization_manager: score_cutoff        : 14.025680329799652 -> 12.875234506416321
0:26:41.116248 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:41.181323 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:41.327166 INFO: === checking if optimization conditions were reached ===
0:26:41.329580 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:26:41.329697 INFO: Updating optimization_manager: classifier_version  : 7 -> 9
0:26:41.329776 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:26:41.329844 INFO: ==============================================
0:26:41.329921 INFO: Starting optimization step 10.
0:26:41.329986 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:26:41.330052 INFO: Using ng extraction backend
0:26:41.330120 PROGRESS: Extracting batch of 100984 precursors
0:26:41.504738 INFO: === Search parameters used ===
0:26:41.505013 INFO: rt_error       : 805.6004638671875
0:26:41.505068 INFO: mobility_error : 0.1
0:26:41.505112 INFO: num_candidates : 3
0:26:41.505157 INFO: ms1_error      : 30
0:26:41.505197 INFO: ms2_error      : 10.0
0:26:41.505236 INFO: fwhm_rt        : 3.0
0:26:41.505273 INFO: quant_window   : 3
0:26:41.505313 INFO: ==============================================
0:26:42.762065 INFO: performing precursor FDR with 40 features
0:26:42.762183 INFO: Decoy channel: -1
0:26:42.762209 INFO: Competetive: True
0:26:42.839865 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:42.942151 INFO: Using random state 163781 for train-test-split
0:26:46.858282 INFO: Test AUC: 0.599
0:26:46.858399 INFO: Train AUC: 0.603
0:26:46.858428 INFO: AUC difference: 0.67%
0:26:47.168704 INFO: Resetting torch num_threads to 80
0:26:47.181750 PROGRESS: === Extracted 302127 precursors and 1609289 fragments ===
0:26:47.182124 INFO: === FDR correction performed with classifier version 9 ===
0:26:47.182606 PROGRESS: ============================= Precursor FDR =============================
0:26:47.182689 PROGRESS: Total precursors accumulated: 351
0:26:47.182745 PROGRESS: Target precursors: 348 (99.15%)
0:26:47.182791 PROGRESS: Decoy precursors: 3 (0.85%)
0:26:47.182835 PROGRESS: 
0:26:47.182877 PROGRESS: Precursor Summary:
0:26:47.183755 PROGRESS: Channel   0:	 0.050 FDR:   348; 0.010 FDR:   348; 0.001 FDR:   106
0:26:47.183843 PROGRESS: 
0:26:47.183895 PROGRESS: Protein Summary:
0:26:47.184966 PROGRESS: Channel   0:	 0.050 FDR:   328; 0.010 FDR:   328; 0.001 FDR:   101
0:26:47.185055 PROGRESS: =========================================================================
0:26:47.190431 INFO: Target number of precursors reached.
0:26:47.295467 INFO: fragments_df: keeping 4272 of 1609289 [sum(precursor_idx_mask)=8611 sum(mass_error_mask)=1609289 stop_rank=4272
0:26:47.579849 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:26:47.706366 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:26:48.271981 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:26:48.272388 INFO: Using score_cutoff 14.027661621379853 (fac=0.99, q=1)
0:26:48.272666 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:26:48.272745 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:26:48.272799 INFO: Updating optimization_manager: score_cutoff        : 12.875234506416321 -> 14.027661621379853
0:26:48.272870 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:48.334934 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:48.488215 INFO: === checking if optimization conditions were reached ===
0:26:48.490859 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:26:48.490982 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:26:48.491052 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:26:48.491117 INFO: ==============================================
0:26:48.491188 PROGRESS: Optimization finished for ms2_error.
0:26:48.765024 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:48.829016 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:48.976584 INFO: Starting optimization step 0.
0:26:48.976946 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:26:48.977033 INFO: Using ng extraction backend
0:26:48.977104 PROGRESS: Extracting batch of 100984 precursors
0:26:49.162024 INFO: === Search parameters used ===
0:26:49.162410 INFO: rt_error       : 805.6004638671875
0:26:49.162468 INFO: mobility_error : 0.1
0:26:49.162517 INFO: num_candidates : 3
0:26:49.162566 INFO: ms1_error      : 30
0:26:49.162610 INFO: ms2_error      : 10.0
0:26:49.162652 INFO: fwhm_rt        : 3.0
0:26:49.162711 INFO: quant_window   : 3
0:26:49.162756 INFO: ==============================================
0:26:50.560838 INFO: performing precursor FDR with 40 features
0:26:50.560997 INFO: Decoy channel: -1
0:26:50.561025 INFO: Competetive: True
0:26:50.675087 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:50.806149 INFO: Using random state 943060 for train-test-split
0:26:56.484719 INFO: Test AUC: 0.596
0:26:56.484910 INFO: Train AUC: 0.607
0:26:56.484942 INFO: AUC difference: 1.73%
0:26:56.871895 INFO: Resetting torch num_threads to 80
0:26:56.891414 PROGRESS: === Extracted 302112 precursors and 1609278 fragments ===
0:26:56.891943 INFO: === FDR correction performed with classifier version 10 ===
0:26:56.892443 PROGRESS: ============================= Precursor FDR =============================
0:26:56.892530 PROGRESS: Total precursors accumulated: 442
0:26:56.892587 PROGRESS: Target precursors: 438 (99.10%)
0:26:56.892637 PROGRESS: Decoy precursors: 4 (0.90%)
0:26:56.892679 PROGRESS: 
0:26:56.892720 PROGRESS: Precursor Summary:
0:26:56.893697 PROGRESS: Channel   0:	 0.050 FDR:   438; 0.010 FDR:   438; 0.001 FDR:   392
0:26:56.893786 PROGRESS: 
0:26:56.893840 PROGRESS: Protein Summary:
0:26:56.895024 PROGRESS: Channel   0:	 0.050 FDR:   411; 0.010 FDR:   411; 0.001 FDR:   367
0:26:56.895110 PROGRESS: =========================================================================
0:26:56.909328 INFO: Target number of precursors reached.
0:26:57.038610 INFO: fragments_df: keeping 5000 of 1609278 [sum(precursor_idx_mask)=10748 sum(mass_error_mask)=1609278 stop_rank=5000
0:26:57.254217 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:26:57.388901 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:26:58.010373 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:26:58.010926 INFO: Using score_cutoff 14.027463541316987 (fac=0.99, q=1)
0:26:58.011255 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:26:58.011335 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:26:58.011389 INFO: Updating optimization_manager: score_cutoff        : 14.027661621379853 -> 14.027463541316987
0:26:58.011444 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:58.042974 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:58.114027 INFO: === checking if optimization conditions were reached ===
0:26:58.114351 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:26:58.116529 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 125.37622524892477
0:26:58.116640 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 125.3762.
0:26:58.116707 INFO: ==============================================
0:26:58.116779 INFO: Starting optimization step 1.
0:26:58.116854 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:26:58.116918 INFO: Using ng extraction backend
0:26:58.116981 PROGRESS: Extracting batch of 50293 precursors
0:26:58.208831 INFO: === Search parameters used ===
0:26:58.209205 INFO: rt_error       : 125.37622524892477
0:26:58.209261 INFO: mobility_error : 0.1
0:26:58.209308 INFO: num_candidates : 3
0:26:58.209351 INFO: ms1_error      : 30
0:26:58.209408 INFO: ms2_error      : 10.0
0:26:58.209449 INFO: fwhm_rt        : 3.0
0:26:58.209489 INFO: quant_window   : 3
0:26:58.209526 INFO: ==============================================
0:26:58.873343 INFO: performing precursor FDR with 40 features
0:26:58.873505 INFO: Decoy channel: -1
0:26:58.873533 INFO: Competetive: True
0:26:58.931018 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:58.982243 INFO: Using random state 943060 for train-test-split
0:27:01.502998 INFO: Test AUC: 0.596
0:27:01.503164 INFO: Train AUC: 0.604
0:27:01.503196 INFO: AUC difference: 1.30%
0:27:01.768314 INFO: Resetting torch num_threads to 80
0:27:01.776478 PROGRESS: === Extracted 147866 precursors and 621652 fragments ===
0:27:01.776899 INFO: === FDR correction performed with classifier version 10 ===
0:27:01.777352 PROGRESS: ============================= Precursor FDR =============================
0:27:01.777437 PROGRESS: Total precursors accumulated: 284
0:27:01.777494 PROGRESS: Target precursors: 282 (99.30%)
0:27:01.777544 PROGRESS: Decoy precursors: 2 (0.70%)
0:27:01.777589 PROGRESS: 
0:27:01.777631 PROGRESS: Precursor Summary:
0:27:01.778528 PROGRESS: Channel   0:	 0.050 FDR:   282; 0.010 FDR:   282; 0.001 FDR:   135
0:27:01.778615 PROGRESS: 
0:27:01.778668 PROGRESS: Protein Summary:
0:27:01.779728 PROGRESS: Channel   0:	 0.050 FDR:   270; 0.010 FDR:   270; 0.001 FDR:   133
0:27:01.779815 PROGRESS: =========================================================================
0:27:01.782671 INFO: Target number of precursors reached.
0:27:01.824990 INFO: fragments_df: keeping 3071 of 621652 [sum(precursor_idx_mask)=6637 sum(mass_error_mask)=621652 stop_rank=3071
0:27:01.992835 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:02.090107 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:02.434129 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:02.434641 INFO: Using score_cutoff 12.80817431230545 (fac=0.99, q=1)
0:27:02.434955 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:02.435034 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:02.435088 INFO: Updating optimization_manager: score_cutoff        : 14.027463541316987 -> 12.80817431230545
0:27:02.435143 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:02.466174 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:02.535236 INFO: === checking if optimization conditions were reached ===
0:27:02.535551 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:27:02.537737 INFO: Updating optimization_manager: rt_error            : 125.37622524892477 -> 94.52726795692804
0:27:02.537846 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 94.5273.
0:27:02.537914 INFO: ==============================================
0:27:02.537984 INFO: Starting optimization step 2.
0:27:02.538041 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:27:02.538101 INFO: Using ng extraction backend
0:27:02.538161 PROGRESS: Extracting batch of 50293 precursors
0:27:02.629341 INFO: === Search parameters used ===
0:27:02.629700 INFO: rt_error       : 94.52726795692804
0:27:02.629756 INFO: mobility_error : 0.1
0:27:02.629822 INFO: num_candidates : 3
0:27:02.629867 INFO: ms1_error      : 30
0:27:02.629912 INFO: ms2_error      : 10.0
0:27:02.629953 INFO: fwhm_rt        : 3.0
0:27:02.629992 INFO: quant_window   : 3
0:27:02.630031 INFO: ==============================================
0:27:03.274262 INFO: performing precursor FDR with 40 features
0:27:03.274426 INFO: Decoy channel: -1
0:27:03.274456 INFO: Competetive: True
0:27:03.331212 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:03.384176 INFO: Using random state 943060 for train-test-split
0:27:05.851540 INFO: Test AUC: 0.591
0:27:05.851711 INFO: Train AUC: 0.605
0:27:05.851744 INFO: AUC difference: 2.33%
0:27:06.110328 INFO: Resetting torch num_threads to 80
0:27:06.118288 PROGRESS: === Extracted 146685 precursors and 590936 fragments ===
0:27:06.118696 INFO: === FDR correction performed with classifier version 10 ===
0:27:06.119140 PROGRESS: ============================= Precursor FDR =============================
0:27:06.119224 PROGRESS: Total precursors accumulated: 252
0:27:06.119281 PROGRESS: Target precursors: 250 (99.21%)
0:27:06.119329 PROGRESS: Decoy precursors: 2 (0.79%)
0:27:06.119372 PROGRESS: 
0:27:06.119414 PROGRESS: Precursor Summary:
0:27:06.120298 PROGRESS: Channel   0:	 0.050 FDR:   250; 0.010 FDR:   250; 0.001 FDR:   162
0:27:06.120383 PROGRESS: 
0:27:06.120438 PROGRESS: Protein Summary:
0:27:06.121477 PROGRESS: Channel   0:	 0.050 FDR:   240; 0.010 FDR:   240; 0.001 FDR:   159
0:27:06.121567 PROGRESS: =========================================================================
0:27:06.124278 INFO: Target number of precursors reached.
0:27:06.165449 INFO: fragments_df: keeping 2797 of 590936 [sum(precursor_idx_mask)=5864 sum(mass_error_mask)=590936 stop_rank=2797
0:27:06.332319 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:06.431901 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:06.742426 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:06.742972 INFO: Using score_cutoff 13.469067403507232 (fac=0.99, q=1)
0:27:06.743284 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:06.743361 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:06.743412 INFO: Updating optimization_manager: score_cutoff        : 12.80817431230545 -> 13.469067403507232
0:27:06.743466 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:06.775247 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:06.849476 INFO: === checking if optimization conditions were reached ===
0:27:06.849804 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:27:06.852126 INFO: Updating optimization_manager: rt_error            : 94.52726795692804 -> 74.02616018320498
0:27:06.852229 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 74.0262.
0:27:06.852303 INFO: ==============================================
0:27:06.852372 INFO: Starting optimization step 3.
0:27:06.852431 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:27:06.852510 INFO: Using ng extraction backend
0:27:06.852576 PROGRESS: Extracting batch of 50293 precursors
0:27:06.944841 INFO: === Search parameters used ===
0:27:06.945202 INFO: rt_error       : 74.02616018320498
0:27:06.945258 INFO: mobility_error : 0.1
0:27:06.945304 INFO: num_candidates : 3
0:27:06.945348 INFO: ms1_error      : 30
0:27:06.945390 INFO: ms2_error      : 10.0
0:27:06.945431 INFO: fwhm_rt        : 3.0
0:27:06.945471 INFO: quant_window   : 3
0:27:06.945511 INFO: ==============================================
0:27:07.594541 INFO: performing precursor FDR with 40 features
0:27:07.594705 INFO: Decoy channel: -1
0:27:07.594733 INFO: Competetive: True
0:27:07.653452 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:07.706574 INFO: Using random state 943060 for train-test-split
0:27:10.237254 INFO: Test AUC: 0.593
0:27:10.237420 INFO: Train AUC: 0.605
0:27:10.237453 INFO: AUC difference: 1.97%
0:27:10.492741 INFO: Resetting torch num_threads to 80
0:27:10.500915 PROGRESS: === Extracted 145479 precursors and 567902 fragments ===
0:27:10.501330 INFO: === FDR correction performed with classifier version 10 ===
0:27:10.501789 PROGRESS: ============================= Precursor FDR =============================
0:27:10.501879 PROGRESS: Total precursors accumulated: 294
0:27:10.501935 PROGRESS: Target precursors: 292 (99.32%)
0:27:10.501983 PROGRESS: Decoy precursors: 2 (0.68%)
0:27:10.502027 PROGRESS: 
0:27:10.502069 PROGRESS: Precursor Summary:
0:27:10.502965 PROGRESS: Channel   0:	 0.050 FDR:   292; 0.010 FDR:   292; 0.001 FDR:   257
0:27:10.503053 PROGRESS: 
0:27:10.503108 PROGRESS: Protein Summary:
0:27:10.504187 PROGRESS: Channel   0:	 0.050 FDR:   278; 0.010 FDR:   278; 0.001 FDR:   245
0:27:10.504276 PROGRESS: =========================================================================
0:27:10.507109 INFO: Target number of precursors reached.
0:27:10.546117 INFO: fragments_df: keeping 3087 of 567902 [sum(precursor_idx_mask)=6645 sum(mass_error_mask)=567902 stop_rank=3087
0:27:10.715408 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:10.811409 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:11.156641 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:11.157190 INFO: Using score_cutoff 12.9831448802948 (fac=0.99, q=1)
0:27:11.157509 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:11.157589 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:11.157640 INFO: Updating optimization_manager: score_cutoff        : 13.469067403507232 -> 12.9831448802948
0:27:11.157694 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:11.190126 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:11.260797 INFO: === checking if optimization conditions were reached ===
0:27:11.261133 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:27:11.263474 INFO: Updating optimization_manager: rt_error            : 74.02616018320498 -> 58.419913413009645
0:27:11.263584 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 58.4199.
0:27:11.263652 INFO: ==============================================
0:27:11.263723 INFO: Starting optimization step 4.
0:27:11.263780 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:27:11.263840 INFO: Using ng extraction backend
0:27:11.263898 PROGRESS: Extracting batch of 50293 precursors
0:27:11.355859 INFO: === Search parameters used ===
0:27:11.356229 INFO: rt_error       : 58.419913413009645
0:27:11.356282 INFO: mobility_error : 0.1
0:27:11.356329 INFO: num_candidates : 3
0:27:11.356373 INFO: ms1_error      : 30
0:27:11.356414 INFO: ms2_error      : 10.0
0:27:11.356455 INFO: fwhm_rt        : 3.0
0:27:11.356494 INFO: quant_window   : 3
0:27:11.356534 INFO: ==============================================
0:27:11.985485 INFO: performing precursor FDR with 40 features
0:27:11.985666 INFO: Decoy channel: -1
0:27:11.985695 INFO: Competetive: True
0:27:12.040500 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:12.093756 INFO: Using random state 943060 for train-test-split
0:27:14.944654 INFO: Test AUC: 0.588
0:27:14.944829 INFO: Train AUC: 0.606
0:27:14.944863 INFO: AUC difference: 2.95%
0:27:15.207956 INFO: Resetting torch num_threads to 80
0:27:15.216043 PROGRESS: === Extracted 142496 precursors and 536701 fragments ===
0:27:15.216454 INFO: === FDR correction performed with classifier version 10 ===
0:27:15.216919 PROGRESS: ============================= Precursor FDR =============================
0:27:15.217009 PROGRESS: Total precursors accumulated: 309
0:27:15.217068 PROGRESS: Target precursors: 306 (99.03%)
0:27:15.217119 PROGRESS: Decoy precursors: 3 (0.97%)
0:27:15.217165 PROGRESS: 
0:27:15.217207 PROGRESS: Precursor Summary:
0:27:15.218134 PROGRESS: Channel   0:	 0.050 FDR:   306; 0.010 FDR:   306; 0.001 FDR:   248
0:27:15.218225 PROGRESS: 
0:27:15.218279 PROGRESS: Protein Summary:
0:27:15.219335 PROGRESS: Channel   0:	 0.050 FDR:   295; 0.010 FDR:   295; 0.001 FDR:   238
0:27:15.219432 PROGRESS: =========================================================================
0:27:15.222200 INFO: Target number of precursors reached.
0:27:15.260339 INFO: fragments_df: keeping 3073 of 536701 [sum(precursor_idx_mask)=6559 sum(mass_error_mask)=536701 stop_rank=3073
0:27:15.429317 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:15.558613 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:15.949690 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:15.950221 INFO: Using score_cutoff 10.588330578804015 (fac=0.99, q=1)
0:27:15.950538 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:15.950618 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:15.950670 INFO: Updating optimization_manager: score_cutoff        : 12.9831448802948 -> 10.588330578804015
0:27:15.950725 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:15.983024 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:16.054086 INFO: === checking if optimization conditions were reached ===
0:27:16.054436 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:27:16.056758 INFO: Updating optimization_manager: rt_error            : 58.419913413009645 -> 43.8364391770784
0:27:16.056882 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 43.8364.
0:27:16.056971 INFO: ==============================================
0:27:16.057056 INFO: Starting optimization step 5.
0:27:16.057120 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:27:16.057195 INFO: Using ng extraction backend
0:27:16.057256 PROGRESS: Extracting batch of 50293 precursors
0:27:16.148555 INFO: === Search parameters used ===
0:27:16.148929 INFO: rt_error       : 43.8364391770784
0:27:16.148992 INFO: mobility_error : 0.1
0:27:16.149040 INFO: num_candidates : 3
0:27:16.149085 INFO: ms1_error      : 30
0:27:16.149124 INFO: ms2_error      : 10.0
0:27:16.149165 INFO: fwhm_rt        : 3.0
0:27:16.149204 INFO: quant_window   : 3
0:27:16.149242 INFO: ==============================================
0:27:16.741757 INFO: performing precursor FDR with 40 features
0:27:16.741914 INFO: Decoy channel: -1
0:27:16.741942 INFO: Competetive: True
0:27:16.795848 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:16.845863 INFO: Using random state 943060 for train-test-split
0:27:18.969750 INFO: Test AUC: 0.595
0:27:18.969913 INFO: Train AUC: 0.602
0:27:18.969944 INFO: AUC difference: 1.27%
0:27:20.455447 INFO: Resetting torch num_threads to 80
0:27:20.466250 PROGRESS: === Extracted 134358 precursors and 492709 fragments ===
0:27:20.466715 INFO: === FDR correction performed with classifier version 10 ===
0:27:20.467190 PROGRESS: ============================= Precursor FDR =============================
0:27:20.467281 PROGRESS: Total precursors accumulated: 311
0:27:20.467342 PROGRESS: Target precursors: 308 (99.04%)
0:27:20.467403 PROGRESS: Decoy precursors: 3 (0.96%)
0:27:20.467456 PROGRESS: 
0:27:20.467502 PROGRESS: Precursor Summary:
0:27:20.468544 PROGRESS: Channel   0:	 0.050 FDR:   308; 0.010 FDR:   308; 0.001 FDR:   211
0:27:20.468798 PROGRESS: 
0:27:20.468891 PROGRESS: Protein Summary:
0:27:20.470131 PROGRESS: Channel   0:	 0.050 FDR:   299; 0.010 FDR:   299; 0.001 FDR:   204
0:27:20.470233 PROGRESS: =========================================================================
0:27:20.473492 INFO: Target number of precursors reached.
0:27:20.515841 INFO: fragments_df: keeping 2877 of 492709 [sum(precursor_idx_mask)=6150 sum(mass_error_mask)=492709 stop_rank=2877
0:27:20.680049 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:20.815859 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:21.272476 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:21.273200 INFO: Using score_cutoff 7.755670631933213 (fac=0.99, q=1)
0:27:21.273704 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:21.273940 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:21.274149 INFO: Updating optimization_manager: score_cutoff        : 10.588330578804015 -> 7.755670631933213
0:27:21.274362 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:21.309956 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:21.396764 INFO: === checking if optimization conditions were reached ===
0:27:21.397059 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:27:21.399569 INFO: Updating optimization_manager: rt_error            : 43.8364391770784 -> 32.08174525470952
0:27:21.399708 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 32.0817.
0:27:21.399789 INFO: ==============================================
0:27:21.399888 INFO: Starting optimization step 6.
0:27:21.399958 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:27:21.400031 INFO: Using ng extraction backend
0:27:21.400099 PROGRESS: Extracting batch of 50293 precursors
0:27:21.495770 INFO: === Search parameters used ===
0:27:21.496029 INFO: rt_error       : 32.08174525470952
0:27:21.496086 INFO: mobility_error : 0.1
0:27:21.496132 INFO: num_candidates : 3
0:27:21.496174 INFO: ms1_error      : 30
0:27:21.496217 INFO: ms2_error      : 10.0
0:27:21.496257 INFO: fwhm_rt        : 3.0
0:27:21.496295 INFO: quant_window   : 3
0:27:21.496333 INFO: ==============================================
0:27:22.161646 INFO: performing precursor FDR with 40 features
0:27:22.161785 INFO: Decoy channel: -1
0:27:22.161818 INFO: Competetive: True
0:27:22.215688 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:22.258998 INFO: Using random state 943060 for train-test-split
0:27:24.096169 INFO: Test AUC: 0.587
0:27:24.096287 INFO: Train AUC: 0.605
0:27:24.096316 INFO: AUC difference: 3.08%
0:27:24.363213 INFO: Resetting torch num_threads to 80
0:27:24.369754 PROGRESS: === Extracted 134318 precursors and 491714 fragments ===
0:27:24.370125 INFO: === FDR correction performed with classifier version 10 ===
0:27:24.370609 PROGRESS: ============================= Precursor FDR =============================
0:27:24.370698 PROGRESS: Total precursors accumulated: 284
0:27:24.370755 PROGRESS: Target precursors: 282 (99.30%)
0:27:24.370806 PROGRESS: Decoy precursors: 2 (0.70%)
0:27:24.370850 PROGRESS: 
0:27:24.370891 PROGRESS: Precursor Summary:
0:27:24.371781 PROGRESS: Channel   0:	 0.050 FDR:   282; 0.010 FDR:   282; 0.001 FDR:   218
0:27:24.371879 PROGRESS: 
0:27:24.371937 PROGRESS: Protein Summary:
0:27:24.373024 PROGRESS: Channel   0:	 0.050 FDR:   273; 0.010 FDR:   273; 0.001 FDR:   211
0:27:24.373117 PROGRESS: =========================================================================
0:27:24.375212 INFO: Target number of precursors reached.
0:27:24.408636 INFO: fragments_df: keeping 2722 of 491714 [sum(precursor_idx_mask)=5670 sum(mass_error_mask)=491714 stop_rank=2722
0:27:24.549434 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:24.655830 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:24.957223 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:24.957634 INFO: Using score_cutoff 11.605147730255126 (fac=0.99, q=1)
0:27:24.957915 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:24.957991 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:24.958042 INFO: Updating optimization_manager: score_cutoff        : 7.755670631933213 -> 11.605147730255126
0:27:24.958094 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:24.990205 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:25.057643 INFO: === checking if optimization conditions were reached ===
0:27:25.057900 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:27:25.060148 INFO: Updating optimization_manager: rt_error            : 32.08174525470952 -> 32.34649191489774
0:27:25.060269 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 32.3465.
0:27:25.060358 INFO: ==============================================
0:27:25.060441 INFO: Starting optimization step 7.
0:27:25.060508 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:27:25.060580 INFO: Using ng extraction backend
0:27:25.060649 PROGRESS: Extracting batch of 50293 precursors
0:27:25.149917 INFO: === Search parameters used ===
0:27:25.150183 INFO: rt_error       : 32.34649191489774
0:27:25.150237 INFO: mobility_error : 0.1
0:27:25.150289 INFO: num_candidates : 3
0:27:25.150333 INFO: ms1_error      : 30
0:27:25.150371 INFO: ms2_error      : 10.0
0:27:25.150410 INFO: fwhm_rt        : 3.0
0:27:25.150449 INFO: quant_window   : 3
0:27:25.150486 INFO: ==============================================
0:27:25.685538 INFO: performing precursor FDR with 40 features
0:27:25.685652 INFO: Decoy channel: -1
0:27:25.685678 INFO: Competetive: True
0:27:25.725428 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:25.757050 INFO: Using random state 943060 for train-test-split
0:27:27.555528 INFO: Test AUC: 0.595
0:27:27.555654 INFO: Train AUC: 0.605
0:27:27.555685 INFO: AUC difference: 1.65%
0:27:27.810774 INFO: Resetting torch num_threads to 80
0:27:27.816957 PROGRESS: === Extracted 134307 precursors and 491881 fragments ===
0:27:27.817296 INFO: === FDR correction performed with classifier version 10 ===
0:27:27.817734 PROGRESS: ============================= Precursor FDR =============================
0:27:27.817828 PROGRESS: Total precursors accumulated: 259
0:27:27.817884 PROGRESS: Target precursors: 257 (99.23%)
0:27:27.817936 PROGRESS: Decoy precursors: 2 (0.77%)
0:27:27.817980 PROGRESS: 
0:27:27.818023 PROGRESS: Precursor Summary:
0:27:27.818913 PROGRESS: Channel   0:	 0.050 FDR:   257; 0.010 FDR:   257; 0.001 FDR:   214
0:27:27.819000 PROGRESS: 
0:27:27.819056 PROGRESS: Protein Summary:
0:27:27.820084 PROGRESS: Channel   0:	 0.050 FDR:   248; 0.010 FDR:   248; 0.001 FDR:   209
0:27:27.820177 PROGRESS: =========================================================================
0:27:27.822156 INFO: Target number of precursors reached.
0:27:27.856220 INFO: fragments_df: keeping 2542 of 491881 [sum(precursor_idx_mask)=5204 sum(mass_error_mask)=491881 stop_rank=2542
0:27:27.988094 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:28.108471 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:28.410739 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:28.411286 INFO: Using score_cutoff 12.63700618286133 (fac=0.99, q=1)
0:27:28.411607 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:28.411688 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:28.411741 INFO: Updating optimization_manager: score_cutoff        : 11.605147730255126 -> 12.63700618286133
0:27:28.411797 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:28.444299 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:28.511251 INFO: === checking if optimization conditions were reached ===
0:27:28.511581 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
0:27:28.513232 INFO: Updating optimization_manager: rt_error            : 32.34649191489774 -> 32.08174525470952
0:27:28.513379 INFO: Updating optimization_manager: classifier_version  : 10 -> 17
0:27:28.513478 INFO: Updating optimization_manager: score_cutoff        : 12.63700618286133 -> 11.605147730255126
0:27:28.513573 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:28.513657 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:28.513743 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 32.0817 found after 8 searches.
0:27:28.513809 INFO: ==============================================
0:27:28.513885 PROGRESS: Optimization finished for rt_error.
0:27:28.763584 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:28.796157 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:28.906227 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:27:28.906514 PROGRESS: ==============================================
0:27:28.906595 PROGRESS: ms2_error      : 10.0000
0:27:28.906651 PROGRESS: rt_error       : 32.0817
0:27:28.906699 PROGRESS: ==============================================
0:27:28.908288 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:36.823338 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:59.948620 INFO: Using ng extraction backend
0:27:59.949095 PROGRESS: Extracting batch of 12001526 precursors
0:28:15.805274 INFO: === Search parameters used ===
0:28:15.805599 INFO: rt_error       : 32.08174525470952
0:28:15.805661 INFO: mobility_error : 0.1
0:28:15.805716 INFO: num_candidates : 3
0:28:15.805758 INFO: ms1_error      : 30
0:28:15.805800 INFO: ms2_error      : 10.0
0:28:15.805839 INFO: fwhm_rt        : 3.0
0:28:15.805881 INFO: quant_window   : 3
0:28:15.805920 INFO: ==============================================
0:28:34.535716 INFO: Removed 25023588 precursors with score below cutoff 11.605147730255126
0:28:42.018212 INFO: performing precursor FDR with 40 features
0:28:42.018337 INFO: Decoy channel: -1
0:28:42.018368 INFO: Competetive: True
0:28:42.886623 INFO: Setting torch num_threads to 2 for FDR classification task
0:28:45.988787 INFO: Using random state 873930 for train-test-split
0:30:35.923994 INFO: Test AUC: 0.623
0:30:35.924220 INFO: Train AUC: 0.624
0:30:35.924254 INFO: AUC difference: 0.24%
0:30:38.538738 INFO: Resetting torch num_threads to 80
0:30:40.403451 PROGRESS: ============================= Precursor FDR =============================
0:30:40.403717 PROGRESS: Total precursors accumulated: 71,917
0:30:40.403783 PROGRESS: Target precursors: 71,205 (99.01%)
0:30:40.403833 PROGRESS: Decoy precursors: 712 (0.99%)
0:30:40.403879 PROGRESS: 
0:30:40.403920 PROGRESS: Precursor Summary:
0:30:40.425242 PROGRESS: Channel   0:	 0.050 FDR: 71,205; 0.010 FDR: 71,205; 0.001 FDR: 49,721
0:30:40.425466 PROGRESS: 
0:30:40.425527 PROGRESS: Protein Summary:
0:30:40.461976 PROGRESS: Channel   0:	 0.050 FDR: 12,445; 0.010 FDR: 12,445; 0.001 FDR: 9,235
0:30:40.462210 PROGRESS: =========================================================================
0:30:40.516206 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/psm.parquet
0:30:40.659170 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.parquet
0:30:40.868666 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:30:41.600365 PROGRESS: 
0:30:41.600514 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark/quant
0:30:41.600587 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/figures
0:30:41.600758 INFO: Initializing TimingManager
0:30:41.601189 INFO: Initializing RawFileManager
0:30:53.257210 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:30:53.262170 INFO: Determining DIA cycle
0:30:53.278669 INFO: Found cycle with start 0.00 min and length 300.
0:30:53.454362 INFO: RT (min)            : 0.0 - 26.9
0:30:53.454484 INFO: RT duration (sec)   : 1611.2
0:30:53.454514 INFO: RT duration (min)   : 26.9
0:30:53.454541 INFO: Cycle len (scans)   : 300
0:30:53.454561 INFO: Cycle len (sec)     : 1.65
0:30:53.454580 INFO: Number of cycles    : 977
0:30:53.454602 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:30:53.454642 INFO: Creating DIA data object took: 11.853354454040527
0:30:54.125264 INFO: Creating DIA data NG object took: 0.6704695224761963
0:30:55.666853 INFO: Initializing CalibrationManager
0:30:55.667262 INFO: Setting up calibration estimators ..
0:30:55.667423 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:30:55.667595 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
0:30:55.667816 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:30:55.667960 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:30:55.668115 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
0:30:55.668767 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:30:55.668879 INFO: Done setting up calibration estimators.
0:30:55.669123 INFO: Initializing OptimizationManager
0:30:55.669331 INFO: initial parameter: ms1_error = 30
0:30:55.669420 INFO: initial parameter: ms2_error = 30
0:30:55.669502 INFO: initial parameter: rt_error = 805.5982666015625
0:30:55.669579 INFO: initial parameter: mobility_error = 0.1
0:30:55.669649 INFO: initial parameter: num_candidates = 1
0:30:55.669719 INFO: initial parameter: fwhm_rt = 5
0:30:55.669789 INFO: initial parameter: fwhm_mobility = 0.01
0:30:55.669857 INFO: initial parameter: score_cutoff = 0
0:30:55.669922 INFO: initial parameter: classifier_version = -1
0:30:55.670020 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:30:55.670367 INFO: FDRManager: loading saved state not requested, will be initialized.
0:30:55.670408 INFO: Initializing FDRManager
0:30:55.670448 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:30:57.195027 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:30:58.079478 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:30:58.079880 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
0:30:58.079989 PROGRESS: Starting initial search for precursors.
0:30:58.080070 INFO: Starting optimization step 0.
0:30:58.080131 PROGRESS: === Extracting elution groups 0 to 200 ===
0:30:58.080188 INFO: Using ng extraction backend
0:30:58.080248 PROGRESS: Extracting batch of 396 precursors
0:30:58.082173 INFO: === Search parameters used ===
0:30:58.082275 INFO: rt_error       : 805.5982666015625
0:30:58.082324 INFO: mobility_error : 0.1
0:30:58.082366 INFO: num_candidates : 1
0:30:58.082406 INFO: ms1_error      : 30
0:30:58.082446 INFO: ms2_error      : 30
0:30:58.082483 INFO: fwhm_rt        : 5
0:30:58.082524 INFO: quant_window   : 3
0:30:58.082561 INFO: ==============================================
0:30:58.109225 INFO: performing precursor FDR with 40 features
0:30:58.109304 INFO: Decoy channel: -1
0:30:58.109331 INFO: Competetive: True
0:30:58.110250 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:58.112523 INFO: Using random state 276994 for train-test-split
0:30:58.119715 INFO: Test AUC: 0.541
0:30:58.119776 INFO: Train AUC: 0.488
0:30:58.119807 INFO: AUC difference: 10.91%
0:30:58.119829 WARNING: AUC difference > 5%. This may indicate overfitting.
0:30:58.330171 INFO: Resetting torch num_threads to 80
0:30:58.331482 PROGRESS: === Extracted 392 precursors and 1853 fragments ===
0:30:58.331806 INFO: === FDR correction performed with classifier version -1 ===
0:30:58.332245 PROGRESS: ============================= Precursor FDR =============================
0:30:58.332331 PROGRESS: Total precursors accumulated: 1
0:30:58.332392 PROGRESS: Target precursors: 1 (100.00%)
0:30:58.332444 PROGRESS: Decoy precursors: 0 (0.00%)
0:30:58.332492 PROGRESS: 
0:30:58.332539 PROGRESS: Precursor Summary:
0:30:58.333436 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:30:58.333530 PROGRESS: 
0:30:58.333587 PROGRESS: Protein Summary:
0:30:58.334572 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:30:58.334662 PROGRESS: =========================================================================
0:30:58.334848 INFO: Target number of precursors not reached yet.
0:30:58.398938 INFO: Starting optimization step 1.
0:30:58.399133 PROGRESS: === Extracting elution groups 200 to 600 ===
0:30:58.399215 INFO: Using ng extraction backend
0:30:58.399276 PROGRESS: Extracting batch of 786 precursors
0:30:58.401903 INFO: === Search parameters used ===
0:30:58.402025 INFO: rt_error       : 805.5982666015625
0:30:58.402080 INFO: mobility_error : 0.1
0:30:58.402127 INFO: num_candidates : 1
0:30:58.402172 INFO: ms1_error      : 30
0:30:58.402214 INFO: ms2_error      : 30
0:30:58.402256 INFO: fwhm_rt        : 5
0:30:58.402296 INFO: quant_window   : 3
0:30:58.402334 INFO: ==============================================
0:30:58.471615 INFO: performing precursor FDR with 40 features
0:30:58.471713 INFO: Decoy channel: -1
0:30:58.471739 INFO: Competetive: True
0:30:58.474517 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:58.475979 INFO: Using random state 259985 for train-test-split
0:30:58.484067 INFO: Test AUC: 0.485
0:30:58.484120 INFO: Train AUC: 0.503
0:30:58.484149 INFO: AUC difference: 3.68%
0:30:58.685565 INFO: Resetting torch num_threads to 80
0:30:58.687557 PROGRESS: === Extracted 1171 precursors and 5469 fragments ===
0:30:58.687881 INFO: === FDR correction performed with classifier version -1 ===
0:30:58.688301 PROGRESS: ============================= Precursor FDR =============================
0:30:58.688385 PROGRESS: Total precursors accumulated: 0
0:30:58.688442 PROGRESS: Target precursors: 0 (0.00%)
0:30:58.688492 PROGRESS: Decoy precursors: 0 (0.00%)
0:30:58.688536 PROGRESS: 
0:30:58.688578 PROGRESS: Precursor Summary:
0:30:58.688690 PROGRESS: 
0:30:58.688752 PROGRESS: Protein Summary:
0:30:58.688829 PROGRESS: =========================================================================
0:30:58.689032 INFO: Target number of precursors not reached yet.
0:30:58.755599 INFO: Starting optimization step 2.
0:30:58.755795 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:30:58.755872 INFO: Using ng extraction backend
0:30:58.755931 PROGRESS: Extracting batch of 1592 precursors
0:30:58.760087 INFO: === Search parameters used ===
0:30:58.760213 INFO: rt_error       : 805.5982666015625
0:30:58.760262 INFO: mobility_error : 0.1
0:30:58.760308 INFO: num_candidates : 1
0:30:58.760349 INFO: ms1_error      : 30
0:30:58.760390 INFO: ms2_error      : 30
0:30:58.760432 INFO: fwhm_rt        : 5
0:30:58.760472 INFO: quant_window   : 3
0:30:58.760511 INFO: ==============================================
0:30:58.791009 INFO: performing precursor FDR with 40 features
0:30:58.791085 INFO: Decoy channel: -1
0:30:58.791110 INFO: Competetive: True
0:30:58.794392 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:58.796200 INFO: Using random state 332994 for train-test-split
0:30:58.807655 INFO: Test AUC: 0.556
0:30:58.807717 INFO: Train AUC: 0.484
0:30:58.807745 INFO: AUC difference: 14.99%
0:30:58.807768 WARNING: AUC difference > 5%. This may indicate overfitting.
0:30:59.010499 INFO: Resetting torch num_threads to 80
0:30:59.012940 PROGRESS: === Extracted 2751 precursors and 13038 fragments ===
0:30:59.013268 INFO: === FDR correction performed with classifier version -1 ===
0:30:59.013689 PROGRESS: ============================= Precursor FDR =============================
0:30:59.013775 PROGRESS: Total precursors accumulated: 0
0:30:59.013841 PROGRESS: Target precursors: 0 (0.00%)
0:30:59.013894 PROGRESS: Decoy precursors: 0 (0.00%)
0:30:59.013940 PROGRESS: 
0:30:59.013982 PROGRESS: Precursor Summary:
0:30:59.014087 PROGRESS: 
0:30:59.014147 PROGRESS: Protein Summary:
0:30:59.014218 PROGRESS: =========================================================================
0:30:59.014421 INFO: Target number of precursors not reached yet.
0:30:59.083588 INFO: Starting optimization step 3.
0:30:59.083789 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:30:59.083866 INFO: Using ng extraction backend
0:30:59.083925 PROGRESS: Extracting batch of 3177 precursors
0:30:59.090750 INFO: === Search parameters used ===
0:30:59.090882 INFO: rt_error       : 805.5982666015625
0:30:59.090933 INFO: mobility_error : 0.1
0:30:59.090980 INFO: num_candidates : 1
0:30:59.091021 INFO: ms1_error      : 30
0:30:59.091061 INFO: ms2_error      : 30
0:30:59.091105 INFO: fwhm_rt        : 5
0:30:59.091144 INFO: quant_window   : 3
0:30:59.091183 INFO: ==============================================
0:30:59.140344 INFO: performing precursor FDR with 40 features
0:30:59.140430 INFO: Decoy channel: -1
0:30:59.140455 INFO: Competetive: True
0:30:59.145434 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:59.147667 INFO: Using random state 291257 for train-test-split
0:30:59.166728 INFO: Test AUC: 0.480
0:30:59.166799 INFO: Train AUC: 0.500
0:30:59.166828 INFO: AUC difference: 3.97%
0:30:59.370900 INFO: Resetting torch num_threads to 80
0:30:59.374015 PROGRESS: === Extracted 5898 precursors and 28051 fragments ===
0:30:59.374349 INFO: === FDR correction performed with classifier version -1 ===
0:30:59.374778 PROGRESS: ============================= Precursor FDR =============================
0:30:59.374863 PROGRESS: Total precursors accumulated: 0
0:30:59.374920 PROGRESS: Target precursors: 0 (0.00%)
0:30:59.374968 PROGRESS: Decoy precursors: 0 (0.00%)
0:30:59.375012 PROGRESS: 
0:30:59.375054 PROGRESS: Precursor Summary:
0:30:59.375157 PROGRESS: 
0:30:59.375216 PROGRESS: Protein Summary:
0:30:59.375287 PROGRESS: =========================================================================
0:30:59.375518 INFO: Target number of precursors not reached yet.
0:30:59.448640 INFO: Starting optimization step 4.
0:30:59.448860 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:30:59.448940 INFO: Using ng extraction backend
0:30:59.449002 PROGRESS: Extracting batch of 6340 precursors
0:30:59.461176 INFO: === Search parameters used ===
0:30:59.461320 INFO: rt_error       : 805.5982666015625
0:30:59.461371 INFO: mobility_error : 0.1
0:30:59.461416 INFO: num_candidates : 1
0:30:59.461458 INFO: ms1_error      : 30
0:30:59.461498 INFO: ms2_error      : 30
0:30:59.461540 INFO: fwhm_rt        : 5
0:30:59.461579 INFO: quant_window   : 3
0:30:59.461630 INFO: ==============================================
0:30:59.531042 INFO: performing precursor FDR with 40 features
0:30:59.531144 INFO: Decoy channel: -1
0:30:59.531170 INFO: Competetive: True
0:30:59.537286 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:59.540533 INFO: Using random state 114948 for train-test-split
0:30:59.574513 INFO: Test AUC: 0.510
0:30:59.574605 INFO: Train AUC: 0.492
0:30:59.574635 INFO: AUC difference: 3.60%
0:30:59.786349 INFO: Resetting torch num_threads to 80
0:30:59.790704 PROGRESS: === Extracted 12176 precursors and 57532 fragments ===
0:30:59.791074 INFO: === FDR correction performed with classifier version -1 ===
0:30:59.791505 PROGRESS: ============================= Precursor FDR =============================
0:30:59.791592 PROGRESS: Total precursors accumulated: 0
0:30:59.791650 PROGRESS: Target precursors: 0 (0.00%)
0:30:59.791698 PROGRESS: Decoy precursors: 0 (0.00%)
0:30:59.791742 PROGRESS: 
0:30:59.791784 PROGRESS: Precursor Summary:
0:30:59.791889 PROGRESS: 
0:30:59.791947 PROGRESS: Protein Summary:
0:30:59.792016 PROGRESS: =========================================================================
0:30:59.792306 INFO: Target number of precursors not reached yet.
0:30:59.873745 INFO: Starting optimization step 5.
0:30:59.873955 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:30:59.874031 INFO: Using ng extraction backend
0:30:59.874092 PROGRESS: Extracting batch of 12663 precursors
0:30:59.897085 INFO: === Search parameters used ===
0:30:59.897256 INFO: rt_error       : 805.5982666015625
0:30:59.897307 INFO: mobility_error : 0.1
0:30:59.897355 INFO: num_candidates : 1
0:30:59.897408 INFO: ms1_error      : 30
0:30:59.897450 INFO: ms2_error      : 30
0:30:59.897491 INFO: fwhm_rt        : 5
0:30:59.897531 INFO: quant_window   : 3
0:30:59.897569 INFO: ==============================================
0:31:00.027016 INFO: performing precursor FDR with 40 features
0:31:00.027126 INFO: Decoy channel: -1
0:31:00.027153 INFO: Competetive: True
0:31:00.038474 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:00.045043 INFO: Using random state 129657 for train-test-split
0:31:00.289657 INFO: Test AUC: 0.532
0:31:00.289757 INFO: Train AUC: 0.527
0:31:00.289788 INFO: AUC difference: 1.01%
0:31:00.508058 INFO: Resetting torch num_threads to 80
0:31:00.514045 PROGRESS: === Extracted 24724 precursors and 116398 fragments ===
0:31:00.514474 INFO: === FDR correction performed with classifier version -1 ===
0:31:00.514926 PROGRESS: ============================= Precursor FDR =============================
0:31:00.515012 PROGRESS: Total precursors accumulated: 0
0:31:00.515070 PROGRESS: Target precursors: 0 (0.00%)
0:31:00.515120 PROGRESS: Decoy precursors: 0 (0.00%)
0:31:00.515164 PROGRESS: 
0:31:00.515206 PROGRESS: Precursor Summary:
0:31:00.515314 PROGRESS: 
0:31:00.515375 PROGRESS: Protein Summary:
0:31:00.515447 PROGRESS: =========================================================================
0:31:00.515885 INFO: Target number of precursors not reached yet.
0:31:00.613496 INFO: Starting optimization step 6.
0:31:00.613722 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:31:00.613802 INFO: Using ng extraction backend
0:31:00.613868 PROGRESS: Extracting batch of 25339 precursors
0:31:00.658534 INFO: === Search parameters used ===
0:31:00.658754 INFO: rt_error       : 805.5982666015625
0:31:00.658806 INFO: mobility_error : 0.1
0:31:00.658852 INFO: num_candidates : 1
0:31:00.658892 INFO: ms1_error      : 30
0:31:00.658933 INFO: ms2_error      : 30
0:31:00.658971 INFO: fwhm_rt        : 5
0:31:00.659010 INFO: quant_window   : 3
0:31:00.659049 INFO: ==============================================
0:31:00.875354 INFO: performing precursor FDR with 40 features
0:31:00.875468 INFO: Decoy channel: -1
0:31:00.875495 INFO: Competetive: True
0:31:00.894530 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:00.906534 INFO: Using random state 700258 for train-test-split
0:31:01.489958 INFO: Test AUC: 0.548
0:31:01.490075 INFO: Train AUC: 0.569
0:31:01.490107 INFO: AUC difference: 3.77%
0:31:01.723641 INFO: Resetting torch num_threads to 80
0:31:01.733736 PROGRESS: === Extracted 49832 precursors and 234547 fragments ===
0:31:01.734265 INFO: === FDR correction performed with classifier version -1 ===
0:31:01.734760 PROGRESS: ============================= Precursor FDR =============================
0:31:01.734852 PROGRESS: Total precursors accumulated: 106
0:31:01.734911 PROGRESS: Target precursors: 105 (99.06%)
0:31:01.734962 PROGRESS: Decoy precursors: 1 (0.94%)
0:31:01.735008 PROGRESS: 
0:31:01.735051 PROGRESS: Precursor Summary:
0:31:01.735920 PROGRESS: Channel   0:	 0.050 FDR:   105; 0.010 FDR:   105; 0.001 FDR:    95
0:31:01.736009 PROGRESS: 
0:31:01.736063 PROGRESS: Protein Summary:
0:31:01.737039 PROGRESS: Channel   0:	 0.050 FDR:   103; 0.010 FDR:   103; 0.001 FDR:    93
0:31:01.737130 PROGRESS: =========================================================================
0:31:01.738221 INFO: Target number of precursors not reached yet.
0:31:01.870093 INFO: Starting optimization step 7.
0:31:01.870330 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:31:01.870411 INFO: Using ng extraction backend
0:31:01.870476 PROGRESS: Extracting batch of 50691 precursors
0:31:01.958019 INFO: === Search parameters used ===
0:31:01.958263 INFO: rt_error       : 805.5982666015625
0:31:01.958317 INFO: mobility_error : 0.1
0:31:01.958364 INFO: num_candidates : 1
0:31:01.958406 INFO: ms1_error      : 30
0:31:01.958446 INFO: ms2_error      : 30
0:31:01.958487 INFO: fwhm_rt        : 5
0:31:01.958525 INFO: quant_window   : 3
0:31:01.958566 INFO: ==============================================
0:31:02.317152 INFO: performing precursor FDR with 40 features
0:31:02.317262 INFO: Decoy channel: -1
0:31:02.317289 INFO: Competetive: True
0:31:02.357889 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:02.383143 INFO: Using random state 356450 for train-test-split
0:31:03.817146 INFO: Test AUC: 0.579
0:31:03.817264 INFO: Train AUC: 0.593
0:31:03.817295 INFO: AUC difference: 2.37%
0:31:04.060185 INFO: Resetting torch num_threads to 80
0:31:04.078926 PROGRESS: === Extracted 100023 precursors and 471000 fragments ===
0:31:04.079663 INFO: === FDR correction performed with classifier version -1 ===
0:31:04.080195 PROGRESS: ============================= Precursor FDR =============================
0:31:04.080286 PROGRESS: Total precursors accumulated: 249
0:31:04.080347 PROGRESS: Target precursors: 247 (99.20%)
0:31:04.080398 PROGRESS: Decoy precursors: 2 (0.80%)
0:31:04.080446 PROGRESS: 
0:31:04.080489 PROGRESS: Precursor Summary:
0:31:04.081433 PROGRESS: Channel   0:	 0.050 FDR:   247; 0.010 FDR:   247; 0.001 FDR:   215
0:31:04.081527 PROGRESS: 
0:31:04.081583 PROGRESS: Protein Summary:
0:31:04.082618 PROGRESS: Channel   0:	 0.050 FDR:   234; 0.010 FDR:   234; 0.001 FDR:   202
0:31:04.082708 PROGRESS: =========================================================================
0:31:04.084358 INFO: Target number of precursors reached.
0:31:04.119913 INFO: fragments_df: keeping 2201 of 471000 [sum(precursor_idx_mask)=2720 sum(mass_error_mask)=471000 stop_rank=2201
0:31:04.324522 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:04.445711 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:04.739331 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:31:04.739730 INFO: Using score_cutoff 14.519655553436278 (fac=0.99, q=1)
0:31:04.740019 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:31:04.740099 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:31:04.740151 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.519655553436278
0:31:04.740204 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:04.802223 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:04.954745 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:31:04.954966 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:31:04.955052 INFO: Starting optimization step 8.
0:31:04.955124 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:31:04.955194 INFO: Using ng extraction backend
0:31:04.955253 PROGRESS: Extracting batch of 100984 precursors
0:31:05.127168 INFO: === Search parameters used ===
0:31:05.127411 INFO: rt_error       : 805.5982666015625
0:31:05.127466 INFO: mobility_error : 0.1
0:31:05.127513 INFO: num_candidates : 3
0:31:05.127554 INFO: ms1_error      : 30
0:31:05.127599 INFO: ms2_error      : 30
0:31:05.127644 INFO: fwhm_rt        : 3.0
0:31:05.127685 INFO: quant_window   : 3
0:31:05.127738 INFO: ==============================================
0:31:06.667780 INFO: performing precursor FDR with 40 features
0:31:06.667902 INFO: Decoy channel: -1
0:31:06.667929 INFO: Competetive: True
0:31:06.750320 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:06.854668 INFO: Using random state 390844 for train-test-split
0:31:10.852537 INFO: Test AUC: 0.589
0:31:10.853272 INFO: Train AUC: 0.604
0:31:10.853310 INFO: AUC difference: 2.34%
0:31:11.157691 INFO: Resetting torch num_threads to 80
0:31:11.171052 PROGRESS: === Extracted 300248 precursors and 1383339 fragments ===
0:31:11.171427 INFO: === FDR correction performed with classifier version 7 ===
0:31:11.171890 PROGRESS: ============================= Precursor FDR =============================
0:31:11.171974 PROGRESS: Total precursors accumulated: 324
0:31:11.172030 PROGRESS: Target precursors: 321 (99.07%)
0:31:11.172079 PROGRESS: Decoy precursors: 3 (0.93%)
0:31:11.172122 PROGRESS: 
0:31:11.172163 PROGRESS: Precursor Summary:
0:31:11.173088 PROGRESS: Channel   0:	 0.050 FDR:   321; 0.010 FDR:   321; 0.001 FDR:   257
0:31:11.173175 PROGRESS: 
0:31:11.173236 PROGRESS: Protein Summary:
0:31:11.174329 PROGRESS: Channel   0:	 0.050 FDR:   302; 0.010 FDR:   302; 0.001 FDR:   240
0:31:11.174415 PROGRESS: =========================================================================
0:31:11.180191 INFO: Target number of precursors reached.
0:31:11.271520 INFO: fragments_df: keeping 3660 of 1383339 [sum(precursor_idx_mask)=6997 sum(mass_error_mask)=1383339 stop_rank=3660
0:31:11.481635 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:11.602420 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:12.078124 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:12.078531 INFO: Using score_cutoff 8.935764947891236 (fac=0.99, q=1)
0:31:12.078805 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:12.078881 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:12.078932 INFO: Updating optimization_manager: score_cutoff        : 14.519655553436278 -> 8.935764947891236
0:31:12.078984 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:12.139996 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:12.291895 INFO: === checking if optimization conditions were reached ===
0:31:12.294105 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:31:12.294221 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:31:12.294296 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:31:12.294363 INFO: ==============================================
0:31:12.294451 INFO: Starting optimization step 9.
0:31:12.294520 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:31:12.294587 INFO: Using ng extraction backend
0:31:12.294652 PROGRESS: Extracting batch of 100984 precursors
0:31:12.470361 INFO: === Search parameters used ===
0:31:12.470604 INFO: rt_error       : 805.5982666015625
0:31:12.470663 INFO: mobility_error : 0.1
0:31:12.470706 INFO: num_candidates : 3
0:31:12.470749 INFO: ms1_error      : 30
0:31:12.470789 INFO: ms2_error      : 10.0
0:31:12.470827 INFO: fwhm_rt        : 3.0
0:31:12.470865 INFO: quant_window   : 3
0:31:12.470904 INFO: ==============================================
0:31:13.728281 INFO: performing precursor FDR with 40 features
0:31:13.728405 INFO: Decoy channel: -1
0:31:13.728432 INFO: Competetive: True
0:31:13.809275 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:13.913097 INFO: Using random state 405630 for train-test-split
0:31:17.974603 INFO: Test AUC: 0.594
0:31:17.974719 INFO: Train AUC: 0.607
0:31:17.974749 INFO: AUC difference: 2.05%
0:31:18.284191 INFO: Resetting torch num_threads to 80
0:31:18.296132 PROGRESS: === Extracted 302362 precursors and 1621768 fragments ===
0:31:18.296514 INFO: === FDR correction performed with classifier version 8 ===
0:31:18.297015 PROGRESS: ============================= Precursor FDR =============================
0:31:18.297114 PROGRESS: Total precursors accumulated: 409
0:31:18.297174 PROGRESS: Target precursors: 405 (99.02%)
0:31:18.297227 PROGRESS: Decoy precursors: 4 (0.98%)
0:31:18.297273 PROGRESS: 
0:31:18.297314 PROGRESS: Precursor Summary:
0:31:18.298208 PROGRESS: Channel   0:	 0.050 FDR:   405; 0.010 FDR:   405; 0.001 FDR:     0
0:31:18.298304 PROGRESS: 
0:31:18.298361 PROGRESS: Protein Summary:
0:31:18.299400 PROGRESS: Channel   0:	 0.050 FDR:   376; 0.010 FDR:   376; 0.001 FDR:     0
0:31:18.299488 PROGRESS: =========================================================================
0:31:18.304878 INFO: Target number of precursors reached.
0:31:18.412172 INFO: fragments_df: keeping 4829 of 1621768 [sum(precursor_idx_mask)=9965 sum(mass_error_mask)=1621768 stop_rank=4829
0:31:18.553161 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:18.661937 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:19.244382 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:19.244784 INFO: Using score_cutoff 13.620695907211303 (fac=0.99, q=1)
0:31:19.245079 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:19.245160 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:19.245214 INFO: Updating optimization_manager: score_cutoff        : 8.935764947891236 -> 13.620695907211303
0:31:19.245268 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:19.275873 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:19.341172 INFO: === checking if optimization conditions were reached ===
0:31:19.343511 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:31:19.343631 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:31:19.343709 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:31:19.343795 INFO: ==============================================
0:31:19.343871 PROGRESS: Optimization finished for ms2_error.
0:31:19.492061 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:19.523266 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:19.587621 INFO: Starting optimization step 0.
0:31:19.587879 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:19.587968 INFO: Using ng extraction backend
0:31:19.588044 PROGRESS: Extracting batch of 50293 precursors
0:31:19.678039 INFO: === Search parameters used ===
0:31:19.678285 INFO: rt_error       : 805.5982666015625
0:31:19.678341 INFO: mobility_error : 0.1
0:31:19.678387 INFO: num_candidates : 3
0:31:19.678432 INFO: ms1_error      : 30
0:31:19.678475 INFO: ms2_error      : 10.0
0:31:19.678515 INFO: fwhm_rt        : 3.0
0:31:19.678556 INFO: quant_window   : 3
0:31:19.678596 INFO: ==============================================
0:31:20.304981 INFO: performing precursor FDR with 40 features
0:31:20.305101 INFO: Decoy channel: -1
0:31:20.305128 INFO: Competetive: True
0:31:20.347417 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:20.383112 INFO: Using random state 120421 for train-test-split
0:31:22.333343 INFO: Test AUC: 0.604
0:31:22.333455 INFO: Train AUC: 0.615
0:31:22.333484 INFO: AUC difference: 1.78%
0:31:22.592875 INFO: Resetting torch num_threads to 80
0:31:22.599510 PROGRESS: === Extracted 150566 precursors and 808192 fragments ===
0:31:22.599854 INFO: === FDR correction performed with classifier version 9 ===
0:31:22.600285 PROGRESS: ============================= Precursor FDR =============================
0:31:22.600371 PROGRESS: Total precursors accumulated: 241
0:31:22.600438 PROGRESS: Target precursors: 239 (99.17%)
0:31:22.600491 PROGRESS: Decoy precursors: 2 (0.83%)
0:31:22.600536 PROGRESS: 
0:31:22.600580 PROGRESS: Precursor Summary:
0:31:22.601449 PROGRESS: Channel   0:	 0.050 FDR:   239; 0.010 FDR:   239; 0.001 FDR:   197
0:31:22.601539 PROGRESS: 
0:31:22.601594 PROGRESS: Protein Summary:
0:31:22.602595 PROGRESS: Channel   0:	 0.050 FDR:   232; 0.010 FDR:   232; 0.001 FDR:   190
0:31:22.602682 PROGRESS: =========================================================================
0:31:22.604952 INFO: Target number of precursors reached.
0:31:22.660166 INFO: fragments_df: keeping 2769 of 808192 [sum(precursor_idx_mask)=5788 sum(mass_error_mask)=808192 stop_rank=2769
0:31:22.794804 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:22.907713 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:23.273073 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:23.273471 INFO: Using score_cutoff 12.27718863143921 (fac=0.99, q=1)
0:31:23.273746 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:23.273828 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:23.273879 INFO: Updating optimization_manager: score_cutoff        : 13.620695907211303 -> 12.27718863143921
0:31:23.273931 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:23.304125 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:23.367232 INFO: === checking if optimization conditions were reached ===
0:31:23.367503 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:31:23.369541 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 203.4914173370229
0:31:23.369661 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 203.4914.
0:31:23.369738 INFO: ==============================================
0:31:23.369817 INFO: Starting optimization step 1.
0:31:23.369883 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:23.369953 INFO: Using ng extraction backend
0:31:23.370018 PROGRESS: Extracting batch of 50293 precursors
0:31:23.459970 INFO: === Search parameters used ===
0:31:23.460217 INFO: rt_error       : 203.4914173370229
0:31:23.460274 INFO: mobility_error : 0.1
0:31:23.460321 INFO: num_candidates : 3
0:31:23.460364 INFO: ms1_error      : 30
0:31:23.460407 INFO: ms2_error      : 10.0
0:31:23.460446 INFO: fwhm_rt        : 3.0
0:31:23.460485 INFO: quant_window   : 3
0:31:23.460524 INFO: ==============================================
0:31:24.105728 INFO: performing precursor FDR with 40 features
0:31:24.105850 INFO: Decoy channel: -1
0:31:24.105877 INFO: Competetive: True
0:31:24.159503 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:24.208878 INFO: Using random state 120421 for train-test-split
0:31:26.908790 INFO: Test AUC: 0.599
0:31:26.908914 INFO: Train AUC: 0.608
0:31:26.908944 INFO: AUC difference: 1.53%
0:31:27.168697 INFO: Resetting torch num_threads to 80
0:31:27.175469 PROGRESS: === Extracted 149321 precursors and 696506 fragments ===
0:31:27.175807 INFO: === FDR correction performed with classifier version 9 ===
0:31:27.176242 PROGRESS: ============================= Precursor FDR =============================
0:31:27.176337 PROGRESS: Total precursors accumulated: 248
0:31:27.176397 PROGRESS: Target precursors: 246 (99.19%)
0:31:27.176446 PROGRESS: Decoy precursors: 2 (0.81%)
0:31:27.176491 PROGRESS: 
0:31:27.176533 PROGRESS: Precursor Summary:
0:31:27.177414 PROGRESS: Channel   0:	 0.050 FDR:   246; 0.010 FDR:   246; 0.001 FDR:   195
0:31:27.177504 PROGRESS: 
0:31:27.177557 PROGRESS: Protein Summary:
0:31:27.178565 PROGRESS: Channel   0:	 0.050 FDR:   239; 0.010 FDR:   239; 0.001 FDR:   188
0:31:27.178653 PROGRESS: =========================================================================
0:31:27.180886 INFO: Target number of precursors reached.
0:31:27.227383 INFO: fragments_df: keeping 2763 of 696506 [sum(precursor_idx_mask)=5902 sum(mass_error_mask)=696506 stop_rank=2763
0:31:27.362184 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:27.461036 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:28.652961 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:28.653363 INFO: Using score_cutoff 13.625363402366638 (fac=0.99, q=1)
0:31:28.653637 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:28.653716 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:28.653780 INFO: Updating optimization_manager: score_cutoff        : 12.27718863143921 -> 13.625363402366638
0:31:28.653834 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:28.683985 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:28.746947 INFO: === checking if optimization conditions were reached ===
0:31:28.747211 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:31:28.749372 INFO: Updating optimization_manager: rt_error            : 203.4914173370229 -> 92.17457710636708
0:31:28.749490 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 92.1746.
0:31:28.749568 INFO: ==============================================
0:31:28.749647 INFO: Starting optimization step 2.
0:31:28.749714 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:28.749785 INFO: Using ng extraction backend
0:31:28.749851 PROGRESS: Extracting batch of 50293 precursors
0:31:28.839635 INFO: === Search parameters used ===
0:31:28.839890 INFO: rt_error       : 92.17457710636708
0:31:28.839946 INFO: mobility_error : 0.1
0:31:28.839994 INFO: num_candidates : 3
0:31:28.840042 INFO: ms1_error      : 30
0:31:28.840085 INFO: ms2_error      : 10.0
0:31:28.840125 INFO: fwhm_rt        : 3.0
0:31:28.840165 INFO: quant_window   : 3
0:31:28.840203 INFO: ==============================================
0:31:29.423876 INFO: performing precursor FDR with 40 features
0:31:29.423994 INFO: Decoy channel: -1
0:31:29.424021 INFO: Competetive: True
0:31:29.465636 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:29.501659 INFO: Using random state 120421 for train-test-split
0:31:31.325518 INFO: Test AUC: 0.594
0:31:31.325631 INFO: Train AUC: 0.609
0:31:31.325661 INFO: AUC difference: 2.34%
0:31:31.580853 INFO: Resetting torch num_threads to 80
0:31:31.587476 PROGRESS: === Extracted 146465 precursors and 590078 fragments ===
0:31:31.587829 INFO: === FDR correction performed with classifier version 9 ===
0:31:31.588271 PROGRESS: ============================= Precursor FDR =============================
0:31:31.588363 PROGRESS: Total precursors accumulated: 230
0:31:31.588422 PROGRESS: Target precursors: 228 (99.13%)
0:31:31.588470 PROGRESS: Decoy precursors: 2 (0.87%)
0:31:31.588516 PROGRESS: 
0:31:31.588558 PROGRESS: Precursor Summary:
0:31:31.589439 PROGRESS: Channel   0:	 0.050 FDR:   228; 0.010 FDR:   228; 0.001 FDR:   209
0:31:31.589537 PROGRESS: 
0:31:31.589591 PROGRESS: Protein Summary:
0:31:31.590606 PROGRESS: Channel   0:	 0.050 FDR:   221; 0.010 FDR:   221; 0.001 FDR:   202
0:31:31.590696 PROGRESS: =========================================================================
0:31:31.592964 INFO: Target number of precursors reached.
0:31:31.631866 INFO: fragments_df: keeping 2570 of 590078 [sum(precursor_idx_mask)=5277 sum(mass_error_mask)=590078 stop_rank=2570
0:31:31.766404 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:31.864730 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:32.145328 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:32.145731 INFO: Using score_cutoff 14.528815887737274 (fac=0.99, q=1)
0:31:32.146008 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:32.146089 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:32.146148 INFO: Updating optimization_manager: score_cutoff        : 13.625363402366638 -> 14.528815887737274
0:31:32.146202 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:32.176737 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:32.242855 INFO: === checking if optimization conditions were reached ===
0:31:32.243116 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:31:32.245356 INFO: Updating optimization_manager: rt_error            : 92.17457710636708 -> 78.04477952768723
0:31:32.245470 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 78.0448.
0:31:32.245562 INFO: ==============================================
0:31:32.245641 INFO: Starting optimization step 3.
0:31:32.245706 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:32.245776 INFO: Using ng extraction backend
0:31:32.245842 PROGRESS: Extracting batch of 50293 precursors
0:31:32.335391 INFO: === Search parameters used ===
0:31:32.335634 INFO: rt_error       : 78.04477952768723
0:31:32.335689 INFO: mobility_error : 0.1
0:31:32.335735 INFO: num_candidates : 3
0:31:32.335779 INFO: ms1_error      : 30
0:31:32.335822 INFO: ms2_error      : 10.0
0:31:32.335863 INFO: fwhm_rt        : 3.0
0:31:32.335903 INFO: quant_window   : 3
0:31:32.335953 INFO: ==============================================
0:31:32.917046 INFO: performing precursor FDR with 40 features
0:31:32.917162 INFO: Decoy channel: -1
0:31:32.917189 INFO: Competetive: True
0:31:32.958635 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:32.993505 INFO: Using random state 120421 for train-test-split
0:31:34.931047 INFO: Test AUC: 0.590
0:31:34.931168 INFO: Train AUC: 0.611
0:31:34.931199 INFO: AUC difference: 3.46%
0:31:35.183008 INFO: Resetting torch num_threads to 80
0:31:35.189665 PROGRESS: === Extracted 145619 precursors and 569467 fragments ===
0:31:35.190008 INFO: === FDR correction performed with classifier version 9 ===
0:31:35.190459 PROGRESS: ============================= Precursor FDR =============================
0:31:35.190547 PROGRESS: Total precursors accumulated: 256
0:31:35.190606 PROGRESS: Target precursors: 254 (99.22%)
0:31:35.190656 PROGRESS: Decoy precursors: 2 (0.78%)
0:31:35.190700 PROGRESS: 
0:31:35.190743 PROGRESS: Precursor Summary:
0:31:35.191626 PROGRESS: Channel   0:	 0.050 FDR:   254; 0.010 FDR:   254; 0.001 FDR:   200
0:31:35.191715 PROGRESS: 
0:31:35.191773 PROGRESS: Protein Summary:
0:31:35.192801 PROGRESS: Channel   0:	 0.050 FDR:   246; 0.010 FDR:   246; 0.001 FDR:   194
0:31:35.192911 PROGRESS: =========================================================================
0:31:35.195213 INFO: Target number of precursors reached.
0:31:35.234962 INFO: fragments_df: keeping 2808 of 569467 [sum(precursor_idx_mask)=5785 sum(mass_error_mask)=569467 stop_rank=2808
0:31:35.369608 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:35.489716 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:35.862357 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:35.862760 INFO: Using score_cutoff 13.584130270957946 (fac=0.99, q=1)
0:31:35.863036 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:35.863124 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:35.863182 INFO: Updating optimization_manager: score_cutoff        : 14.528815887737274 -> 13.584130270957946
0:31:35.863236 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:35.893631 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:35.960522 INFO: === checking if optimization conditions were reached ===
0:31:35.960776 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:31:35.963045 INFO: Updating optimization_manager: rt_error            : 78.04477952768723 -> 62.53815305867439
0:31:35.963161 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 62.5382.
0:31:35.963238 INFO: ==============================================
0:31:35.963318 INFO: Starting optimization step 4.
0:31:35.963382 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:35.963453 INFO: Using ng extraction backend
0:31:35.963518 PROGRESS: Extracting batch of 50293 precursors
0:31:36.053475 INFO: === Search parameters used ===
0:31:36.053724 INFO: rt_error       : 62.53815305867439
0:31:36.053780 INFO: mobility_error : 0.1
0:31:36.053826 INFO: num_candidates : 3
0:31:36.053869 INFO: ms1_error      : 30
0:31:36.053911 INFO: ms2_error      : 10.0
0:31:36.053951 INFO: fwhm_rt        : 3.0
0:31:36.054016 INFO: quant_window   : 3
0:31:36.054060 INFO: ==============================================
0:31:36.639222 INFO: performing precursor FDR with 40 features
0:31:36.639336 INFO: Decoy channel: -1
0:31:36.639363 INFO: Competetive: True
0:31:36.680238 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:36.714465 INFO: Using random state 120421 for train-test-split
0:31:38.504335 INFO: Test AUC: 0.595
0:31:38.504452 INFO: Train AUC: 0.609
0:31:38.504481 INFO: AUC difference: 2.24%
0:31:38.764305 INFO: Resetting torch num_threads to 80
0:31:38.770829 PROGRESS: === Extracted 143289 precursors and 536988 fragments ===
0:31:38.771174 INFO: === FDR correction performed with classifier version 9 ===
0:31:38.771617 PROGRESS: ============================= Precursor FDR =============================
0:31:38.771706 PROGRESS: Total precursors accumulated: 240
0:31:38.771766 PROGRESS: Target precursors: 238 (99.17%)
0:31:38.771815 PROGRESS: Decoy precursors: 2 (0.83%)
0:31:38.771859 PROGRESS: 
0:31:38.771899 PROGRESS: Precursor Summary:
0:31:38.772774 PROGRESS: Channel   0:	 0.050 FDR:   238; 0.010 FDR:   238; 0.001 FDR:   227
0:31:38.772868 PROGRESS: 
0:31:38.772926 PROGRESS: Protein Summary:
0:31:38.773955 PROGRESS: Channel   0:	 0.050 FDR:   231; 0.010 FDR:   231; 0.001 FDR:   221
0:31:38.774043 PROGRESS: =========================================================================
0:31:38.776205 INFO: Target number of precursors reached.
0:31:38.812693 INFO: fragments_df: keeping 2610 of 536988 [sum(precursor_idx_mask)=5290 sum(mass_error_mask)=536988 stop_rank=2610
0:31:38.970857 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:39.086568 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:39.430186 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:39.430590 INFO: Using score_cutoff 13.368178561878205 (fac=0.99, q=1)
0:31:39.430869 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:39.430948 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:39.431004 INFO: Updating optimization_manager: score_cutoff        : 13.584130270957946 -> 13.368178561878205
0:31:39.431058 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:39.462005 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:39.526421 INFO: === checking if optimization conditions were reached ===
0:31:39.526688 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:31:39.528945 INFO: Updating optimization_manager: rt_error            : 62.53815305867439 -> 47.4805627012549
0:31:39.529063 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 47.4806.
0:31:39.529140 INFO: ==============================================
0:31:39.529219 INFO: Starting optimization step 5.
0:31:39.529286 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:39.529357 INFO: Using ng extraction backend
0:31:39.529425 PROGRESS: Extracting batch of 50293 precursors
0:31:39.618752 INFO: === Search parameters used ===
0:31:39.619005 INFO: rt_error       : 47.4805627012549
0:31:39.619060 INFO: mobility_error : 0.1
0:31:39.619106 INFO: num_candidates : 3
0:31:39.619150 INFO: ms1_error      : 30
0:31:39.619206 INFO: ms2_error      : 10.0
0:31:39.619248 INFO: fwhm_rt        : 3.0
0:31:39.619289 INFO: quant_window   : 3
0:31:39.619327 INFO: ==============================================
0:31:40.137516 INFO: performing precursor FDR with 40 features
0:31:40.137635 INFO: Decoy channel: -1
0:31:40.137661 INFO: Competetive: True
0:31:40.174460 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:40.207680 INFO: Using random state 120421 for train-test-split
0:31:41.957663 INFO: Test AUC: 0.594
0:31:41.957785 INFO: Train AUC: 0.610
0:31:41.957816 INFO: AUC difference: 2.55%
0:31:42.212041 INFO: Resetting torch num_threads to 80
0:31:42.218343 PROGRESS: === Extracted 133621 precursors and 480083 fragments ===
0:31:42.218687 INFO: === FDR correction performed with classifier version 9 ===
0:31:42.219117 PROGRESS: ============================= Precursor FDR =============================
0:31:42.219199 PROGRESS: Total precursors accumulated: 246
0:31:42.219255 PROGRESS: Target precursors: 244 (99.19%)
0:31:42.219302 PROGRESS: Decoy precursors: 2 (0.81%)
0:31:42.219346 PROGRESS: 
0:31:42.219387 PROGRESS: Precursor Summary:
0:31:42.220247 PROGRESS: Channel   0:	 0.050 FDR:   244; 0.010 FDR:   244; 0.001 FDR:   183
0:31:42.220331 PROGRESS: 
0:31:42.220385 PROGRESS: Protein Summary:
0:31:42.221416 PROGRESS: Channel   0:	 0.050 FDR:   235; 0.010 FDR:   235; 0.001 FDR:   179
0:31:42.221503 PROGRESS: =========================================================================
0:31:42.223511 INFO: Target number of precursors reached.
0:31:42.255933 INFO: fragments_df: keeping 2484 of 480083 [sum(precursor_idx_mask)=4955 sum(mass_error_mask)=480083 stop_rank=2484
0:31:42.389813 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:42.510075 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:42.836756 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:42.837172 INFO: Using score_cutoff 13.217362762355805 (fac=0.99, q=1)
0:31:42.837445 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:42.837519 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:42.837570 INFO: Updating optimization_manager: score_cutoff        : 13.368178561878205 -> 13.217362762355805
0:31:42.837620 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:42.869243 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:42.936380 INFO: === checking if optimization conditions were reached ===
0:31:42.936656 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:31:42.938968 INFO: Updating optimization_manager: rt_error            : 47.4805627012549 -> 35.62713220762808
0:31:42.939092 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 35.6271.
0:31:42.939168 INFO: ==============================================
0:31:42.939250 INFO: Starting optimization step 6.
0:31:42.939317 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:42.939388 INFO: Using ng extraction backend
0:31:42.939457 PROGRESS: Extracting batch of 50293 precursors
0:31:43.029504 INFO: === Search parameters used ===
0:31:43.029753 INFO: rt_error       : 35.62713220762808
0:31:43.029806 INFO: mobility_error : 0.1
0:31:43.029863 INFO: num_candidates : 3
0:31:43.029907 INFO: ms1_error      : 30
0:31:43.029948 INFO: ms2_error      : 10.0
0:31:43.029992 INFO: fwhm_rt        : 3.0
0:31:43.030030 INFO: quant_window   : 3
0:31:43.030067 INFO: ==============================================
0:31:43.545391 INFO: performing precursor FDR with 40 features
0:31:43.545510 INFO: Decoy channel: -1
0:31:43.545541 INFO: Competetive: True
0:31:43.584146 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:43.617625 INFO: Using random state 120421 for train-test-split
0:31:45.356408 INFO: Test AUC: 0.593
0:31:45.356530 INFO: Train AUC: 0.608
0:31:45.356560 INFO: AUC difference: 2.58%
0:31:45.615034 INFO: Resetting torch num_threads to 80
0:31:45.621387 PROGRESS: === Extracted 133769 precursors and 481022 fragments ===
0:31:45.621726 INFO: === FDR correction performed with classifier version 9 ===
0:31:45.622168 PROGRESS: ============================= Precursor FDR =============================
0:31:45.622249 PROGRESS: Total precursors accumulated: 260
0:31:45.622305 PROGRESS: Target precursors: 258 (99.23%)
0:31:45.622354 PROGRESS: Decoy precursors: 2 (0.77%)
0:31:45.622397 PROGRESS: 
0:31:45.622439 PROGRESS: Precursor Summary:
0:31:45.623297 PROGRESS: Channel   0:	 0.050 FDR:   258; 0.010 FDR:   258; 0.001 FDR:   177
0:31:45.623381 PROGRESS: 
0:31:45.623434 PROGRESS: Protein Summary:
0:31:45.624436 PROGRESS: Channel   0:	 0.050 FDR:   252; 0.010 FDR:   252; 0.001 FDR:   174
0:31:45.624520 PROGRESS: =========================================================================
0:31:45.626554 INFO: Target number of precursors reached.
0:31:45.658626 INFO: fragments_df: keeping 2550 of 481022 [sum(precursor_idx_mask)=5177 sum(mass_error_mask)=481022 stop_rank=2550
0:31:45.792565 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:45.911813 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:46.246890 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:46.247293 INFO: Using score_cutoff 10.820579263687135 (fac=0.99, q=1)
0:31:46.247571 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:46.247648 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:46.247702 INFO: Updating optimization_manager: score_cutoff        : 13.217362762355805 -> 10.820579263687135
0:31:46.247755 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:46.279851 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:46.351682 INFO: === checking if optimization conditions were reached ===
0:31:46.351958 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:31:46.354231 INFO: Updating optimization_manager: rt_error            : 35.62713220762808 -> 33.38592804383585
0:31:46.354349 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 33.3859.
0:31:46.354425 INFO: ==============================================
0:31:46.354504 INFO: Starting optimization step 7.
0:31:46.354571 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:46.354638 INFO: Using ng extraction backend
0:31:46.354702 PROGRESS: Extracting batch of 50293 precursors
0:31:46.444659 INFO: === Search parameters used ===
0:31:46.444933 INFO: rt_error       : 33.38592804383585
0:31:46.444990 INFO: mobility_error : 0.1
0:31:46.445035 INFO: num_candidates : 3
0:31:46.445078 INFO: ms1_error      : 30
0:31:46.445118 INFO: ms2_error      : 10.0
0:31:46.445157 INFO: fwhm_rt        : 3.0
0:31:46.445196 INFO: quant_window   : 3
0:31:46.445234 INFO: ==============================================
0:31:46.978191 INFO: performing precursor FDR with 40 features
0:31:46.978306 INFO: Decoy channel: -1
0:31:46.978333 INFO: Competetive: True
0:31:47.015445 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:47.049429 INFO: Using random state 120421 for train-test-split
0:31:48.690934 INFO: Test AUC: 0.591
0:31:48.691053 INFO: Train AUC: 0.609
0:31:48.691083 INFO: AUC difference: 2.97%
0:31:48.944779 INFO: Resetting torch num_threads to 80
0:31:48.951781 PROGRESS: === Extracted 133978 precursors and 485430 fragments ===
0:31:48.952149 INFO: === FDR correction performed with classifier version 9 ===
0:31:48.952572 PROGRESS: ============================= Precursor FDR =============================
0:31:48.952654 PROGRESS: Total precursors accumulated: 192
0:31:48.952713 PROGRESS: Target precursors: 191 (99.48%)
0:31:48.952764 PROGRESS: Decoy precursors: 1 (0.52%)
0:31:48.952816 PROGRESS: 
0:31:48.952862 PROGRESS: Precursor Summary:
0:31:48.953703 PROGRESS: Channel   0:	 0.050 FDR:   191; 0.010 FDR:   191; 0.001 FDR:   184
0:31:48.953792 PROGRESS: 
0:31:48.953846 PROGRESS: Protein Summary:
0:31:48.954833 PROGRESS: Channel   0:	 0.050 FDR:   186; 0.010 FDR:   186; 0.001 FDR:   181
0:31:48.954921 PROGRESS: =========================================================================
0:31:48.957044 INFO: Target number of precursors not reached yet.
0:31:49.096458 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:49.129224 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:49.197530 INFO: === skipping optimization until target number of precursors are found ===
0:31:49.197782 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
0:31:49.197883 INFO: Starting optimization step 8.
0:31:49.197955 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:31:49.198030 INFO: Using ng extraction backend
0:31:49.198112 PROGRESS: Extracting batch of 50691 precursors
0:31:49.288881 INFO: === Search parameters used ===
0:31:49.289125 INFO: rt_error       : 33.38592804383585
0:31:49.289183 INFO: mobility_error : 0.1
0:31:49.289229 INFO: num_candidates : 3
0:31:49.289272 INFO: ms1_error      : 30
0:31:49.289311 INFO: ms2_error      : 10.0
0:31:49.289351 INFO: fwhm_rt        : 3.0
0:31:49.289390 INFO: quant_window   : 3
0:31:49.289427 INFO: ==============================================
0:31:49.881960 INFO: performing precursor FDR with 40 features
0:31:49.882072 INFO: Decoy channel: -1
0:31:49.882099 INFO: Competetive: True
0:31:49.990418 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:50.083184 INFO: Using random state 120421 for train-test-split
0:31:53.874248 INFO: Test AUC: 0.598
0:31:53.874364 INFO: Train AUC: 0.605
0:31:53.874396 INFO: AUC difference: 1.22%
0:31:54.175531 INFO: Resetting torch num_threads to 80
0:31:54.215098 PROGRESS: === Extracted 269433 precursors and 973311 fragments ===
0:31:54.215674 INFO: === FDR correction performed with classifier version 9 ===
0:31:54.216310 PROGRESS: ============================= Precursor FDR =============================
0:31:54.216398 PROGRESS: Total precursors accumulated: 557
0:31:54.216469 PROGRESS: Target precursors: 552 (99.10%)
0:31:54.216522 PROGRESS: Decoy precursors: 5 (0.90%)
0:31:54.216570 PROGRESS: 
0:31:54.216614 PROGRESS: Precursor Summary:
0:31:54.217611 PROGRESS: Channel   0:	 0.050 FDR:   552; 0.010 FDR:   552; 0.001 FDR:   375
0:31:54.217704 PROGRESS: 
0:31:54.217764 PROGRESS: Protein Summary:
0:31:54.218969 PROGRESS: Channel   0:	 0.050 FDR:   516; 0.010 FDR:   516; 0.001 FDR:   350
0:31:54.219060 PROGRESS: =========================================================================
0:31:54.223508 INFO: Target number of precursors reached.
0:31:54.294084 INFO: fragments_df: keeping 5000 of 973311 [sum(precursor_idx_mask)=11068 sum(mass_error_mask)=973311 stop_rank=5000
0:31:54.434910 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:54.628422 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:55.391173 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:55.391600 INFO: Using score_cutoff 11.409853345298766 (fac=0.99, q=1)
0:31:55.391883 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:55.391959 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:55.392012 INFO: Updating optimization_manager: score_cutoff        : 10.820579263687135 -> 11.409853345298766
0:31:55.392064 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:55.423721 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:55.487102 INFO: === checking if optimization conditions were reached ===
0:31:55.487381 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
0:31:55.489868 INFO: Updating optimization_manager: rt_error            : 33.38592804383585 -> 32.73235839896531
0:31:55.489983 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 32.7324.
0:31:55.490060 INFO: ==============================================
0:31:55.490141 INFO: Starting optimization step 9.
0:31:55.490207 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:31:55.490278 INFO: Using ng extraction backend
0:31:55.490345 PROGRESS: Extracting batch of 50293 precursors
0:31:55.580144 INFO: === Search parameters used ===
0:31:55.580389 INFO: rt_error       : 32.73235839896531
0:31:55.580442 INFO: mobility_error : 0.1
0:31:55.580487 INFO: num_candidates : 3
0:31:55.580529 INFO: ms1_error      : 30
0:31:55.580569 INFO: ms2_error      : 10.0
0:31:55.580608 INFO: fwhm_rt        : 3.0
0:31:55.580649 INFO: quant_window   : 3
0:31:55.580687 INFO: ==============================================
0:31:56.109963 INFO: performing precursor FDR with 40 features
0:31:56.110073 INFO: Decoy channel: -1
0:31:56.110099 INFO: Competetive: True
0:31:56.149347 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:56.182559 INFO: Using random state 120421 for train-test-split
0:31:57.923456 INFO: Test AUC: 0.589
0:31:57.923574 INFO: Train AUC: 0.606
0:31:57.923604 INFO: AUC difference: 2.84%
0:31:58.176454 INFO: Resetting torch num_threads to 80
0:31:58.182849 PROGRESS: === Extracted 134179 precursors and 487315 fragments ===
0:31:58.183203 INFO: === FDR correction performed with classifier version 9 ===
0:31:58.183659 PROGRESS: ============================= Precursor FDR =============================
0:31:58.183746 PROGRESS: Total precursors accumulated: 237
0:31:58.183806 PROGRESS: Target precursors: 235 (99.16%)
0:31:58.183855 PROGRESS: Decoy precursors: 2 (0.84%)
0:31:58.183901 PROGRESS: 
0:31:58.183944 PROGRESS: Precursor Summary:
0:31:58.184827 PROGRESS: Channel   0:	 0.050 FDR:   235; 0.010 FDR:   235; 0.001 FDR:   172
0:31:58.184916 PROGRESS: 
0:31:58.184979 PROGRESS: Protein Summary:
0:31:58.185973 PROGRESS: Channel   0:	 0.050 FDR:   229; 0.010 FDR:   229; 0.001 FDR:   169
0:31:58.186062 PROGRESS: =========================================================================
0:31:58.188166 INFO: Target number of precursors reached.
0:31:58.225133 INFO: fragments_df: keeping 2384 of 487315 [sum(precursor_idx_mask)=4751 sum(mass_error_mask)=487315 stop_rank=2384
0:31:58.359991 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:58.489188 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:58.804574 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:58.804983 INFO: Using score_cutoff 12.44514872303009 (fac=0.99, q=1)
0:31:58.805265 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:58.805342 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:58.805393 INFO: Updating optimization_manager: score_cutoff        : 11.409853345298766 -> 12.44514872303009
0:31:58.805452 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:58.837510 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:58.903764 INFO: === checking if optimization conditions were reached ===
0:31:58.904049 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
0:31:58.905398 INFO: Updating optimization_manager: rt_error            : 32.73235839896531 -> 33.38592804383585
0:31:58.905545 INFO: Updating optimization_manager: classifier_version  : 9 -> 18
0:31:58.905653 INFO: Updating optimization_manager: score_cutoff        : 12.44514872303009 -> 11.409853345298766
0:31:58.905752 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:58.905848 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:58.905948 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 33.3859 found after 9 searches.
0:31:58.906026 INFO: ==============================================
0:31:58.906111 PROGRESS: Optimization finished for rt_error.
0:31:59.056373 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:59.089161 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:59.186342 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:31:59.186577 PROGRESS: ==============================================
0:31:59.186659 PROGRESS: ms2_error      : 10.0000
0:31:59.186723 PROGRESS: rt_error       : 33.3859
0:31:59.186780 PROGRESS: ==============================================
0:31:59.187435 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:32:07.202092 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:32:24.898885 INFO: Using ng extraction backend
0:32:24.899192 PROGRESS: Extracting batch of 12001526 precursors
0:32:40.682181 INFO: === Search parameters used ===
0:32:40.682508 INFO: rt_error       : 33.38592804383585
0:32:40.682572 INFO: mobility_error : 0.1
0:32:40.682619 INFO: num_candidates : 3
0:32:40.682663 INFO: ms1_error      : 30
0:32:40.682708 INFO: ms2_error      : 10.0
0:32:40.682764 INFO: fwhm_rt        : 3.0
0:32:40.682816 INFO: quant_window   : 3
0:32:40.682858 INFO: ==============================================
0:33:03.484270 INFO: Removed 24791613 precursors with score below cutoff 11.409853345298766
0:33:11.059442 INFO: performing precursor FDR with 40 features
0:33:11.059562 INFO: Decoy channel: -1
0:33:11.059590 INFO: Competetive: True
0:33:11.864384 INFO: Setting torch num_threads to 2 for FDR classification task
0:33:14.943501 INFO: Using random state 790 for train-test-split
0:35:09.360191 INFO: Test AUC: 0.624
0:35:09.360326 INFO: Train AUC: 0.625
0:35:09.360359 INFO: AUC difference: 0.22%
0:35:12.103960 INFO: Resetting torch num_threads to 80
0:35:13.792048 PROGRESS: ============================= Precursor FDR =============================
0:35:13.792749 PROGRESS: Total precursors accumulated: 74,140
0:35:13.792825 PROGRESS: Target precursors: 73,406 (99.01%)
0:35:13.792892 PROGRESS: Decoy precursors: 734 (0.99%)
0:35:13.792948 PROGRESS: 
0:35:13.792999 PROGRESS: Precursor Summary:
0:35:13.817575 PROGRESS: Channel   0:	 0.050 FDR: 73,406; 0.010 FDR: 73,406; 0.001 FDR: 52,437
0:35:13.817789 PROGRESS: 
0:35:13.817863 PROGRESS: Protein Summary:
0:35:13.856160 PROGRESS: Channel   0:	 0.050 FDR: 12,233; 0.010 FDR: 12,233; 0.001 FDR: 9,131
0:35:13.856373 PROGRESS: =========================================================================
0:35:13.910801 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/psm.parquet
0:35:14.080631 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.parquet
0:35:14.297168 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:35:14.892208 PROGRESS: 
0:35:14.892348 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark/quant
0:35:14.892426 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/figures
0:35:14.892608 INFO: Initializing TimingManager
0:35:14.893041 INFO: Initializing RawFileManager
0:35:26.462524 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.
0:35:26.466818 INFO: Determining DIA cycle
0:35:26.483133 INFO: Found cycle with start 0.00 min and length 300.
0:35:26.657407 INFO: RT (min)            : 0.0 - 26.9
0:35:26.657508 INFO: RT duration (sec)   : 1611.2
0:35:26.657536 INFO: RT duration (min)   : 26.9
0:35:26.657559 INFO: Cycle len (scans)   : 300
0:35:26.657579 INFO: Cycle len (sec)     : 1.65
0:35:26.657597 INFO: Number of cycles    : 977
0:35:26.657615 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:35:26.657642 INFO: Creating DIA data object took: 11.764484405517578
0:35:27.359530 INFO: Creating DIA data NG object took: 0.7017838954925537
0:35:28.615998 INFO: Initializing CalibrationManager
0:35:28.616257 INFO: Setting up calibration estimators ..
0:35:28.616314 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:35:28.616387 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'}' ..
0:35:28.616462 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:35:28.616508 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:35:28.616558 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}}' ..
0:35:28.616603 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:35:28.616645 INFO: Done setting up calibration estimators.
0:35:28.616836 INFO: Initializing OptimizationManager
0:35:28.616996 INFO: initial parameter: ms1_error = 30
0:35:28.617046 INFO: initial parameter: ms2_error = 30
0:35:28.617090 INFO: initial parameter: rt_error = 805.6002197265625
0:35:28.617130 INFO: initial parameter: mobility_error = 0.1
0:35:28.617170 INFO: initial parameter: num_candidates = 1
0:35:28.617213 INFO: initial parameter: fwhm_rt = 5
0:35:28.617254 INFO: initial parameter: fwhm_mobility = 0.01
0:35:28.617293 INFO: initial parameter: score_cutoff = 0
0:35:28.617330 INFO: initial parameter: classifier_version = -1
0:35:28.617393 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:35:28.617595 INFO: FDRManager: loading saved state not requested, will be initialized.
0:35:28.617630 INFO: Initializing FDRManager
0:35:28.617666 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:35:30.054600 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:35:30.932475 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:35:30.932860 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
0:35:30.932961 PROGRESS: Starting initial search for precursors.
0:35:30.933040 INFO: Starting optimization step 0.
0:35:30.933100 PROGRESS: === Extracting elution groups 0 to 200 ===
0:35:30.933156 INFO: Using ng extraction backend
0:35:30.933219 PROGRESS: Extracting batch of 396 precursors
0:35:30.935152 INFO: === Search parameters used ===
0:35:30.935245 INFO: rt_error       : 805.6002197265625
0:35:30.935293 INFO: mobility_error : 0.1
0:35:30.935336 INFO: num_candidates : 1
0:35:30.935376 INFO: ms1_error      : 30
0:35:30.935416 INFO: ms2_error      : 30
0:35:30.935454 INFO: fwhm_rt        : 5
0:35:30.935492 INFO: quant_window   : 3
0:35:30.935531 INFO: ==============================================
0:35:30.961053 INFO: performing precursor FDR with 40 features
0:35:30.961118 INFO: Decoy channel: -1
0:35:30.961150 INFO: Competetive: True
0:35:30.962057 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:30.963984 INFO: Using random state 905059 for train-test-split
0:35:30.970409 INFO: Test AUC: 0.496
0:35:30.970463 INFO: Train AUC: 0.493
0:35:30.970500 INFO: AUC difference: 0.63%
0:35:31.176926 INFO: Resetting torch num_threads to 80
0:35:31.178228 PROGRESS: === Extracted 393 precursors and 1847 fragments ===
0:35:31.178580 INFO: === FDR correction performed with classifier version -1 ===
0:35:31.179028 PROGRESS: ============================= Precursor FDR =============================
0:35:31.179119 PROGRESS: Total precursors accumulated: 0
0:35:31.179191 PROGRESS: Target precursors: 0 (0.00%)
0:35:31.179251 PROGRESS: Decoy precursors: 0 (0.00%)
0:35:31.179307 PROGRESS: 
0:35:31.179363 PROGRESS: Precursor Summary:
0:35:31.179490 PROGRESS: 
0:35:31.179561 PROGRESS: Protein Summary:
0:35:31.179648 PROGRESS: =========================================================================
0:35:31.179854 INFO: Target number of precursors not reached yet.
0:35:31.244174 INFO: Starting optimization step 1.
0:35:31.244387 PROGRESS: === Extracting elution groups 200 to 600 ===
0:35:31.244484 INFO: Using ng extraction backend
0:35:31.244558 PROGRESS: Extracting batch of 786 precursors
0:35:31.247208 INFO: === Search parameters used ===
0:35:31.247317 INFO: rt_error       : 805.6002197265625
0:35:31.247382 INFO: mobility_error : 0.1
0:35:31.247440 INFO: num_candidates : 1
0:35:31.247493 INFO: ms1_error      : 30
0:35:31.247545 INFO: ms2_error      : 30
0:35:31.247598 INFO: fwhm_rt        : 5
0:35:31.247649 INFO: quant_window   : 3
0:35:31.247698 INFO: ==============================================
0:35:31.306628 INFO: performing precursor FDR with 40 features
0:35:31.306710 INFO: Decoy channel: -1
0:35:31.306743 INFO: Competetive: True
0:35:31.309511 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:31.310984 INFO: Using random state 828289 for train-test-split
0:35:31.318899 INFO: Test AUC: 0.432
0:35:31.318966 INFO: Train AUC: 0.520
0:35:31.319004 INFO: AUC difference: 17.01%
0:35:31.319032 WARNING: AUC difference > 5%. This may indicate overfitting.
0:35:31.521416 INFO: Resetting torch num_threads to 80
0:35:31.523443 PROGRESS: === Extracted 1172 precursors and 5527 fragments ===
0:35:31.523810 INFO: === FDR correction performed with classifier version -1 ===
0:35:31.524260 PROGRESS: ============================= Precursor FDR =============================
0:35:31.524352 PROGRESS: Total precursors accumulated: 0
0:35:31.524423 PROGRESS: Target precursors: 0 (0.00%)
0:35:31.524484 PROGRESS: Decoy precursors: 0 (0.00%)
0:35:31.524540 PROGRESS: 
0:35:31.524594 PROGRESS: Precursor Summary:
0:35:31.524721 PROGRESS: 
0:35:31.524795 PROGRESS: Protein Summary:
0:35:31.524906 PROGRESS: =========================================================================
0:35:31.525155 INFO: Target number of precursors not reached yet.
0:35:31.591777 INFO: Starting optimization step 2.
0:35:31.591984 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:35:31.592085 INFO: Using ng extraction backend
0:35:31.592159 PROGRESS: Extracting batch of 1592 precursors
0:35:31.596285 INFO: === Search parameters used ===
0:35:31.596403 INFO: rt_error       : 805.6002197265625
0:35:31.596469 INFO: mobility_error : 0.1
0:35:31.596526 INFO: num_candidates : 1
0:35:31.596579 INFO: ms1_error      : 30
0:35:31.596632 INFO: ms2_error      : 30
0:35:31.596685 INFO: fwhm_rt        : 5
0:35:31.596735 INFO: quant_window   : 3
0:35:31.596785 INFO: ==============================================
0:35:31.629147 INFO: performing precursor FDR with 40 features
0:35:31.629245 INFO: Decoy channel: -1
0:35:31.629270 INFO: Competetive: True
0:35:31.633502 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:31.635291 INFO: Using random state 562294 for train-test-split
0:35:31.646252 INFO: Test AUC: 0.466
0:35:31.646309 INFO: Train AUC: 0.512
0:35:31.646338 INFO: AUC difference: 9.05%
0:35:31.646360 WARNING: AUC difference > 5%. This may indicate overfitting.
0:35:31.852512 INFO: Resetting torch num_threads to 80
0:35:31.854944 PROGRESS: === Extracted 2754 precursors and 13075 fragments ===
0:35:31.855276 INFO: === FDR correction performed with classifier version -1 ===
0:35:31.855695 PROGRESS: ============================= Precursor FDR =============================
0:35:31.855778 PROGRESS: Total precursors accumulated: 0
0:35:31.855835 PROGRESS: Target precursors: 0 (0.00%)
0:35:31.855884 PROGRESS: Decoy precursors: 0 (0.00%)
0:35:31.855928 PROGRESS: 
0:35:31.855980 PROGRESS: Precursor Summary:
0:35:31.856087 PROGRESS: 
0:35:31.856146 PROGRESS: Protein Summary:
0:35:31.856215 PROGRESS: =========================================================================
0:35:31.856419 INFO: Target number of precursors not reached yet.
0:35:31.925561 INFO: Starting optimization step 3.
0:35:31.925767 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:35:31.925846 INFO: Using ng extraction backend
0:35:31.925905 PROGRESS: Extracting batch of 3177 precursors
0:35:31.932722 INFO: === Search parameters used ===
0:35:31.932871 INFO: rt_error       : 805.6002197265625
0:35:31.932922 INFO: mobility_error : 0.1
0:35:31.932970 INFO: num_candidates : 1
0:35:31.933016 INFO: ms1_error      : 30
0:35:31.933057 INFO: ms2_error      : 30
0:35:31.933097 INFO: fwhm_rt        : 5
0:35:31.933136 INFO: quant_window   : 3
0:35:31.933175 INFO: ==============================================
0:35:31.977653 INFO: performing precursor FDR with 40 features
0:35:31.977739 INFO: Decoy channel: -1
0:35:31.977764 INFO: Competetive: True
0:35:31.981750 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:31.983942 INFO: Using random state 2327 for train-test-split
0:35:32.002554 INFO: Test AUC: 0.500
0:35:32.002624 INFO: Train AUC: 0.500
0:35:32.002652 INFO: AUC difference: 0.17%
0:35:32.209306 INFO: Resetting torch num_threads to 80
0:35:32.212491 PROGRESS: === Extracted 5901 precursors and 27847 fragments ===
0:35:32.212834 INFO: === FDR correction performed with classifier version -1 ===
0:35:32.213287 PROGRESS: ============================= Precursor FDR =============================
0:35:32.213373 PROGRESS: Total precursors accumulated: 1
0:35:32.213434 PROGRESS: Target precursors: 1 (100.00%)
0:35:32.213485 PROGRESS: Decoy precursors: 0 (0.00%)
0:35:32.213528 PROGRESS: 
0:35:32.213570 PROGRESS: Precursor Summary:
0:35:32.214458 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:35:32.214545 PROGRESS: 
0:35:32.214598 PROGRESS: Protein Summary:
0:35:32.215574 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:35:32.215660 PROGRESS: =========================================================================
0:35:32.215906 INFO: Target number of precursors not reached yet.
0:35:32.289093 INFO: Starting optimization step 4.
0:35:32.289312 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:35:32.289388 INFO: Using ng extraction backend
0:35:32.289451 PROGRESS: Extracting batch of 6340 precursors
0:35:32.301624 INFO: === Search parameters used ===
0:35:32.301752 INFO: rt_error       : 805.6002197265625
0:35:32.301801 INFO: mobility_error : 0.1
0:35:32.301845 INFO: num_candidates : 1
0:35:32.301885 INFO: ms1_error      : 30
0:35:32.301924 INFO: ms2_error      : 30
0:35:32.301964 INFO: fwhm_rt        : 5
0:35:32.302015 INFO: quant_window   : 3
0:35:32.302058 INFO: ==============================================
0:35:32.373354 INFO: performing precursor FDR with 40 features
0:35:32.373450 INFO: Decoy channel: -1
0:35:32.373475 INFO: Competetive: True
0:35:32.380208 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:32.383792 INFO: Using random state 874829 for train-test-split
0:35:32.420774 INFO: Test AUC: 0.494
0:35:32.420888 INFO: Train AUC: 0.497
0:35:32.420917 INFO: AUC difference: 0.46%
0:35:32.636458 INFO: Resetting torch num_threads to 80
0:35:32.640725 PROGRESS: === Extracted 12165 precursors and 57133 fragments ===
0:35:32.641097 INFO: === FDR correction performed with classifier version -1 ===
0:35:32.641550 PROGRESS: ============================= Precursor FDR =============================
0:35:32.641636 PROGRESS: Total precursors accumulated: 4
0:35:32.641692 PROGRESS: Target precursors: 4 (100.00%)
0:35:32.641741 PROGRESS: Decoy precursors: 0 (0.00%)
0:35:32.641784 PROGRESS: 
0:35:32.641826 PROGRESS: Precursor Summary:
0:35:32.642715 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:35:32.642802 PROGRESS: 
0:35:32.642855 PROGRESS: Protein Summary:
0:35:32.643839 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:35:32.643924 PROGRESS: =========================================================================
0:35:32.644253 INFO: Target number of precursors not reached yet.
0:35:32.725526 INFO: Starting optimization step 5.
0:35:32.725747 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:35:32.725825 INFO: Using ng extraction backend
0:35:32.725886 PROGRESS: Extracting batch of 12663 precursors
0:35:32.748888 INFO: === Search parameters used ===
0:35:32.749062 INFO: rt_error       : 805.6002197265625
0:35:32.749113 INFO: mobility_error : 0.1
0:35:32.749157 INFO: num_candidates : 1
0:35:32.749197 INFO: ms1_error      : 30
0:35:32.749237 INFO: ms2_error      : 30
0:35:32.749275 INFO: fwhm_rt        : 5
0:35:32.749314 INFO: quant_window   : 3
0:35:32.749351 INFO: ==============================================
0:35:32.872831 INFO: performing precursor FDR with 40 features
0:35:32.872942 INFO: Decoy channel: -1
0:35:32.872967 INFO: Competetive: True
0:35:32.882585 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:32.888283 INFO: Using random state 882412 for train-test-split
0:35:33.128065 INFO: Test AUC: 0.504
0:35:33.128162 INFO: Train AUC: 0.495
0:35:33.128191 INFO: AUC difference: 1.85%
0:35:33.347458 INFO: Resetting torch num_threads to 80
0:35:33.353343 PROGRESS: === Extracted 24723 precursors and 116071 fragments ===
0:35:33.353776 INFO: === FDR correction performed with classifier version -1 ===
0:35:33.354234 PROGRESS: ============================= Precursor FDR =============================
0:35:33.354318 PROGRESS: Total precursors accumulated: 0
0:35:33.354376 PROGRESS: Target precursors: 0 (0.00%)
0:35:33.354429 PROGRESS: Decoy precursors: 0 (0.00%)
0:35:33.354474 PROGRESS: 
0:35:33.354518 PROGRESS: Precursor Summary:
0:35:33.354624 PROGRESS: 
0:35:33.354683 PROGRESS: Protein Summary:
0:35:33.354753 PROGRESS: =========================================================================
0:35:33.355166 INFO: Target number of precursors not reached yet.
0:35:33.452441 INFO: Starting optimization step 6.
0:35:33.452684 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:35:33.452784 INFO: Using ng extraction backend
0:35:33.452860 PROGRESS: Extracting batch of 25339 precursors
0:35:33.497446 INFO: === Search parameters used ===
0:35:33.497641 INFO: rt_error       : 805.6002197265625
0:35:33.497692 INFO: mobility_error : 0.1
0:35:33.497736 INFO: num_candidates : 1
0:35:33.497782 INFO: ms1_error      : 30
0:35:33.497825 INFO: ms2_error      : 30
0:35:33.497866 INFO: fwhm_rt        : 5
0:35:33.497906 INFO: quant_window   : 3
0:35:33.497945 INFO: ==============================================
0:35:33.712906 INFO: performing precursor FDR with 40 features
0:35:33.713017 INFO: Decoy channel: -1
0:35:33.713043 INFO: Competetive: True
0:35:33.732847 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:33.744122 INFO: Using random state 603510 for train-test-split
0:35:34.317150 INFO: Test AUC: 0.542
0:35:34.317260 INFO: Train AUC: 0.544
0:35:34.317289 INFO: AUC difference: 0.44%
0:35:34.546685 INFO: Resetting torch num_threads to 80
0:35:34.556016 PROGRESS: === Extracted 49768 precursors and 233056 fragments ===
0:35:34.556467 INFO: === FDR correction performed with classifier version -1 ===
0:35:34.556991 PROGRESS: ============================= Precursor FDR =============================
0:35:34.557085 PROGRESS: Total precursors accumulated: 4
0:35:34.557143 PROGRESS: Target precursors: 4 (100.00%)
0:35:34.557194 PROGRESS: Decoy precursors: 0 (0.00%)
0:35:34.557237 PROGRESS: 
0:35:34.557280 PROGRESS: Precursor Summary:
0:35:34.558183 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:35:34.558269 PROGRESS: 
0:35:34.558321 PROGRESS: Protein Summary:
0:35:34.559312 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
0:35:34.559398 PROGRESS: =========================================================================
0:35:34.560106 INFO: Target number of precursors not reached yet.
0:35:34.690315 INFO: Starting optimization step 7.
0:35:34.690556 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:35:34.690636 INFO: Using ng extraction backend
0:35:34.690702 PROGRESS: Extracting batch of 50691 precursors
0:35:34.778219 INFO: === Search parameters used ===
0:35:34.778468 INFO: rt_error       : 805.6002197265625
0:35:34.778521 INFO: mobility_error : 0.1
0:35:34.778567 INFO: num_candidates : 1
0:35:34.778608 INFO: ms1_error      : 30
0:35:34.778649 INFO: ms2_error      : 30
0:35:34.778687 INFO: fwhm_rt        : 5
0:35:34.778726 INFO: quant_window   : 3
0:35:34.778763 INFO: ==============================================
0:35:35.133409 INFO: performing precursor FDR with 40 features
0:35:35.133519 INFO: Decoy channel: -1
0:35:35.133545 INFO: Competetive: True
0:35:35.174179 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:35.200939 INFO: Using random state 289569 for train-test-split
0:35:36.743933 INFO: Test AUC: 0.565
0:35:36.744048 INFO: Train AUC: 0.581
0:35:36.744078 INFO: AUC difference: 2.78%
0:35:36.994914 INFO: Resetting torch num_threads to 80
0:35:37.014449 PROGRESS: === Extracted 99957 precursors and 468918 fragments ===
0:35:37.014983 INFO: === FDR correction performed with classifier version -1 ===
0:35:37.015559 PROGRESS: ============================= Precursor FDR =============================
0:35:37.015660 PROGRESS: Total precursors accumulated: 284
0:35:37.015723 PROGRESS: Target precursors: 282 (99.30%)
0:35:37.015795 PROGRESS: Decoy precursors: 2 (0.70%)
0:35:37.015845 PROGRESS: 
0:35:37.015892 PROGRESS: Precursor Summary:
0:35:37.016832 PROGRESS: Channel   0:	 0.050 FDR:   282; 0.010 FDR:   282; 0.001 FDR:   239
0:35:37.016925 PROGRESS: 
0:35:37.016980 PROGRESS: Protein Summary:
0:35:37.018061 PROGRESS: Channel   0:	 0.050 FDR:   263; 0.010 FDR:   263; 0.001 FDR:   224
0:35:37.018152 PROGRESS: =========================================================================
0:35:37.019637 INFO: Target number of precursors reached.
0:35:37.055368 INFO: fragments_df: keeping 2381 of 468918 [sum(precursor_idx_mask)=3051 sum(mass_error_mask)=468918 stop_rank=2381
0:35:37.257920 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:35:37.373793 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:35:37.690612 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:35:37.691023 INFO: Using score_cutoff 13.914229015159606 (fac=0.99, q=1)
0:35:37.691319 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:35:37.691400 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:35:37.691457 INFO: Updating optimization_manager: score_cutoff        : 0 -> 13.914229015159606
0:35:37.691513 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:35:37.753048 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:35:37.902514 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:35:37.902815 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:35:37.902920 INFO: Starting optimization step 8.
0:35:37.902989 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:35:37.903064 INFO: Using ng extraction backend
0:35:37.903134 PROGRESS: Extracting batch of 100984 precursors
0:35:38.079382 INFO: === Search parameters used ===
0:35:38.079634 INFO: rt_error       : 805.6002197265625
0:35:38.079689 INFO: mobility_error : 0.1
0:35:38.079735 INFO: num_candidates : 3
0:35:38.079777 INFO: ms1_error      : 30
0:35:38.079819 INFO: ms2_error      : 30
0:35:38.079858 INFO: fwhm_rt        : 3.0
0:35:38.079899 INFO: quant_window   : 3
0:35:38.079938 INFO: ==============================================
0:35:39.322588 INFO: performing precursor FDR with 40 features
0:35:39.322704 INFO: Decoy channel: -1
0:35:39.322731 INFO: Competetive: True
0:35:39.401565 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:39.507243 INFO: Using random state 648978 for train-test-split
0:35:43.526199 INFO: Test AUC: 0.590
0:35:43.526323 INFO: Train AUC: 0.602
0:35:43.526354 INFO: AUC difference: 2.07%
0:35:43.834771 INFO: Resetting torch num_threads to 80
0:35:43.846526 PROGRESS: === Extracted 300109 precursors and 1378946 fragments ===
0:35:43.847064 INFO: === FDR correction performed with classifier version 7 ===
0:35:43.847512 PROGRESS: ============================= Precursor FDR =============================
0:35:43.847599 PROGRESS: Total precursors accumulated: 245
0:35:43.847658 PROGRESS: Target precursors: 243 (99.18%)
0:35:43.847709 PROGRESS: Decoy precursors: 2 (0.82%)
0:35:43.847754 PROGRESS: 
0:35:43.847798 PROGRESS: Precursor Summary:
0:35:43.848664 PROGRESS: Channel   0:	 0.050 FDR:   243; 0.010 FDR:   243; 0.001 FDR:     0
0:35:43.848752 PROGRESS: 
0:35:43.848815 PROGRESS: Protein Summary:
0:35:43.849814 PROGRESS: Channel   0:	 0.050 FDR:   228; 0.010 FDR:   228; 0.001 FDR:     0
0:35:43.849904 PROGRESS: =========================================================================
0:35:43.854995 INFO: Target number of precursors reached.
0:35:43.946468 INFO: fragments_df: keeping 3082 of 1378946 [sum(precursor_idx_mask)=5611 sum(mass_error_mask)=1378946 stop_rank=3082
0:35:44.153904 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:35:44.266972 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:35:44.674013 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:35:44.674417 INFO: Using score_cutoff 15.213435411071776 (fac=0.99, q=1)
0:35:44.674694 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:35:44.674781 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:35:44.674834 INFO: Updating optimization_manager: score_cutoff        : 13.914229015159606 -> 15.213435411071776
0:35:44.674887 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:35:44.736854 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:35:44.886853 INFO: === checking if optimization conditions were reached ===
0:35:44.888964 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:35:44.889081 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:35:44.889176 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:35:44.889246 INFO: ==============================================
0:35:44.889322 INFO: Starting optimization step 9.
0:35:44.889387 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:35:44.889453 INFO: Using ng extraction backend
0:35:44.889518 PROGRESS: Extracting batch of 100984 precursors
0:35:45.064025 INFO: === Search parameters used ===
0:35:45.064272 INFO: rt_error       : 805.6002197265625
0:35:45.064329 INFO: mobility_error : 0.1
0:35:45.064376 INFO: num_candidates : 3
0:35:45.064420 INFO: ms1_error      : 30
0:35:45.064462 INFO: ms2_error      : 10.0
0:35:45.064502 INFO: fwhm_rt        : 3.0
0:35:45.064543 INFO: quant_window   : 3
0:35:45.064582 INFO: ==============================================
0:35:46.278884 INFO: performing precursor FDR with 40 features
0:35:46.278998 INFO: Decoy channel: -1
0:35:46.279023 INFO: Competetive: True
0:35:46.358395 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:46.465407 INFO: Using random state 77627 for train-test-split
0:35:50.617077 INFO: Test AUC: 0.595
0:35:50.617197 INFO: Train AUC: 0.604
0:35:50.617229 INFO: AUC difference: 1.49%
0:35:52.010710 INFO: Resetting torch num_threads to 80
0:35:52.023046 PROGRESS: === Extracted 302319 precursors and 1617913 fragments ===
0:35:52.023421 INFO: === FDR correction performed with classifier version 8 ===
0:35:52.023906 PROGRESS: ============================= Precursor FDR =============================
0:35:52.023995 PROGRESS: Total precursors accumulated: 538
0:35:52.024053 PROGRESS: Target precursors: 533 (99.07%)
0:35:52.024102 PROGRESS: Decoy precursors: 5 (0.93%)
0:35:52.024158 PROGRESS: 
0:35:52.024203 PROGRESS: Precursor Summary:
0:35:52.025195 PROGRESS: Channel   0:	 0.050 FDR:   533; 0.010 FDR:   533; 0.001 FDR:   397
0:35:52.025294 PROGRESS: 
0:35:52.025351 PROGRESS: Protein Summary:
0:35:52.026538 PROGRESS: Channel   0:	 0.050 FDR:   498; 0.010 FDR:   498; 0.001 FDR:   370
0:35:52.026628 PROGRESS: =========================================================================
0:35:52.032006 INFO: Target number of precursors reached.
0:35:52.136477 INFO: fragments_df: keeping 5000 of 1617913 [sum(precursor_idx_mask)=12658 sum(mass_error_mask)=1617913 stop_rank=5000
0:35:52.277559 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:35:52.415417 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:35:53.094808 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:35:53.095205 INFO: Using score_cutoff 9.712777632522585 (fac=0.99, q=1)
0:35:53.095488 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:35:53.095568 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:35:53.095620 INFO: Updating optimization_manager: score_cutoff        : 15.213435411071776 -> 9.712777632522585
0:35:53.095673 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:35:53.126255 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:35:53.192571 INFO: === checking if optimization conditions were reached ===
0:35:53.195022 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:35:53.195195 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:35:53.195273 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:35:53.195342 INFO: ==============================================
0:35:53.195433 PROGRESS: Optimization finished for ms2_error.
0:35:53.342912 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:35:53.373638 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:35:53.439283 INFO: Starting optimization step 0.
0:35:53.439535 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:35:53.439625 INFO: Using ng extraction backend
0:35:53.439695 PROGRESS: Extracting batch of 50293 precursors
0:35:53.529554 INFO: === Search parameters used ===
0:35:53.529817 INFO: rt_error       : 805.6002197265625
0:35:53.529870 INFO: mobility_error : 0.1
0:35:53.529913 INFO: num_candidates : 3
0:35:53.529954 INFO: ms1_error      : 30
0:35:53.529995 INFO: ms2_error      : 10.0
0:35:53.530040 INFO: fwhm_rt        : 3.0
0:35:53.530079 INFO: quant_window   : 3
0:35:53.530116 INFO: ==============================================
0:35:54.160412 INFO: performing precursor FDR with 40 features
0:35:54.160536 INFO: Decoy channel: -1
0:35:54.160562 INFO: Competetive: True
0:35:54.201327 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:54.238371 INFO: Using random state 53502 for train-test-split
0:35:56.164549 INFO: Test AUC: 0.592
0:35:56.164658 INFO: Train AUC: 0.612
0:35:56.164689 INFO: AUC difference: 3.30%
0:35:56.433965 INFO: Resetting torch num_threads to 80
0:35:56.441420 PROGRESS: === Extracted 150570 precursors and 805151 fragments ===
0:35:56.441779 INFO: === FDR correction performed with classifier version 9 ===
0:35:56.442241 PROGRESS: ============================= Precursor FDR =============================
0:35:56.442328 PROGRESS: Total precursors accumulated: 278
0:35:56.442384 PROGRESS: Target precursors: 276 (99.28%)
0:35:56.442432 PROGRESS: Decoy precursors: 2 (0.72%)
0:35:56.442475 PROGRESS: 
0:35:56.442516 PROGRESS: Precursor Summary:
0:35:56.443399 PROGRESS: Channel   0:	 0.050 FDR:   276; 0.010 FDR:   276; 0.001 FDR:   203
0:35:56.443483 PROGRESS: 
0:35:56.443536 PROGRESS: Protein Summary:
0:35:56.444603 PROGRESS: Channel   0:	 0.050 FDR:   267; 0.010 FDR:   267; 0.001 FDR:   195
0:35:56.444688 PROGRESS: =========================================================================
0:35:56.447439 INFO: Target number of precursors reached.
0:35:56.502569 INFO: fragments_df: keeping 3046 of 805151 [sum(precursor_idx_mask)=6548 sum(mass_error_mask)=805151 stop_rank=3046
0:35:56.639850 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:35:56.761510 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:35:57.163285 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:35:57.163710 INFO: Using score_cutoff 10.616007735729218 (fac=0.99, q=1)
0:35:57.163984 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:35:57.164059 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:35:57.164111 INFO: Updating optimization_manager: score_cutoff        : 9.712777632522585 -> 10.616007735729218
0:35:57.164167 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:35:57.194842 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:35:57.260654 INFO: === checking if optimization conditions were reached ===
0:35:57.260926 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:35:57.262972 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 255.79071712361326
0:35:57.263083 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 255.7907.
0:35:57.263155 INFO: ==============================================
0:35:57.263230 INFO: Starting optimization step 1.
0:35:57.263292 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:35:57.263358 INFO: Using ng extraction backend
0:35:57.263420 PROGRESS: Extracting batch of 50293 precursors
0:35:57.353071 INFO: === Search parameters used ===
0:35:57.353328 INFO: rt_error       : 255.79071712361326
0:35:57.353379 INFO: mobility_error : 0.1
0:35:57.353422 INFO: num_candidates : 3
0:35:57.353475 INFO: ms1_error      : 30
0:35:57.353514 INFO: ms2_error      : 10.0
0:35:57.353551 INFO: fwhm_rt        : 3.0
0:35:57.353588 INFO: quant_window   : 3
0:35:57.353624 INFO: ==============================================
0:35:57.927100 INFO: performing precursor FDR with 40 features
0:35:57.927213 INFO: Decoy channel: -1
0:35:57.927238 INFO: Competetive: True
0:35:57.967168 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:58.003057 INFO: Using random state 53502 for train-test-split
0:35:59.976572 INFO: Test AUC: 0.595
0:35:59.976691 INFO: Train AUC: 0.607
0:35:59.976721 INFO: AUC difference: 1.83%
0:36:00.244747 INFO: Resetting torch num_threads to 80
0:36:00.251455 PROGRESS: === Extracted 149740 precursors and 739438 fragments ===
0:36:00.251829 INFO: === FDR correction performed with classifier version 9 ===
0:36:00.252276 PROGRESS: ============================= Precursor FDR =============================
0:36:00.252359 PROGRESS: Total precursors accumulated: 282
0:36:00.252414 PROGRESS: Target precursors: 280 (99.29%)
0:36:00.252465 PROGRESS: Decoy precursors: 2 (0.71%)
0:36:00.252509 PROGRESS: 
0:36:00.252550 PROGRESS: Precursor Summary:
0:36:00.253483 PROGRESS: Channel   0:	 0.050 FDR:   280; 0.010 FDR:   280; 0.001 FDR:   240
0:36:00.253575 PROGRESS: 
0:36:00.253628 PROGRESS: Protein Summary:
0:36:00.254698 PROGRESS: Channel   0:	 0.050 FDR:   271; 0.010 FDR:   271; 0.001 FDR:   232
0:36:00.254783 PROGRESS: =========================================================================
0:36:00.256977 INFO: Target number of precursors reached.
0:36:00.306292 INFO: fragments_df: keeping 3104 of 739438 [sum(precursor_idx_mask)=6690 sum(mass_error_mask)=739438 stop_rank=3104
0:36:00.440774 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:36:00.560166 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:36:00.969882 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:36:00.970297 INFO: Using score_cutoff 11.923460078144073 (fac=0.99, q=1)
0:36:00.970573 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:36:00.970656 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:36:00.970712 INFO: Updating optimization_manager: score_cutoff        : 10.616007735729218 -> 11.923460078144073
0:36:00.970762 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:01.001324 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:01.067358 INFO: === checking if optimization conditions were reached ===
0:36:01.067615 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:36:01.069824 INFO: Updating optimization_manager: rt_error            : 255.79071712361326 -> 154.80457625989027
0:36:01.069937 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 154.8046.
0:36:01.070011 INFO: ==============================================
0:36:01.070090 INFO: Starting optimization step 2.
0:36:01.070155 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:36:01.070223 INFO: Using ng extraction backend
0:36:01.070288 PROGRESS: Extracting batch of 50293 precursors
0:36:01.159820 INFO: === Search parameters used ===
0:36:01.160074 INFO: rt_error       : 154.80457625989027
0:36:01.160126 INFO: mobility_error : 0.1
0:36:01.160171 INFO: num_candidates : 3
0:36:01.160212 INFO: ms1_error      : 30
0:36:01.160251 INFO: ms2_error      : 10.0
0:36:01.160291 INFO: fwhm_rt        : 3.0
0:36:01.160328 INFO: quant_window   : 3
0:36:01.160376 INFO: ==============================================
0:36:01.738999 INFO: performing precursor FDR with 40 features
0:36:01.739111 INFO: Decoy channel: -1
0:36:01.739138 INFO: Competetive: True
0:36:01.779784 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:01.816920 INFO: Using random state 53502 for train-test-split
0:36:03.756769 INFO: Test AUC: 0.590
0:36:03.756897 INFO: Train AUC: 0.603
0:36:03.756927 INFO: AUC difference: 2.13%
0:36:04.019842 INFO: Resetting torch num_threads to 80
0:36:04.026636 PROGRESS: === Extracted 148469 precursors and 650442 fragments ===
0:36:04.026999 INFO: === FDR correction performed with classifier version 9 ===
0:36:04.027447 PROGRESS: ============================= Precursor FDR =============================
0:36:04.027534 PROGRESS: Total precursors accumulated: 293
0:36:04.027590 PROGRESS: Target precursors: 291 (99.32%)
0:36:04.027638 PROGRESS: Decoy precursors: 2 (0.68%)
0:36:04.027680 PROGRESS: 
0:36:04.027721 PROGRESS: Precursor Summary:
0:36:04.028597 PROGRESS: Channel   0:	 0.050 FDR:   291; 0.010 FDR:   291; 0.001 FDR:   221
0:36:04.028681 PROGRESS: 
0:36:04.028734 PROGRESS: Protein Summary:
0:36:04.029784 PROGRESS: Channel   0:	 0.050 FDR:   280; 0.010 FDR:   280; 0.001 FDR:   214
0:36:04.029871 PROGRESS: =========================================================================
0:36:04.032040 INFO: Target number of precursors reached.
0:36:04.077277 INFO: fragments_df: keeping 3238 of 650442 [sum(precursor_idx_mask)=6836 sum(mass_error_mask)=650442 stop_rank=3238
0:36:04.211514 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:36:04.325343 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:36:04.750326 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:36:04.750750 INFO: Using score_cutoff 11.537617195129394 (fac=0.99, q=1)
0:36:04.751038 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:36:04.751113 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:36:04.751166 INFO: Updating optimization_manager: score_cutoff        : 11.923460078144073 -> 11.537617195129394
0:36:04.751218 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:04.782209 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:04.850129 INFO: === checking if optimization conditions were reached ===
0:36:04.850391 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:36:04.852736 INFO: Updating optimization_manager: rt_error            : 154.80457625989027 -> 105.76719664118255
0:36:04.852859 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 105.7672.
0:36:04.852936 INFO: ==============================================
0:36:04.853014 INFO: Starting optimization step 3.
0:36:04.853079 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:36:04.853146 INFO: Using ng extraction backend
0:36:04.853212 PROGRESS: Extracting batch of 50293 precursors
0:36:04.943145 INFO: === Search parameters used ===
0:36:04.943388 INFO: rt_error       : 105.76719664118255
0:36:04.943441 INFO: mobility_error : 0.1
0:36:04.943486 INFO: num_candidates : 3
0:36:04.943525 INFO: ms1_error      : 30
0:36:04.943565 INFO: ms2_error      : 10.0
0:36:04.944048 INFO: fwhm_rt        : 3.0
0:36:04.944097 INFO: quant_window   : 3
0:36:04.944134 INFO: ==============================================
0:36:05.518982 INFO: performing precursor FDR with 40 features
0:36:05.519099 INFO: Decoy channel: -1
0:36:05.519125 INFO: Competetive: True
0:36:05.558514 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:05.593815 INFO: Using random state 53502 for train-test-split
0:36:07.707236 INFO: Test AUC: 0.591
0:36:07.707351 INFO: Train AUC: 0.605
0:36:07.707381 INFO: AUC difference: 2.28%
0:36:07.972941 INFO: Resetting torch num_threads to 80
0:36:07.979860 PROGRESS: === Extracted 147215 precursors and 603306 fragments ===
0:36:07.980221 INFO: === FDR correction performed with classifier version 9 ===
0:36:07.980668 PROGRESS: ============================= Precursor FDR =============================
0:36:07.980753 PROGRESS: Total precursors accumulated: 321
0:36:07.980821 PROGRESS: Target precursors: 318 (99.07%)
0:36:07.980875 PROGRESS: Decoy precursors: 3 (0.93%)
0:36:07.980920 PROGRESS: 
0:36:07.980962 PROGRESS: Precursor Summary:
0:36:07.981840 PROGRESS: Channel   0:	 0.050 FDR:   318; 0.010 FDR:   318; 0.001 FDR:   257
0:36:07.981927 PROGRESS: 
0:36:07.981981 PROGRESS: Protein Summary:
0:36:07.983056 PROGRESS: Channel   0:	 0.050 FDR:   306; 0.010 FDR:   306; 0.001 FDR:   248
0:36:07.983143 PROGRESS: =========================================================================
0:36:07.985377 INFO: Target number of precursors reached.
0:36:08.026989 INFO: fragments_df: keeping 3374 of 603306 [sum(precursor_idx_mask)=7314 sum(mass_error_mask)=603306 stop_rank=3374
0:36:08.175143 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:36:08.295023 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:36:08.736910 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:36:08.737309 INFO: Using score_cutoff 11.418707373046875 (fac=0.99, q=1)
0:36:08.737588 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:36:08.737666 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:36:08.737719 INFO: Updating optimization_manager: score_cutoff        : 11.537617195129394 -> 11.418707373046875
0:36:08.737771 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:08.768845 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:08.837828 INFO: === checking if optimization conditions were reached ===
0:36:08.838089 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:36:08.840356 INFO: Updating optimization_manager: rt_error            : 105.76719664118255 -> 92.17367643105133
0:36:08.840470 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 92.1737.
0:36:08.840544 INFO: ==============================================
0:36:08.840623 INFO: Starting optimization step 4.
0:36:08.840691 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:36:08.840760 INFO: Using ng extraction backend
0:36:08.840837 PROGRESS: Extracting batch of 50293 precursors
0:36:08.930012 INFO: === Search parameters used ===
0:36:08.930266 INFO: rt_error       : 92.17367643105133
0:36:08.930320 INFO: mobility_error : 0.1
0:36:08.930364 INFO: num_candidates : 3
0:36:08.930421 INFO: ms1_error      : 30
0:36:08.930465 INFO: ms2_error      : 10.0
0:36:08.930506 INFO: fwhm_rt        : 3.0
0:36:08.930550 INFO: quant_window   : 3
0:36:08.930591 INFO: ==============================================
0:36:09.524877 INFO: performing precursor FDR with 40 features
0:36:09.525020 INFO: Decoy channel: -1
0:36:09.525048 INFO: Competetive: True
0:36:09.563511 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:09.599058 INFO: Using random state 53502 for train-test-split
0:36:11.580960 INFO: Test AUC: 0.592
0:36:11.581075 INFO: Train AUC: 0.605
0:36:11.581108 INFO: AUC difference: 2.23%
0:36:11.834506 INFO: Resetting torch num_threads to 80
0:36:11.841052 PROGRESS: === Extracted 146449 precursors and 586053 fragments ===
0:36:11.841400 INFO: === FDR correction performed with classifier version 9 ===
0:36:11.841864 PROGRESS: ============================= Precursor FDR =============================
0:36:11.841952 PROGRESS: Total precursors accumulated: 276
0:36:11.842011 PROGRESS: Target precursors: 274 (99.28%)
0:36:11.842064 PROGRESS: Decoy precursors: 2 (0.72%)
0:36:11.842110 PROGRESS: 
0:36:11.842153 PROGRESS: Precursor Summary:
0:36:11.843031 PROGRESS: Channel   0:	 0.050 FDR:   274; 0.010 FDR:   274; 0.001 FDR:   216
0:36:11.843117 PROGRESS: 
0:36:11.843171 PROGRESS: Protein Summary:
0:36:11.844212 PROGRESS: Channel   0:	 0.050 FDR:   263; 0.010 FDR:   263; 0.001 FDR:   208
0:36:11.844300 PROGRESS: =========================================================================
0:36:11.846417 INFO: Target number of precursors reached.
0:36:11.885971 INFO: fragments_df: keeping 3022 of 586053 [sum(precursor_idx_mask)=6353 sum(mass_error_mask)=586053 stop_rank=3022
0:36:12.024589 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:36:12.147030 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:36:12.546817 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:36:12.547400 INFO: Using score_cutoff 11.509925866699218 (fac=0.99, q=1)
0:36:12.547706 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:36:12.547785 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:36:12.547839 INFO: Updating optimization_manager: score_cutoff        : 11.418707373046875 -> 11.509925866699218
0:36:12.547896 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:12.580076 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:12.649673 INFO: === checking if optimization conditions were reached ===
0:36:12.649939 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:36:12.652521 INFO: Updating optimization_manager: rt_error            : 92.17367643105133 -> 66.21443970373429
0:36:12.652640 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 66.2144.
0:36:12.652715 INFO: ==============================================
0:36:12.652802 INFO: Starting optimization step 5.
0:36:12.652889 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:36:12.652974 INFO: Using ng extraction backend
0:36:12.653063 PROGRESS: Extracting batch of 50293 precursors
0:36:12.744727 INFO: === Search parameters used ===
0:36:12.744987 INFO: rt_error       : 66.21443970373429
0:36:12.745054 INFO: mobility_error : 0.1
0:36:12.745109 INFO: num_candidates : 3
0:36:12.745152 INFO: ms1_error      : 30
0:36:12.745192 INFO: ms2_error      : 10.0
0:36:12.745231 INFO: fwhm_rt        : 3.0
0:36:12.745270 INFO: quant_window   : 3
0:36:12.745310 INFO: ==============================================
0:36:13.341959 INFO: performing precursor FDR with 40 features
0:36:13.342071 INFO: Decoy channel: -1
0:36:13.342098 INFO: Competetive: True
0:36:13.385260 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:13.423855 INFO: Using random state 53502 for train-test-split
0:36:15.378097 INFO: Test AUC: 0.588
0:36:15.378207 INFO: Train AUC: 0.602
0:36:15.378237 INFO: AUC difference: 2.31%
0:36:15.633502 INFO: Resetting torch num_threads to 80
0:36:15.640332 PROGRESS: === Extracted 143587 precursors and 541565 fragments ===
0:36:15.640710 INFO: === FDR correction performed with classifier version 9 ===
0:36:15.641164 PROGRESS: ============================= Precursor FDR =============================
0:36:15.641250 PROGRESS: Total precursors accumulated: 303
0:36:15.641306 PROGRESS: Target precursors: 300 (99.01%)
0:36:15.641354 PROGRESS: Decoy precursors: 3 (0.99%)
0:36:15.641400 PROGRESS: 
0:36:15.641444 PROGRESS: Precursor Summary:
0:36:15.642334 PROGRESS: Channel   0:	 0.050 FDR:   300; 0.010 FDR:   296; 0.001 FDR:   277
0:36:15.642421 PROGRESS: 
0:36:15.642475 PROGRESS: Protein Summary:
0:36:15.643541 PROGRESS: Channel   0:	 0.050 FDR:   294; 0.010 FDR:   290; 0.001 FDR:   271
0:36:15.643628 PROGRESS: =========================================================================
0:36:15.645756 INFO: Target number of precursors reached.
0:36:15.683169 INFO: fragments_df: keeping 2865 of 541565 [sum(precursor_idx_mask)=6202 sum(mass_error_mask)=541565 stop_rank=2865
0:36:15.817847 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:36:15.943364 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:36:16.323646 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:36:16.324074 INFO: Using score_cutoff 2.751582800745964 (fac=0.99, q=1)
0:36:16.324389 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:36:16.324467 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:36:16.324520 INFO: Updating optimization_manager: score_cutoff        : 11.509925866699218 -> 2.751582800745964
0:36:16.324577 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:16.355341 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:16.426428 INFO: === checking if optimization conditions were reached ===
0:36:16.426699 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:36:16.429050 INFO: Updating optimization_manager: rt_error            : 66.21443970373429 -> 50.39894757303985
0:36:16.429162 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 50.3989.
0:36:16.429237 INFO: ==============================================
0:36:16.429316 INFO: Starting optimization step 6.
0:36:16.429380 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:36:16.429454 INFO: Using ng extraction backend
0:36:16.429521 PROGRESS: Extracting batch of 50293 precursors
0:36:16.520307 INFO: === Search parameters used ===
0:36:16.520562 INFO: rt_error       : 50.39894757303985
0:36:16.520616 INFO: mobility_error : 0.1
0:36:16.520661 INFO: num_candidates : 3
0:36:16.520702 INFO: ms1_error      : 30
0:36:16.520741 INFO: ms2_error      : 10.0
0:36:16.520779 INFO: fwhm_rt        : 3.0
0:36:16.520827 INFO: quant_window   : 3
0:36:16.520867 INFO: ==============================================
0:36:17.043175 INFO: performing precursor FDR with 40 features
0:36:17.043299 INFO: Decoy channel: -1
0:36:17.043325 INFO: Competetive: True
0:36:17.080714 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:17.117593 INFO: Using random state 53502 for train-test-split
0:36:18.890079 INFO: Test AUC: 0.591
0:36:18.890193 INFO: Train AUC: 0.604
0:36:18.890222 INFO: AUC difference: 2.18%
0:36:19.148800 INFO: Resetting torch num_threads to 80
0:36:19.155276 PROGRESS: === Extracted 134243 precursors and 480997 fragments ===
0:36:19.155622 INFO: === FDR correction performed with classifier version 9 ===
0:36:19.156070 PROGRESS: ============================= Precursor FDR =============================
0:36:19.156154 PROGRESS: Total precursors accumulated: 309
0:36:19.156210 PROGRESS: Target precursors: 306 (99.03%)
0:36:19.156257 PROGRESS: Decoy precursors: 3 (0.97%)
0:36:19.156299 PROGRESS: 
0:36:19.156340 PROGRESS: Precursor Summary:
0:36:19.157233 PROGRESS: Channel   0:	 0.050 FDR:   306; 0.010 FDR:   306; 0.001 FDR:   222
0:36:19.157320 PROGRESS: 
0:36:19.157374 PROGRESS: Protein Summary:
0:36:19.158416 PROGRESS: Channel   0:	 0.050 FDR:   298; 0.010 FDR:   298; 0.001 FDR:   215
0:36:19.158503 PROGRESS: =========================================================================
0:36:19.160501 INFO: Target number of precursors reached.
0:36:19.194370 INFO: fragments_df: keeping 2897 of 480997 [sum(precursor_idx_mask)=6037 sum(mass_error_mask)=480997 stop_rank=2897
0:36:19.334563 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:36:19.446158 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:36:19.766768 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:36:19.767169 INFO: Using score_cutoff 8.305770411014558 (fac=0.99, q=1)
0:36:19.767445 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:36:19.767522 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:36:19.767573 INFO: Updating optimization_manager: score_cutoff        : 2.751582800745964 -> 8.305770411014558
0:36:19.767624 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:19.798485 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:19.869429 INFO: === checking if optimization conditions were reached ===
0:36:19.869686 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:36:19.871629 INFO: Updating optimization_manager: rt_error            : 50.39894757303985 -> 38.28639283050635
0:36:19.871740 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 38.2864.
0:36:19.871824 INFO: ==============================================
0:36:19.871914 INFO: Starting optimization step 7.
0:36:19.871992 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:36:19.872071 INFO: Using ng extraction backend
0:36:19.872161 PROGRESS: Extracting batch of 50293 precursors
0:36:19.959205 INFO: === Search parameters used ===
0:36:19.959468 INFO: rt_error       : 38.28639283050635
0:36:19.959541 INFO: mobility_error : 0.1
0:36:19.959621 INFO: num_candidates : 3
0:36:19.959684 INFO: ms1_error      : 30
0:36:19.959745 INFO: ms2_error      : 10.0
0:36:19.959801 INFO: fwhm_rt        : 3.0
0:36:19.959860 INFO: quant_window   : 3
0:36:19.959917 INFO: ==============================================
0:36:20.476298 INFO: performing precursor FDR with 40 features
0:36:20.476418 INFO: Decoy channel: -1
0:36:20.476445 INFO: Competetive: True
0:36:20.512642 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:20.545579 INFO: Using random state 53502 for train-test-split
0:36:22.270397 INFO: Test AUC: 0.592
0:36:22.270513 INFO: Train AUC: 0.605
0:36:22.270544 INFO: AUC difference: 2.04%
0:36:22.525585 INFO: Resetting torch num_threads to 80
0:36:22.531966 PROGRESS: === Extracted 132729 precursors and 472391 fragments ===
0:36:22.532310 INFO: === FDR correction performed with classifier version 9 ===
0:36:22.532753 PROGRESS: ============================= Precursor FDR =============================
0:36:22.532851 PROGRESS: Total precursors accumulated: 307
0:36:22.532921 PROGRESS: Target precursors: 304 (99.02%)
0:36:22.532983 PROGRESS: Decoy precursors: 3 (0.98%)
0:36:22.533041 PROGRESS: 
0:36:22.533096 PROGRESS: Precursor Summary:
0:36:22.533981 PROGRESS: Channel   0:	 0.050 FDR:   304; 0.010 FDR:   304; 0.001 FDR:   222
0:36:22.534067 PROGRESS: 
0:36:22.534120 PROGRESS: Protein Summary:
0:36:22.535175 PROGRESS: Channel   0:	 0.050 FDR:   297; 0.010 FDR:   297; 0.001 FDR:   215
0:36:22.535272 PROGRESS: =========================================================================
0:36:22.537271 INFO: Target number of precursors reached.
0:36:22.569407 INFO: fragments_df: keeping 2857 of 472391 [sum(precursor_idx_mask)=6008 sum(mass_error_mask)=472391 stop_rank=2857
0:36:22.702620 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:36:22.829721 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:36:23.207929 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:36:23.208330 INFO: Using score_cutoff 11.112139860534667 (fac=0.99, q=1)
0:36:23.208605 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:36:23.208681 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:36:23.208734 INFO: Updating optimization_manager: score_cutoff        : 8.305770411014558 -> 11.112139860534667
0:36:23.208786 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:23.240307 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:23.307730 INFO: === checking if optimization conditions were reached ===
0:36:23.307955 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
0:36:23.309907 INFO: Updating optimization_manager: rt_error            : 38.28639283050635 -> 34.44295571059649
0:36:23.310006 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 34.4430.
0:36:23.310072 INFO: ==============================================
0:36:23.310139 INFO: Starting optimization step 8.
0:36:23.310637 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:36:23.310707 INFO: Using ng extraction backend
0:36:23.310765 PROGRESS: Extracting batch of 50293 precursors
0:36:23.397964 INFO: === Search parameters used ===
0:36:23.398216 INFO: rt_error       : 34.44295571059649
0:36:23.398270 INFO: mobility_error : 0.1
0:36:23.398316 INFO: num_candidates : 3
0:36:23.398358 INFO: ms1_error      : 30
0:36:23.398398 INFO: ms2_error      : 10.0
0:36:23.398437 INFO: fwhm_rt        : 3.0
0:36:23.398477 INFO: quant_window   : 3
0:36:23.398518 INFO: ==============================================
0:36:23.921010 INFO: performing precursor FDR with 40 features
0:36:23.921121 INFO: Decoy channel: -1
0:36:23.921147 INFO: Competetive: True
0:36:23.957677 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:23.989548 INFO: Using random state 53502 for train-test-split
0:36:25.677112 INFO: Test AUC: 0.594
0:36:25.677228 INFO: Train AUC: 0.604
0:36:25.677259 INFO: AUC difference: 1.56%
0:36:25.938160 INFO: Resetting torch num_threads to 80
0:36:25.944530 PROGRESS: === Extracted 132975 precursors and 473626 fragments ===
0:36:25.944877 INFO: === FDR correction performed with classifier version 9 ===
0:36:25.945324 PROGRESS: ============================= Precursor FDR =============================
0:36:25.945409 PROGRESS: Total precursors accumulated: 309
0:36:25.945467 PROGRESS: Target precursors: 306 (99.03%)
0:36:25.945516 PROGRESS: Decoy precursors: 3 (0.97%)
0:36:25.945564 PROGRESS: 
0:36:25.945608 PROGRESS: Precursor Summary:
0:36:25.946501 PROGRESS: Channel   0:	 0.050 FDR:   306; 0.010 FDR:   306; 0.001 FDR:   225
0:36:25.946595 PROGRESS: 
0:36:25.946660 PROGRESS: Protein Summary:
0:36:25.947721 PROGRESS: Channel   0:	 0.050 FDR:   298; 0.010 FDR:   298; 0.001 FDR:   218
0:36:25.947809 PROGRESS: =========================================================================
0:36:25.949789 INFO: Target number of precursors reached.
0:36:25.982432 INFO: fragments_df: keeping 2843 of 473626 [sum(precursor_idx_mask)=6070 sum(mass_error_mask)=473626 stop_rank=2843
0:36:26.115144 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:36:26.237687 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:36:26.614506 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:36:26.614907 INFO: Using score_cutoff 10.996160575389862 (fac=0.99, q=1)
0:36:26.615208 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:36:26.615298 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:36:26.615362 INFO: Updating optimization_manager: score_cutoff        : 11.112139860534667 -> 10.996160575389862
0:36:26.615425 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:26.646860 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:26.713433 INFO: === checking if optimization conditions were reached ===
0:36:26.713658 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
0:36:26.715569 INFO: Updating optimization_manager: rt_error            : 34.44295571059649 -> 33.55433345720098
0:36:26.715665 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 33.5543.
0:36:26.715729 INFO: ==============================================
0:36:26.715808 INFO: Starting optimization step 9.
0:36:26.715865 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:36:26.715924 INFO: Using ng extraction backend
0:36:26.715978 PROGRESS: Extracting batch of 50293 precursors
0:36:26.802899 INFO: === Search parameters used ===
0:36:26.803154 INFO: rt_error       : 33.55433345720098
0:36:26.803210 INFO: mobility_error : 0.1
0:36:26.803255 INFO: num_candidates : 3
0:36:26.803296 INFO: ms1_error      : 30
0:36:26.803335 INFO: ms2_error      : 10.0
0:36:26.803374 INFO: fwhm_rt        : 3.0
0:36:26.803414 INFO: quant_window   : 3
0:36:26.803453 INFO: ==============================================
0:36:27.322351 INFO: performing precursor FDR with 40 features
0:36:27.322470 INFO: Decoy channel: -1
0:36:27.322495 INFO: Competetive: True
0:36:27.356228 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:27.387374 INFO: Using random state 53502 for train-test-split
0:36:29.193027 INFO: Test AUC: 0.591
0:36:29.193140 INFO: Train AUC: 0.607
0:36:29.193169 INFO: AUC difference: 2.55%
0:36:29.447634 INFO: Resetting torch num_threads to 80
0:36:29.453975 PROGRESS: === Extracted 133160 precursors and 474785 fragments ===
0:36:29.454315 INFO: === FDR correction performed with classifier version 9 ===
0:36:29.454771 PROGRESS: ============================= Precursor FDR =============================
0:36:29.454854 PROGRESS: Total precursors accumulated: 306
0:36:29.454911 PROGRESS: Target precursors: 303 (99.02%)
0:36:29.454958 PROGRESS: Decoy precursors: 3 (0.98%)
0:36:29.455002 PROGRESS: 
0:36:29.455045 PROGRESS: Precursor Summary:
0:36:29.455963 PROGRESS: Channel   0:	 0.050 FDR:   303; 0.010 FDR:   303; 0.001 FDR:   254
0:36:29.456051 PROGRESS: 
0:36:29.456112 PROGRESS: Protein Summary:
0:36:29.457184 PROGRESS: Channel   0:	 0.050 FDR:   297; 0.010 FDR:   297; 0.001 FDR:   248
0:36:29.457275 PROGRESS: =========================================================================
0:36:29.459221 INFO: Target number of precursors reached.
0:36:29.491921 INFO: fragments_df: keeping 2802 of 474785 [sum(precursor_idx_mask)=5933 sum(mass_error_mask)=474785 stop_rank=2802
0:36:29.625758 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:36:29.749303 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:36:30.121280 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:36:30.121678 INFO: Using score_cutoff 10.212316498374937 (fac=0.99, q=1)
0:36:30.121954 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:36:30.122032 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:36:30.122086 INFO: Updating optimization_manager: score_cutoff        : 10.996160575389862 -> 10.212316498374937
0:36:30.122138 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:30.153467 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:30.220548 INFO: === checking if optimization conditions were reached ===
0:36:30.220777 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 2 ===
0:36:30.221883 INFO: Updating optimization_manager: rt_error            : 33.55433345720098 -> 33.55433345720098
0:36:30.222020 INFO: Updating optimization_manager: classifier_version  : 9 -> 19
0:36:30.222115 INFO: Updating optimization_manager: score_cutoff        : 10.212316498374937 -> 10.212316498374937
0:36:30.222202 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:36:30.222282 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:36:30.222363 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 33.5543 found after 10 searches.
0:36:30.222425 INFO: ==============================================
0:36:30.222492 PROGRESS: Optimization finished for rt_error.
0:36:30.359151 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:30.390817 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:30.482867 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:36:30.483057 PROGRESS: ==============================================
0:36:30.483125 PROGRESS: ms2_error      : 10.0000
0:36:30.483180 PROGRESS: rt_error       : 33.5543
0:36:30.483225 PROGRESS: ==============================================
0:36:30.483735 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:38.290722 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:55.588633 INFO: Using ng extraction backend
0:36:55.588902 PROGRESS: Extracting batch of 12001526 precursors
0:37:11.341567 INFO: === Search parameters used ===
0:37:11.341812 INFO: rt_error       : 33.55433345720098
0:37:11.341882 INFO: mobility_error : 0.1
0:37:11.341933 INFO: num_candidates : 3
0:37:11.341979 INFO: ms1_error      : 30
0:37:11.342022 INFO: ms2_error      : 10.0
0:37:11.342064 INFO: fwhm_rt        : 3.0
0:37:11.342104 INFO: quant_window   : 3
0:37:11.342143 INFO: ==============================================
0:37:33.631986 INFO: Removed 23033244 precursors with score below cutoff 10.212316498374937
0:37:44.655494 INFO: performing precursor FDR with 40 features
0:37:44.655607 INFO: Decoy channel: -1
0:37:44.655635 INFO: Competetive: True
0:37:45.735864 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:49.922611 INFO: Using random state 800996 for train-test-split
0:40:11.793245 INFO: Test AUC: 0.624
0:40:11.793465 INFO: Train AUC: 0.625
0:40:11.793503 INFO: AUC difference: 0.17%
0:40:14.908852 INFO: Resetting torch num_threads to 80
0:40:16.752958 PROGRESS: ============================= Precursor FDR =============================
0:40:16.753229 PROGRESS: Total precursors accumulated: 73,361
0:40:16.753295 PROGRESS: Target precursors: 72,635 (99.01%)
0:40:16.753359 PROGRESS: Decoy precursors: 726 (0.99%)
0:40:16.753407 PROGRESS: 
0:40:16.753450 PROGRESS: Precursor Summary:
0:40:16.776498 PROGRESS: Channel   0:	 0.050 FDR: 72,635; 0.010 FDR: 72,635; 0.001 FDR: 48,518
0:40:16.776735 PROGRESS: 
0:40:16.776794 PROGRESS: Protein Summary:
0:40:16.812344 PROGRESS: Channel   0:	 0.050 FDR: 12,307; 0.010 FDR: 12,307; 0.001 FDR: 8,778
0:40:16.812573 PROGRESS: =========================================================================
0:40:16.878840 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/psm.parquet
0:40:17.034526 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.parquet
0:40:17.246060 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:40:17.917059 PROGRESS: 
0:40:17.917207 INFO: Quantification results path: run_output_Astral/alphadia_1.12.1_rs_benchmark/quant
0:40:17.917275 INFO: Creating folder run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/figures
0:40:17.917438 INFO: Initializing TimingManager
0:40:17.917858 INFO: Initializing RawFileManager
0:40:29.827502 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:40:29.832276 INFO: Determining DIA cycle
0:40:29.847728 INFO: Found cycle with start 0.00 min and length 300.
0:40:30.013066 INFO: RT (min)            : 0.0 - 26.9
0:40:30.013157 INFO: RT duration (sec)   : 1611.2
0:40:30.013186 INFO: RT duration (min)   : 26.9
0:40:30.013210 INFO: Cycle len (scans)   : 300
0:40:30.013230 INFO: Cycle len (sec)     : 1.65
0:40:30.013250 INFO: Number of cycles    : 978
0:40:30.013272 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:40:30.013323 INFO: Creating DIA data object took: 12.095369338989258
0:40:30.658092 INFO: Creating DIA data NG object took: 0.6446397304534912
0:40:32.132196 INFO: Initializing CalibrationManager
0:40:32.132456 INFO: Setting up calibration estimators ..
0:40:32.132515 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:40:32.132603 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
0:40:32.132688 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:40:32.132737 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:40:32.132792 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
0:40:32.132852 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:40:32.132900 INFO: Done setting up calibration estimators.
0:40:32.133093 INFO: Initializing OptimizationManager
0:40:32.133244 INFO: initial parameter: ms1_error = 30
0:40:32.133295 INFO: initial parameter: ms2_error = 30
0:40:32.133343 INFO: initial parameter: rt_error = 805.611083984375
0:40:32.133389 INFO: initial parameter: mobility_error = 0.1
0:40:32.133433 INFO: initial parameter: num_candidates = 1
0:40:32.133472 INFO: initial parameter: fwhm_rt = 5
0:40:32.133512 INFO: initial parameter: fwhm_mobility = 0.01
0:40:32.133554 INFO: initial parameter: score_cutoff = 0
0:40:32.133593 INFO: initial parameter: classifier_version = -1
0:40:32.133664 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:40:32.133962 INFO: FDRManager: loading saved state not requested, will be initialized.
0:40:32.133999 INFO: Initializing FDRManager
0:40:32.134036 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:40:33.553367 PROGRESS: Initializing spectral library: 6,026,252 target precursors potentially observable (97,794 removed)
0:40:34.432939 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:40:34.433323 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
0:40:34.433428 PROGRESS: Starting initial search for precursors.
0:40:34.433510 INFO: Starting optimization step 0.
0:40:34.433574 PROGRESS: === Extracting elution groups 0 to 200 ===
0:40:34.433632 INFO: Using ng extraction backend
0:40:34.433694 PROGRESS: Extracting batch of 396 precursors
0:40:34.435582 INFO: === Search parameters used ===
0:40:34.435672 INFO: rt_error       : 805.611083984375
0:40:34.435720 INFO: mobility_error : 0.1
0:40:34.435763 INFO: num_candidates : 1
0:40:34.435804 INFO: ms1_error      : 30
0:40:34.435843 INFO: ms2_error      : 30
0:40:34.435885 INFO: fwhm_rt        : 5
0:40:34.435924 INFO: quant_window   : 3
0:40:34.435961 INFO: ==============================================
0:40:34.456155 INFO: performing precursor FDR with 40 features
0:40:34.456256 INFO: Decoy channel: -1
0:40:34.456283 INFO: Competetive: True
0:40:34.457227 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:34.459517 INFO: Using random state 329154 for train-test-split
0:40:34.466590 INFO: Test AUC: 0.519
0:40:34.466645 INFO: Train AUC: 0.481
0:40:34.466674 INFO: AUC difference: 7.85%
0:40:34.466696 WARNING: AUC difference > 5%. This may indicate overfitting.
0:40:34.672030 INFO: Resetting torch num_threads to 80
0:40:34.673335 PROGRESS: === Extracted 393 precursors and 1907 fragments ===
0:40:34.673660 INFO: === FDR correction performed with classifier version -1 ===
0:40:34.674101 PROGRESS: ============================= Precursor FDR =============================
0:40:34.674189 PROGRESS: Total precursors accumulated: 1
0:40:34.674247 PROGRESS: Target precursors: 1 (100.00%)
0:40:34.674298 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:34.674342 PROGRESS: 
0:40:34.674386 PROGRESS: Precursor Summary:
0:40:34.675282 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:40:34.675369 PROGRESS: 
0:40:34.675426 PROGRESS: Protein Summary:
0:40:34.676402 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:40:34.676490 PROGRESS: =========================================================================
0:40:34.676676 INFO: Target number of precursors not reached yet.
0:40:34.740979 INFO: Starting optimization step 1.
0:40:34.741169 PROGRESS: === Extracting elution groups 200 to 600 ===
0:40:34.741256 INFO: Using ng extraction backend
0:40:34.741321 PROGRESS: Extracting batch of 786 precursors
0:40:34.743932 INFO: === Search parameters used ===
0:40:34.744034 INFO: rt_error       : 805.611083984375
0:40:34.744082 INFO: mobility_error : 0.1
0:40:34.744126 INFO: num_candidates : 1
0:40:34.744168 INFO: ms1_error      : 30
0:40:34.744208 INFO: ms2_error      : 30
0:40:34.744247 INFO: fwhm_rt        : 5
0:40:34.744287 INFO: quant_window   : 3
0:40:34.744323 INFO: ==============================================
0:40:34.792710 INFO: performing precursor FDR with 40 features
0:40:34.792821 INFO: Decoy channel: -1
0:40:34.792849 INFO: Competetive: True
0:40:34.795696 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:34.797209 INFO: Using random state 701066 for train-test-split
0:40:34.805269 INFO: Test AUC: 0.508
0:40:34.805322 INFO: Train AUC: 0.487
0:40:34.805352 INFO: AUC difference: 4.36%
0:40:35.014896 INFO: Resetting torch num_threads to 80
0:40:35.016898 PROGRESS: === Extracted 1172 precursors and 5583 fragments ===
0:40:35.017218 INFO: === FDR correction performed with classifier version -1 ===
0:40:35.017663 PROGRESS: ============================= Precursor FDR =============================
0:40:35.017751 PROGRESS: Total precursors accumulated: 1
0:40:35.017809 PROGRESS: Target precursors: 1 (100.00%)
0:40:35.017857 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:35.017902 PROGRESS: 
0:40:35.017946 PROGRESS: Precursor Summary:
0:40:35.018846 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:40:35.018933 PROGRESS: 
0:40:35.018989 PROGRESS: Protein Summary:
0:40:35.019963 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:40:35.020049 PROGRESS: =========================================================================
0:40:35.020251 INFO: Target number of precursors not reached yet.
0:40:35.086839 INFO: Starting optimization step 2.
0:40:35.087032 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:40:35.087109 INFO: Using ng extraction backend
0:40:35.087170 PROGRESS: Extracting batch of 1592 precursors
0:40:35.091225 INFO: === Search parameters used ===
0:40:35.091343 INFO: rt_error       : 805.611083984375
0:40:35.091394 INFO: mobility_error : 0.1
0:40:35.091439 INFO: num_candidates : 1
0:40:35.091480 INFO: ms1_error      : 30
0:40:35.091518 INFO: ms2_error      : 30
0:40:35.091558 INFO: fwhm_rt        : 5
0:40:35.091595 INFO: quant_window   : 3
0:40:35.091634 INFO: ==============================================
0:40:35.130160 INFO: performing precursor FDR with 40 features
0:40:35.130238 INFO: Decoy channel: -1
0:40:35.130265 INFO: Competetive: True
0:40:35.133590 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:35.135294 INFO: Using random state 905880 for train-test-split
0:40:35.147184 INFO: Test AUC: 0.539
0:40:35.147244 INFO: Train AUC: 0.479
0:40:35.147273 INFO: AUC difference: 12.53%
0:40:35.147295 WARNING: AUC difference > 5%. This may indicate overfitting.
0:40:35.353774 INFO: Resetting torch num_threads to 80
0:40:35.356191 PROGRESS: === Extracted 2760 precursors and 13238 fragments ===
0:40:35.356517 INFO: === FDR correction performed with classifier version -1 ===
0:40:35.356947 PROGRESS: ============================= Precursor FDR =============================
0:40:35.357033 PROGRESS: Total precursors accumulated: 0
0:40:35.357090 PROGRESS: Target precursors: 0 (0.00%)
0:40:35.357138 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:35.357182 PROGRESS: 
0:40:35.357226 PROGRESS: Precursor Summary:
0:40:35.357327 PROGRESS: 
0:40:35.357385 PROGRESS: Protein Summary:
0:40:35.357455 PROGRESS: =========================================================================
0:40:35.357664 INFO: Target number of precursors not reached yet.
0:40:35.427674 INFO: Starting optimization step 3.
0:40:35.427874 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:40:35.427952 INFO: Using ng extraction backend
0:40:35.428011 PROGRESS: Extracting batch of 3177 precursors
0:40:35.434811 INFO: === Search parameters used ===
0:40:35.434933 INFO: rt_error       : 805.611083984375
0:40:35.434982 INFO: mobility_error : 0.1
0:40:35.435026 INFO: num_candidates : 1
0:40:35.435070 INFO: ms1_error      : 30
0:40:35.435111 INFO: ms2_error      : 30
0:40:35.435151 INFO: fwhm_rt        : 5
0:40:35.435193 INFO: quant_window   : 3
0:40:35.435243 INFO: ==============================================
0:40:35.478661 INFO: performing precursor FDR with 40 features
0:40:35.478752 INFO: Decoy channel: -1
0:40:35.478778 INFO: Competetive: True
0:40:35.483132 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:35.485394 INFO: Using random state 868848 for train-test-split
0:40:35.504216 INFO: Test AUC: 0.478
0:40:35.504285 INFO: Train AUC: 0.494
0:40:35.504316 INFO: AUC difference: 3.34%
0:40:35.712258 INFO: Resetting torch num_threads to 80
0:40:35.715412 PROGRESS: === Extracted 5916 precursors and 28236 fragments ===
0:40:35.715744 INFO: === FDR correction performed with classifier version -1 ===
0:40:35.716165 PROGRESS: ============================= Precursor FDR =============================
0:40:35.716250 PROGRESS: Total precursors accumulated: 0
0:40:35.716306 PROGRESS: Target precursors: 0 (0.00%)
0:40:35.716357 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:35.716401 PROGRESS: 
0:40:35.716444 PROGRESS: Precursor Summary:
0:40:35.716548 PROGRESS: 
0:40:35.716608 PROGRESS: Protein Summary:
0:40:35.716677 PROGRESS: =========================================================================
0:40:35.716928 INFO: Target number of precursors not reached yet.
0:40:35.791605 INFO: Starting optimization step 4.
0:40:35.791818 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:40:35.791898 INFO: Using ng extraction backend
0:40:35.791957 PROGRESS: Extracting batch of 6340 precursors
0:40:35.804023 INFO: === Search parameters used ===
0:40:35.804154 INFO: rt_error       : 805.611083984375
0:40:35.804203 INFO: mobility_error : 0.1
0:40:35.804252 INFO: num_candidates : 1
0:40:35.804295 INFO: ms1_error      : 30
0:40:35.804347 INFO: ms2_error      : 30
0:40:35.804392 INFO: fwhm_rt        : 5
0:40:35.804432 INFO: quant_window   : 3
0:40:35.804472 INFO: ==============================================
0:40:35.878042 INFO: performing precursor FDR with 40 features
0:40:35.878145 INFO: Decoy channel: -1
0:40:35.878172 INFO: Competetive: True
0:40:35.885047 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:35.888361 INFO: Using random state 257323 for train-test-split
0:40:35.924581 INFO: Test AUC: 0.480
0:40:35.924685 INFO: Train AUC: 0.494
0:40:35.924715 INFO: AUC difference: 2.87%
0:40:36.135676 INFO: Resetting torch num_threads to 80
0:40:36.139817 PROGRESS: === Extracted 12186 precursors and 57773 fragments ===
0:40:36.140167 INFO: === FDR correction performed with classifier version -1 ===
0:40:36.140625 PROGRESS: ============================= Precursor FDR =============================
0:40:36.140716 PROGRESS: Total precursors accumulated: 1
0:40:36.140777 PROGRESS: Target precursors: 1 (100.00%)
0:40:36.140835 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:36.140882 PROGRESS: 
0:40:36.140924 PROGRESS: Precursor Summary:
0:40:36.141818 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:40:36.141906 PROGRESS: 
0:40:36.141961 PROGRESS: Protein Summary:
0:40:36.142943 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:40:36.143032 PROGRESS: =========================================================================
0:40:36.143344 INFO: Target number of precursors not reached yet.
0:40:36.227108 INFO: Starting optimization step 5.
0:40:36.227326 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:40:36.227405 INFO: Using ng extraction backend
0:40:36.227484 PROGRESS: Extracting batch of 12663 precursors
0:40:36.250347 INFO: === Search parameters used ===
0:40:36.250504 INFO: rt_error       : 805.611083984375
0:40:36.250555 INFO: mobility_error : 0.1
0:40:36.250602 INFO: num_candidates : 1
0:40:36.250644 INFO: ms1_error      : 30
0:40:36.250685 INFO: ms2_error      : 30
0:40:36.250726 INFO: fwhm_rt        : 5
0:40:36.250767 INFO: quant_window   : 3
0:40:36.250808 INFO: ==============================================
0:40:36.376987 INFO: performing precursor FDR with 40 features
0:40:36.377097 INFO: Decoy channel: -1
0:40:36.377124 INFO: Competetive: True
0:40:36.386972 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:36.392687 INFO: Using random state 20662 for train-test-split
0:40:36.631852 INFO: Test AUC: 0.524
0:40:36.631963 INFO: Train AUC: 0.526
0:40:36.631994 INFO: AUC difference: 0.36%
0:40:36.848289 INFO: Resetting torch num_threads to 80
0:40:36.854236 PROGRESS: === Extracted 24708 precursors and 116540 fragments ===
0:40:36.854652 INFO: === FDR correction performed with classifier version -1 ===
0:40:36.855136 PROGRESS: ============================= Precursor FDR =============================
0:40:36.855227 PROGRESS: Total precursors accumulated: 26
0:40:36.855287 PROGRESS: Target precursors: 26 (100.00%)
0:40:36.855339 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:36.855391 PROGRESS: 
0:40:36.855435 PROGRESS: Precursor Summary:
0:40:36.856338 PROGRESS: Channel   0:	 0.050 FDR:    26; 0.010 FDR:    26; 0.001 FDR:    26
0:40:36.856428 PROGRESS: 
0:40:36.856483 PROGRESS: Protein Summary:
0:40:36.857506 PROGRESS: Channel   0:	 0.050 FDR:    26; 0.010 FDR:    26; 0.001 FDR:    26
0:40:36.857607 PROGRESS: =========================================================================
0:40:36.858061 INFO: Target number of precursors not reached yet.
0:40:36.957586 INFO: Starting optimization step 6.
0:40:36.957818 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:40:36.957900 INFO: Using ng extraction backend
0:40:36.957962 PROGRESS: Extracting batch of 25339 precursors
0:40:37.002265 INFO: === Search parameters used ===
0:40:37.002470 INFO: rt_error       : 805.611083984375
0:40:37.002520 INFO: mobility_error : 0.1
0:40:37.002567 INFO: num_candidates : 1
0:40:37.002609 INFO: ms1_error      : 30
0:40:37.002652 INFO: ms2_error      : 30
0:40:37.002700 INFO: fwhm_rt        : 5
0:40:37.002742 INFO: quant_window   : 3
0:40:37.002781 INFO: ==============================================
0:40:37.220731 INFO: performing precursor FDR with 40 features
0:40:37.220851 INFO: Decoy channel: -1
0:40:37.220881 INFO: Competetive: True
0:40:37.240463 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:37.251821 INFO: Using random state 112282 for train-test-split
0:40:37.867626 INFO: Test AUC: 0.558
0:40:37.867743 INFO: Train AUC: 0.581
0:40:37.867774 INFO: AUC difference: 4.00%
0:40:38.101454 INFO: Resetting torch num_threads to 80
0:40:38.111378 PROGRESS: === Extracted 49785 precursors and 233156 fragments ===
0:40:38.111906 INFO: === FDR correction performed with classifier version -1 ===
0:40:38.112468 PROGRESS: ============================= Precursor FDR =============================
0:40:38.112561 PROGRESS: Total precursors accumulated: 93
0:40:38.112621 PROGRESS: Target precursors: 93 (100.00%)
0:40:38.112672 PROGRESS: Decoy precursors: 0 (0.00%)
0:40:38.112731 PROGRESS: 
0:40:38.112779 PROGRESS: Precursor Summary:
0:40:38.113732 PROGRESS: Channel   0:	 0.050 FDR:    93; 0.010 FDR:    93; 0.001 FDR:    93
0:40:38.113826 PROGRESS: 
0:40:38.113884 PROGRESS: Protein Summary:
0:40:38.114915 PROGRESS: Channel   0:	 0.050 FDR:    91; 0.010 FDR:    91; 0.001 FDR:    91
0:40:38.115007 PROGRESS: =========================================================================
0:40:38.115786 INFO: Target number of precursors not reached yet.
0:40:38.246729 INFO: Starting optimization step 7.
0:40:38.246965 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:40:38.247045 INFO: Using ng extraction backend
0:40:38.247108 PROGRESS: Extracting batch of 50691 precursors
0:40:38.334337 INFO: === Search parameters used ===
0:40:38.334585 INFO: rt_error       : 805.611083984375
0:40:38.334635 INFO: mobility_error : 0.1
0:40:38.334682 INFO: num_candidates : 1
0:40:38.334722 INFO: ms1_error      : 30
0:40:38.334762 INFO: ms2_error      : 30
0:40:38.334802 INFO: fwhm_rt        : 5
0:40:38.334839 INFO: quant_window   : 3
0:40:38.334876 INFO: ==============================================
0:40:38.694232 INFO: performing precursor FDR with 40 features
0:40:38.694349 INFO: Decoy channel: -1
0:40:38.694375 INFO: Competetive: True
0:40:38.735809 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:38.761488 INFO: Using random state 159808 for train-test-split
0:40:40.194182 INFO: Test AUC: 0.574
0:40:40.194299 INFO: Train AUC: 0.601
0:40:40.194329 INFO: AUC difference: 4.50%
0:40:40.443572 INFO: Resetting torch num_threads to 80
0:40:40.462161 PROGRESS: === Extracted 99985 precursors and 468362 fragments ===
0:40:40.462734 INFO: === FDR correction performed with classifier version -1 ===
0:40:40.463292 PROGRESS: ============================= Precursor FDR =============================
0:40:40.463384 PROGRESS: Total precursors accumulated: 252
0:40:40.463443 PROGRESS: Target precursors: 250 (99.21%)
0:40:40.463491 PROGRESS: Decoy precursors: 2 (0.79%)
0:40:40.463537 PROGRESS: 
0:40:40.463580 PROGRESS: Precursor Summary:
0:40:40.464489 PROGRESS: Channel   0:	 0.050 FDR:   250; 0.010 FDR:   250; 0.001 FDR:   225
0:40:40.464579 PROGRESS: 
0:40:40.464634 PROGRESS: Protein Summary:
0:40:40.465696 PROGRESS: Channel   0:	 0.050 FDR:   229; 0.010 FDR:   229; 0.001 FDR:   210
0:40:40.465787 PROGRESS: =========================================================================
0:40:40.467446 INFO: Target number of precursors reached.
0:40:40.502418 INFO: fragments_df: keeping 2201 of 468362 [sum(precursor_idx_mask)=2746 sum(mass_error_mask)=468362 stop_rank=2201
0:40:40.704223 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:40.822487 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:41.112138 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:40:41.112529 INFO: Using score_cutoff 14.284050827693939 (fac=0.99, q=1)
0:40:41.112828 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:40:41.112909 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:40:41.112972 INFO: Updating optimization_manager: score_cutoff        : 0 -> 14.284050827693939
0:40:41.113031 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:41.174614 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:41.313718 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:40:41.313952 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:40:41.314042 INFO: Starting optimization step 8.
0:40:41.314104 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:40:41.314170 INFO: Using ng extraction backend
0:40:41.314228 PROGRESS: Extracting batch of 100984 precursors
0:40:41.485905 INFO: === Search parameters used ===
0:40:41.486155 INFO: rt_error       : 805.611083984375
0:40:41.486207 INFO: mobility_error : 0.1
0:40:41.486253 INFO: num_candidates : 3
0:40:41.486294 INFO: ms1_error      : 30
0:40:41.486334 INFO: ms2_error      : 30
0:40:41.486374 INFO: fwhm_rt        : 3.0
0:40:41.486412 INFO: quant_window   : 3
0:40:41.486453 INFO: ==============================================
0:40:42.727891 INFO: performing precursor FDR with 40 features
0:40:42.728009 INFO: Decoy channel: -1
0:40:42.728036 INFO: Competetive: True
0:40:42.807270 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:42.911762 INFO: Using random state 814754 for train-test-split
0:40:46.905628 INFO: Test AUC: 0.593
0:40:46.905745 INFO: Train AUC: 0.608
0:40:46.905776 INFO: AUC difference: 2.39%
0:40:47.206396 INFO: Resetting torch num_threads to 80
0:40:47.218603 PROGRESS: === Extracted 300163 precursors and 1376668 fragments ===
0:40:47.218985 INFO: === FDR correction performed with classifier version 7 ===
0:40:47.219444 PROGRESS: ============================= Precursor FDR =============================
0:40:47.219539 PROGRESS: Total precursors accumulated: 297
0:40:47.219600 PROGRESS: Target precursors: 295 (99.33%)
0:40:47.219650 PROGRESS: Decoy precursors: 2 (0.67%)
0:40:47.219696 PROGRESS: 
0:40:47.219738 PROGRESS: Precursor Summary:
0:40:47.220623 PROGRESS: Channel   0:	 0.050 FDR:   295; 0.010 FDR:   295; 0.001 FDR:   261
0:40:47.220711 PROGRESS: 
0:40:47.220764 PROGRESS: Protein Summary:
0:40:47.221818 PROGRESS: Channel   0:	 0.050 FDR:   274; 0.010 FDR:   274; 0.001 FDR:   242
0:40:47.221911 PROGRESS: =========================================================================
0:40:47.227084 INFO: Target number of precursors reached.
0:40:47.320157 INFO: fragments_df: keeping 3406 of 1376668 [sum(precursor_idx_mask)=6433 sum(mass_error_mask)=1376668 stop_rank=3406
0:40:47.529350 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:47.627557 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:48.005113 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:48.005522 INFO: Using score_cutoff 12.614522830581665 (fac=0.99, q=1)
0:40:48.005800 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:48.005879 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:48.005934 INFO: Updating optimization_manager: score_cutoff        : 14.284050827693939 -> 12.614522830581665
0:40:48.005987 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:48.067576 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:48.204462 INFO: === checking if optimization conditions were reached ===
0:40:48.206321 INFO: Updating optimization_manager: ms2_error           : 30 -> 10.0
0:40:48.206424 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:40:48.206488 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:40:48.206548 INFO: ==============================================
0:40:48.206613 INFO: Starting optimization step 9.
0:40:48.206668 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:40:48.206724 INFO: Using ng extraction backend
0:40:48.206781 PROGRESS: Extracting batch of 100984 precursors
0:40:48.378482 INFO: === Search parameters used ===
0:40:48.378735 INFO: rt_error       : 805.611083984375
0:40:48.378789 INFO: mobility_error : 0.1
0:40:48.378836 INFO: num_candidates : 3
0:40:48.378878 INFO: ms1_error      : 30
0:40:48.378918 INFO: ms2_error      : 10.0
0:40:48.378959 INFO: fwhm_rt        : 3.0
0:40:48.378997 INFO: quant_window   : 3
0:40:48.379037 INFO: ==============================================
0:40:49.641182 INFO: performing precursor FDR with 40 features
0:40:49.641302 INFO: Decoy channel: -1
0:40:49.641329 INFO: Competetive: True
0:40:49.720766 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:49.823750 INFO: Using random state 814022 for train-test-split
0:40:53.938337 INFO: Test AUC: 0.594
0:40:53.938463 INFO: Train AUC: 0.609
0:40:53.938493 INFO: AUC difference: 2.39%
0:40:55.511532 INFO: Resetting torch num_threads to 80
0:40:55.523577 PROGRESS: === Extracted 302279 precursors and 1615349 fragments ===
0:40:55.523956 INFO: === FDR correction performed with classifier version 8 ===
0:40:55.524454 PROGRESS: ============================= Precursor FDR =============================
0:40:55.524548 PROGRESS: Total precursors accumulated: 521
0:40:55.524605 PROGRESS: Target precursors: 516 (99.04%)
0:40:55.524655 PROGRESS: Decoy precursors: 5 (0.96%)
0:40:55.524699 PROGRESS: 
0:40:55.524744 PROGRESS: Precursor Summary:
0:40:55.525737 PROGRESS: Channel   0:	 0.050 FDR:   516; 0.010 FDR:   516; 0.001 FDR:   348
0:40:55.525834 PROGRESS: 
0:40:55.525890 PROGRESS: Protein Summary:
0:40:55.527072 PROGRESS: Channel   0:	 0.050 FDR:   486; 0.010 FDR:   486; 0.001 FDR:   326
0:40:55.527164 PROGRESS: =========================================================================
0:40:55.532336 INFO: Target number of precursors reached.
0:40:55.636309 INFO: fragments_df: keeping 5000 of 1615349 [sum(precursor_idx_mask)=12053 sum(mass_error_mask)=1615349 stop_rank=5000
0:40:55.820595 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:55.936697 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:56.551981 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:56.552386 INFO: Using score_cutoff 9.492345660209654 (fac=0.99, q=1)
0:40:56.552670 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:56.552750 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:56.552804 INFO: Updating optimization_manager: score_cutoff        : 12.614522830581665 -> 9.492345660209654
0:40:56.552883 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:56.583551 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:56.650849 INFO: === checking if optimization conditions were reached ===
0:40:56.652928 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:40:56.653033 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:40:56.653101 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:40:56.653159 INFO: ==============================================
0:40:56.653224 PROGRESS: Optimization finished for ms2_error.
0:40:56.785444 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:56.816366 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:56.883885 INFO: Starting optimization step 0.
0:40:56.884112 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:40:56.884191 INFO: Using ng extraction backend
0:40:56.884254 PROGRESS: Extracting batch of 50293 precursors
0:40:56.971083 INFO: === Search parameters used ===
0:40:56.971373 INFO: rt_error       : 805.611083984375
0:40:56.971427 INFO: mobility_error : 0.1
0:40:56.971473 INFO: num_candidates : 3
0:40:56.971517 INFO: ms1_error      : 30
0:40:56.971558 INFO: ms2_error      : 10.0
0:40:56.971605 INFO: fwhm_rt        : 3.0
0:40:56.971648 INFO: quant_window   : 3
0:40:56.971688 INFO: ==============================================
0:40:57.608741 INFO: performing precursor FDR with 40 features
0:40:57.608866 INFO: Decoy channel: -1
0:40:57.608894 INFO: Competetive: True
0:40:57.647568 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:57.683022 INFO: Using random state 807974 for train-test-split
0:40:59.594297 INFO: Test AUC: 0.602
0:40:59.594414 INFO: Train AUC: 0.616
0:40:59.594446 INFO: AUC difference: 2.30%
0:40:59.860297 INFO: Resetting torch num_threads to 80
0:40:59.866753 PROGRESS: === Extracted 150531 precursors and 804285 fragments ===
0:40:59.867097 INFO: === FDR correction performed with classifier version 9 ===
0:40:59.867538 PROGRESS: ============================= Precursor FDR =============================
0:40:59.867630 PROGRESS: Total precursors accumulated: 235
0:40:59.867688 PROGRESS: Target precursors: 233 (99.15%)
0:40:59.867739 PROGRESS: Decoy precursors: 2 (0.85%)
0:40:59.867784 PROGRESS: 
0:40:59.867827 PROGRESS: Precursor Summary:
0:40:59.868719 PROGRESS: Channel   0:	 0.050 FDR:   233; 0.010 FDR:   233; 0.001 FDR:   180
0:40:59.868819 PROGRESS: 
0:40:59.868879 PROGRESS: Protein Summary:
0:40:59.869906 PROGRESS: Channel   0:	 0.050 FDR:   228; 0.010 FDR:   228; 0.001 FDR:   175
0:40:59.869997 PROGRESS: =========================================================================
0:40:59.872166 INFO: Target number of precursors reached.
0:40:59.925861 INFO: fragments_df: keeping 2689 of 804285 [sum(precursor_idx_mask)=5676 sum(mass_error_mask)=804285 stop_rank=2689
0:41:00.060145 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:00.154025 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:00.450648 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:00.451068 INFO: Using score_cutoff 12.976960854721069 (fac=0.99, q=1)
0:41:00.451351 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:00.451430 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:00.451483 INFO: Updating optimization_manager: score_cutoff        : 9.492345660209654 -> 12.976960854721069
0:41:00.451538 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:00.481892 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:00.547744 INFO: === checking if optimization conditions were reached ===
0:41:00.547981 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
0:41:00.549723 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 157.8115758908721
0:41:00.549825 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 157.8116.
0:41:00.549890 INFO: ==============================================
0:41:00.549960 INFO: Starting optimization step 1.
0:41:00.550017 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:41:00.550077 INFO: Using ng extraction backend
0:41:00.550133 PROGRESS: Extracting batch of 50293 precursors
0:41:00.637080 INFO: === Search parameters used ===
0:41:00.637343 INFO: rt_error       : 157.8115758908721
0:41:00.637397 INFO: mobility_error : 0.1
0:41:00.637440 INFO: num_candidates : 3
0:41:00.637481 INFO: ms1_error      : 30
0:41:00.637534 INFO: ms2_error      : 10.0
0:41:00.637574 INFO: fwhm_rt        : 3.0
0:41:00.637612 INFO: quant_window   : 3
0:41:00.637649 INFO: ==============================================
0:41:01.210786 INFO: performing precursor FDR with 40 features
0:41:01.210899 INFO: Decoy channel: -1
0:41:01.210926 INFO: Competetive: True
0:41:01.249759 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:01.285609 INFO: Using random state 807974 for train-test-split
0:41:03.116827 INFO: Test AUC: 0.589
0:41:03.116942 INFO: Train AUC: 0.609
0:41:03.116973 INFO: AUC difference: 3.28%
0:41:03.379157 INFO: Resetting torch num_threads to 80
0:41:03.385578 PROGRESS: === Extracted 148641 precursors and 653906 fragments ===
0:41:03.385921 INFO: === FDR correction performed with classifier version 9 ===
0:41:03.386356 PROGRESS: ============================= Precursor FDR =============================
0:41:03.386448 PROGRESS: Total precursors accumulated: 237
0:41:03.386507 PROGRESS: Target precursors: 235 (99.16%)
0:41:03.386556 PROGRESS: Decoy precursors: 2 (0.84%)
0:41:03.386601 PROGRESS: 
0:41:03.386643 PROGRESS: Precursor Summary:
0:41:03.387506 PROGRESS: Channel   0:	 0.050 FDR:   235; 0.010 FDR:   235; 0.001 FDR:   210
0:41:03.387594 PROGRESS: 
0:41:03.387647 PROGRESS: Protein Summary:
0:41:03.388649 PROGRESS: Channel   0:	 0.050 FDR:   229; 0.010 FDR:   229; 0.001 FDR:   205
0:41:03.388737 PROGRESS: =========================================================================
0:41:03.390850 INFO: Target number of precursors reached.
0:41:03.433971 INFO: fragments_df: keeping 2719 of 653906 [sum(precursor_idx_mask)=5619 sum(mass_error_mask)=653906 stop_rank=2719
0:41:03.568193 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:03.659285 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:03.959231 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:03.959638 INFO: Using score_cutoff 13.914608501815795 (fac=0.99, q=1)
0:41:03.959915 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:03.959996 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:03.960050 INFO: Updating optimization_manager: score_cutoff        : 12.976960854721069 -> 13.914608501815795
0:41:03.960105 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:03.990967 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:04.057962 INFO: === checking if optimization conditions were reached ===
0:41:04.058196 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
0:41:04.060005 INFO: Updating optimization_manager: rt_error            : 157.8115758908721 -> 109.84997954418647
0:41:04.060106 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 109.8500.
0:41:04.060169 INFO: ==============================================
0:41:04.060238 INFO: Starting optimization step 2.
0:41:04.060294 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:41:04.060354 INFO: Using ng extraction backend
0:41:04.060410 PROGRESS: Extracting batch of 50293 precursors
0:41:04.147337 INFO: === Search parameters used ===
0:41:04.147609 INFO: rt_error       : 109.84997954418647
0:41:04.147666 INFO: mobility_error : 0.1
0:41:04.148405 INFO: num_candidates : 3
0:41:04.148461 INFO: ms1_error      : 30
0:41:04.148505 INFO: ms2_error      : 10.0
0:41:04.148548 INFO: fwhm_rt        : 3.0
0:41:04.148587 INFO: quant_window   : 3
0:41:04.148626 INFO: ==============================================
0:41:04.729796 INFO: performing precursor FDR with 40 features
0:41:04.729916 INFO: Decoy channel: -1
0:41:04.729944 INFO: Competetive: True
0:41:04.770000 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:04.806136 INFO: Using random state 807974 for train-test-split
0:41:06.714952 INFO: Test AUC: 0.596
0:41:06.715071 INFO: Train AUC: 0.605
0:41:06.715102 INFO: AUC difference: 1.63%
0:41:06.971650 INFO: Resetting torch num_threads to 80
0:41:06.978148 PROGRESS: === Extracted 147548 precursors and 611486 fragments ===
0:41:06.978495 INFO: === FDR correction performed with classifier version 9 ===
0:41:06.978934 PROGRESS: ============================= Precursor FDR =============================
0:41:06.979025 PROGRESS: Total precursors accumulated: 252
0:41:06.979082 PROGRESS: Target precursors: 250 (99.21%)
0:41:06.979131 PROGRESS: Decoy precursors: 2 (0.79%)
0:41:06.979176 PROGRESS: 
0:41:06.979217 PROGRESS: Precursor Summary:
0:41:06.980113 PROGRESS: Channel   0:	 0.050 FDR:   250; 0.010 FDR:   250; 0.001 FDR:   199
0:41:06.980208 PROGRESS: 
0:41:06.980266 PROGRESS: Protein Summary:
0:41:06.981295 PROGRESS: Channel   0:	 0.050 FDR:   243; 0.010 FDR:   243; 0.001 FDR:   194
0:41:06.981388 PROGRESS: =========================================================================
0:41:06.983526 INFO: Target number of precursors reached.
0:41:07.024449 INFO: fragments_df: keeping 2838 of 611486 [sum(precursor_idx_mask)=5876 sum(mass_error_mask)=611486 stop_rank=2838
0:41:07.159039 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:07.273583 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:07.650275 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:07.650683 INFO: Using score_cutoff 13.01873410835266 (fac=0.99, q=1)
0:41:07.650964 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:07.651047 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:07.651100 INFO: Updating optimization_manager: score_cutoff        : 13.914608501815795 -> 13.01873410835266
0:41:07.651154 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:07.681828 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:07.748158 INFO: === checking if optimization conditions were reached ===
0:41:07.748425 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
0:41:07.750715 INFO: Updating optimization_manager: rt_error            : 109.84997954418647 -> 89.52980750922133
0:41:07.750830 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 89.5298.
0:41:07.750906 INFO: ==============================================
0:41:07.750987 INFO: Starting optimization step 3.
0:41:07.751052 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:41:07.751122 INFO: Using ng extraction backend
0:41:07.751186 PROGRESS: Extracting batch of 50293 precursors
0:41:07.838721 INFO: === Search parameters used ===
0:41:07.838998 INFO: rt_error       : 89.52980750922133
0:41:07.839054 INFO: mobility_error : 0.1
0:41:07.839099 INFO: num_candidates : 3
0:41:07.839142 INFO: ms1_error      : 30
0:41:07.839182 INFO: ms2_error      : 10.0
0:41:07.839222 INFO: fwhm_rt        : 3.0
0:41:07.839261 INFO: quant_window   : 3
0:41:07.839299 INFO: ==============================================
0:41:08.425320 INFO: performing precursor FDR with 40 features
0:41:08.425439 INFO: Decoy channel: -1
0:41:08.425470 INFO: Competetive: True
0:41:08.464307 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:08.498767 INFO: Using random state 807974 for train-test-split
0:41:10.353060 INFO: Test AUC: 0.593
0:41:10.353182 INFO: Train AUC: 0.609
0:41:10.353213 INFO: AUC difference: 2.62%
0:41:10.613370 INFO: Resetting torch num_threads to 80
0:41:10.620041 PROGRESS: === Extracted 146628 precursors and 585681 fragments ===
0:41:10.620385 INFO: === FDR correction performed with classifier version 9 ===
0:41:10.620844 PROGRESS: ============================= Precursor FDR =============================
0:41:10.620933 PROGRESS: Total precursors accumulated: 303
0:41:10.620997 PROGRESS: Target precursors: 300 (99.01%)
0:41:10.621046 PROGRESS: Decoy precursors: 3 (0.99%)
0:41:10.621092 PROGRESS: 
0:41:10.621135 PROGRESS: Precursor Summary:
0:41:10.622032 PROGRESS: Channel   0:	 0.050 FDR:   300; 0.010 FDR:   290; 0.001 FDR:   231
0:41:10.622120 PROGRESS: 
0:41:10.622174 PROGRESS: Protein Summary:
0:41:10.623226 PROGRESS: Channel   0:	 0.050 FDR:   288; 0.010 FDR:   279; 0.001 FDR:   224
0:41:10.623314 PROGRESS: =========================================================================
0:41:10.625418 INFO: Target number of precursors reached.
0:41:10.666029 INFO: fragments_df: keeping 3112 of 585681 [sum(precursor_idx_mask)=6698 sum(mass_error_mask)=585681 stop_rank=3112
0:41:10.799581 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:10.913371 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:11.323015 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:11.323418 INFO: Using score_cutoff 12.911580942249298 (fac=0.99, q=1)
0:41:11.323699 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:11.323777 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:11.323829 INFO: Updating optimization_manager: score_cutoff        : 13.01873410835266 -> 12.911580942249298
0:41:11.323883 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:11.354682 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:11.420973 INFO: === checking if optimization conditions were reached ===
0:41:11.421228 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
0:41:11.423497 INFO: Updating optimization_manager: rt_error            : 89.52980750922133 -> 66.03327369239696
0:41:11.423614 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 66.0333.
0:41:11.423687 INFO: ==============================================
0:41:11.423767 INFO: Starting optimization step 4.
0:41:11.423833 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:41:11.423904 INFO: Using ng extraction backend
0:41:11.423984 PROGRESS: Extracting batch of 50293 precursors
0:41:11.513702 INFO: === Search parameters used ===
0:41:11.513951 INFO: rt_error       : 66.03327369239696
0:41:11.514003 INFO: mobility_error : 0.1
0:41:11.514048 INFO: num_candidates : 3
0:41:11.514088 INFO: ms1_error      : 30
0:41:11.514128 INFO: ms2_error      : 10.0
0:41:11.514169 INFO: fwhm_rt        : 3.0
0:41:11.514208 INFO: quant_window   : 3
0:41:11.514246 INFO: ==============================================
0:41:12.087152 INFO: performing precursor FDR with 40 features
0:41:12.087286 INFO: Decoy channel: -1
0:41:12.087312 INFO: Competetive: True
0:41:12.126648 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:12.160177 INFO: Using random state 807974 for train-test-split
0:41:13.934397 INFO: Test AUC: 0.593
0:41:13.934512 INFO: Train AUC: 0.607
0:41:13.934543 INFO: AUC difference: 2.32%
0:41:14.194663 INFO: Resetting torch num_threads to 80
0:41:14.201070 PROGRESS: === Extracted 144215 precursors and 544043 fragments ===
0:41:14.201411 INFO: === FDR correction performed with classifier version 9 ===
0:41:14.201845 PROGRESS: ============================= Precursor FDR =============================
0:41:14.201932 PROGRESS: Total precursors accumulated: 254
0:41:14.201989 PROGRESS: Target precursors: 252 (99.21%)
0:41:14.202040 PROGRESS: Decoy precursors: 2 (0.79%)
0:41:14.202085 PROGRESS: 
0:41:14.202129 PROGRESS: Precursor Summary:
0:41:14.202996 PROGRESS: Channel   0:	 0.050 FDR:   252; 0.010 FDR:   252; 0.001 FDR:    95
0:41:14.203089 PROGRESS: 
0:41:14.203145 PROGRESS: Protein Summary:
0:41:14.204151 PROGRESS: Channel   0:	 0.050 FDR:   243; 0.010 FDR:   243; 0.001 FDR:    93
0:41:14.204249 PROGRESS: =========================================================================
0:41:14.206308 INFO: Target number of precursors reached.
0:41:14.244063 INFO: fragments_df: keeping 2624 of 544043 [sum(precursor_idx_mask)=5518 sum(mass_error_mask)=544043 stop_rank=2624
0:41:14.377312 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:14.472725 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:14.758750 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:14.759284 INFO: Using score_cutoff 6.086819845819473 (fac=0.99, q=1)
0:41:14.759566 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:14.759646 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:14.759700 INFO: Updating optimization_manager: score_cutoff        : 12.911580942249298 -> 6.086819845819473
0:41:14.759755 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:14.790794 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:14.858014 INFO: === checking if optimization conditions were reached ===
0:41:14.858265 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
0:41:14.860170 INFO: Updating optimization_manager: rt_error            : 66.03327369239696 -> 47.527704954030646
0:41:14.860272 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 47.5277.
0:41:14.860336 INFO: ==============================================
0:41:14.860406 INFO: Starting optimization step 5.
0:41:14.860463 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:41:14.860529 INFO: Using ng extraction backend
0:41:14.860587 PROGRESS: Extracting batch of 50293 precursors
0:41:14.947553 INFO: === Search parameters used ===
0:41:14.947806 INFO: rt_error       : 47.527704954030646
0:41:14.947859 INFO: mobility_error : 0.1
0:41:14.947902 INFO: num_candidates : 3
0:41:14.947946 INFO: ms1_error      : 30
0:41:14.947986 INFO: ms2_error      : 10.0
0:41:14.948024 INFO: fwhm_rt        : 3.0
0:41:14.948062 INFO: quant_window   : 3
0:41:14.948098 INFO: ==============================================
0:41:15.469267 INFO: performing precursor FDR with 40 features
0:41:15.469383 INFO: Decoy channel: -1
0:41:15.469410 INFO: Competetive: True
0:41:15.504648 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:15.535616 INFO: Using random state 807974 for train-test-split
0:41:17.203273 INFO: Test AUC: 0.595
0:41:17.203389 INFO: Train AUC: 0.609
0:41:17.203420 INFO: AUC difference: 2.35%
0:41:17.460328 INFO: Resetting torch num_threads to 80
0:41:17.466375 PROGRESS: === Extracted 133268 precursors and 475397 fragments ===
0:41:17.466716 INFO: === FDR correction performed with classifier version 9 ===
0:41:17.467151 PROGRESS: ============================= Precursor FDR =============================
0:41:17.467237 PROGRESS: Total precursors accumulated: 230
0:41:17.467294 PROGRESS: Target precursors: 228 (99.13%)
0:41:17.467345 PROGRESS: Decoy precursors: 2 (0.87%)
0:41:17.467390 PROGRESS: 
0:41:17.467435 PROGRESS: Precursor Summary:
0:41:17.468289 PROGRESS: Channel   0:	 0.050 FDR:   228; 0.010 FDR:   228; 0.001 FDR:   161
0:41:17.468376 PROGRESS: 
0:41:17.468440 PROGRESS: Protein Summary:
0:41:17.469474 PROGRESS: Channel   0:	 0.050 FDR:   225; 0.010 FDR:   225; 0.001 FDR:   159
0:41:17.469567 PROGRESS: =========================================================================
0:41:17.471519 INFO: Target number of precursors reached.
0:41:17.503758 INFO: fragments_df: keeping 2343 of 475397 [sum(precursor_idx_mask)=4672 sum(mass_error_mask)=475397 stop_rank=2343
0:41:17.637658 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:17.731234 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:17.989091 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:17.989489 INFO: Using score_cutoff 13.130322530651092 (fac=0.99, q=1)
0:41:17.989767 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:17.989847 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:17.989900 INFO: Updating optimization_manager: score_cutoff        : 6.086819845819473 -> 13.130322530651092
0:41:17.989952 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:18.021183 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:18.086572 INFO: === checking if optimization conditions were reached ===
0:41:18.086797 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
0:41:18.088666 INFO: Updating optimization_manager: rt_error            : 47.527704954030646 -> 36.66285444770147
0:41:18.088767 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 36.6629.
0:41:18.088850 INFO: ==============================================
0:41:18.088935 INFO: Starting optimization step 6.
0:41:18.088996 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:41:18.089056 INFO: Using ng extraction backend
0:41:18.089114 PROGRESS: Extracting batch of 50293 precursors
0:41:18.176343 INFO: === Search parameters used ===
0:41:18.176600 INFO: rt_error       : 36.66285444770147
0:41:18.176656 INFO: mobility_error : 0.1
0:41:18.176701 INFO: num_candidates : 3
0:41:18.176742 INFO: ms1_error      : 30
0:41:18.176785 INFO: ms2_error      : 10.0
0:41:18.176834 INFO: fwhm_rt        : 3.0
0:41:18.176876 INFO: quant_window   : 3
0:41:18.176916 INFO: ==============================================
0:41:18.703602 INFO: performing precursor FDR with 40 features
0:41:18.703720 INFO: Decoy channel: -1
0:41:18.703748 INFO: Competetive: True
0:41:18.740389 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:18.772099 INFO: Using random state 807974 for train-test-split
0:41:20.451335 INFO: Test AUC: 0.594
0:41:20.451452 INFO: Train AUC: 0.610
0:41:20.451484 INFO: AUC difference: 2.55%
0:41:20.712614 INFO: Resetting torch num_threads to 80
0:41:20.718783 PROGRESS: === Extracted 133563 precursors and 475613 fragments ===
0:41:20.719121 INFO: === FDR correction performed with classifier version 9 ===
0:41:20.719549 PROGRESS: ============================= Precursor FDR =============================
0:41:20.719633 PROGRESS: Total precursors accumulated: 237
0:41:20.719690 PROGRESS: Target precursors: 235 (99.16%)
0:41:20.719739 PROGRESS: Decoy precursors: 2 (0.84%)
0:41:20.719784 PROGRESS: 
0:41:20.719827 PROGRESS: Precursor Summary:
0:41:20.720682 PROGRESS: Channel   0:	 0.050 FDR:   235; 0.010 FDR:   235; 0.001 FDR:   164
0:41:20.720779 PROGRESS: 
0:41:20.720844 PROGRESS: Protein Summary:
0:41:20.721844 PROGRESS: Channel   0:	 0.050 FDR:   229; 0.010 FDR:   229; 0.001 FDR:   161
0:41:20.721932 PROGRESS: =========================================================================
0:41:20.723891 INFO: Target number of precursors reached.
0:41:20.756621 INFO: fragments_df: keeping 2342 of 475613 [sum(precursor_idx_mask)=4670 sum(mass_error_mask)=475613 stop_rank=2342
0:41:20.889806 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:21.009024 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:21.331282 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:21.331688 INFO: Using score_cutoff 6.308986940002441 (fac=0.99, q=1)
0:41:21.331968 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:21.332046 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:21.332100 INFO: Updating optimization_manager: score_cutoff        : 13.130322530651092 -> 6.308986940002441
0:41:21.332155 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:21.363338 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:21.459941 INFO: === checking if optimization conditions were reached ===
0:41:21.460215 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
0:41:21.462477 INFO: Updating optimization_manager: rt_error            : 36.66285444770147 -> 33.721367649789165
0:41:21.462592 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 33.7214.
0:41:21.463532 INFO: ==============================================
0:41:21.463630 INFO: Starting optimization step 7.
0:41:21.463698 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:41:21.463769 INFO: Using ng extraction backend
0:41:21.463837 PROGRESS: Extracting batch of 50293 precursors
0:41:21.552159 INFO: === Search parameters used ===
0:41:21.552399 INFO: rt_error       : 33.721367649789165
0:41:21.552452 INFO: mobility_error : 0.1
0:41:21.552496 INFO: num_candidates : 3
0:41:21.552538 INFO: ms1_error      : 30
0:41:21.552577 INFO: ms2_error      : 10.0
0:41:21.552618 INFO: fwhm_rt        : 3.0
0:41:21.552656 INFO: quant_window   : 3
0:41:21.552693 INFO: ==============================================
0:41:22.098794 INFO: performing precursor FDR with 40 features
0:41:22.099639 INFO: Decoy channel: -1
0:41:22.099689 INFO: Competetive: True
0:41:22.137325 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:22.170153 INFO: Using random state 807974 for train-test-split
0:41:24.030538 INFO: Test AUC: 0.593
0:41:24.030652 INFO: Train AUC: 0.609
0:41:24.030683 INFO: AUC difference: 2.71%
0:41:24.291768 INFO: Resetting torch num_threads to 80
0:41:24.297952 PROGRESS: === Extracted 133592 precursors and 475852 fragments ===
0:41:24.298292 INFO: === FDR correction performed with classifier version 9 ===
0:41:24.298717 PROGRESS: ============================= Precursor FDR =============================
0:41:24.298803 PROGRESS: Total precursors accumulated: 229
0:41:24.298859 PROGRESS: Target precursors: 227 (99.13%)
0:41:24.298909 PROGRESS: Decoy precursors: 2 (0.87%)
0:41:24.298953 PROGRESS: 
0:41:24.299004 PROGRESS: Precursor Summary:
0:41:24.299873 PROGRESS: Channel   0:	 0.050 FDR:   227; 0.010 FDR:   227; 0.001 FDR:   175
0:41:24.299962 PROGRESS: 
0:41:24.300018 PROGRESS: Protein Summary:
0:41:24.301027 PROGRESS: Channel   0:	 0.050 FDR:   221; 0.010 FDR:   221; 0.001 FDR:   172
0:41:24.301117 PROGRESS: =========================================================================
0:41:24.303102 INFO: Target number of precursors reached.
0:41:24.335828 INFO: fragments_df: keeping 2300 of 475852 [sum(precursor_idx_mask)=4629 sum(mass_error_mask)=475852 stop_rank=2300
0:41:24.471755 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:24.629965 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:24.893960 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:24.894363 INFO: Using score_cutoff 13.130272765159607 (fac=0.99, q=1)
0:41:24.894643 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:24.894722 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:24.894778 INFO: Updating optimization_manager: score_cutoff        : 6.308986940002441 -> 13.130272765159607
0:41:24.894831 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:24.926180 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:25.009190 INFO: === checking if optimization conditions were reached ===
0:41:25.009458 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
0:41:25.011698 INFO: Updating optimization_manager: rt_error            : 33.721367649789165 -> 34.70547897528892
0:41:25.011814 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 34.7055.
0:41:25.011891 INFO: ==============================================
0:41:25.011972 INFO: Starting optimization step 8.
0:41:25.012038 PROGRESS: === Extracting elution groups 0 to 25400 ===
0:41:25.012109 INFO: Using ng extraction backend
0:41:25.012175 PROGRESS: Extracting batch of 50293 precursors
0:41:25.124051 INFO: === Search parameters used ===
0:41:25.124324 INFO: rt_error       : 34.70547897528892
0:41:25.124384 INFO: mobility_error : 0.1
0:41:25.124430 INFO: num_candidates : 3
0:41:25.124477 INFO: ms1_error      : 30
0:41:25.124517 INFO: ms2_error      : 10.0
0:41:25.124556 INFO: fwhm_rt        : 3.0
0:41:25.124593 INFO: quant_window   : 3
0:41:25.124631 INFO: ==============================================
0:41:25.652132 INFO: performing precursor FDR with 40 features
0:41:25.652248 INFO: Decoy channel: -1
0:41:25.652274 INFO: Competetive: True
0:41:25.689187 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:25.722047 INFO: Using random state 807974 for train-test-split
0:41:27.676340 INFO: Test AUC: 0.596
0:41:27.676462 INFO: Train AUC: 0.611
0:41:27.676493 INFO: AUC difference: 2.44%
0:41:27.933671 INFO: Resetting torch num_threads to 80
0:41:27.939806 PROGRESS: === Extracted 134002 precursors and 479793 fragments ===
0:41:27.940145 INFO: === FDR correction performed with classifier version 9 ===
0:41:27.940582 PROGRESS: ============================= Precursor FDR =============================
0:41:27.940673 PROGRESS: Total precursors accumulated: 246
0:41:27.940732 PROGRESS: Target precursors: 244 (99.19%)
0:41:27.940791 PROGRESS: Decoy precursors: 2 (0.81%)
0:41:27.940861 PROGRESS: 
0:41:27.940916 PROGRESS: Precursor Summary:
0:41:27.941793 PROGRESS: Channel   0:	 0.050 FDR:   244; 0.010 FDR:   244; 0.001 FDR:   205
0:41:27.941880 PROGRESS: 
0:41:27.941933 PROGRESS: Protein Summary:
0:41:27.942936 PROGRESS: Channel   0:	 0.050 FDR:   237; 0.010 FDR:   237; 0.001 FDR:   199
0:41:27.943028 PROGRESS: =========================================================================
0:41:27.945014 INFO: Target number of precursors reached.
0:41:27.977415 INFO: fragments_df: keeping 2392 of 479793 [sum(precursor_idx_mask)=4912 sum(mass_error_mask)=479793 stop_rank=2392
0:41:28.110497 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:28.228116 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:28.542854 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:28.543250 INFO: Using score_cutoff 11.160871294784545 (fac=0.99, q=1)
0:41:28.543524 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:28.543604 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:28.543659 INFO: Updating optimization_manager: score_cutoff        : 13.130272765159607 -> 11.160871294784545
0:41:28.543713 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:28.575244 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:28.638795 INFO: === checking if optimization conditions were reached ===
0:41:28.639042 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
0:41:28.640065 INFO: Updating optimization_manager: rt_error            : 34.70547897528892 -> 89.52980750922133
0:41:28.640189 INFO: Updating optimization_manager: classifier_version  : 9 -> 13
0:41:28.640284 INFO: Updating optimization_manager: score_cutoff        : 11.160871294784545 -> 12.911580942249298
0:41:28.640370 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:28.640449 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:28.640530 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 89.5298 found after 9 searches.
0:41:28.640590 INFO: ==============================================
0:41:28.640655 PROGRESS: Optimization finished for rt_error.
0:41:28.772179 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:28.804000 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:28.892624 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:41:28.892836 PROGRESS: ==============================================
0:41:28.892907 PROGRESS: ms2_error      : 10.0000
0:41:28.892962 PROGRESS: rt_error       : 89.5298
0:41:28.893009 PROGRESS: ==============================================
0:41:28.893422 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:36.799843 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:54.256971 INFO: Using ng extraction backend
0:41:54.257262 PROGRESS: Extracting batch of 12001526 precursors
0:42:10.081713 INFO: === Search parameters used ===
0:42:10.081964 INFO: rt_error       : 89.52980750922133
0:42:10.082024 INFO: mobility_error : 0.1
0:42:10.082075 INFO: num_candidates : 3
0:42:10.082119 INFO: ms1_error      : 30
0:42:10.082161 INFO: ms2_error      : 10.0
0:42:10.082203 INFO: fwhm_rt        : 3.0
0:42:10.082243 INFO: quant_window   : 3
0:42:10.082283 INFO: ==============================================
0:42:37.002654 INFO: Removed 26384036 precursors with score below cutoff 12.911580942249298
0:42:47.758822 INFO: performing precursor FDR with 40 features
0:42:47.758970 INFO: Decoy channel: -1
0:42:47.759003 INFO: Competetive: True
0:42:49.191669 INFO: Setting torch num_threads to 2 for FDR classification task
0:42:53.182878 INFO: Using random state 331433 for train-test-split
0:45:04.181342 INFO: Test AUC: 0.623
0:45:04.181480 INFO: Train AUC: 0.624
0:45:04.181515 INFO: AUC difference: 0.06%
0:45:07.199271 INFO: Resetting torch num_threads to 80
0:45:08.791739 PROGRESS: ============================= Precursor FDR =============================
0:45:08.791981 PROGRESS: Total precursors accumulated: 86,436
0:45:08.792044 PROGRESS: Target precursors: 85,581 (99.01%)
0:45:08.792102 PROGRESS: Decoy precursors: 855 (0.99%)
0:45:08.792149 PROGRESS: 
0:45:08.792192 PROGRESS: Precursor Summary:
0:45:08.821118 PROGRESS: Channel   0:	 0.050 FDR: 85,581; 0.010 FDR: 85,581; 0.001 FDR: 63,502
0:45:08.821352 PROGRESS: 
0:45:08.821415 PROGRESS: Protein Summary:
0:45:08.865134 PROGRESS: Channel   0:	 0.050 FDR: 13,013; 0.010 FDR: 13,013; 0.001 FDR: 9,802
0:45:08.865364 PROGRESS: =========================================================================
0:45:08.928903 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/psm.parquet
0:45:09.114817 INFO: Saving results to run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.parquet
0:45:09.354461 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:45:41.382434 PROGRESS: Processing search outputs
0:45:41.382538 PROGRESS: Performing protein grouping and FDR
0:45:41.382571 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:45:41.436487 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:45:41.470115 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:45:41.509334 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:45:41.550215 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:45:41.588530 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:45:41.635510 INFO: Building combined output
0:45:41.657768 INFO: Performing protein inference
0:45:42.179770 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
0:46:24.451621 INFO: Performing protein FDR
0:46:29.733081 INFO: Normalizing q-values using 17,903 targets and 3,470 decoys
0:46:29.736607 INFO: Test AUC: 0.864
0:46:29.736658 INFO: Train AUC: 0.863
0:46:29.736690 INFO: AUC difference: 0.18%
0:46:30.292212 PROGRESS: ================ Protein FDR =================
0:46:30.292342 PROGRESS: Unique protein groups in output
0:46:30.292374 PROGRESS:   1% protein FDR: 10,219
0:46:30.292397 PROGRESS: 
0:46:30.292416 PROGRESS: Unique precursor in output
0:46:30.292434 PROGRESS:   1% protein FDR: 119,661
0:46:30.292456 PROGRESS: ================================================
0:46:30.355525 PROGRESS: Building search statistics
0:46:30.443818 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
0:46:30.444020 INFO: Initializing OptimizationManager
0:46:30.444238 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
0:46:30.444321 INFO: Initializing CalibrationManager
0:46:30.444516 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
0:46:30.444586 INFO: Initializing RawFileManager
0:46:30.473637 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
0:46:30.473815 INFO: Initializing OptimizationManager
0:46:30.474008 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
0:46:30.474079 INFO: Initializing CalibrationManager
0:46:30.474272 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
0:46:30.474345 INFO: Initializing RawFileManager
0:46:30.503242 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
0:46:30.503676 INFO: Initializing OptimizationManager
0:46:30.503885 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
0:46:30.503956 INFO: Initializing CalibrationManager
0:46:30.504139 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
0:46:30.504206 INFO: Initializing RawFileManager
0:46:30.532380 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
0:46:30.532555 INFO: Initializing OptimizationManager
0:46:30.532745 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
0:46:30.532823 INFO: Initializing CalibrationManager
0:46:30.533019 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
0:46:30.533089 INFO: Initializing RawFileManager
0:46:30.561302 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
0:46:30.561475 INFO: Initializing OptimizationManager
0:46:30.561660 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
0:46:30.561729 INFO: Initializing CalibrationManager
0:46:30.561914 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
0:46:30.561985 INFO: Initializing RawFileManager
0:46:30.593342 INFO: Loaded OptimizationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
0:46:30.593528 INFO: Initializing OptimizationManager
0:46:30.593740 INFO: Loaded CalibrationManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
0:46:30.593814 INFO: Initializing CalibrationManager
0:46:30.593999 INFO: Loaded RawFileManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
0:46:30.594073 INFO: Initializing RawFileManager
0:46:30.597887 INFO: Writing stat output to disk
0:46:30.597954 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark/stat.tsv to disk
0:46:30.606264 PROGRESS: Building internal statistics
0:46:30.606499 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
0:46:30.606542 INFO: Initializing TimingManager
0:46:30.606824 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
0:46:30.606867 INFO: Initializing TimingManager
0:46:30.607056 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
0:46:30.607094 INFO: Initializing TimingManager
0:46:30.607265 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
0:46:30.607303 INFO: Initializing TimingManager
0:46:30.607471 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
0:46:30.607508 INFO: Initializing TimingManager
0:46:30.607672 INFO: Loaded TimingManager from run_output_Astral/alphadia_1.12.1_rs_benchmark/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
0:46:30.607708 INFO: Initializing TimingManager
0:46:30.608080 INFO: Writing internal output to disk
0:46:30.608126 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark/internal.tsv to disk
0:46:30.608577 PROGRESS: Performing label free quantification
0:46:30.664370 INFO: Accumulating fragment data
0:46:30.664526 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:46:30.873832 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:46:32.095534 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:46:33.263786 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
0:46:34.526479 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
0:46:35.851526 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
0:46:37.552948 PROGRESS: Performing label free quantification on the precursor level
0:46:37.553074 INFO: Filtering fragments by quality
0:46:37.910381 INFO: Performing label-free quantification using directLFQ
0:46:39.504341 INFO: 119661 lfq-groups total
0:47:30.045280 INFO: using 80 processes
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0:47:30.421016 INFO: lfq-object 100
0:47:30.477930 INFO: lfq-object 400
0:47:30.512439 INFO: lfq-object 200
0:47:30.588331 INFO: lfq-object 500
0:47:30.604623 INFO: lfq-object 800
0:47:30.608095 INFO: lfq-object 300
0:47:30.687171 INFO: lfq-object 600
0:47:30.710667 INFO: lfq-object 900
0:47:30.714816 INFO: lfq-object 1200
0:47:30.729164 INFO: lfq-object 1500
0:47:30.785723 INFO: lfq-object 700
0:47:30.806456 INFO: lfq-object 1000
0:47:30.807475 INFO: lfq-object 1300
0:47:30.822220 INFO: lfq-object 1600
0:47:30.837057 INFO: lfq-object 1900
0:47:30.902095 INFO: lfq-object 1100
0:47:30.902722 INFO: lfq-object 1400
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0:47:30.932580 INFO: lfq-object 2000
0:47:31.011230 INFO: lfq-object 1800
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0:47:31.239854 INFO: lfq-object 3000
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0:47:31.937279 INFO: lfq-object 5000
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0:48:47.824897 INFO: lfq-object 116300
0:48:47.843746 INFO: lfq-object 116600
0:48:47.870139 INFO: lfq-object 117200
0:48:47.872017 INFO: lfq-object 116900
0:48:47.951053 INFO: lfq-object 117500
0:48:47.964491 INFO: lfq-object 117300
0:48:47.966370 INFO: lfq-object 117000
0:48:48.045432 INFO: lfq-object 117600
0:48:48.063142 INFO: lfq-object 117400
0:48:48.143562 INFO: lfq-object 117700
0:48:48.143599 INFO: lfq-object 117900
0:48:48.241263 INFO: lfq-object 117800
0:48:48.244299 INFO: lfq-object 118000
0:48:48.256093 INFO: lfq-object 118200
0:48:48.335400 INFO: lfq-object 118100
0:48:48.358354 INFO: lfq-object 118300
0:48:48.453346 INFO: lfq-object 118400
0:48:48.547928 INFO: lfq-object 118500
0:48:48.660922 INFO: lfq-object 118600
0:48:48.753799 INFO: lfq-object 118700
0:48:48.848149 INFO: lfq-object 118800
0:48:48.934659 INFO: lfq-object 118900
0:48:49.070453 INFO: lfq-object 119000
0:48:49.171799 INFO: lfq-object 119100
0:48:49.221546 INFO: lfq-object 119400
0:48:49.269670 INFO: lfq-object 119200
0:48:49.313697 INFO: lfq-object 119500
0:48:49.363108 INFO: lfq-object 119300
0:48:49.410803 INFO: lfq-object 119600
0:48:58.147974 INFO: Writing precursor output to disk
0:48:58.148300 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark/precursor.matrix.tsv to disk
0:48:58.674839 PROGRESS: Performing label free quantification on the pg level
0:48:58.674944 INFO: Filtering fragments by quality
0:48:59.026919 INFO: Performing label-free quantification using directLFQ
0:48:59.341268 INFO: 10219 lfq-groups total
0:49:28.767995 INFO: using 80 processes
0:49:28.893649 INFO: lfq-object 0
0:49:28.933918 INFO: lfq-object 100
0:49:29.138918 INFO: lfq-object 200
0:49:29.174436 INFO: lfq-object 800
0:49:29.187412 INFO: lfq-object 400
0:49:29.221102 INFO: lfq-object 300
0:49:29.245653 INFO: lfq-object 500
0:49:29.392866 INFO: lfq-object 900
0:49:29.411575 INFO: lfq-object 600
0:49:29.476631 INFO: lfq-object 1100
0:49:29.496300 INFO: lfq-object 1200
0:49:29.508830 INFO: lfq-object 1600
0:49:29.525682 INFO: lfq-object 1000
0:49:29.527330 INFO: lfq-object 700
0:49:29.566762 INFO: lfq-object 1700
0:49:29.647026 INFO: lfq-object 1900
0:49:29.764208 INFO: lfq-object 1400
0:49:29.789860 INFO: lfq-object 1500
0:49:29.813793 INFO: lfq-object 2400
0:49:29.832272 INFO: lfq-object 2000
0:49:29.833333 INFO: lfq-object 1800
0:49:29.845754 INFO: lfq-object 1300
0:49:29.853074 INFO: lfq-object 2500
0:49:29.927807 INFO: lfq-object 2100
0:49:29.929523 INFO: lfq-object 2700
0:49:30.069160 INFO: lfq-object 2900
0:49:30.069408 INFO: lfq-object 2800
0:49:30.098485 INFO: lfq-object 2600
0:49:30.119148 INFO: lfq-object 2300
0:49:30.125013 INFO: lfq-object 2200
0:49:30.156945 INFO: lfq-object 3000
0:49:30.167424 INFO: lfq-object 3200
0:49:30.270373 INFO: lfq-object 3300
0:49:30.287381 INFO: lfq-object 3100
0:49:30.357677 INFO: lfq-object 3500
0:49:30.382721 INFO: lfq-object 3400
0:49:30.399442 INFO: lfq-object 3700
0:49:30.407154 INFO: lfq-object 3600
0:49:30.482367 INFO: lfq-object 3800
0:49:30.541488 INFO: lfq-object 4000
0:49:30.658029 INFO: lfq-object 4100
0:49:30.688463 INFO: lfq-object 3900
0:49:30.703666 INFO: lfq-object 4200
0:49:30.749266 INFO: lfq-object 4300
0:49:30.868584 INFO: lfq-object 4500
0:49:30.896220 INFO: lfq-object 4600
0:49:30.918267 INFO: lfq-object 4800
0:49:30.944415 INFO: lfq-object 4400
0:49:30.959696 INFO: lfq-object 4900
0:49:30.987277 INFO: lfq-object 5000
0:49:31.040819 INFO: lfq-object 4700
0:49:31.098111 INFO: lfq-object 5100
0:49:31.253133 INFO: lfq-object 5300
0:49:31.260840 INFO: lfq-object 5600
0:49:31.305757 INFO: lfq-object 5700
0:49:31.308657 INFO: lfq-object 5200
0:49:31.321467 INFO: lfq-object 5400
0:49:31.337537 INFO: lfq-object 5800
0:49:31.363536 INFO: lfq-object 5900
0:49:31.441166 INFO: lfq-object 6000
0:49:31.443182 INFO: lfq-object 6100
0:49:31.482351 INFO: lfq-object 5500
0:49:31.529888 INFO: lfq-object 6300
0:49:31.546649 INFO: lfq-object 6400
0:49:31.609191 INFO: lfq-object 6500
0:49:31.624001 INFO: lfq-object 6200
0:49:31.658293 INFO: lfq-object 6600
0:49:31.796107 INFO: lfq-object 6700
0:49:31.824117 INFO: lfq-object 6800
0:49:31.883257 INFO: lfq-object 7000
0:49:31.908503 INFO: lfq-object 7100
0:49:31.916831 INFO: lfq-object 7200
0:49:31.943904 INFO: lfq-object 6900
0:49:31.947558 INFO: lfq-object 7300
0:49:32.014538 INFO: lfq-object 7400
0:49:32.051513 INFO: lfq-object 7500
0:49:32.139822 INFO: lfq-object 7600
0:49:32.178684 INFO: lfq-object 7700
0:49:32.247740 INFO: lfq-object 7800
0:49:32.330381 INFO: lfq-object 8000
0:49:32.370224 INFO: lfq-object 8100
0:49:32.373602 INFO: lfq-object 7900
0:49:32.405873 INFO: lfq-object 8200
0:49:32.464979 INFO: lfq-object 8300
0:49:32.486401 INFO: lfq-object 8400
0:49:32.562407 INFO: lfq-object 8500
0:49:32.579412 INFO: lfq-object 8600
0:49:32.587166 INFO: lfq-object 8800
0:49:32.621067 INFO: lfq-object 8900
0:49:32.676261 INFO: lfq-object 9000
0:49:32.743158 INFO: lfq-object 8700
0:49:32.762329 INFO: lfq-object 9100
0:49:32.782025 INFO: lfq-object 9200
0:49:32.832892 INFO: lfq-object 9300
0:49:32.876832 INFO: lfq-object 9400
0:49:32.895779 INFO: lfq-object 9600
0:49:32.939469 INFO: lfq-object 9500
0:49:32.984208 INFO: lfq-object 9800
0:49:33.004836 INFO: lfq-object 9700
0:49:33.075954 INFO: lfq-object 9900
0:49:33.081649 INFO: lfq-object 10000
0:49:33.211834 INFO: lfq-object 10100
0:49:33.215754 INFO: lfq-object 10200
0:49:35.354816 INFO: Writing pg output to disk
0:49:35.354993 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark/pg.matrix.tsv to disk
0:49:35.578273 INFO: Writing psm output to disk
0:49:35.578411 INFO: Saving run_output_Astral/alphadia_1.12.1_rs_benchmark/precursors.tsv to disk
0:49:43.939222 PROGRESS: Building MBR spectral library
0:49:44.005351 INFO: Running MbrLibraryBuilder
0:49:47.979392 INFO: MBR spectral library contains 119,661 precursors, 10,219 proteins
0:49:47.979576 INFO: Writing MBR spectral library to disk
0:49:48.993825 PROGRESS: =================== Search Finished ===================
0:49:50.247852 WARNING: WARNING: Temp mmap arrays were written to /tmp/temp_mmap_hnjihxi6. Cleanup of this folder is OS dependant, and might need to be triggered manually! Current space: 1,070,895,579,136
