0:00:00.000026 INFO: Moved old log file ./run_output/alphadia_1.12.1_rs_benchmark/log.txt to run_output/alphadia_1.12.1_rs_benchmark/log.5.bkp.txt
0:00:00.000159 INFO: Output directory: /home/robbe/ProteoBench_diaPASEF/run_output/alphadia_1.12.1_rs_benchmark, cwd: /home/robbe/ProteoBench_diaPASEF.
0:00:00.000193 INFO: User provided config file: config_alphadia112_rs_diaPASEF.yaml.
0:00:00.000220 INFO: User provided config dict: {}.
0:00:00.011995 PROGRESS:           _      _         ___ ___   _   
0:00:00.012055 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.012082 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.012109 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.012133 PROGRESS:            |_|                           
0:00:00.012153 PROGRESS: 
0:00:00.012172 PROGRESS: version: 1.12.1
0:00:00.012198 INFO: hostname: thestral
0:00:00.012246 INFO: date: 2025-10-17 15:44:56
0:00:00.012269 INFO: ================ AlphaX Environment ===============
0:00:00.012289 INFO: alphatims       : 1.0.9
0:00:00.012309 INFO: alpharaw        : 0.4.7
0:00:00.012327 INFO: alphabase       : 1.7.1
0:00:00.012345 INFO: alphapeptdeep   : 1.3.2
0:00:00.012368 INFO: directlfq       : 0.3.1
0:00:00.012385 INFO: ===================================================
0:00:00.012401 INFO: ================= Pip Environment =================
0:00:00.073346 INFO: peptdeep==1.3.2 pytz==2025.2 click==8.1.8 partd==1.4.2 wget==3.2 uri-template==1.3.0 nvidia-nvjitlink-cu12==12.4.127 huggingface-hub==0.30.2 fqdn==1.5.1 jsonref==1.1.0 rdkit==2024.9.6 simplejson==3.20.1 alphabase==1.7.1 tornado==6.4.2 s3transfer==0.11.4 tqdm==4.67.1 psutil==7.0.0 arrow==1.3.0 dask==2024.11.2 torchmetrics==1.7.1 numpy==1.26.4 directlfq==0.3.1 gitdb==4.0.12 contextlib2==21.6.0 future==1.0.0 toolz==1.0.0 monotonic==1.6 argparse==1.4.0 nvidia-cuda-cupti-cu12==12.4.127 importlib_resources==6.5.2 packaging==24.2 SQLAlchemy==2.0.39 pyarrow==19.0.1 alphadia-search-rs==0.2.0 joblib==1.4.2 requests-oauthlib==2.0.0 transformers==4.51.2 webcolors==24.11.1 cffi==1.17.1 nvidia-cuda-nvrtc-cu12==12.4.127 numba==0.61.2 protobuf==5.29.3 pyteomics==4.7.5 alphadia==1.12.1 mpmath==1.3.0 multiprocess==0.70.17 lightning-utilities==0.14.3 MarkupSafe==3.0.2 pyzstd==0.16.2 six==1.17.0 cycler==0.12.1 charset-normalizer==3.4.1 tenacity==9.0.0 fsspec==2025.3.2 xxhash==3.5.0 attrs==25.2.0 pip==23.0.1 threadpoolctl==3.6.0 pythonnet==3.0.5 requests==2.32.3 triton==3.2.0 alphatims==1.0.9 h5py==3.13.0 oauthlib==3.2.2 zstandard==0.22.0 pyahocorasick==2.1.0 swagger-spec-validator==3.0.4 blinker==1.9.0 pycparser==2.22 regex==2024.11.6 streamlit-aggrid==1.1.1 streamlit==1.43.2 websocket-client==1.8.0 certifi==2025.1.31 narwhals==1.30.0 isoduration==20.11.0 python-dateutil==2.9.0.post0 botocore==1.37.11 locket==1.0.0 alpharaw==0.4.7 referencing==0.36.2 torch==2.6.0 setuptools==78.1.0 nvidia-cusparse-cu12==12.3.1.170 rocket-fft==0.2.5 neptune==1.10.4 importlib_metadata==8.6.1 cloudpickle==3.1.1 clr_loader==0.2.7.post0 pandas==2.2.3 dill==0.3.9 pyparsing==3.2.3 typing_extensions==4.13.2 jsonschema-specifications==2024.10.1 networkx==3.4.2 biopython==1.85 urllib3==2.4.0 types-python-dateutil==2.9.0.20241206 seaborn==0.13.2 toml==0.10.2 zipp==3.21.0 rfc3339-validator==0.1.4 altair==5.5.0 llvmlite==0.44.0 greenlet==3.1.1 fonttools==4.57.0 scipy==1.12.0 tzdata==2025.2 filelock==3.18.0 matplotlib==3.10.1 contourpy==1.3.1 pydeck==0.9.1 lxml==5.3.2 Jinja2==3.1.6 bravado-core==6.1.1 msgpack==1.1.0 nvidia-nvtx-cu12==12.4.127 nvidia-cusolver-cu12==11.6.1.9 safetensors==0.5.3 idna==3.10 cachetools==5.5.2 jsonpointer==3.0.0 rpds-py==0.23.1 nvidia-cufft-cu12==11.2.1.3 jsonschema==4.23.0 watchdog==6.0.0 python-decouple==3.8 sympy==1.13.1 boto3==1.37.11 dask-expr==1.1.19 pillow==11.1.0 plotly==6.0.0 nvidia-cublas-cu12==12.4.5.8 nvidia-cudnn-cu12==9.1.0.70 tokenizers==0.21.1 smmap==5.0.2 nvidia-curand-cu12==10.3.5.147 GitPython==3.1.44 progressbar==2.5 PyJWT==2.10.1 kiwisolver==1.4.8 nvidia-cuda-runtime-cu12==12.4.127 scikit-learn==1.6.1 nvidia-nccl-cu12==2.21.5 jmespath==1.0.1 rfc3986-validator==0.1.1 bravado==11.1.0 nvidia-cusparselt-cu12==0.6.2 PyYAML==6.0.2 more-itertools==10.3.0 wheel==0.45.1 autocommand==2.2.2 packaging==24.2 typing_extensions==4.12.2 tomli==2.0.1 backports.tarfile==1.2.0 jaraco.functools==4.0.1 jaraco.text==3.12.1 platformdirs==4.2.2 jaraco.collections==5.1.0 typeguard==4.3.0 jaraco.context==5.3.0 importlib_metadata==8.0.0 inflect==7.3.1 zipp==3.19.2
0:00:00.073577 INFO: ===================================================
0:00:00.073614 INFO: Running step 'library'
0:00:00.073670 INFO: loading default config from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.084640 INFO: loading additional config provided via CLI
0:00:00.084705 INFO: loading additional config provided via CLI parameters
0:00:00.085086 INFO: Updating config with 'user defined'
0:00:00.085220 INFO: Updating config with 'user defined (cli)'
0:00:00.085316 INFO: updating config with user defined values: [{'version': 1, 'workflow_name': None, 'output_directory': None, 'library_path': None, 'raw_paths': ['./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d'], 'fasta_paths': [], 'quant_directory': None, 'general': {'thread_count': 80, 'transfer_step_enabled': False, 'mbr_step_enabled': 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': False, 'enzyme': 'trypsin/p', 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M;Acetyl@Protein_N-term', 'max_var_mod_num': 1, 'missed_cleavages': 1, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [400, 1000], 'fragment_mz': [50, 2000], 'nce': 25.0, 'fragment_types': ['b', 'y'], 'max_fragment_charge': 2, 'instrument': 'timsTOF', 'peptdeep_model_path': None, 'peptdeep_model_type': 'generic'}, 'custom_modifications': [{'name': 'Dimethyl:d12@K', 'composition': 'H(-2)2H(8)13C(2)'}, {'name': 'Dimethyl:d12@Any_N-term', 'composition': 'H(-2)2H(8)13C(2)'}, {'name': 'Dimethyl:d12@Protein_N-term', 'composition': 'H(-2)2H(8)13C(2)'}, {'name': 'mTRAQ:d12@K', 'composition': 'H(12)C(1)13C(10)15N(2)O(1)'}, {'name': 'mTRAQ:d12@Any_N-term', 'composition': 'H(12)C(1)13C(14)15N(2)O(1)'}, {'name': 'mTRAQ:d12@Protein_N-term', 'composition': 'H(12)C(1)13C(14)15N(2)O(1)'}, {'name': 'Label:13C(12)@K', 'composition': 'C(12)'}], 'search': {'extraction_backend': 'classic', 'target_ms1_tolerance': 15, 'target_ms2_tolerance': 15, 'target_rt_tolerance': 0.0, 'target_mobility_tolerance': 0.0, 'quant_window': 3, 'target_num_candidates': 3, 'channel_filter': '', 'exclude_shared_ions': True, 'compete_for_fragments': True, 'quant_all': True, 'top_k_fragments_selection': 12, 'top_k_fragments_scoring': 12, 'min_fragment_intensity': 0.01, 'experimental_xic': True, 'optimized_peak_group_score': False}, 'calibration': {'batch_size': 200, 'optimization_lock_target': 200, 'max_steps': 20, 'min_steps': 2, 'max_skips': 1, 'max_fragments': 5000, 'min_correlation': 0.7}, 'search_initial': {'initial_num_candidates': 1, 'initial_ms1_tolerance': 30, 'initial_ms2_tolerance': 30, 'initial_mobility_tolerance': 0.1, 'initial_rt_tolerance': 0.5}, 'selection_config': {'peak_len_rt': 10.0, 'sigma_scale_rt': 0.5, 'peak_len_mobility': 0.01, 'sigma_scale_mobility': 1.0, 'top_k_precursors': 3, 'kernel_size': 30, 'f_mobility': 1.0, 'f_rt': 0.99, 'center_fraction': 0.5, 'min_size_mobility': 8, 'min_size_rt': 3, 'max_size_mobility': 20, 'max_size_rt': 15, 'group_channels': False, 'use_weighted_score': True, 'join_close_candidates': False, 'join_close_candidates_scan_threshold': 0.6, 'join_close_candidates_cycle_threshold': 0.6}, 'scoring_config': {'score_grouped': False, 'top_k_isotopes': 3, 'reference_channel': -1, 'precursor_mz_tolerance': 10, 'fragment_mz_tolerance': 15}, 'library_multiplexing': {'enabled': False, 'input_channel': 0, 'multiplex_mapping': []}, 'multiplexing': {'enabled': False, 'target_channels': '4,8', 'decoy_channel': 12, 'reference_channel': 0, 'competetive_scoring': True}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins', 'inference_strategy': 'heuristic', 'competetive_scoring': True, 'keep_decoys': False, 'channel_wise_fdr': False, 'enable_two_step_classifier': False, 'two_step_classifier_max_iterations': 5, 'enable_nn_hyperparameter_tuning': False}, 'search_output': {'file_format': 'tsv', 'peptide_level_lfq': False, 'precursor_level_lfq': True, 'save_fragment_quant_matrix': False, 'min_k_fragments': 12, 'min_correlation': 0.9, 'num_samples_quadratic': 50, 'min_nonnan': 3, 'normalize_lfq': True}, 'optimization': {'order_of_optimization': None, 'ms2_error': {'targeted_update_percentile_range': 0.95, 'targeted_update_factor': 1.0, 'automatic_update_percentile_range': 0.99, 'automatic_update_factor': 1.1, 'try_narrower_values': True, 'maximal_decrease': 0.5, 'favour_narrower_optimum': False, 'maximum_decrease_from_maximum': 0.1}, 'ms1_error': {'targeted_update_percentile_range': 0.95, 'targeted_update_factor': 1.0, 'automatic_update_percentile_range': 0.99, 'automatic_update_factor': 1.1, 'try_narrower_values': False, 'maximal_decrease': 0.2, 'favour_narrower_optimum': False, 'maximum_decrease_from_maximum': 0.1}, 'mobility_error': {'targeted_update_percentile_range': 0.95, 'targeted_update_factor': 1.0, 'automatic_update_percentile_range': 0.99, 'automatic_update_factor': 1.1, 'try_narrower_values': False, 'maximal_decrease': 0.2, 'favour_narrower_optimum': False, 'maximum_decrease_from_maximum': 0.1}, 'rt_error': {'targeted_update_percentile_range': 0.95, 'targeted_update_factor': 1.0, 'automatic_update_percentile_range': 0.99, 'automatic_update_factor': 1.1, 'try_narrower_values': True, 'maximal_decrease': 0.2, 'favour_narrower_optimum': True, 'maximum_decrease_from_maximum': 0.1}}, 'optimization_manager': {'fwhm_rt': 5, 'fwhm_mobility': 0.01, 'score_cutoff': 0}, 'transfer_library': {'enabled': False, 'fragment_types': ['b', 'y'], 'max_charge': 2, 'top_k_samples': 3, 'norm_delta_max': True, 'precursor_correlation_cutoff': 0.5, 'fragment_correlation_ratio': 0.75}, 'transfer_learning': {'enabled': False, 'batch_size': 2000, 'max_lr': 0.0001, 'train_fraction': 0.7, 'validation_fraction': 0.2, 'test_fraction': 0.1, 'test_interval': 1, 'lr_patience': 3, 'epochs': 51, 'warmup_epochs': 5, 'nce': 25, 'instrument': 'timsTOF'}}, {'raw_paths': ['./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d', './raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d'], 'library_path': '/home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf', 'fasta_paths': ['./ProteoBenchFASTA_DDAQuantification.fasta']}]
0:00:00.085568 INFO: Updating config with 'user defined'
0:00:00.085682 INFO: Updating config with 'user defined (cli)'
0:00:00.085719 INFO: ├──version: 1
0:00:00.085744 INFO: ├──workflow_name: None
0:00:00.085766 INFO: ├──output_directory: None
0:00:00.085788 INFO: [32;20m├──library_path: /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf [user defined (cli), default: None][0m
0:00:00.085810 INFO: ├──raw_paths:
0:00:00.085830 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d [user defined (cli), default: None][0m
0:00:00.085855 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d [user defined (cli), default: None][0m
0:00:00.085874 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d [user defined (cli), default: None][0m
0:00:00.085897 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d [user defined (cli), default: None][0m
0:00:00.085916 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d [user defined (cli), default: None][0m
0:00:00.085935 INFO: │   [32;20m- ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d [user defined (cli), default: None][0m
0:00:00.085955 INFO: ├──fasta_paths:
0:00:00.085973 INFO: │   [32;20m- ./ProteoBenchFASTA_DDAQuantification.fasta [user defined (cli), default: None][0m
0:00:00.085993 INFO: ├──quant_directory: None
0:00:00.086013 INFO: ├──general
0:00:00.086034 INFO: │   [32;20m├──thread_count: 80 [user defined, default: 10][0m
0:00:00.086053 INFO: │   ├──transfer_step_enabled: False
0:00:00.086073 INFO: │   ├──mbr_step_enabled: False
0:00:00.086091 INFO: │   ├──reuse_calibration: False
0:00:00.086108 INFO: │   ├──reuse_quant: False
0:00:00.086127 INFO: │   ├──astral_ms1: False
0:00:00.086144 INFO: │   ├──log_level: INFO
0:00:00.086162 INFO: │   ├──mmap_detector_events: False
0:00:00.086182 INFO: │   [32;20m├──use_gpu: False [user defined, default: True][0m
0:00:00.086202 INFO: │   ├──save_figures: True
0:00:00.086222 INFO: │   ├──save_library: True
0:00:00.086242 INFO: │   ├──save_flat_library: False
0:00:00.086262 INFO: │   ├──input_library_type: base
0:00:00.086282 INFO: │   ├──save_mbr_library: True
0:00:00.086300 INFO: │   └──random_state: None
0:00:00.086318 INFO: ├──library_loading
0:00:00.086339 INFO: │   └──rt_heuristic: 180
0:00:00.086358 INFO: ├──library_prediction
0:00:00.086380 INFO: │   ├──enabled: False
0:00:00.086399 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.086418 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.086436 INFO: │   ├──variable_modifications: Oxidation@M;Acetyl@Protein_N-term
0:00:00.086456 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.086474 INFO: │   ├──missed_cleavages: 1
0:00:00.086493 INFO: │   ├──precursor_len:
0:00:00.086513 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.086533 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.086553 INFO: │   ├──precursor_charge:
0:00:00.086572 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.086589 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.086609 INFO: │   ├──precursor_mz:
0:00:00.086628 INFO: │   │   - 400
0:00:00.086646 INFO: │   │   [32;20m- 1000 [user defined, default: 1200][0m
0:00:00.086663 INFO: │   ├──fragment_mz:
0:00:00.086682 INFO: │   │   [32;20m- 50 [user defined, default: 200][0m
0:00:00.086699 INFO: │   │   - 2000
0:00:00.086717 INFO: │   ├──nce: 25.0
0:00:00.086736 INFO: │   ├──fragment_types:
0:00:00.086753 INFO: │   │   - b
0:00:00.086771 INFO: │   │   - y
0:00:00.086809 INFO: │   ├──max_fragment_charge: 2
0:00:00.086828 INFO: │   [32;20m├──instrument: timsTOF [user defined, default: Lumos][0m
0:00:00.086846 INFO: │   ├──peptdeep_model_path: None
0:00:00.086866 INFO: │   └──peptdeep_model_type: generic
0:00:00.086884 INFO: ├──custom_modifications:
0:00:00.086902 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.086921 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.086939 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.086956 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.086975 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.087002 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.087022 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.087039 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.087057 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.087076 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.087094 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.087111 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.087131 INFO: │   ├──name: Label:13C(12)@K
0:00:00.087149 INFO: │   └──composition: C(12)
0:00:00.087166 INFO: ├──search
0:00:00.087187 INFO: │   ├──extraction_backend: classic
0:00:00.087205 INFO: │   [32;20m├──target_ms1_tolerance: 15 [user defined, default: 5][0m
0:00:00.087223 INFO: │   [32;20m├──target_ms2_tolerance: 15 [user defined, default: 10][0m
0:00:00.087243 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.087261 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.087279 INFO: │   ├──quant_window: 3
0:00:00.087298 INFO: │   ├──target_num_candidates: 3
0:00:00.087317 INFO: │   ├──channel_filter: 
0:00:00.087336 INFO: │   ├──exclude_shared_ions: True
0:00:00.087355 INFO: │   ├──compete_for_fragments: True
0:00:00.087373 INFO: │   ├──quant_all: True
0:00:00.087391 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.087410 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.087429 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.087447 INFO: │   ├──experimental_xic: True
0:00:00.087467 INFO: │   └──optimized_peak_group_score: False
0:00:00.087484 INFO: ├──calibration
0:00:00.087502 INFO: │   [32;20m├──batch_size: 200 [user defined, default: 8000][0m
0:00:00.087521 INFO: │   ├──optimization_lock_target: 200
0:00:00.087540 INFO: │   ├──max_steps: 20
0:00:00.087559 INFO: │   ├──min_steps: 2
0:00:00.087579 INFO: │   ├──max_skips: 1
0:00:00.087597 INFO: │   ├──max_fragments: 5000
0:00:00.087615 INFO: │   └──min_correlation: 0.7
0:00:00.087635 INFO: ├──search_initial
0:00:00.087654 INFO: │   ├──initial_num_candidates: 1
0:00:00.087672 INFO: │   ├──initial_ms1_tolerance: 30
0:00:00.087691 INFO: │   ├──initial_ms2_tolerance: 30
0:00:00.087710 INFO: │   ├──initial_mobility_tolerance: 0.1
0:00:00.087729 INFO: │   └──initial_rt_tolerance: 0.5
0:00:00.087748 INFO: ├──selection_config
0:00:00.087766 INFO: │   ├──peak_len_rt: 10.0
0:00:00.087784 INFO: │   ├──sigma_scale_rt: 0.5
0:00:00.087804 INFO: │   ├──peak_len_mobility: 0.01
0:00:00.087823 INFO: │   ├──sigma_scale_mobility: 1.0
0:00:00.087841 INFO: │   ├──top_k_precursors: 3
0:00:00.087860 INFO: │   ├──kernel_size: 30
0:00:00.087878 INFO: │   ├──f_mobility: 1.0
0:00:00.087896 INFO: │   ├──f_rt: 0.99
0:00:00.087915 INFO: │   ├──center_fraction: 0.5
0:00:00.087932 INFO: │   ├──min_size_mobility: 8
0:00:00.087950 INFO: │   ├──min_size_rt: 3
0:00:00.087969 INFO: │   ├──max_size_mobility: 20
0:00:00.087986 INFO: │   ├──max_size_rt: 15
0:00:00.088003 INFO: │   ├──group_channels: False
0:00:00.088022 INFO: │   ├──use_weighted_score: True
0:00:00.088040 INFO: │   ├──join_close_candidates: False
0:00:00.088058 INFO: │   ├──join_close_candidates_scan_threshold: 0.6
0:00:00.088076 INFO: │   └──join_close_candidates_cycle_threshold: 0.6
0:00:00.088094 INFO: ├──scoring_config
0:00:00.088113 INFO: │   ├──score_grouped: False
0:00:00.088132 INFO: │   ├──top_k_isotopes: 3
0:00:00.088149 INFO: │   ├──reference_channel: -1
0:00:00.088166 INFO: │   ├──precursor_mz_tolerance: 10
0:00:00.088186 INFO: │   └──fragment_mz_tolerance: 15
0:00:00.088204 INFO: ├──library_multiplexing
0:00:00.088221 INFO: │   ├──enabled: False
0:00:00.088244 INFO: │   ├──input_channel: 0
0:00:00.088261 INFO: │   └──multiplex_mapping:
0:00:00.088278 INFO: ├──multiplexing
0:00:00.088298 INFO: │   ├──enabled: False
0:00:00.088315 INFO: │   ├──target_channels: 4,8
0:00:00.088332 INFO: │   ├──decoy_channel: 12
0:00:00.088349 INFO: │   ├──reference_channel: 0
0:00:00.088368 INFO: │   └──competetive_scoring: True
0:00:00.088385 INFO: ├──fdr
0:00:00.088403 INFO: │   ├──fdr: 0.01
0:00:00.088421 INFO: │   ├──group_level: proteins
0:00:00.088439 INFO: │   ├──inference_strategy: heuristic
0:00:00.088456 INFO: │   ├──competetive_scoring: True
0:00:00.088475 INFO: │   ├──keep_decoys: False
0:00:00.088493 INFO: │   ├──channel_wise_fdr: False
0:00:00.088511 INFO: │   ├──enable_two_step_classifier: False
0:00:00.088530 INFO: │   ├──two_step_classifier_max_iterations: 5
0:00:00.088548 INFO: │   └──enable_nn_hyperparameter_tuning: False
0:00:00.088565 INFO: ├──search_output
0:00:00.088584 INFO: │   ├──file_format: tsv
0:00:00.088602 INFO: │   ├──peptide_level_lfq: False
0:00:00.088619 INFO: │   [32;20m├──precursor_level_lfq: True [user defined, default: False][0m
0:00:00.088639 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.088657 INFO: │   ├──min_k_fragments: 12
0:00:00.088676 INFO: │   ├──min_correlation: 0.9
0:00:00.088695 INFO: │   ├──num_samples_quadratic: 50
0:00:00.088712 INFO: │   ├──min_nonnan: 3
0:00:00.088730 INFO: │   └──normalize_lfq: True
0:00:00.088748 INFO: ├──optimization
0:00:00.088766 INFO: │   ├──order_of_optimization: None
0:00:00.088784 INFO: │   ├──ms2_error
0:00:00.088805 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.088823 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.088842 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.088863 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.088881 INFO: │   │   ├──try_narrower_values: True
0:00:00.088899 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.088919 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.088938 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.088955 INFO: │   ├──ms1_error
0:00:00.088975 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.088993 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.089011 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.089031 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.089048 INFO: │   │   ├──try_narrower_values: False
0:00:00.089066 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.089086 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.089104 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.089121 INFO: │   ├──mobility_error
0:00:00.089140 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.089158 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.089177 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.089196 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.089214 INFO: │   │   ├──try_narrower_values: False
0:00:00.089231 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.089250 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.089268 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.089285 INFO: │   └──rt_error
0:00:00.089304 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.089323 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.089341 INFO: │       ├──automatic_update_percentile_range: 0.99
0:00:00.089361 INFO: │       ├──automatic_update_factor: 1.1
0:00:00.089378 INFO: │       ├──try_narrower_values: True
0:00:00.089395 INFO: │       ├──maximal_decrease: 0.2
0:00:00.089420 INFO: │       ├──favour_narrower_optimum: True
0:00:00.089438 INFO: │       └──maximum_decrease_from_maximum: 0.1
0:00:00.089455 INFO: ├──optimization_manager
0:00:00.089474 INFO: │   ├──fwhm_rt: 5
0:00:00.089491 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.089509 INFO: │   └──score_cutoff: 0
0:00:00.089527 INFO: ├──transfer_library
0:00:00.089545 INFO: │   ├──enabled: False
0:00:00.089561 INFO: │   ├──fragment_types:
0:00:00.089579 INFO: │   │   - b
0:00:00.089598 INFO: │   │   - y
0:00:00.089615 INFO: │   ├──max_charge: 2
0:00:00.089633 INFO: │   ├──top_k_samples: 3
0:00:00.089652 INFO: │   ├──norm_delta_max: True
0:00:00.089670 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.089688 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.089707 INFO: └──transfer_learning
0:00:00.089725 INFO:     ├──enabled: False
0:00:00.089742 INFO:     ├──batch_size: 2000
0:00:00.089761 INFO:     ├──max_lr: 0.0001
0:00:00.089779 INFO:     ├──train_fraction: 0.7
0:00:00.089796 INFO:     ├──validation_fraction: 0.2
0:00:00.089815 INFO:     ├──test_fraction: 0.1
0:00:00.089832 INFO:     ├──test_interval: 1
0:00:00.089849 INFO:     ├──lr_patience: 3
0:00:00.089868 INFO:     ├──epochs: 51
0:00:00.089885 INFO:     ├──warmup_epochs: 5
0:00:00.089903 INFO:     ├──nce: 25
0:00:00.089923 INFO:     [32;20m└──instrument: timsTOF [user defined, default: Lumos][0m
0:00:00.094682 INFO: Moved existing config file run_output/alphadia_1.12.1_rs_benchmark/frozen_config.yaml to run_output/alphadia_1.12.1_rs_benchmark/frozen_config.5.bkp.yaml
0:00:00.094903 INFO: Registering 7 custom modifications
0:00:00.121834 INFO: Searching 6 files:
0:00:00.121902 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:00:00.121927 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
0:00:00.121950 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
0:00:00.121970 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
0:00:00.121988 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
0:00:00.122005 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
0:00:00.122023 INFO: Using 1 fasta files:
0:00:00.122043 INFO:   ./ProteoBenchFASTA_DDAQuantification.fasta
0:00:00.122061 INFO: Using library: /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf
0:00:00.122079 INFO: Saving output to: run_output/alphadia_1.12.1_rs_benchmark
0:00:00.122106 PROGRESS: Loading spectral library
0:00:00.122130 PROGRESS: Loading library (type: base) from disk..
0:00:00.122155 INFO: Running DynamicLoader
0:00:00.122202 INFO: Loading .hdf library from /home/robbe/ProteoBench_diaPASEF/run_output_Astral/alphadia_1.12.1_rs_benchmark/speclib.hdf
0:00:26.414426 INFO: Running PrecursorInitializer
0:00:26.414741 INFO: Running AnnotateFasta
0:00:26.541092 INFO: Dropping decoys from input library before annotation
0:00:46.680829 INFO: Running IsotopeGenerator
0:00:46.681101 WARNING: Input library already contains isotope information. Skipping isotope generation. 
 Please note that isotope generation outside of alphabase is not supported.
0:00:46.681140 INFO: Running RTNormalization
0:00:46.681199 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:00:46.681243 INFO: Saving library to run_output/alphadia_1.12.1_rs_benchmark/speclib.hdf
0:01:21.656528 INFO: Running DecoyGenerator
0:02:59.376875 INFO: Running FlattenLibrary
0:03:33.673805 INFO: Running InitFlatColumns
0:03:33.971144 INFO: Running LogFlatLibraryStats
0:03:33.971276 INFO: ============ Library Stats ============
0:03:33.971315 INFO: Number of precursors: 12,218,312
0:03:35.900577 INFO: 	thereof targets:6,124,046
0:03:35.900720 INFO: 	thereof decoys: 6,094,266
0:03:35.982133 INFO: Number of elution groups: 6,124,046
0:03:35.982258 INFO: 	average size: 2.00
0:03:36.273559 INFO: Number of proteins: 117,993
0:03:36.303061 INFO: Number of channels: 1 ([0])
0:03:36.303240 INFO: Isotopes Distribution for 4 isotopes
0:03:36.303270 INFO: =======================================
0:03:36.311961 PROGRESS: Starting Search Workflows
0:03:36.312129 PROGRESS: 
0:03:36.312210 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark/quant
0:03:36.312340 INFO: Initializing TimingManager
0:03:36.312945 INFO: Initializing RawFileManager
0:03:36.313073 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:36.313136 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:36.313179 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:36.514921 INFO: Reading 39,128 frames with 2,835,410,867 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:46.235528 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d...
0:03:46.239846 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:46.251187 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:46.251481 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:46.251804 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:46.253427 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:46.275312 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:46.275634 INFO: Indexing quadrupole dimension
0:03:46.776232 INFO: Transposing detector events
0:03:56.667100 INFO: Finished transposing data
0:03:56.702125 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:03:56.702997 INFO: RT (min)            : 0.0 - 70.0
0:03:56.703089 INFO: RT duration (sec)   : 4199.9
0:03:56.703144 INFO: RT duration (min)   : 70.0
0:03:56.703193 INFO: Cycle len (scans)   : 9
0:03:56.703239 INFO: Cycle len (sec)     : 0.97
0:03:56.703283 INFO: Number of cycles    : 4347
0:03:56.703331 INFO: MS2 range (m/z)     : 400.0 - 1000.0
0:03:56.703434 INFO: Creating DIA data object took: 20.39037561416626
0:03:58.328234 INFO: Initializing CalibrationManager
0:03:58.328497 INFO: Setting up calibration estimators ..
0:03:58.328561 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:03:58.328636 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'}' ..
0:03:58.328739 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:03:58.328802 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
0:03:58.328861 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}}' ..
0:03:58.328926 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
0:03:58.328977 INFO: Done setting up calibration estimators.
0:03:58.329097 INFO: Initializing OptimizationManager
0:03:58.329191 INFO: initial parameter: ms1_error = 30
0:03:58.329240 INFO: initial parameter: ms2_error = 30
0:03:58.329285 INFO: initial parameter: rt_error = 2099.928159
0:03:58.329327 INFO: initial parameter: mobility_error = 0.1
0:03:58.329375 INFO: initial parameter: num_candidates = 1
0:03:58.329416 INFO: initial parameter: fwhm_rt = 5
0:03:58.329457 INFO: initial parameter: fwhm_mobility = 0.01
0:03:58.329499 INFO: initial parameter: score_cutoff = 0
0:03:58.329538 INFO: initial parameter: classifier_version = -1
0:03:58.329610 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
0:03:58.329866 INFO: FDRManager: loading saved state not requested, will be initialized.
0:03:58.329904 INFO: Initializing FDRManager
0:03:58.329943 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
0:03:59.571234 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
0:04:00.842157 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:04:00.842597 INFO: Updating optimization_manager: rt_error            : 2099.928159 -> 2099.928159
0:04:00.842693 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
0:04:00.842882 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
0:04:00.842992 PROGRESS: Starting initial search for precursors.
0:04:00.843076 INFO: Starting optimization step 0.
0:04:00.843143 PROGRESS: === Extracting elution groups 0 to 200 ===
0:04:00.843213 INFO: Using classic extraction backend
0:04:00.843391 PROGRESS: Extracting batch of 390 precursors
0:04:00.843460 INFO: === Search parameters used ===
0:04:00.843507 INFO: rt_error       : 2099.928159
0:04:00.843550 INFO: mobility_error : 0.1
0:04:00.843596 INFO: num_candidates : 1
0:04:00.843638 INFO: ms1_error      : 30
0:04:00.843678 INFO: ms2_error      : 30
0:04:00.843719 INFO: fwhm_rt        : 5
0:04:00.843758 INFO: quant_window   : 3
0:04:00.843797 INFO: ==============================================
0:04:02.799127 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:04:02.799314 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:04:02.799346 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:04:02.799368 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:04:04.762214 INFO: Starting candidate selection
0:05:09.549990 INFO: Starting candidate scoring
0:10:20.844232 INFO: Finished candidate processing
0:10:20.844463 INFO: Collecting candidate features
0:10:21.365691 INFO: Collecting fragment features
0:10:23.090375 INFO: Finished candidate scoring
0:10:23.092482 INFO: performing precursor FDR with 47 features
0:10:23.092535 INFO: Decoy channel: -1
0:10:23.092560 INFO: Competetive: True
0:10:23.093889 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:23.097299 INFO: Using random state 43716 for train-test-split
0:10:23.114418 INFO: Test AUC: 0.503
0:10:23.114482 INFO: Train AUC: 0.507
0:10:23.114514 INFO: AUC difference: 0.94%
0:10:23.351341 INFO: Resetting torch num_threads to 80
0:10:23.351848 PROGRESS: === Extracted 364 precursors and 3956 fragments ===
0:10:23.352323 INFO: === FDR correction performed with classifier version -1 ===
0:10:23.352856 PROGRESS: ============================= Precursor FDR =============================
0:10:23.352942 PROGRESS: Total precursors accumulated: 188
0:10:23.353004 PROGRESS: Target precursors: 177 (94.15%)
0:10:23.353055 PROGRESS: Decoy precursors: 11 (5.85%)
0:10:23.353101 PROGRESS: 
0:10:23.353145 PROGRESS: Precursor Summary:
0:10:23.353975 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:10:23.354058 PROGRESS: 
0:10:23.354112 PROGRESS: Protein Summary:
0:10:23.355042 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:10:23.355130 PROGRESS: =========================================================================
0:10:23.355415 INFO: Target number of precursors not reached yet.
0:10:23.445151 INFO: Starting optimization step 1.
0:10:23.445403 PROGRESS: === Extracting elution groups 200 to 600 ===
0:10:23.445541 INFO: Using classic extraction backend
0:10:23.445766 PROGRESS: Extracting batch of 783 precursors
0:10:23.445865 INFO: === Search parameters used ===
0:10:23.445948 INFO: rt_error       : 2099.928159
0:10:23.446013 INFO: mobility_error : 0.1
0:10:23.446074 INFO: num_candidates : 1
0:10:23.446133 INFO: ms1_error      : 30
0:10:23.446191 INFO: ms2_error      : 30
0:10:23.446249 INFO: fwhm_rt        : 5
0:10:23.446307 INFO: quant_window   : 3
0:10:23.446364 INFO: ==============================================
0:10:23.447407 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:10:23.447464 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:10:23.447513 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:10:23.447545 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:10:23.462229 INFO: Starting candidate selection
0:10:33.164797 INFO: Starting candidate scoring
0:10:33.297928 INFO: Finished candidate processing
0:10:33.298101 INFO: Collecting candidate features
0:10:33.311932 INFO: Collecting fragment features
0:10:33.315085 INFO: Finished candidate scoring
0:10:33.317543 INFO: performing precursor FDR with 47 features
0:10:33.317646 INFO: Decoy channel: -1
0:10:33.317672 INFO: Competetive: True
0:10:33.321273 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:33.323464 INFO: Using random state 717991 for train-test-split
0:10:33.332817 INFO: Test AUC: 0.479
0:10:33.332926 INFO: Train AUC: 0.507
0:10:33.332955 INFO: AUC difference: 5.50%
0:10:33.332978 WARNING: AUC difference > 5%. This may indicate overfitting.
0:10:34.185343 INFO: Resetting torch num_threads to 80
0:10:34.186482 PROGRESS: === Extracted 1120 precursors and 12173 fragments ===
0:10:34.186881 INFO: === FDR correction performed with classifier version -1 ===
0:10:34.187430 PROGRESS: ============================= Precursor FDR =============================
0:10:34.187516 PROGRESS: Total precursors accumulated: 577
0:10:34.187575 PROGRESS: Target precursors: 547 (94.80%)
0:10:34.187633 PROGRESS: Decoy precursors: 30 (5.20%)
0:10:34.187681 PROGRESS: 
0:10:34.187725 PROGRESS: Precursor Summary:
0:10:34.188548 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:10:34.188631 PROGRESS: 
0:10:34.188687 PROGRESS: Protein Summary:
0:10:34.189588 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
0:10:34.189671 PROGRESS: =========================================================================
0:10:34.189798 INFO: Target number of precursors not reached yet.
0:10:34.265471 INFO: Starting optimization step 2.
0:10:34.265669 PROGRESS: === Extracting elution groups 600 to 1400 ===
0:10:34.265749 INFO: Using classic extraction backend
0:10:34.265873 PROGRESS: Extracting batch of 1576 precursors
0:10:34.265946 INFO: === Search parameters used ===
0:10:34.265996 INFO: rt_error       : 2099.928159
0:10:34.266041 INFO: mobility_error : 0.1
0:10:34.266085 INFO: num_candidates : 1
0:10:34.266125 INFO: ms1_error      : 30
0:10:34.266165 INFO: ms2_error      : 30
0:10:34.266205 INFO: fwhm_rt        : 5
0:10:34.266246 INFO: quant_window   : 3
0:10:34.266284 INFO: ==============================================
0:10:34.267059 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:10:34.267105 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:10:34.267132 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:10:34.267154 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:10:34.271319 INFO: Starting candidate selection
0:10:51.049266 INFO: Starting candidate scoring
0:10:51.329543 INFO: Finished candidate processing
0:10:51.329718 INFO: Collecting candidate features
0:10:51.345680 INFO: Collecting fragment features
0:10:51.349963 INFO: Finished candidate scoring
0:10:51.354903 INFO: performing precursor FDR with 47 features
0:10:51.355019 INFO: Decoy channel: -1
0:10:51.355050 INFO: Competetive: True
0:10:51.359857 INFO: Setting torch num_threads to 2 for FDR classification task
0:10:51.362924 INFO: Using random state 956319 for train-test-split
0:10:51.378921 INFO: Test AUC: 0.525
0:10:51.379071 INFO: Train AUC: 0.498
0:10:51.379112 INFO: AUC difference: 5.30%
0:10:51.379143 WARNING: AUC difference > 5%. This may indicate overfitting.
0:10:51.636165 INFO: Resetting torch num_threads to 80
0:10:51.638034 PROGRESS: === Extracted 2644 precursors and 28607 fragments ===
0:10:51.638560 INFO: === FDR correction performed with classifier version -1 ===
0:10:51.639281 PROGRESS: ============================= Precursor FDR =============================
0:10:51.639379 PROGRESS: Total precursors accumulated: 1,357
0:10:51.639440 PROGRESS: Target precursors: 1,283 (94.55%)
0:10:51.639493 PROGRESS: Decoy precursors: 74 (5.45%)
0:10:51.639542 PROGRESS: 
0:10:51.639588 PROGRESS: Precursor Summary:
0:10:51.640469 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:10:51.640566 PROGRESS: 
0:10:51.640624 PROGRESS: Protein Summary:
0:10:51.641585 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:10:51.641671 PROGRESS: =========================================================================
0:10:51.641832 INFO: Target number of precursors not reached yet.
0:10:51.744242 INFO: Starting optimization step 3.
0:10:51.744495 PROGRESS: === Extracting elution groups 1400 to 3000 ===
0:10:51.744579 INFO: Using classic extraction backend
0:10:51.744718 PROGRESS: Extracting batch of 3162 precursors
0:10:51.744793 INFO: === Search parameters used ===
0:10:51.744844 INFO: rt_error       : 2099.928159
0:10:51.744888 INFO: mobility_error : 0.1
0:10:51.744944 INFO: num_candidates : 1
0:10:51.744989 INFO: ms1_error      : 30
0:10:51.745031 INFO: ms2_error      : 30
0:10:51.745072 INFO: fwhm_rt        : 5
0:10:51.745112 INFO: quant_window   : 3
0:10:51.745151 INFO: ==============================================
0:10:51.746607 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:10:51.746673 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:10:51.746704 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:10:51.746727 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:10:51.781759 INFO: Starting candidate selection
0:11:25.600044 INFO: Starting candidate scoring
0:11:25.915258 INFO: Finished candidate processing
0:11:25.915429 INFO: Collecting candidate features
0:11:25.940613 INFO: Collecting fragment features
0:11:25.946292 INFO: Finished candidate scoring
0:11:25.975254 INFO: performing precursor FDR with 47 features
0:11:25.975411 INFO: Decoy channel: -1
0:11:25.975437 INFO: Competetive: True
0:11:25.985772 INFO: Setting torch num_threads to 2 for FDR classification task
0:11:25.990734 INFO: Using random state 331513 for train-test-split
0:11:26.014667 INFO: Test AUC: 0.495
0:11:26.014790 INFO: Train AUC: 0.503
0:11:26.014826 INFO: AUC difference: 1.63%
0:11:26.230522 INFO: Resetting torch num_threads to 80
0:11:26.232936 PROGRESS: === Extracted 5675 precursors and 61258 fragments ===
0:11:26.233450 INFO: === FDR correction performed with classifier version -1 ===
0:11:26.234299 PROGRESS: ============================= Precursor FDR =============================
0:11:26.234385 PROGRESS: Total precursors accumulated: 2,903
0:11:26.234447 PROGRESS: Target precursors: 2,732 (94.11%)
0:11:26.234498 PROGRESS: Decoy precursors: 171 (5.89%)
0:11:26.234545 PROGRESS: 
0:11:26.234591 PROGRESS: Precursor Summary:
0:11:26.235489 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:11:26.235575 PROGRESS: 
0:11:26.235631 PROGRESS: Protein Summary:
0:11:26.236587 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:11:26.236673 PROGRESS: =========================================================================
0:11:26.236891 INFO: Target number of precursors not reached yet.
0:11:26.375471 INFO: Starting optimization step 4.
0:11:26.375862 PROGRESS: === Extracting elution groups 3000 to 6200 ===
0:11:26.376006 INFO: Using classic extraction backend
0:11:26.376279 PROGRESS: Extracting batch of 6312 precursors
0:11:26.376395 INFO: === Search parameters used ===
0:11:26.376462 INFO: rt_error       : 2099.928159
0:11:26.376521 INFO: mobility_error : 0.1
0:11:26.376577 INFO: num_candidates : 1
0:11:26.376631 INFO: ms1_error      : 30
0:11:26.376696 INFO: ms2_error      : 30
0:11:26.376751 INFO: fwhm_rt        : 5
0:11:26.376805 INFO: quant_window   : 3
0:11:26.376859 INFO: ==============================================
0:11:26.381319 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:11:26.381435 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:11:26.381485 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:11:26.381517 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:11:26.387277 INFO: Starting candidate selection
0:12:29.606173 INFO: Starting candidate scoring
0:12:30.155417 INFO: Finished candidate processing
0:12:30.155544 INFO: Collecting candidate features
0:12:30.181930 INFO: Collecting fragment features
0:12:30.189769 INFO: Finished candidate scoring
0:12:30.217606 INFO: performing precursor FDR with 47 features
0:12:30.217767 INFO: Decoy channel: -1
0:12:30.217816 INFO: Competetive: True
0:12:30.228236 INFO: Setting torch num_threads to 2 for FDR classification task
0:12:30.233666 INFO: Using random state 741875 for train-test-split
0:12:30.269136 INFO: Test AUC: 0.495
0:12:30.269262 INFO: Train AUC: 0.499
0:12:30.269297 INFO: AUC difference: 0.95%
0:12:30.515167 INFO: Resetting torch num_threads to 80
0:12:30.520527 PROGRESS: === Extracted 11704 precursors and 126135 fragments ===
0:12:30.521209 INFO: === FDR correction performed with classifier version -1 ===
0:12:30.522783 PROGRESS: ============================= Precursor FDR =============================
0:12:30.522880 PROGRESS: Total precursors accumulated: 5,987
0:12:30.522947 PROGRESS: Target precursors: 5,628 (94.00%)
0:12:30.522999 PROGRESS: Decoy precursors: 359 (6.00%)
0:12:30.523046 PROGRESS: 
0:12:30.523091 PROGRESS: Precursor Summary:
0:12:30.524009 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:12:30.524095 PROGRESS: 
0:12:30.524165 PROGRESS: Protein Summary:
0:12:30.525148 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:12:30.525236 PROGRESS: =========================================================================
0:12:30.525551 INFO: Target number of precursors not reached yet.
0:12:30.675502 INFO: Starting optimization step 5.
0:12:30.675751 PROGRESS: === Extracting elution groups 6200 to 12600 ===
0:12:30.675843 INFO: Using classic extraction backend
0:12:30.676022 PROGRESS: Extracting batch of 12615 precursors
0:12:30.676105 INFO: === Search parameters used ===
0:12:30.676156 INFO: rt_error       : 2099.928159
0:12:30.676202 INFO: mobility_error : 0.1
0:12:30.676246 INFO: num_candidates : 1
0:12:30.676289 INFO: ms1_error      : 30
0:12:30.676330 INFO: ms2_error      : 30
0:12:30.676370 INFO: fwhm_rt        : 5
0:12:30.676416 INFO: quant_window   : 3
0:12:30.676457 INFO: ==============================================
0:12:30.680774 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:12:30.680870 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:12:30.680909 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:12:30.680933 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:12:30.686885 INFO: Starting candidate selection
0:14:52.512172 INFO: Starting candidate scoring
0:14:53.552489 INFO: Finished candidate processing
0:14:53.552624 INFO: Collecting candidate features
0:14:53.604801 WARNING: height_correlation has 1 NaNs ( 0.01 % out of 12042)
0:14:53.610697 INFO: Collecting fragment features
0:14:53.625550 INFO: Finished candidate scoring
0:14:53.688780 INFO: performing precursor FDR with 47 features
0:14:53.688930 INFO: Decoy channel: -1
0:14:53.688961 INFO: Competetive: True
0:14:53.713258 INFO: Setting torch num_threads to 2 for FDR classification task
0:14:53.722053 WARNING: dropped 1 decoy PSMs due to missing features
0:14:53.728951 INFO: Using random state 409118 for train-test-split
0:14:54.048857 INFO: Test AUC: 0.534
0:14:54.048986 INFO: Train AUC: 0.544
0:14:54.049017 INFO: AUC difference: 1.85%
0:14:54.306467 INFO: Resetting torch num_threads to 80
0:14:54.316729 PROGRESS: === Extracted 23746 precursors and 255624 fragments ===
0:14:54.317529 INFO: === FDR correction performed with classifier version -1 ===
0:14:54.320816 PROGRESS: ============================= Precursor FDR =============================
0:14:54.321011 PROGRESS: Total precursors accumulated: 12,162
0:14:54.321103 PROGRESS: Target precursors: 6,846 (56.29%)
0:14:54.321172 PROGRESS: Decoy precursors: 5,316 (43.71%)
0:14:54.321235 PROGRESS: 
0:14:54.321296 PROGRESS: Precursor Summary:
0:14:54.322609 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:14:54.322724 PROGRESS: 
0:14:54.322812 PROGRESS: Protein Summary:
0:14:54.323946 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
0:14:54.324041 PROGRESS: =========================================================================
0:14:54.324620 INFO: Target number of precursors not reached yet.
0:14:54.536798 INFO: Starting optimization step 6.
0:14:54.537063 PROGRESS: === Extracting elution groups 12600 to 25400 ===
0:14:54.537164 INFO: Using classic extraction backend
0:14:54.537355 PROGRESS: Extracting batch of 25223 precursors
0:14:54.537441 INFO: === Search parameters used ===
0:14:54.537497 INFO: rt_error       : 2099.928159
0:14:54.537550 INFO: mobility_error : 0.1
0:14:54.537600 INFO: num_candidates : 1
0:14:54.537645 INFO: ms1_error      : 30
0:14:54.537690 INFO: ms2_error      : 30
0:14:54.537734 INFO: fwhm_rt        : 5
0:14:54.537777 INFO: quant_window   : 3
0:14:54.537833 INFO: ==============================================
0:14:54.546756 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:14:54.546899 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:14:54.546940 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:14:54.546965 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:14:54.562993 INFO: Starting candidate selection
0:19:55.926242 INFO: Starting candidate scoring
0:19:57.791156 INFO: Finished candidate processing
0:19:57.791306 INFO: Collecting candidate features
0:19:57.843436 WARNING: intensity_correlation has 5 NaNs ( 0.02 % out of 24137)
0:19:57.848151 INFO: Collecting fragment features
0:19:57.868866 INFO: Finished candidate scoring
0:19:58.005839 INFO: performing precursor FDR with 47 features
0:19:58.006018 INFO: Decoy channel: -1
0:19:58.006046 INFO: Competetive: True
0:19:58.035094 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:58.047913 WARNING: dropped 1 target PSMs due to missing features
0:19:58.048088 WARNING: dropped 5 decoy PSMs due to missing features
0:19:58.066627 INFO: Using random state 852652 for train-test-split
0:19:59.072298 INFO: Test AUC: 0.560
0:19:59.072526 INFO: Train AUC: 0.584
0:19:59.072583 INFO: AUC difference: 4.09%
0:19:59.367667 INFO: Resetting torch num_threads to 80
0:19:59.388140 PROGRESS: === Extracted 47883 precursors and 515441 fragments ===
0:19:59.389302 INFO: === FDR correction performed with classifier version -1 ===
0:19:59.396674 PROGRESS: ============================= Precursor FDR =============================
0:19:59.396977 PROGRESS: Total precursors accumulated: 24,522
0:19:59.397061 PROGRESS: Target precursors: 14,858 (60.59%)
0:19:59.397124 PROGRESS: Decoy precursors: 9,664 (39.41%)
0:19:59.397178 PROGRESS: 
0:19:59.397227 PROGRESS: Precursor Summary:
0:19:59.398514 PROGRESS: Channel   0:	 0.050 FDR:   101; 0.010 FDR:    44; 0.001 FDR:    44
0:19:59.398607 PROGRESS: 
0:19:59.398666 PROGRESS: Protein Summary:
0:19:59.399884 PROGRESS: Channel   0:	 0.050 FDR:   100; 0.010 FDR:    43; 0.001 FDR:    43
0:19:59.399981 PROGRESS: =========================================================================
0:19:59.401047 INFO: Target number of precursors not reached yet.
0:20:00.706195 INFO: Starting optimization step 7.
0:20:00.706574 PROGRESS: === Extracting elution groups 25400 to 51000 ===
0:20:00.706721 INFO: Using classic extraction backend
0:20:00.707068 PROGRESS: Extracting batch of 50469 precursors
0:20:00.707175 INFO: === Search parameters used ===
0:20:00.707231 INFO: rt_error       : 2099.928159
0:20:00.707292 INFO: mobility_error : 0.1
0:20:00.707347 INFO: num_candidates : 1
0:20:00.707393 INFO: ms1_error      : 30
0:20:00.707433 INFO: ms2_error      : 30
0:20:00.707473 INFO: fwhm_rt        : 5
0:20:00.707512 INFO: quant_window   : 3
0:20:00.707552 INFO: ==============================================
0:20:00.725984 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:20:00.726171 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:20:00.726243 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:20:00.726270 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:20:00.735012 INFO: Starting candidate selection
0:29:04.146347 INFO: Starting candidate scoring
0:29:07.712081 INFO: Finished candidate processing
0:29:07.712238 INFO: Collecting candidate features
0:29:07.958752 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 48203)
0:29:07.964927 INFO: Collecting fragment features
0:29:08.004900 INFO: Finished candidate scoring
0:29:08.295630 INFO: performing precursor FDR with 47 features
0:29:08.296154 INFO: Decoy channel: -1
0:29:08.296188 INFO: Competetive: True
0:29:08.370095 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:08.396620 WARNING: dropped 2 target PSMs due to missing features
0:29:08.396785 WARNING: dropped 7 decoy PSMs due to missing features
0:29:08.422732 INFO: Using random state 241156 for train-test-split
0:29:10.378804 INFO: Test AUC: 0.563
0:29:10.378990 INFO: Train AUC: 0.597
0:29:10.379040 INFO: AUC difference: 5.56%
0:29:10.379075 WARNING: AUC difference > 5%. This may indicate overfitting.
0:29:10.671556 INFO: Resetting torch num_threads to 80
0:29:10.704709 PROGRESS: === Extracted 96086 precursors and 1034079 fragments ===
0:29:10.705704 INFO: === FDR correction performed with classifier version -1 ===
0:29:10.720067 PROGRESS: ============================= Precursor FDR =============================
0:29:10.720422 PROGRESS: Total precursors accumulated: 49,211
0:29:10.720495 PROGRESS: Target precursors: 30,466 (61.91%)
0:29:10.720554 PROGRESS: Decoy precursors: 18,745 (38.09%)
0:29:10.720607 PROGRESS: 
0:29:10.720657 PROGRESS: Precursor Summary:
0:29:10.722312 PROGRESS: Channel   0:	 0.050 FDR:   305; 0.010 FDR:   224; 0.001 FDR:   157
0:29:10.722434 PROGRESS: 
0:29:10.722497 PROGRESS: Protein Summary:
0:29:10.723917 PROGRESS: Channel   0:	 0.050 FDR:   289; 0.010 FDR:   214; 0.001 FDR:   153
0:29:10.724017 PROGRESS: =========================================================================
0:29:10.726630 INFO: Target number of precursors reached.
0:29:10.806664 INFO: fragments_df: keeping 2120 of 1034079 [sum(precursor_idx_mask)=2553 sum(mass_error_mask)=1034079 stop_rank=2120
0:29:11.357309 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
0:29:11.510299 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:29:11.659448 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
0:29:11.806905 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:29:12.107851 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:29:12.108419 INFO: Using score_cutoff 53.95759131774902 (fac=0.99, q=1)
0:29:12.109169 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0344762802124023
0:29:12.109254 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.01116950809955597
0:29:12.109313 INFO: Updating optimization_manager: score_cutoff        : 0 -> 53.95759131774902
0:29:12.109431 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:29:12.125274 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:29:12.191350 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:29:12.214942 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:29:12.360746 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:29:12.361109 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:29:12.361258 INFO: Starting optimization step 8.
0:29:12.361453 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:29:12.361688 INFO: Using classic extraction backend
0:29:12.362083 PROGRESS: Extracting batch of 100530 precursors
0:29:12.362200 INFO: === Search parameters used ===
0:29:12.362263 INFO: rt_error       : 2099.928159
0:29:12.362317 INFO: mobility_error : 0.1
0:29:12.362367 INFO: num_candidates : 3
0:29:12.362414 INFO: ms1_error      : 30
0:29:12.362468 INFO: ms2_error      : 30
0:29:12.362518 INFO: fwhm_rt        : 3.0344762802124023
0:29:12.362566 INFO: quant_window   : 3
0:29:12.362615 INFO: ==============================================
0:29:12.410025 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:29:12.410349 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:29:12.410479 INFO: FWHM in RT is 3.03 seconds, sigma is 0.67
0:29:12.410561 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.18
0:29:12.418544 INFO: Starting candidate selection
0:45:39.202611 INFO: Starting candidate scoring
0:46:02.542909 INFO: Finished candidate processing
0:46:02.543263 INFO: Collecting candidate features
0:46:03.474695 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 279322)
0:46:03.488785 INFO: Collecting fragment features
0:46:03.673120 INFO: Finished candidate scoring
0:46:03.998310 INFO: performing precursor FDR with 47 features
0:46:03.998470 INFO: Decoy channel: -1
0:46:03.998497 INFO: Competetive: True
0:46:04.120093 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:04.192641 WARNING: dropped 2 target PSMs due to missing features
0:46:04.192810 WARNING: dropped 1 decoy PSMs due to missing features
0:46:04.285122 INFO: Using random state 98532 for train-test-split
0:46:10.057028 INFO: Test AUC: 0.564
0:46:10.057184 INFO: Train AUC: 0.584
0:46:10.057219 INFO: AUC difference: 3.44%
0:46:10.382164 INFO: Resetting torch num_threads to 80
0:46:10.389440 PROGRESS: === Extracted 279322 precursors and 3040198 fragments ===
0:46:10.390118 INFO: === FDR correction performed with classifier version 7 ===
0:46:10.403236 PROGRESS: ============================= Precursor FDR =============================
0:46:10.403606 PROGRESS: Total precursors accumulated: 50,107
0:46:10.403681 PROGRESS: Target precursors: 31,245 (62.36%)
0:46:10.403741 PROGRESS: Decoy precursors: 18,862 (37.64%)
0:46:10.403794 PROGRESS: 
0:46:10.403844 PROGRESS: Precursor Summary:
0:46:10.405511 PROGRESS: Channel   0:	 0.050 FDR:   308; 0.010 FDR:   231; 0.001 FDR:   164
0:46:10.405629 PROGRESS: 
0:46:10.405691 PROGRESS: Protein Summary:
0:46:10.407118 PROGRESS: Channel   0:	 0.050 FDR:   293; 0.010 FDR:   221; 0.001 FDR:   156
0:46:10.407250 PROGRESS: =========================================================================
0:46:10.410417 INFO: Target number of precursors reached.
0:46:10.620239 INFO: fragments_df: keeping 3705 of 3040198 [sum(precursor_idx_mask)=7655 sum(mass_error_mask)=3040197 stop_rank=3705
0:46:10.931040 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
0:46:11.064822 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:11.181953 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
0:46:11.305814 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:11.796014 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:11.796513 INFO: Using score_cutoff 54.253253059387205 (fac=0.99, q=1)
0:46:11.796907 INFO: Updating optimization_manager: fwhm_rt             : 3.0344762802124023 -> 2.8772470951080322
0:46:11.797005 INFO: Updating optimization_manager: fwhm_mobility       : 0.01116950809955597 -> 0.010380592197179794
0:46:11.797081 INFO: Updating optimization_manager: score_cutoff        : 53.95759131774902 -> 54.253253059387205
0:46:11.797177 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
0:46:11.812283 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:11.873753 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
0:46:11.892103 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:12.038812 INFO: === checking if optimization conditions were reached ===
0:46:12.041407 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
0:46:12.041603 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:46:12.041764 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
0:46:12.043022 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
0:46:12.043203 INFO: Updating optimization_manager: classifier_version  : 8 -> 8
0:46:12.043346 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
0:46:12.043493 INFO: ==============================================
0:46:12.043658 INFO: Starting optimization step 9.
0:46:12.046083 PROGRESS: === Extracting elution groups 0 to 51000 ===
0:46:12.046505 INFO: Using classic extraction backend
0:46:12.046796 PROGRESS: Extracting batch of 100530 precursors
0:46:12.046962 INFO: === Search parameters used ===
0:46:12.047102 INFO: rt_error       : 2099.928159
0:46:12.047217 INFO: mobility_error : 0.1
0:46:12.047330 INFO: num_candidates : 3
0:46:12.047439 INFO: ms1_error      : 15.0
0:46:12.047547 INFO: ms2_error      : 15.0
0:46:12.047654 INFO: fwhm_rt        : 2.8772470951080322
0:46:12.047768 INFO: quant_window   : 3
0:46:12.047871 INFO: ==============================================
0:46:12.087688 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:46:12.087988 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:46:12.088125 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
0:46:12.088223 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.81
0:46:12.095467 INFO: Starting candidate selection
1:03:09.720712 INFO: Starting candidate scoring
1:03:28.056070 INFO: Finished candidate processing
1:03:28.056230 INFO: Collecting candidate features
1:03:28.918757 WARNING: intensity_correlation has 10 NaNs ( 0.00 % out of 278792)
1:03:28.919567 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 278792)
1:03:28.938856 INFO: Collecting fragment features
1:03:29.221391 INFO: Finished candidate scoring
1:03:29.716888 INFO: performing precursor FDR with 47 features
1:03:29.717103 INFO: Decoy channel: -1
1:03:29.717137 INFO: Competetive: True
1:03:29.907801 INFO: Setting torch num_threads to 2 for FDR classification task
1:03:30.034801 WARNING: dropped 7 target PSMs due to missing features
1:03:30.035038 WARNING: dropped 5 decoy PSMs due to missing features
1:03:30.278377 INFO: Using random state 738957 for train-test-split
1:03:36.127752 INFO: Test AUC: 0.571
1:03:36.128045 INFO: Train AUC: 0.596
1:03:36.128086 INFO: AUC difference: 4.19%
1:03:36.462303 INFO: Resetting torch num_threads to 80
1:03:36.470260 PROGRESS: === Extracted 278792 precursors and 2886022 fragments ===
1:03:36.471083 INFO: === FDR correction performed with classifier version 8 ===
1:03:36.483706 PROGRESS: ============================= Precursor FDR =============================
1:03:36.484065 PROGRESS: Total precursors accumulated: 50,018
1:03:36.484141 PROGRESS: Target precursors: 31,483 (62.94%)
1:03:36.484200 PROGRESS: Decoy precursors: 18,535 (37.06%)
1:03:36.484254 PROGRESS: 
1:03:36.484306 PROGRESS: Precursor Summary:
1:03:36.485964 PROGRESS: Channel   0:	 0.050 FDR:   487; 0.010 FDR:   349; 0.001 FDR:   272
1:03:36.486071 PROGRESS: 
1:03:36.486133 PROGRESS: Protein Summary:
1:03:36.487674 PROGRESS: Channel   0:	 0.050 FDR:   458; 0.010 FDR:   328; 0.001 FDR:   260
1:03:36.487777 PROGRESS: =========================================================================
1:03:36.490690 INFO: Target number of precursors reached.
1:03:36.685988 INFO: fragments_df: keeping 5000 of 2886022 [sum(precursor_idx_mask)=11331 sum(mass_error_mask)=2886022 stop_rank=5000
1:03:37.082747 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:03:37.223562 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:03:37.357036 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:03:37.486685 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:03:38.188200 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:03:38.188704 INFO: Using score_cutoff 44.812542453002926 (fac=0.99, q=1)
1:03:38.189096 INFO: Updating optimization_manager: fwhm_rt             : 2.8772470951080322 -> 2.712045192718506
1:03:38.189183 INFO: Updating optimization_manager: fwhm_mobility       : 0.010380592197179794 -> 0.009111340157687664
1:03:38.189240 INFO: Updating optimization_manager: score_cutoff        : 54.253253059387205 -> 44.812542453002926
1:03:38.189311 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:03:38.203393 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:03:38.265594 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:03:38.283512 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:03:38.423586 INFO: === checking if optimization conditions were reached ===
1:03:38.426386 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1:03:38.426551 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:03:38.426649 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1:03:38.427884 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1:03:38.428008 INFO: Updating optimization_manager: classifier_version  : 9 -> 9
1:03:38.428079 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1:03:38.428144 INFO: ==============================================
1:03:38.428254 PROGRESS: Optimization finished for ms2_error, ms1_error.
1:03:38.662450 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:03:38.676793 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:03:38.738819 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:03:38.756649 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:03:38.897249 INFO: Starting optimization step 0.
1:03:38.897609 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:03:38.897713 INFO: Using classic extraction backend
1:03:38.897940 PROGRESS: Extracting batch of 100530 precursors
1:03:38.898038 INFO: === Search parameters used ===
1:03:38.898098 INFO: rt_error       : 2099.928159
1:03:38.898152 INFO: mobility_error : 0.1
1:03:38.898204 INFO: num_candidates : 3
1:03:38.898255 INFO: ms1_error      : 15.0
1:03:38.898305 INFO: ms2_error      : 15.0
1:03:38.898356 INFO: fwhm_rt        : 2.712045192718506
1:03:38.898405 INFO: quant_window   : 3
1:03:38.898454 INFO: ==============================================
1:03:38.940713 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:03:38.940897 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:03:38.940962 INFO: FWHM in RT is 2.71 seconds, sigma is 0.60
1:03:38.940989 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.23
1:03:38.987082 INFO: Starting candidate selection
1:19:41.254865 INFO: Starting candidate scoring
1:19:54.311592 INFO: Finished candidate processing
1:19:54.311975 INFO: Collecting candidate features
1:19:55.438872 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 278721)
1:19:55.439660 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 278721)
1:19:55.458515 INFO: Collecting fragment features
1:19:55.729828 INFO: Finished candidate scoring
1:19:56.335034 INFO: performing precursor FDR with 47 features
1:19:56.335258 INFO: Decoy channel: -1
1:19:56.335287 INFO: Competetive: True
1:19:56.496502 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:56.595202 WARNING: dropped 8 target PSMs due to missing features
1:19:56.595520 WARNING: dropped 4 decoy PSMs due to missing features
1:19:56.825014 INFO: Using random state 322229 for train-test-split
1:20:04.134117 INFO: Test AUC: 0.579
1:20:04.134326 INFO: Train AUC: 0.606
1:20:04.134371 INFO: AUC difference: 4.45%
1:20:04.663300 INFO: Resetting torch num_threads to 80
1:20:04.705719 PROGRESS: === Extracted 278721 precursors and 2879326 fragments ===
1:20:04.707648 INFO: === FDR correction performed with classifier version 9 ===
1:20:04.734369 PROGRESS: ============================= Precursor FDR =============================
1:20:04.734902 PROGRESS: Total precursors accumulated: 50,032
1:20:04.735012 PROGRESS: Target precursors: 31,964 (63.89%)
1:20:04.735078 PROGRESS: Decoy precursors: 18,068 (36.11%)
1:20:04.735136 PROGRESS: 
1:20:04.735192 PROGRESS: Precursor Summary:
1:20:04.738304 PROGRESS: Channel   0:	 0.050 FDR:   510; 0.010 FDR:   378; 0.001 FDR:   271
1:20:04.738468 PROGRESS: 
1:20:04.738542 PROGRESS: Protein Summary:
1:20:04.743898 PROGRESS: Channel   0:	 0.050 FDR:   483; 0.010 FDR:   356; 0.001 FDR:   256
1:20:04.744205 PROGRESS: =========================================================================
1:20:04.750761 INFO: Target number of precursors reached.
1:20:05.083929 INFO: fragments_df: keeping 5000 of 2879326 [sum(precursor_idx_mask)=12118 sum(mass_error_mask)=2879326 stop_rank=5000
1:20:05.773218 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:20:05.951193 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:20:06.154969 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:20:06.402811 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:20:08.750721 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:20:08.751260 INFO: Using score_cutoff 47.529588208007816 (fac=0.99, q=1)
1:20:08.751651 INFO: Updating optimization_manager: fwhm_rt             : 2.712045192718506 -> 2.7830631732940674
1:20:08.751748 INFO: Updating optimization_manager: fwhm_mobility       : 0.009111340157687664 -> 0.00907430611550808
1:20:08.751821 INFO: Updating optimization_manager: score_cutoff        : 44.812542453002926 -> 47.529588208007816
1:20:08.751895 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:20:08.767157 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:20:08.833662 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:20:08.848670 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:20:09.013405 INFO: === checking if optimization conditions were reached ===
1:20:09.020849 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1:20:09.023621 INFO: Updating optimization_manager: rt_error            : 2099.928159 -> 482.9028138342245
1:20:09.026564 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 482.9028.
1:20:09.026872 INFO: ==============================================
1:20:09.027355 INFO: Starting optimization step 1.
1:20:09.027581 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:20:09.027795 INFO: Using classic extraction backend
1:20:09.028084 PROGRESS: Extracting batch of 100530 precursors
1:20:09.028390 INFO: === Search parameters used ===
1:20:09.028594 INFO: rt_error       : 482.9028138342245
1:20:09.028769 INFO: mobility_error : 0.1
1:20:09.028938 INFO: num_candidates : 3
1:20:09.029112 INFO: ms1_error      : 15.0
1:20:09.029279 INFO: ms2_error      : 15.0
1:20:09.029442 INFO: fwhm_rt        : 2.7830631732940674
1:20:09.029608 INFO: quant_window   : 3
1:20:09.029772 INFO: ==============================================
1:20:09.067292 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:20:09.067600 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:20:09.067690 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
1:20:09.067757 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.21
1:20:09.124876 INFO: Starting candidate selection
1:23:03.607734 INFO: Starting candidate scoring
1:23:16.000304 INFO: Finished candidate processing
1:23:16.000690 INFO: Collecting candidate features
1:23:16.625187 WARNING: intensity_correlation has 69 NaNs ( 0.03 % out of 269911)
1:23:16.625711 WARNING: height_correlation has 9 NaNs ( 0.00 % out of 269911)
1:23:16.638572 INFO: Collecting fragment features
1:23:16.831638 INFO: Finished candidate scoring
1:23:17.116880 INFO: performing precursor FDR with 47 features
1:23:17.117041 INFO: Decoy channel: -1
1:23:17.117078 INFO: Competetive: True
1:23:17.214403 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:17.267475 WARNING: dropped 40 target PSMs due to missing features
1:23:17.267676 WARNING: dropped 34 decoy PSMs due to missing features
1:23:17.346468 INFO: Using random state 322229 for train-test-split
1:23:22.981790 INFO: Test AUC: 0.559
1:23:22.981956 INFO: Train AUC: 0.583
1:23:22.981989 INFO: AUC difference: 4.04%
1:23:23.313687 INFO: Resetting torch num_threads to 80
1:23:23.336831 PROGRESS: === Extracted 269911 precursors and 2729439 fragments ===
1:23:23.337475 INFO: === FDR correction performed with classifier version 9 ===
1:23:23.346998 PROGRESS: ============================= Precursor FDR =============================
1:23:23.347265 PROGRESS: Total precursors accumulated: 49,209
1:23:23.347330 PROGRESS: Target precursors: 29,998 (60.96%)
1:23:23.347383 PROGRESS: Decoy precursors: 19,211 (39.04%)
1:23:23.347427 PROGRESS: 
1:23:23.347469 PROGRESS: Precursor Summary:
1:23:23.348941 PROGRESS: Channel   0:	 0.050 FDR:   547; 0.010 FDR:   373; 0.001 FDR:   304
1:23:23.349033 PROGRESS: 
1:23:23.349094 PROGRESS: Protein Summary:
1:23:23.350556 PROGRESS: Channel   0:	 0.050 FDR:   516; 0.010 FDR:   351; 0.001 FDR:   288
1:23:23.350647 PROGRESS: =========================================================================
1:23:23.365487 INFO: Target number of precursors reached.
1:23:23.557441 INFO: fragments_df: keeping 5000 of 2729439 [sum(precursor_idx_mask)=11949 sum(mass_error_mask)=2729437 stop_rank=5000
1:23:23.950997 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:23:24.091026 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:24.215962 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:23:24.341437 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:25.020915 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:25.021401 INFO: Using score_cutoff 48.84510509033203 (fac=0.99, q=1)
1:23:25.021834 INFO: Updating optimization_manager: fwhm_rt             : 2.7830631732940674 -> 2.7856290340423584
1:23:25.021919 INFO: Updating optimization_manager: fwhm_mobility       : 0.00907430611550808 -> 0.009015197865664959
1:23:25.021972 INFO: Updating optimization_manager: score_cutoff        : 47.529588208007816 -> 48.84510509033203
1:23:25.022059 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:23:25.035869 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:25.096977 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:23:25.114264 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:25.256028 INFO: === checking if optimization conditions were reached ===
1:23:25.256461 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1:23:25.259476 INFO: Updating optimization_manager: rt_error            : 482.9028138342245 -> 338.9840465198701
1:23:25.259916 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 338.9840.
1:23:25.260029 INFO: ==============================================
1:23:25.260187 INFO: Starting optimization step 2.
1:23:25.260258 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:23:25.260376 INFO: Using classic extraction backend
1:23:25.260703 PROGRESS: Extracting batch of 100530 precursors
1:23:25.260795 INFO: === Search parameters used ===
1:23:25.260848 INFO: rt_error       : 338.9840465198701
1:23:25.260893 INFO: mobility_error : 0.1
1:23:25.260933 INFO: num_candidates : 3
1:23:25.260987 INFO: ms1_error      : 15.0
1:23:25.261042 INFO: ms2_error      : 15.0
1:23:25.261100 INFO: fwhm_rt        : 2.7856290340423584
1:23:25.261156 INFO: quant_window   : 3
1:23:25.261209 INFO: ==============================================
1:23:25.299245 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:23:25.299429 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:23:25.299504 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1:23:25.299536 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.18
1:23:25.327572 INFO: Starting candidate selection
1:25:44.085457 INFO: Starting candidate scoring
1:25:57.346598 INFO: Finished candidate processing
1:25:57.346857 INFO: Collecting candidate features
1:25:57.843401 WARNING: intensity_correlation has 70 NaNs ( 0.03 % out of 267587)
1:25:57.843908 WARNING: height_correlation has 12 NaNs ( 0.00 % out of 267587)
1:25:57.856387 INFO: Collecting fragment features
1:25:58.041976 INFO: Finished candidate scoring
1:25:58.297116 INFO: performing precursor FDR with 47 features
1:25:58.297252 INFO: Decoy channel: -1
1:25:58.297280 INFO: Competetive: True
1:25:58.386199 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:58.434041 WARNING: dropped 44 target PSMs due to missing features
1:25:58.434186 WARNING: dropped 35 decoy PSMs due to missing features
1:25:58.505107 INFO: Using random state 322229 for train-test-split
1:26:03.548281 INFO: Test AUC: 0.553
1:26:03.548429 INFO: Train AUC: 0.580
1:26:03.548468 INFO: AUC difference: 4.56%
1:26:03.868676 INFO: Resetting torch num_threads to 80
1:26:03.874444 PROGRESS: === Extracted 267587 precursors and 2680552 fragments ===
1:26:03.875048 INFO: === FDR correction performed with classifier version 9 ===
1:26:03.883621 PROGRESS: ============================= Precursor FDR =============================
1:26:03.883886 PROGRESS: Total precursors accumulated: 48,886
1:26:03.883954 PROGRESS: Target precursors: 29,649 (60.65%)
1:26:03.884006 PROGRESS: Decoy precursors: 19,237 (39.35%)
1:26:03.884053 PROGRESS: 
1:26:03.884099 PROGRESS: Precursor Summary:
1:26:03.885482 PROGRESS: Channel   0:	 0.050 FDR:   548; 0.010 FDR:   396; 0.001 FDR:   332
1:26:03.885571 PROGRESS: 
1:26:03.885630 PROGRESS: Protein Summary:
1:26:03.887090 PROGRESS: Channel   0:	 0.050 FDR:   516; 0.010 FDR:   373; 0.001 FDR:   314
1:26:03.887183 PROGRESS: =========================================================================
1:26:03.888682 INFO: Target number of precursors reached.
1:26:04.076361 INFO: fragments_df: keeping 5000 of 2680552 [sum(precursor_idx_mask)=12584 sum(mass_error_mask)=2680548 stop_rank=5000
1:26:04.473561 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:26:04.693796 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:26:04.865969 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:26:04.994550 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:26:05.685615 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:26:05.686092 INFO: Using score_cutoff 41.095994670867924 (fac=0.99, q=1)
1:26:05.686476 INFO: Updating optimization_manager: fwhm_rt             : 2.7856290340423584 -> 2.746732711791992
1:26:05.686568 INFO: Updating optimization_manager: fwhm_mobility       : 0.009015197865664959 -> 0.009009331464767456
1:26:05.686636 INFO: Updating optimization_manager: score_cutoff        : 48.84510509033203 -> 41.095994670867924
1:26:05.686721 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:26:05.700562 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:26:05.764138 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:26:05.781141 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:26:05.914928 INFO: === checking if optimization conditions were reached ===
1:26:05.915368 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1:26:05.918369 INFO: Updating optimization_manager: rt_error            : 338.9840465198701 -> 346.5833864927306
1:26:05.918550 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 346.5834.
1:26:05.918693 INFO: ==============================================
1:26:05.918885 INFO: Starting optimization step 3.
1:26:05.919066 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:26:05.919196 INFO: Using classic extraction backend
1:26:05.919424 PROGRESS: Extracting batch of 100530 precursors
1:26:05.919592 INFO: === Search parameters used ===
1:26:05.919801 INFO: rt_error       : 346.5833864927306
1:26:05.919929 INFO: mobility_error : 0.1
1:26:05.920042 INFO: num_candidates : 3
1:26:05.920236 INFO: ms1_error      : 15.0
1:26:05.920364 INFO: ms2_error      : 15.0
1:26:05.920480 INFO: fwhm_rt        : 2.746732711791992
1:26:05.920606 INFO: quant_window   : 3
1:26:05.920732 INFO: ==============================================
1:26:05.960825 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:26:05.961106 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:26:05.961247 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1:26:05.961349 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.18
1:26:05.972732 INFO: Starting candidate selection
1:28:10.425218 INFO: Starting candidate scoring
1:28:23.413178 INFO: Finished candidate processing
1:28:23.413537 INFO: Collecting candidate features
1:28:24.098269 WARNING: intensity_correlation has 81 NaNs ( 0.03 % out of 268901)
1:28:24.098932 WARNING: height_correlation has 5 NaNs ( 0.00 % out of 268901)
1:28:24.113181 INFO: Collecting fragment features
1:28:24.316350 INFO: Finished candidate scoring
1:28:24.661204 INFO: performing precursor FDR with 47 features
1:28:24.661357 INFO: Decoy channel: -1
1:28:24.661387 INFO: Competetive: True
1:28:24.777507 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:24.847728 WARNING: dropped 44 target PSMs due to missing features
1:28:24.847921 WARNING: dropped 40 decoy PSMs due to missing features
1:28:24.953561 INFO: Using random state 322229 for train-test-split
1:28:30.897093 INFO: Test AUC: 0.556
1:28:30.897409 INFO: Train AUC: 0.581
1:28:30.897451 INFO: AUC difference: 4.33%
1:28:31.262772 INFO: Resetting torch num_threads to 80
1:28:31.272496 PROGRESS: === Extracted 268901 precursors and 2693403 fragments ===
1:28:31.273487 INFO: === FDR correction performed with classifier version 9 ===
1:28:31.288894 PROGRESS: ============================= Precursor FDR =============================
1:28:31.289251 PROGRESS: Total precursors accumulated: 49,118
1:28:31.289325 PROGRESS: Target precursors: 29,959 (60.99%)
1:28:31.289383 PROGRESS: Decoy precursors: 19,159 (39.01%)
1:28:31.289436 PROGRESS: 
1:28:31.289485 PROGRESS: Precursor Summary:
1:28:31.291245 PROGRESS: Channel   0:	 0.050 FDR:   589; 0.010 FDR:   349; 0.001 FDR:   282
1:28:31.291358 PROGRESS: 
1:28:31.291436 PROGRESS: Protein Summary:
1:28:31.293054 PROGRESS: Channel   0:	 0.050 FDR:   558; 0.010 FDR:   330; 0.001 FDR:   267
1:28:31.293162 PROGRESS: =========================================================================
1:28:31.299064 INFO: Target number of precursors reached.
1:28:31.596853 INFO: fragments_df: keeping 5000 of 2693403 [sum(precursor_idx_mask)=11177 sum(mass_error_mask)=2693400 stop_rank=5000
1:28:32.101134 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:28:32.330221 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:28:32.650125 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:28:32.842911 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:28:33.615935 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:28:33.616469 INFO: Using score_cutoff 50.205257624816895 (fac=0.99, q=1)
1:28:33.616909 INFO: Updating optimization_manager: fwhm_rt             : 2.746732711791992 -> 2.810281753540039
1:28:33.617002 INFO: Updating optimization_manager: fwhm_mobility       : 0.009009331464767456 -> 0.009299930185079575
1:28:33.617060 INFO: Updating optimization_manager: score_cutoff        : 41.095994670867924 -> 50.205257624816895
1:28:33.617145 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:28:33.631642 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:33.718366 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:28:33.756841 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:33.929982 INFO: === checking if optimization conditions were reached ===
1:28:33.930435 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1:28:33.936933 INFO: Updating optimization_manager: rt_error            : 346.5833864927306 -> 338.9840465198701
1:28:33.937117 INFO: Updating optimization_manager: classifier_version  : 9 -> 12
1:28:33.937246 INFO: Updating optimization_manager: score_cutoff        : 50.205257624816895 -> 41.095994670867924
1:28:33.937365 INFO: Updating optimization_manager: fwhm_rt             : 2.810281753540039 -> 2.746732711791992
1:28:33.937507 INFO: Updating optimization_manager: fwhm_mobility       : 0.009299930185079575 -> 0.009009331464767456
1:28:33.937633 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 338.9840 found after 4 searches.
1:28:33.937723 INFO: ==============================================
1:28:33.937856 PROGRESS: Optimization finished for rt_error.
1:28:34.335903 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:28:34.352160 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:28:34.438262 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:28:34.456108 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:34.714414 INFO: Starting optimization step 0.
1:28:34.714719 PROGRESS: === Extracting elution groups 0 to 51000 ===
1:28:34.714853 INFO: Using classic extraction backend
1:28:34.715219 PROGRESS: Extracting batch of 100530 precursors
1:28:34.715342 INFO: === Search parameters used ===
1:28:34.715415 INFO: rt_error       : 338.9840465198701
1:28:34.715498 INFO: mobility_error : 0.1
1:28:34.715562 INFO: num_candidates : 3
1:28:34.715626 INFO: ms1_error      : 15.0
1:28:34.715688 INFO: ms2_error      : 15.0
1:28:34.715748 INFO: fwhm_rt        : 2.746732711791992
1:28:34.715809 INFO: quant_window   : 3
1:28:34.715869 INFO: ==============================================
1:28:34.774220 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:28:34.774582 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:28:34.774805 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1:28:34.774924 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.18
1:28:34.819152 INFO: Starting candidate selection
1:30:42.106759 INFO: Starting candidate scoring
1:30:54.202386 INFO: Finished candidate processing
1:30:54.202723 INFO: Collecting candidate features
1:30:54.746334 WARNING: intensity_correlation has 67 NaNs ( 0.02 % out of 269988)
1:30:54.746869 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 269988)
1:30:54.760062 INFO: Collecting fragment features
1:30:54.926230 INFO: Finished candidate scoring
1:30:55.173034 INFO: performing precursor FDR with 47 features
1:30:55.173183 INFO: Decoy channel: -1
1:30:55.173210 INFO: Competetive: True
1:30:55.258407 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:55.319293 WARNING: dropped 36 target PSMs due to missing features
1:30:55.319467 WARNING: dropped 37 decoy PSMs due to missing features
1:30:55.424614 INFO: Using random state 667451 for train-test-split
1:31:00.384446 INFO: Test AUC: 0.565
1:31:00.384724 INFO: Train AUC: 0.590
1:31:00.384761 INFO: AUC difference: 4.28%
1:31:00.747780 INFO: Resetting torch num_threads to 80
1:31:00.756484 PROGRESS: === Extracted 269988 precursors and 2703473 fragments ===
1:31:00.757214 INFO: === FDR correction performed with classifier version 12 ===
1:31:00.769594 PROGRESS: ============================= Precursor FDR =============================
1:31:00.769912 PROGRESS: Total precursors accumulated: 49,274
1:31:00.769994 PROGRESS: Target precursors: 30,398 (61.69%)
1:31:00.770063 PROGRESS: Decoy precursors: 18,876 (38.31%)
1:31:00.770119 PROGRESS: 
1:31:00.770178 PROGRESS: Precursor Summary:
1:31:00.772053 PROGRESS: Channel   0:	 0.050 FDR:   612; 0.010 FDR:   419; 0.001 FDR:   319
1:31:00.772162 PROGRESS: 
1:31:00.772229 PROGRESS: Protein Summary:
1:31:00.774181 PROGRESS: Channel   0:	 0.050 FDR:   578; 0.010 FDR:   398; 0.001 FDR:   302
1:31:00.774287 PROGRESS: =========================================================================
1:31:00.777213 INFO: Target number of precursors reached.
1:31:00.971476 INFO: fragments_df: keeping 5000 of 2703473 [sum(precursor_idx_mask)=13362 sum(mass_error_mask)=2703472 stop_rank=5000
1:31:01.909376 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:31:02.018658 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:31:02.184721 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:31:02.313542 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:31:02.990687 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:31:02.991220 INFO: Using score_cutoff 44.99298610153198 (fac=0.99, q=1)
1:31:02.991603 INFO: Updating optimization_manager: fwhm_rt             : 2.746732711791992 -> 2.81162166595459
1:31:02.991681 INFO: Updating optimization_manager: fwhm_mobility       : 0.009009331464767456 -> 0.009023557417094707
1:31:02.991735 INFO: Updating optimization_manager: score_cutoff        : 41.095994670867924 -> 44.99298610153198
1:31:02.991791 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:31:02.999412 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:31:03.030901 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:31:03.038776 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:31:03.104403 INFO: === checking if optimization conditions were reached ===
1:31:03.104784 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1:31:03.107450 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07029822977335301
1:31:03.107570 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0703.
1:31:03.107661 INFO: ==============================================
1:31:03.107766 INFO: Starting optimization step 1.
1:31:03.107839 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:31:03.107964 INFO: Using classic extraction backend
1:31:03.108317 PROGRESS: Extracting batch of 50061 precursors
1:31:03.108415 INFO: === Search parameters used ===
1:31:03.108476 INFO: rt_error       : 338.9840465198701
1:31:03.108530 INFO: mobility_error : 0.07029822977335301
1:31:03.108588 INFO: num_candidates : 3
1:31:03.108641 INFO: ms1_error      : 15.0
1:31:03.108692 INFO: ms2_error      : 15.0
1:31:03.108743 INFO: fwhm_rt        : 2.81162166595459
1:31:03.108793 INFO: quant_window   : 3
1:31:03.108841 INFO: ==============================================
1:31:03.136092 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:31:03.136245 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:31:03.136307 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1:31:03.136335 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.19
1:31:03.145934 INFO: Starting candidate selection
1:32:02.858752 INFO: Starting candidate scoring
1:32:09.463822 INFO: Finished candidate processing
1:32:09.463957 INFO: Collecting candidate features
1:32:09.679488 WARNING: intensity_correlation has 35 NaNs ( 0.03 % out of 131805)
1:32:09.679869 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 131805)
1:32:09.688111 INFO: Collecting fragment features
1:32:09.778832 INFO: Finished candidate scoring
1:32:09.876800 INFO: performing precursor FDR with 47 features
1:32:09.876959 INFO: Decoy channel: -1
1:32:09.876985 INFO: Competetive: True
1:32:09.925224 INFO: Setting torch num_threads to 2 for FDR classification task
1:32:09.950970 WARNING: dropped 23 target PSMs due to missing features
1:32:09.951143 WARNING: dropped 14 decoy PSMs due to missing features
1:32:09.977371 INFO: Using random state 667451 for train-test-split
1:32:12.472616 INFO: Test AUC: 0.555
1:32:12.472775 INFO: Train AUC: 0.594
1:32:12.472807 INFO: AUC difference: 6.64%
1:32:12.472829 WARNING: AUC difference > 5%. This may indicate overfitting.
1:32:12.774555 INFO: Resetting torch num_threads to 80
1:32:12.783989 PROGRESS: === Extracted 131805 precursors and 1307041 fragments ===
1:32:12.784840 INFO: === FDR correction performed with classifier version 12 ===
1:32:12.791312 PROGRESS: ============================= Precursor FDR =============================
1:32:12.791674 PROGRESS: Total precursors accumulated: 24,170
1:32:12.791743 PROGRESS: Target precursors: 14,851 (61.44%)
1:32:12.791795 PROGRESS: Decoy precursors: 9,319 (38.56%)
1:32:12.791842 PROGRESS: 
1:32:12.791888 PROGRESS: Precursor Summary:
1:32:12.793295 PROGRESS: Channel   0:	 0.050 FDR:   368; 0.010 FDR:   255; 0.001 FDR:   151
1:32:12.793406 PROGRESS: 
1:32:12.793463 PROGRESS: Protein Summary:
1:32:12.794774 PROGRESS: Channel   0:	 0.050 FDR:   359; 0.010 FDR:   250; 0.001 FDR:   147
1:32:12.794905 PROGRESS: =========================================================================
1:32:12.827960 INFO: Target number of precursors reached.
1:32:12.918684 INFO: fragments_df: keeping 3506 of 1307041 [sum(precursor_idx_mask)=8034 sum(mass_error_mask)=1307038 stop_rank=3506
1:32:13.268635 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:32:13.394521 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:32:13.520366 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:32:13.689350 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:32:14.231994 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:32:14.234349 INFO: Using score_cutoff 40.51756553878784 (fac=0.99, q=1)
1:32:14.235254 INFO: Updating optimization_manager: fwhm_rt             : 2.81162166595459 -> 2.7949740886688232
1:32:14.235348 INFO: Updating optimization_manager: fwhm_mobility       : 0.009023557417094707 -> 0.008914326317608356
1:32:14.235403 INFO: Updating optimization_manager: score_cutoff        : 44.99298610153198 -> 40.51756553878784
1:32:14.235510 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:32:14.245879 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:32:14.284156 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:32:14.292523 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:32:14.361824 INFO: === checking if optimization conditions were reached ===
1:32:14.362168 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1:32:14.365573 INFO: Updating optimization_manager: mobility_error      : 0.07029822977335301 -> 0.06276555162602103
1:32:14.365694 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0628.
1:32:14.365782 INFO: ==============================================
1:32:14.365885 INFO: Starting optimization step 2.
1:32:14.365995 PROGRESS: === Extracting elution groups 0 to 25400 ===
1:32:14.366101 INFO: Using classic extraction backend
1:32:14.366473 PROGRESS: Extracting batch of 50061 precursors
1:32:14.366580 INFO: === Search parameters used ===
1:32:14.366645 INFO: rt_error       : 338.9840465198701
1:32:14.366702 INFO: mobility_error : 0.06276555162602103
1:32:14.366755 INFO: num_candidates : 3
1:32:14.366825 INFO: ms1_error      : 15.0
1:32:14.366880 INFO: ms2_error      : 15.0
1:32:14.366932 INFO: fwhm_rt        : 2.7949740886688232
1:32:14.366983 INFO: quant_window   : 3
1:32:14.367035 INFO: ==============================================
1:32:14.437244 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:32:14.437484 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:32:14.437549 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1:32:14.437582 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.13
1:32:14.463351 INFO: Starting candidate selection
1:33:02.935721 INFO: Starting candidate scoring
1:33:08.963718 INFO: Finished candidate processing
1:33:08.963921 INFO: Collecting candidate features
1:33:09.190439 WARNING: intensity_correlation has 38 NaNs ( 0.03 % out of 131152)
1:33:09.190828 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 131152)
1:33:09.198638 INFO: Collecting fragment features
1:33:09.273142 INFO: Finished candidate scoring
1:33:09.357280 INFO: performing precursor FDR with 47 features
1:33:09.357438 INFO: Decoy channel: -1
1:33:09.357465 INFO: Competetive: True
1:33:09.407201 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:09.435998 WARNING: dropped 21 target PSMs due to missing features
1:33:09.436171 WARNING: dropped 20 decoy PSMs due to missing features
1:33:09.459655 INFO: Using random state 667451 for train-test-split
1:33:12.078681 INFO: Test AUC: 0.566
1:33:12.078864 INFO: Train AUC: 0.593
1:33:12.078900 INFO: AUC difference: 4.50%
1:33:12.360036 INFO: Resetting torch num_threads to 80
1:33:12.365379 PROGRESS: === Extracted 131152 precursors and 1294774 fragments ===
1:33:12.366057 INFO: === FDR correction performed with classifier version 12 ===
1:33:12.371006 PROGRESS: ============================= Precursor FDR =============================
1:33:12.371151 PROGRESS: Total precursors accumulated: 24,060
1:33:12.371219 PROGRESS: Target precursors: 14,934 (62.07%)
1:33:12.371274 PROGRESS: Decoy precursors: 9,126 (37.93%)
1:33:12.371328 PROGRESS: 
1:33:12.371372 PROGRESS: Precursor Summary:
1:33:12.372569 PROGRESS: Channel   0:	 0.050 FDR:   338; 0.010 FDR:   202; 0.001 FDR:   156
1:33:12.372661 PROGRESS: 
1:33:12.372718 PROGRESS: Protein Summary:
1:33:12.373962 PROGRESS: Channel   0:	 0.050 FDR:   331; 0.010 FDR:   198; 0.001 FDR:   152
1:33:12.374248 PROGRESS: =========================================================================
1:33:12.375589 INFO: Target number of precursors reached.
1:33:12.463226 INFO: fragments_df: keeping 2867 of 1294774 [sum(precursor_idx_mask)=6311 sum(mass_error_mask)=1294770 stop_rank=2867
1:33:13.360373 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:33:13.490921 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:33:13.609612 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:33:13.727851 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:33:14.124047 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:33:14.124583 INFO: Using score_cutoff 39.65058205718994 (fac=0.99, q=1)
1:33:14.124972 INFO: Updating optimization_manager: fwhm_rt             : 2.7949740886688232 -> 2.790301561355591
1:33:14.125052 INFO: Updating optimization_manager: fwhm_mobility       : 0.008914326317608356 -> 0.009212719276547432
1:33:14.125108 INFO: Updating optimization_manager: score_cutoff        : 40.51756553878784 -> 39.65058205718994
1:33:14.125167 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:33:14.132936 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:33:14.163412 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:33:14.171566 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:33:14.237941 INFO: === checking if optimization conditions were reached ===
1:33:14.238339 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1:33:14.239758 INFO: Updating optimization_manager: mobility_error      : 0.06276555162602103 -> 0.07029822977335301
1:33:14.239902 INFO: Updating optimization_manager: classifier_version  : 12 -> 15
1:33:14.240007 INFO: Updating optimization_manager: score_cutoff        : 39.65058205718994 -> 40.51756553878784
1:33:14.240103 INFO: Updating optimization_manager: fwhm_rt             : 2.790301561355591 -> 2.7949740886688232
1:33:14.240202 INFO: Updating optimization_manager: fwhm_mobility       : 0.009212719276547432 -> 0.008914326317608356
1:33:14.240314 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0703 found after 3 searches.
1:33:14.240388 INFO: ==============================================
1:33:14.240476 PROGRESS: Optimization finished for mobility_error.
1:33:14.402355 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:33:14.410635 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:33:14.443400 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:33:14.451607 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:33:14.549121 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:33:14.549350 PROGRESS: ==============================================
1:33:14.549491 PROGRESS: ms2_error      : 15.0000
1:33:14.549566 PROGRESS: ms1_error      : 15.0000
1:33:14.549631 PROGRESS: rt_error       : 338.9840
1:33:14.549691 PROGRESS: mobility_error : 0.0703
1:33:14.549747 PROGRESS: ==============================================
1:33:14.554636 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:33:16.238167 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:33:24.267973 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:33:26.336519 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:33:44.689883 INFO: Using classic extraction backend
1:33:44.692967 PROGRESS: Extracting batch of 12073114 precursors
1:33:44.693134 INFO: === Search parameters used ===
1:33:44.693197 INFO: rt_error       : 338.9840465198701
1:33:44.693246 INFO: mobility_error : 0.07029822977335301
1:33:44.693292 INFO: num_candidates : 3
1:33:44.693352 INFO: ms1_error      : 15.0
1:33:44.693397 INFO: ms2_error      : 15.0
1:33:44.693440 INFO: fwhm_rt        : 2.7949740886688232
1:33:44.693481 INFO: quant_window   : 3
1:33:44.693523 INFO: ==============================================
1:33:48.801283 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:33:48.801679 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:33:48.801769 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1:33:48.801797 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.13
1:33:48.804647 INFO: Starting candidate selection
4:22:25.882989 INFO: Removed 15470082 precursors with score below cutoff 40.51756553878784
4:22:29.108639 INFO: Starting candidate scoring
4:37:22.611768 INFO: Finished candidate processing
4:37:22.612636 INFO: Collecting candidate features
4:38:14.030806 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 17624843)
4:38:14.695308 INFO: Collecting fragment features
4:38:39.264561 INFO: Finished candidate scoring
4:39:02.681832 INFO: === Performing FDR correction with classifier version 15 ===
4:39:02.685226 INFO: performing precursor FDR with 47 features
4:39:02.685282 INFO: Decoy channel: -1
4:39:02.685313 INFO: Competetive: True
4:39:07.812927 INFO: Setting torch num_threads to 2 for FDR classification task
4:39:12.537019 WARNING: dropped 1 decoy PSMs due to missing features
4:39:27.517447 INFO: Using random state 590724 for train-test-split
4:45:43.462421 INFO: Test AUC: 0.569
4:45:43.462740 INFO: Train AUC: 0.571
4:45:43.462811 INFO: AUC difference: 0.23%
4:45:47.897604 INFO: Resetting torch num_threads to 80
4:45:48.440974 INFO: Removing fragments below FDR threshold
4:45:50.149431 PROGRESS: ============================= Precursor FDR =============================
4:45:50.149721 PROGRESS: Total precursors accumulated: 68,213
4:45:50.149787 PROGRESS: Target precursors: 67,538 (99.01%)
4:45:50.149839 PROGRESS: Decoy precursors: 675 (0.99%)
4:45:50.149886 PROGRESS: 
4:45:50.149931 PROGRESS: Precursor Summary:
4:45:50.174302 PROGRESS: Channel   0:	 0.050 FDR: 67,538; 0.010 FDR: 67,538; 0.001 FDR: 46,807
4:45:50.174587 PROGRESS: 
4:45:50.174650 PROGRESS: Protein Summary:
4:45:50.205910 PROGRESS: Channel   0:	 0.050 FDR: 10,977; 0.010 FDR: 10,977; 0.001 FDR: 8,646
4:45:50.206176 PROGRESS: =========================================================================
4:45:50.441779 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/psm.parquet
4:45:50.862080 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/frag.parquet
4:45:51.117435 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
4:45:51.715223 PROGRESS: 
4:45:51.715430 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark/quant
4:45:51.715576 INFO: Initializing TimingManager
4:45:51.716401 INFO: Initializing RawFileManager
4:45:51.716560 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:45:51.716654 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:45:51.716733 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:45:52.054337 INFO: Reading 39,128 frames with 2,860,596,893 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:46:03.446819 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d...
4:46:03.450971 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:46:03.455670 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:46:03.456175 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:46:03.457225 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:46:03.460575 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:46:03.482907 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:46:03.483336 INFO: Indexing quadrupole dimension
4:46:04.241666 INFO: Transposing detector events
4:46:16.422713 INFO: Finished transposing data
4:46:16.457572 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
4:46:16.459569 INFO: RT (min)            : 0.0 - 70.0
4:46:16.459630 INFO: RT duration (sec)   : 4199.8
4:46:16.459661 INFO: RT duration (min)   : 70.0
4:46:16.459690 INFO: Cycle len (scans)   : 9
4:46:16.459717 INFO: Cycle len (sec)     : 0.97
4:46:16.459741 INFO: Number of cycles    : 4347
4:46:16.459777 INFO: MS2 range (m/z)     : 400.0 - 1000.0
4:46:16.459849 INFO: Creating DIA data object took: 24.74334192276001
4:46:18.710934 INFO: Initializing CalibrationManager
4:46:18.711275 INFO: Setting up calibration estimators ..
4:46:18.711344 INFO: Found 1 estimator(s) in calibration group 'fragment'
4:46:18.711465 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
4:46:18.711645 INFO: Found 3 estimator(s) in calibration group 'precursor'
4:46:18.711714 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
4:46:18.711772 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
4:46:18.711842 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
4:46:18.711896 INFO: Done setting up calibration estimators.
4:46:18.712046 INFO: Initializing OptimizationManager
4:46:18.712164 INFO: initial parameter: ms1_error = 30
4:46:18.712216 INFO: initial parameter: ms2_error = 30
4:46:18.712264 INFO: initial parameter: rt_error = 2099.894844
4:46:18.712310 INFO: initial parameter: mobility_error = 0.1
4:46:18.712352 INFO: initial parameter: num_candidates = 1
4:46:18.712391 INFO: initial parameter: fwhm_rt = 5
4:46:18.712432 INFO: initial parameter: fwhm_mobility = 0.01
4:46:18.712471 INFO: initial parameter: score_cutoff = 0
4:46:18.712512 INFO: initial parameter: classifier_version = -1
4:46:18.712585 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
4:46:18.712952 INFO: FDRManager: loading saved state not requested, will be initialized.
4:46:18.712987 INFO: Initializing FDRManager
4:46:18.713044 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
4:46:20.155877 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
4:46:21.062945 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
4:46:21.063471 INFO: Updating optimization_manager: rt_error            : 2099.894844 -> 2099.894844
4:46:21.063604 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
4:46:21.063809 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
4:46:21.063939 PROGRESS: Starting initial search for precursors.
4:46:21.064047 INFO: Starting optimization step 0.
4:46:21.064124 PROGRESS: === Extracting elution groups 0 to 200 ===
4:46:21.064201 INFO: Using classic extraction backend
4:46:21.064480 PROGRESS: Extracting batch of 390 precursors
4:46:21.064558 INFO: === Search parameters used ===
4:46:21.064608 INFO: rt_error       : 2099.894844
4:46:21.064652 INFO: mobility_error : 0.1
4:46:21.064693 INFO: num_candidates : 1
4:46:21.064733 INFO: ms1_error      : 30
4:46:21.064771 INFO: ms2_error      : 30
4:46:21.064813 INFO: fwhm_rt        : 5
4:46:21.064853 INFO: quant_window   : 3
4:46:21.064891 INFO: ==============================================
4:46:21.066040 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:46:21.066091 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:46:21.066148 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
4:46:21.066174 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:46:21.119443 INFO: Starting candidate selection
4:46:26.127504 INFO: Starting candidate scoring
4:46:26.267772 INFO: Finished candidate processing
4:46:26.267867 INFO: Collecting candidate features
4:46:26.275384 WARNING: intensity_correlation has 1 NaNs ( 0.28 % out of 363)
4:46:26.278890 INFO: Collecting fragment features
4:46:26.282016 INFO: Finished candidate scoring
4:46:26.283611 INFO: performing precursor FDR with 47 features
4:46:26.283691 INFO: Decoy channel: -1
4:46:26.283715 INFO: Competetive: True
4:46:26.285676 INFO: Setting torch num_threads to 2 for FDR classification task
4:46:26.287230 WARNING: dropped 1 decoy PSMs due to missing features
4:46:26.290012 INFO: Using random state 244194 for train-test-split
4:46:26.304109 INFO: Test AUC: 0.585
4:46:26.304220 INFO: Train AUC: 0.484
4:46:26.304253 INFO: AUC difference: 20.90%
4:46:26.304275 WARNING: AUC difference > 5%. This may indicate overfitting.
4:46:26.538249 INFO: Resetting torch num_threads to 80
4:46:26.538809 PROGRESS: === Extracted 363 precursors and 3948 fragments ===
4:46:26.539406 INFO: === FDR correction performed with classifier version -1 ===
4:46:26.539998 PROGRESS: ============================= Precursor FDR =============================
4:46:26.540087 PROGRESS: Total precursors accumulated: 187
4:46:26.540155 PROGRESS: Target precursors: 107 (57.22%)
4:46:26.540211 PROGRESS: Decoy precursors: 80 (42.78%)
4:46:26.540260 PROGRESS: 
4:46:26.540303 PROGRESS: Precursor Summary:
4:46:26.541208 PROGRESS: Channel   0:	 0.050 FDR:    59; 0.010 FDR:    59; 0.001 FDR:    59
4:46:26.541296 PROGRESS: 
4:46:26.541358 PROGRESS: Protein Summary:
4:46:26.542350 PROGRESS: Channel   0:	 0.050 FDR:    59; 0.010 FDR:    59; 0.001 FDR:    59
4:46:26.542439 PROGRESS: =========================================================================
4:46:26.542548 INFO: Target number of precursors not reached yet.
4:46:26.613362 INFO: Starting optimization step 1.
4:46:26.613595 PROGRESS: === Extracting elution groups 200 to 600 ===
4:46:26.613713 INFO: Using classic extraction backend
4:46:26.613909 PROGRESS: Extracting batch of 783 precursors
4:46:26.614005 INFO: === Search parameters used ===
4:46:26.614070 INFO: rt_error       : 2099.894844
4:46:26.614129 INFO: mobility_error : 0.1
4:46:26.614177 INFO: num_candidates : 1
4:46:26.614219 INFO: ms1_error      : 30
4:46:26.614278 INFO: ms2_error      : 30
4:46:26.614330 INFO: fwhm_rt        : 5
4:46:26.614385 INFO: quant_window   : 3
4:46:26.614429 INFO: ==============================================
4:46:26.616166 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:46:26.616216 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:46:26.616258 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
4:46:26.616286 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:46:26.617178 INFO: Starting candidate selection
4:46:34.527549 INFO: Starting candidate scoring
4:46:34.717925 INFO: Finished candidate processing
4:46:34.718024 INFO: Collecting candidate features
4:46:34.733672 INFO: Collecting fragment features
4:46:34.737080 INFO: Finished candidate scoring
4:46:34.741512 INFO: performing precursor FDR with 47 features
4:46:34.741575 INFO: Decoy channel: -1
4:46:34.741609 INFO: Competetive: True
4:46:34.746327 INFO: Setting torch num_threads to 2 for FDR classification task
4:46:34.747961 WARNING: dropped 1 decoy PSMs due to missing features
4:46:34.749186 INFO: Using random state 482749 for train-test-split
4:46:34.761125 INFO: Test AUC: 0.457
4:46:34.761197 INFO: Train AUC: 0.522
4:46:34.761236 INFO: AUC difference: 12.60%
4:46:34.761266 WARNING: AUC difference > 5%. This may indicate overfitting.
4:46:34.982327 INFO: Resetting torch num_threads to 80
4:46:34.983618 PROGRESS: === Extracted 1116 precursors and 12181 fragments ===
4:46:34.984013 INFO: === FDR correction performed with classifier version -1 ===
4:46:34.984603 PROGRESS: ============================= Precursor FDR =============================
4:46:34.984694 PROGRESS: Total precursors accumulated: 575
4:46:34.984755 PROGRESS: Target precursors: 326 (56.70%)
4:46:34.984811 PROGRESS: Decoy precursors: 249 (43.30%)
4:46:34.984859 PROGRESS: 
4:46:34.984904 PROGRESS: Precursor Summary:
4:46:34.985831 PROGRESS: Channel   0:	 0.050 FDR:   172; 0.010 FDR:   172; 0.001 FDR:   172
4:46:34.985920 PROGRESS: 
4:46:34.985977 PROGRESS: Protein Summary:
4:46:34.987023 PROGRESS: Channel   0:	 0.050 FDR:   172; 0.010 FDR:   172; 0.001 FDR:   172
4:46:34.987113 PROGRESS: =========================================================================
4:46:34.987252 INFO: Target number of precursors not reached yet.
4:46:35.059943 INFO: Starting optimization step 2.
4:46:35.060165 PROGRESS: === Extracting elution groups 600 to 1400 ===
4:46:35.060245 INFO: Using classic extraction backend
4:46:35.060373 PROGRESS: Extracting batch of 1576 precursors
4:46:35.060445 INFO: === Search parameters used ===
4:46:35.060496 INFO: rt_error       : 2099.894844
4:46:35.060542 INFO: mobility_error : 0.1
4:46:35.060584 INFO: num_candidates : 1
4:46:35.060626 INFO: ms1_error      : 30
4:46:35.060665 INFO: ms2_error      : 30
4:46:35.060706 INFO: fwhm_rt        : 5
4:46:35.060746 INFO: quant_window   : 3
4:46:35.060785 INFO: ==============================================
4:46:35.061638 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:46:35.061685 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:46:35.061714 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
4:46:35.061735 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
4:46:35.089396 INFO: Starting candidate selection
4:46:49.293275 INFO: Starting candidate scoring
4:46:49.461756 INFO: Finished candidate processing
4:46:49.461890 INFO: Collecting candidate features
4:46:49.474690 INFO: Collecting fragment features
4:46:49.478088 INFO: Finished candidate scoring
4:46:49.481573 INFO: performing precursor FDR with 47 features
4:46:49.481636 INFO: Decoy channel: -1
4:46:49.481660 INFO: Competetive: True
4:46:49.485096 INFO: Setting torch num_threads to 2 for FDR classification task
4:46:49.486409 WARNING: dropped 1 decoy PSMs due to missing features
4:46:49.487396 INFO: Using random state 301758 for train-test-split
4:46:49.498758 INFO: Test AUC: 0.479
4:46:49.503736 INFO: Train AUC: 0.502
4:46:49.503787 INFO: AUC difference: 4.63%
4:46:49.721543 INFO: Resetting torch num_threads to 80
4:46:49.723365 PROGRESS: === Extracted 2636 precursors and 28710 fragments ===
4:46:49.723855 INFO: === FDR correction performed with classifier version -1 ===
4:46:49.724602 PROGRESS: ============================= Precursor FDR =============================
4:46:49.724716 PROGRESS: Total precursors accumulated: 1,353
4:46:49.724776 PROGRESS: Target precursors: 783 (57.87%)
4:46:49.724826 PROGRESS: Decoy precursors: 570 (42.13%)
4:46:49.724871 PROGRESS: 
4:46:49.724915 PROGRESS: Precursor Summary:
4:46:49.725942 PROGRESS: Channel   0:	 0.050 FDR:   395; 0.010 FDR:   395; 0.001 FDR:   395
4:46:49.726030 PROGRESS: 
4:46:49.726084 PROGRESS: Protein Summary:
4:46:49.727276 PROGRESS: Channel   0:	 0.050 FDR:   393; 0.010 FDR:   393; 0.001 FDR:   393
4:46:49.727368 PROGRESS: =========================================================================
4:46:49.727531 INFO: Target number of precursors reached.
4:46:49.731810 INFO: fragments_df: keeping 759 of 28710 [sum(precursor_idx_mask)=4332 sum(mass_error_mask)=28710 stop_rank=759
4:46:49.873413 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:46:50.010046 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:46:50.144358 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:46:50.281489 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:46:50.438089 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
4:46:50.438628 INFO: Using score_cutoff 35.04484362030029 (fac=0.99, q=1)
4:46:50.439023 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.575263023376465
4:46:50.439106 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.00818940531462431
4:46:50.439160 INFO: Updating optimization_manager: score_cutoff        : 0 -> 35.04484362030029
4:46:50.439219 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:46:50.440590 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:46:50.442832 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:46:50.443818 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:46:50.448902 INFO: Updating optimization_manager: classifier_version  : -1 -> 2
4:46:50.449007 PROGRESS: Required number of precursors found. Starting search parameter optimization.
4:46:50.449086 INFO: Starting optimization step 3.
4:46:50.449144 PROGRESS: === Extracting elution groups 0 to 1400 ===
4:46:50.449200 INFO: Using classic extraction backend
4:46:50.449313 PROGRESS: Extracting batch of 2749 precursors
4:46:50.449375 INFO: === Search parameters used ===
4:46:50.449421 INFO: rt_error       : 2099.894844
4:46:50.449467 INFO: mobility_error : 0.1
4:46:50.449507 INFO: num_candidates : 3
4:46:50.449546 INFO: ms1_error      : 30
4:46:50.449586 INFO: ms2_error      : 30
4:46:50.449634 INFO: fwhm_rt        : 3.575263023376465
4:46:50.449676 INFO: quant_window   : 3
4:46:50.449714 INFO: ==============================================
4:46:50.451033 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:46:50.451079 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:46:50.451113 INFO: FWHM in RT is 3.58 seconds, sigma is 0.79
4:46:50.451135 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.80
4:46:50.451948 INFO: Starting candidate selection
4:47:20.165121 INFO: Starting candidate scoring
4:47:21.039057 INFO: Finished candidate processing
4:47:21.039200 INFO: Collecting candidate features
4:47:21.083210 INFO: Collecting fragment features
4:47:21.099420 INFO: Finished candidate scoring
4:47:21.110540 INFO: performing precursor FDR with 47 features
4:47:21.110687 INFO: Decoy channel: -1
4:47:21.110722 INFO: Competetive: True
4:47:21.122127 INFO: Setting torch num_threads to 2 for FDR classification task
4:47:21.129323 INFO: Using random state 721378 for train-test-split
4:47:21.159853 INFO: Test AUC: 0.501
4:47:21.159976 INFO: Train AUC: 0.499
4:47:21.160012 INFO: AUC difference: 0.44%
4:47:21.420877 INFO: Resetting torch num_threads to 80
4:47:21.421917 PROGRESS: === Extracted 7579 precursors and 82888 fragments ===
4:47:21.422515 INFO: === FDR correction performed with classifier version 2 ===
4:47:21.423468 PROGRESS: ============================= Precursor FDR =============================
4:47:21.423576 PROGRESS: Total precursors accumulated: 1,374
4:47:21.423642 PROGRESS: Target precursors: 888 (64.63%)
4:47:21.423694 PROGRESS: Decoy precursors: 486 (35.37%)
4:47:21.423740 PROGRESS: 
4:47:21.423784 PROGRESS: Precursor Summary:
4:47:21.424936 PROGRESS: Channel   0:	 0.050 FDR:   647; 0.010 FDR:   647; 0.001 FDR:   647
4:47:21.425028 PROGRESS: 
4:47:21.425086 PROGRESS: Protein Summary:
4:47:21.426485 PROGRESS: Channel   0:	 0.050 FDR:   636; 0.010 FDR:   636; 0.001 FDR:   636
4:47:21.426575 PROGRESS: =========================================================================
4:47:21.427032 INFO: Target number of precursors reached.
4:47:21.438786 INFO: fragments_df: keeping 3832 of 82888 [sum(precursor_idx_mask)=20230 sum(mass_error_mask)=82888 stop_rank=3832
4:47:21.548957 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:47:21.741597 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:47:22.016898 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:47:22.325541 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:47:22.937245 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:47:22.937769 INFO: Using score_cutoff 36.40781701126099 (fac=0.99, q=1)
4:47:22.938193 INFO: Updating optimization_manager: fwhm_rt             : 3.575263023376465 -> 3.4627487659454346
4:47:22.938275 INFO: Updating optimization_manager: fwhm_mobility       : 0.00818940531462431 -> 0.007894948124885559
4:47:22.938328 INFO: Updating optimization_manager: score_cutoff        : 35.04484362030029 -> 36.40781701126099
4:47:22.938387 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:47:22.939701 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:47:22.941158 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:47:22.941946 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:47:22.944336 INFO: === checking if optimization conditions were reached ===
4:47:22.946020 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.036425234917573
4:47:22.946130 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
4:47:22.946204 PROGRESS: ❌ ms2_error      : 17.0364 > 15.0000 or insufficient steps taken.
4:47:22.947247 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.45875449391151
4:47:22.947345 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
4:47:22.947407 PROGRESS: ❌ ms1_error      : 15.4588 > 15.0000 or insufficient steps taken.
4:47:22.947462 INFO: ==============================================
4:47:22.947567 INFO: Starting optimization step 4.
4:47:22.947633 PROGRESS: === Extracting elution groups 0 to 600 ===
4:47:22.947707 INFO: Using classic extraction backend
4:47:22.947968 PROGRESS: Extracting batch of 1173 precursors
4:47:22.948046 INFO: === Search parameters used ===
4:47:22.948096 INFO: rt_error       : 2099.894844
4:47:22.948139 INFO: mobility_error : 0.1
4:47:22.948180 INFO: num_candidates : 3
4:47:22.948218 INFO: ms1_error      : 15.45875449391151
4:47:22.948256 INFO: ms2_error      : 17.036425234917573
4:47:22.948297 INFO: fwhm_rt        : 3.4627487659454346
4:47:22.948336 INFO: quant_window   : 3
4:47:22.948375 INFO: ==============================================
4:47:22.949871 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:47:22.949926 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:47:22.949990 INFO: FWHM in RT is 3.46 seconds, sigma is 0.76
4:47:22.950016 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
4:47:23.007216 INFO: Starting candidate selection
4:47:36.646017 INFO: Starting candidate scoring
4:47:36.896750 INFO: Finished candidate processing
4:47:36.896920 INFO: Collecting candidate features
4:47:36.915270 INFO: Collecting fragment features
4:47:36.920813 INFO: Finished candidate scoring
4:47:36.925098 INFO: performing precursor FDR with 47 features
4:47:36.925256 INFO: Decoy channel: -1
4:47:36.925286 INFO: Competetive: True
4:47:36.930306 INFO: Setting torch num_threads to 2 for FDR classification task
4:47:36.933914 INFO: Using random state 917082 for train-test-split
4:47:36.951415 INFO: Test AUC: 0.502
4:47:36.951600 INFO: Train AUC: 0.501
4:47:36.951638 INFO: AUC difference: 0.14%
4:47:37.228548 INFO: Resetting torch num_threads to 80
4:47:37.230088 PROGRESS: === Extracted 3221 precursors and 33962 fragments ===
4:47:37.230620 INFO: === FDR correction performed with classifier version 3 ===
4:47:37.231309 PROGRESS: ============================= Precursor FDR =============================
4:47:37.231409 PROGRESS: Total precursors accumulated: 588
4:47:37.231472 PROGRESS: Target precursors: 348 (59.18%)
4:47:37.231521 PROGRESS: Decoy precursors: 240 (40.82%)
4:47:37.231565 PROGRESS: 
4:47:37.231607 PROGRESS: Precursor Summary:
4:47:37.232558 PROGRESS: Channel   0:	 0.050 FDR:   185; 0.010 FDR:   185; 0.001 FDR:   185
4:47:37.234262 PROGRESS: 
4:47:37.234334 PROGRESS: Protein Summary:
4:47:37.235470 PROGRESS: Channel   0:	 0.050 FDR:   184; 0.010 FDR:   184; 0.001 FDR:   184
4:47:37.235563 PROGRESS: =========================================================================
4:47:37.235811 INFO: Target number of precursors not reached yet.
4:47:37.330267 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:47:37.331782 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:47:37.333563 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:47:37.334481 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:47:37.338052 INFO: === skipping optimization until target number of precursors are found ===
4:47:37.338234 INFO: Starting optimization step 5.
4:47:37.338307 PROGRESS: === Extracting elution groups 600 to 1400 ===
4:47:37.338380 INFO: Using classic extraction backend
4:47:37.338507 PROGRESS: Extracting batch of 1576 precursors
4:47:37.338583 INFO: === Search parameters used ===
4:47:37.338630 INFO: rt_error       : 2099.894844
4:47:37.338672 INFO: mobility_error : 0.1
4:47:37.338712 INFO: num_candidates : 3
4:47:37.338751 INFO: ms1_error      : 15.45875449391151
4:47:37.338800 INFO: ms2_error      : 17.036425234917573
4:47:37.338855 INFO: fwhm_rt        : 3.4627487659454346
4:47:37.338896 INFO: quant_window   : 3
4:47:37.338934 INFO: ==============================================
4:47:37.340131 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:47:37.340180 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:47:37.340218 INFO: FWHM in RT is 3.46 seconds, sigma is 0.76
4:47:37.340240 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
4:47:37.351063 INFO: Starting candidate selection
4:48:02.626762 INFO: Starting candidate scoring
4:48:02.960325 INFO: Finished candidate processing
4:48:02.960486 INFO: Collecting candidate features
4:48:02.986498 INFO: Collecting fragment features
4:48:02.993283 INFO: Finished candidate scoring
4:48:03.003557 INFO: performing precursor FDR with 47 features
4:48:03.003770 INFO: Decoy channel: -1
4:48:03.003801 INFO: Competetive: True
4:48:03.009915 INFO: Setting torch num_threads to 2 for FDR classification task
4:48:03.014725 INFO: Using random state 917082 for train-test-split
4:48:03.037268 INFO: Test AUC: 0.518
4:48:03.037436 INFO: Train AUC: 0.497
4:48:03.037472 INFO: AUC difference: 4.24%
4:48:03.286885 INFO: Resetting torch num_threads to 80
4:48:03.290602 PROGRESS: === Extracted 7580 precursors and 79691 fragments ===
4:48:03.291311 INFO: === FDR correction performed with classifier version 3 ===
4:48:03.292253 PROGRESS: ============================= Precursor FDR =============================
4:48:03.292364 PROGRESS: Total precursors accumulated: 1,372
4:48:03.292443 PROGRESS: Target precursors: 817 (59.55%)
4:48:03.292508 PROGRESS: Decoy precursors: 555 (40.45%)
4:48:03.292567 PROGRESS: 
4:48:03.292621 PROGRESS: Precursor Summary:
4:48:03.293773 PROGRESS: Channel   0:	 0.050 FDR:   438; 0.010 FDR:   438; 0.001 FDR:   438
4:48:03.293882 PROGRESS: 
4:48:03.293958 PROGRESS: Protein Summary:
4:48:03.295301 PROGRESS: Channel   0:	 0.050 FDR:   436; 0.010 FDR:   436; 0.001 FDR:   436
4:48:03.295430 PROGRESS: =========================================================================
4:48:03.295799 INFO: Target number of precursors reached.
4:48:03.306594 INFO: fragments_df: keeping 2143 of 79691 [sum(precursor_idx_mask)=13226 sum(mass_error_mask)=79691 stop_rank=2143
4:48:03.433259 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:48:03.566681 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:48:03.711819 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:48:03.919042 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:48:04.225106 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:48:04.225947 INFO: Using score_cutoff 34.372207081604 (fac=0.99, q=1)
4:48:04.226870 INFO: Updating optimization_manager: fwhm_rt             : 3.4627487659454346 -> 2.9617791175842285
4:48:04.226962 INFO: Updating optimization_manager: fwhm_mobility       : 0.007894948124885559 -> 0.006196620408445597
4:48:04.227018 INFO: Updating optimization_manager: score_cutoff        : 36.40781701126099 -> 34.372207081604
4:48:04.227087 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:48:04.228744 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:48:04.231188 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:48:04.232292 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:48:04.237868 INFO: === checking if optimization conditions were reached ===
4:48:04.239571 INFO: Updating optimization_manager: ms2_error           : 17.036425234917573 -> 15.0
4:48:04.239720 INFO: Updating optimization_manager: classifier_version  : 3 -> 5
4:48:04.239796 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
4:48:04.240901 INFO: Updating optimization_manager: ms1_error           : 15.45875449391151 -> 15.0
4:48:04.241006 INFO: Updating optimization_manager: classifier_version  : 5 -> 5
4:48:04.241068 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
4:48:04.241131 INFO: ==============================================
4:48:04.241227 PROGRESS: Optimization finished for ms2_error, ms1_error.
4:48:04.363261 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:48:04.364932 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:48:04.367367 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:48:04.368413 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:48:04.373523 INFO: Starting optimization step 0.
4:48:04.373799 PROGRESS: === Extracting elution groups 0 to 1400 ===
4:48:04.373924 INFO: Using classic extraction backend
4:48:04.374193 PROGRESS: Extracting batch of 2749 precursors
4:48:04.374281 INFO: === Search parameters used ===
4:48:04.374334 INFO: rt_error       : 2099.894844
4:48:04.374378 INFO: mobility_error : 0.1
4:48:04.374421 INFO: num_candidates : 3
4:48:04.374462 INFO: ms1_error      : 15.0
4:48:04.374502 INFO: ms2_error      : 15.0
4:48:04.374541 INFO: fwhm_rt        : 2.9617791175842285
4:48:04.374582 INFO: quant_window   : 3
4:48:04.374621 INFO: ==============================================
4:48:04.376723 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:48:04.376784 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:48:04.376833 INFO: FWHM in RT is 2.96 seconds, sigma is 0.65
4:48:04.376856 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.87
4:48:04.378225 INFO: Starting candidate selection
4:48:35.317973 INFO: Starting candidate scoring
4:48:35.806509 INFO: Finished candidate processing
4:48:35.806656 INFO: Collecting candidate features
4:48:35.836140 INFO: Collecting fragment features
4:48:35.847573 INFO: Finished candidate scoring
4:48:35.858454 INFO: performing precursor FDR with 47 features
4:48:35.858619 INFO: Decoy channel: -1
4:48:35.858649 INFO: Competetive: True
4:48:35.865950 INFO: Setting torch num_threads to 2 for FDR classification task
4:48:35.871988 INFO: Using random state 199930 for train-test-split
4:48:35.903740 INFO: Test AUC: 0.496
4:48:35.905609 INFO: Train AUC: 0.502
4:48:35.905722 INFO: AUC difference: 1.29%
4:48:36.186712 INFO: Resetting torch num_threads to 80
4:48:36.187697 PROGRESS: === Extracted 7575 precursors and 78308 fragments ===
4:48:36.188281 INFO: === FDR correction performed with classifier version 5 ===
4:48:36.189176 PROGRESS: ============================= Precursor FDR =============================
4:48:36.189289 PROGRESS: Total precursors accumulated: 1,371
4:48:36.189354 PROGRESS: Target precursors: 802 (58.50%)
4:48:36.189406 PROGRESS: Decoy precursors: 569 (41.50%)
4:48:36.189453 PROGRESS: 
4:48:36.189498 PROGRESS: Precursor Summary:
4:48:36.190572 PROGRESS: Channel   0:	 0.050 FDR:   436; 0.010 FDR:   436; 0.001 FDR:   436
4:48:36.190669 PROGRESS: 
4:48:36.190727 PROGRESS: Protein Summary:
4:48:36.191976 PROGRESS: Channel   0:	 0.050 FDR:   434; 0.010 FDR:   434; 0.001 FDR:   434
4:48:36.192072 PROGRESS: =========================================================================
4:48:36.192281 INFO: Target number of precursors reached.
4:48:36.202036 INFO: fragments_df: keeping 2165 of 78308 [sum(precursor_idx_mask)=12876 sum(mass_error_mask)=78308 stop_rank=2165
4:48:36.324455 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:48:36.501169 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:48:36.680229 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:48:36.851275 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:48:37.200434 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:48:37.201120 INFO: Using score_cutoff 31.755229637145995 (fac=0.99, q=1)
4:48:37.201669 INFO: Updating optimization_manager: fwhm_rt             : 2.9617791175842285 -> 2.852908134460449
4:48:37.201812 INFO: Updating optimization_manager: fwhm_mobility       : 0.006196620408445597 -> 0.005691644735634327
4:48:37.201890 INFO: Updating optimization_manager: score_cutoff        : 34.372207081604 -> 31.755229637145995
4:48:37.201965 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:48:37.203806 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:48:37.206739 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:48:37.208240 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:48:37.213795 INFO: === checking if optimization conditions were reached ===
4:48:37.214135 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
4:48:37.217386 INFO: Updating optimization_manager: rt_error            : 2099.894844 -> 1287.516659954022
4:48:37.217640 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1287.5167.
4:48:37.217741 INFO: ==============================================
4:48:37.217830 INFO: Starting optimization step 1.
4:48:37.217904 PROGRESS: === Extracting elution groups 0 to 1400 ===
4:48:37.217976 INFO: Using classic extraction backend
4:48:37.218134 PROGRESS: Extracting batch of 2749 precursors
4:48:37.218223 INFO: === Search parameters used ===
4:48:37.218283 INFO: rt_error       : 1287.516659954022
4:48:37.218333 INFO: mobility_error : 0.1
4:48:37.218383 INFO: num_candidates : 3
4:48:37.218429 INFO: ms1_error      : 15.0
4:48:37.218476 INFO: ms2_error      : 15.0
4:48:37.218542 INFO: fwhm_rt        : 2.852908134460449
4:48:37.218589 INFO: quant_window   : 3
4:48:37.218635 INFO: ==============================================
4:48:37.221747 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:48:37.221833 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:48:37.221879 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
4:48:37.221906 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.64
4:48:37.222992 INFO: Starting candidate selection
4:49:02.713677 INFO: Starting candidate scoring
4:49:03.124948 INFO: Finished candidate processing
4:49:03.125060 INFO: Collecting candidate features
4:49:03.149197 INFO: Collecting fragment features
4:49:03.159528 INFO: Finished candidate scoring
4:49:03.164338 INFO: performing precursor FDR with 47 features
4:49:03.164421 INFO: Decoy channel: -1
4:49:03.164445 INFO: Competetive: True
4:49:03.170138 INFO: Setting torch num_threads to 2 for FDR classification task
4:49:03.174087 INFO: Using random state 199930 for train-test-split
4:49:03.196463 INFO: Test AUC: 0.492
4:49:03.196584 INFO: Train AUC: 0.500
4:49:03.196617 INFO: AUC difference: 1.55%
4:49:03.433566 INFO: Resetting torch num_threads to 80
4:49:03.434541 PROGRESS: === Extracted 7555 precursors and 77932 fragments ===
4:49:03.435141 INFO: === FDR correction performed with classifier version 5 ===
4:49:03.435949 PROGRESS: ============================= Precursor FDR =============================
4:49:03.436053 PROGRESS: Total precursors accumulated: 1,373
4:49:03.436135 PROGRESS: Target precursors: 800 (58.27%)
4:49:03.436207 PROGRESS: Decoy precursors: 573 (41.73%)
4:49:03.436276 PROGRESS: 
4:49:03.436341 PROGRESS: Precursor Summary:
4:49:03.437425 PROGRESS: Channel   0:	 0.050 FDR:   443; 0.010 FDR:   443; 0.001 FDR:   443
4:49:03.437529 PROGRESS: 
4:49:03.437605 PROGRESS: Protein Summary:
4:49:03.438873 PROGRESS: Channel   0:	 0.050 FDR:   440; 0.010 FDR:   440; 0.001 FDR:   440
4:49:03.438987 PROGRESS: =========================================================================
4:49:03.439633 INFO: Target number of precursors reached.
4:49:03.449106 INFO: fragments_df: keeping 2121 of 77932 [sum(precursor_idx_mask)=12872 sum(mass_error_mask)=77932 stop_rank=2121
4:49:04.089272 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:49:04.313137 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:49:04.574538 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:49:04.773671 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:49:05.077769 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:49:05.078314 INFO: Using score_cutoff 31.55837487602234 (fac=0.99, q=1)
4:49:05.078744 INFO: Updating optimization_manager: fwhm_rt             : 2.852908134460449 -> 2.86564302444458
4:49:05.078838 INFO: Updating optimization_manager: fwhm_mobility       : 0.005691644735634327 -> 0.005575174931436777
4:49:05.078905 INFO: Updating optimization_manager: score_cutoff        : 31.755229637145995 -> 31.55837487602234
4:49:05.078976 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:49:05.080433 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:49:05.082731 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:49:05.083729 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:49:05.090788 INFO: === checking if optimization conditions were reached ===
4:49:05.091071 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
4:49:05.093471 INFO: Updating optimization_manager: rt_error            : 1287.516659954022 -> 893.3496605903266
4:49:05.093598 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 893.3497.
4:49:05.093668 INFO: ==============================================
4:49:05.093746 INFO: Starting optimization step 2.
4:49:05.093807 PROGRESS: === Extracting elution groups 0 to 1400 ===
4:49:05.093873 INFO: Using classic extraction backend
4:49:05.094039 PROGRESS: Extracting batch of 2749 precursors
4:49:05.094111 INFO: === Search parameters used ===
4:49:05.094160 INFO: rt_error       : 893.3496605903266
4:49:05.094203 INFO: mobility_error : 0.1
4:49:05.094246 INFO: num_candidates : 3
4:49:05.094285 INFO: ms1_error      : 15.0
4:49:05.094325 INFO: ms2_error      : 15.0
4:49:05.094364 INFO: fwhm_rt        : 2.86564302444458
4:49:05.094402 INFO: quant_window   : 3
4:49:05.094441 INFO: ==============================================
4:49:05.096344 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:49:05.096400 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:49:05.096478 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
4:49:05.096513 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.59
4:49:05.105242 INFO: Starting candidate selection
4:49:18.014501 INFO: Starting candidate scoring
4:49:18.522333 INFO: Finished candidate processing
4:49:18.522494 INFO: Collecting candidate features
4:49:18.549535 INFO: Collecting fragment features
4:49:18.559576 INFO: Finished candidate scoring
4:49:18.563985 INFO: performing precursor FDR with 47 features
4:49:18.564069 INFO: Decoy channel: -1
4:49:18.564093 INFO: Competetive: True
4:49:18.570194 INFO: Setting torch num_threads to 2 for FDR classification task
4:49:18.573993 INFO: Using random state 199930 for train-test-split
4:49:18.596147 INFO: Test AUC: 0.508
4:49:18.596273 INFO: Train AUC: 0.496
4:49:18.596304 INFO: AUC difference: 2.42%
4:49:18.817368 INFO: Resetting torch num_threads to 80
4:49:18.818296 PROGRESS: === Extracted 7567 precursors and 77991 fragments ===
4:49:18.818849 INFO: === FDR correction performed with classifier version 5 ===
4:49:18.819686 PROGRESS: ============================= Precursor FDR =============================
4:49:18.819786 PROGRESS: Total precursors accumulated: 1,374
4:49:18.819864 PROGRESS: Target precursors: 804 (58.52%)
4:49:18.819929 PROGRESS: Decoy precursors: 570 (41.48%)
4:49:18.819992 PROGRESS: 
4:49:18.820054 PROGRESS: Precursor Summary:
4:49:18.821144 PROGRESS: Channel   0:	 0.050 FDR:   450; 0.010 FDR:   450; 0.001 FDR:   450
4:49:18.821242 PROGRESS: 
4:49:18.821327 PROGRESS: Protein Summary:
4:49:18.822596 PROGRESS: Channel   0:	 0.050 FDR:   449; 0.010 FDR:   449; 0.001 FDR:   449
4:49:18.822713 PROGRESS: =========================================================================
4:49:18.823119 INFO: Target number of precursors reached.
4:49:18.832362 INFO: fragments_df: keeping 2176 of 77991 [sum(precursor_idx_mask)=13112 sum(mass_error_mask)=77991 stop_rank=2176
4:49:18.992514 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:49:19.257079 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:49:19.736355 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:49:20.184858 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:49:20.818517 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:49:20.819255 INFO: Using score_cutoff 30.983645800209047 (fac=0.99, q=1)
4:49:20.819742 INFO: Updating optimization_manager: fwhm_rt             : 2.86564302444458 -> 2.867550849914551
4:49:20.819836 INFO: Updating optimization_manager: fwhm_mobility       : 0.005575174931436777 -> 0.00564435962587595
4:49:20.819902 INFO: Updating optimization_manager: score_cutoff        : 31.55837487602234 -> 30.983645800209047
4:49:20.819976 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:49:20.821891 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:49:20.824835 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:49:20.826610 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:49:20.848066 INFO: === checking if optimization conditions were reached ===
4:49:20.848505 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
4:49:20.854397 INFO: Updating optimization_manager: rt_error            : 893.3496605903266 -> 849.0278031192261
4:49:20.854648 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 849.0278.
4:49:20.854746 INFO: ==============================================
4:49:20.854877 INFO: Starting optimization step 3.
4:49:20.854962 PROGRESS: === Extracting elution groups 0 to 1400 ===
4:49:20.855059 INFO: Using classic extraction backend
4:49:20.855308 PROGRESS: Extracting batch of 2749 precursors
4:49:20.855418 INFO: === Search parameters used ===
4:49:20.855489 INFO: rt_error       : 849.0278031192261
4:49:20.855553 INFO: mobility_error : 0.1
4:49:20.855615 INFO: num_candidates : 3
4:49:20.855673 INFO: ms1_error      : 15.0
4:49:20.855732 INFO: ms2_error      : 15.0
4:49:20.855789 INFO: fwhm_rt        : 2.867550849914551
4:49:20.855845 INFO: quant_window   : 3
4:49:20.855918 INFO: ==============================================
4:49:20.859805 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:49:20.859893 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:49:20.859966 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
4:49:20.859998 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.62
4:49:21.059128 INFO: Starting candidate selection
4:49:32.950017 INFO: Starting candidate scoring
4:49:33.565001 INFO: Finished candidate processing
4:49:33.565147 INFO: Collecting candidate features
4:49:33.591704 INFO: Collecting fragment features
4:49:33.600106 INFO: Finished candidate scoring
4:49:33.606586 INFO: performing precursor FDR with 47 features
4:49:33.606710 INFO: Decoy channel: -1
4:49:33.606735 INFO: Competetive: True
4:49:33.612401 INFO: Setting torch num_threads to 2 for FDR classification task
4:49:33.616109 INFO: Using random state 199930 for train-test-split
4:49:33.637941 INFO: Test AUC: 0.498
4:49:33.638071 INFO: Train AUC: 0.500
4:49:33.638100 INFO: AUC difference: 0.44%
4:49:33.875840 INFO: Resetting torch num_threads to 80
4:49:33.876662 PROGRESS: === Extracted 7583 precursors and 78224 fragments ===
4:49:33.877120 INFO: === FDR correction performed with classifier version 5 ===
4:49:33.877836 PROGRESS: ============================= Precursor FDR =============================
4:49:33.877930 PROGRESS: Total precursors accumulated: 1,374
4:49:33.878004 PROGRESS: Target precursors: 794 (57.79%)
4:49:33.878060 PROGRESS: Decoy precursors: 580 (42.21%)
4:49:33.878106 PROGRESS: 
4:49:33.878148 PROGRESS: Precursor Summary:
4:49:33.879185 PROGRESS: Channel   0:	 0.050 FDR:   449; 0.010 FDR:   449; 0.001 FDR:   449
4:49:33.879279 PROGRESS: 
4:49:33.879356 PROGRESS: Protein Summary:
4:49:33.880574 PROGRESS: Channel   0:	 0.050 FDR:   446; 0.010 FDR:   446; 0.001 FDR:   446
4:49:33.880669 PROGRESS: =========================================================================
4:49:33.880864 INFO: Target number of precursors reached.
4:49:33.890039 INFO: fragments_df: keeping 2157 of 78224 [sum(precursor_idx_mask)=13099 sum(mass_error_mask)=78224 stop_rank=2157
4:49:34.031266 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:49:34.236227 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:49:35.508158 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:49:35.761688 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:49:36.159628 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:49:36.160140 INFO: Using score_cutoff 30.593681501770018 (fac=0.99, q=1)
4:49:36.160471 INFO: Updating optimization_manager: fwhm_rt             : 2.867550849914551 -> 2.868030071258545
4:49:36.160560 INFO: Updating optimization_manager: fwhm_mobility       : 0.00564435962587595 -> 0.005583030171692371
4:49:36.160620 INFO: Updating optimization_manager: score_cutoff        : 30.983645800209047 -> 30.593681501770018
4:49:36.160692 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:49:36.162091 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:49:36.164420 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:49:36.165400 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:49:36.170268 INFO: === checking if optimization conditions were reached ===
4:49:36.170384 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
4:49:36.171617 INFO: Updating optimization_manager: rt_error            : 849.0278031192261 -> 849.0278031192261
4:49:36.171743 INFO: Updating optimization_manager: classifier_version  : 5 -> 9
4:49:36.171852 INFO: Updating optimization_manager: score_cutoff        : 30.593681501770018 -> 30.593681501770018
4:49:36.171942 INFO: Updating optimization_manager: fwhm_rt             : 2.868030071258545 -> 2.868030071258545
4:49:36.172027 INFO: Updating optimization_manager: fwhm_mobility       : 0.005583030171692371 -> 0.005583030171692371
4:49:36.172113 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 849.0278 found after 4 searches.
4:49:36.172187 INFO: ==============================================
4:49:36.172257 PROGRESS: Optimization finished for rt_error.
4:49:36.311013 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:49:36.312811 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:49:36.315061 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:49:36.316030 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:49:36.346448 INFO: Starting optimization step 0.
4:49:36.346617 PROGRESS: === Extracting elution groups 0 to 1400 ===
4:49:36.346749 INFO: Using classic extraction backend
4:49:36.347067 PROGRESS: Extracting batch of 2749 precursors
4:49:36.347164 INFO: === Search parameters used ===
4:49:36.347220 INFO: rt_error       : 849.0278031192261
4:49:36.347267 INFO: mobility_error : 0.1
4:49:36.347309 INFO: num_candidates : 3
4:49:36.347349 INFO: ms1_error      : 15.0
4:49:36.347388 INFO: ms2_error      : 15.0
4:49:36.347430 INFO: fwhm_rt        : 2.868030071258545
4:49:36.347471 INFO: quant_window   : 3
4:49:36.347511 INFO: ==============================================
4:49:36.348876 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:49:36.348923 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:49:36.348964 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
4:49:36.348987 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.59
4:49:36.349774 INFO: Starting candidate selection
4:49:46.223868 INFO: Starting candidate scoring
4:49:46.642516 INFO: Finished candidate processing
4:49:46.642736 INFO: Collecting candidate features
4:49:46.664900 INFO: Collecting fragment features
4:49:46.672869 INFO: Finished candidate scoring
4:49:46.677931 INFO: performing precursor FDR with 47 features
4:49:46.678010 INFO: Decoy channel: -1
4:49:46.678035 INFO: Competetive: True
4:49:46.684617 INFO: Setting torch num_threads to 2 for FDR classification task
4:49:46.688478 INFO: Using random state 111459 for train-test-split
4:49:46.708674 INFO: Test AUC: 0.493
4:49:46.708785 INFO: Train AUC: 0.498
4:49:46.708816 INFO: AUC difference: 0.96%
4:49:46.933958 INFO: Resetting torch num_threads to 80
4:49:46.934719 PROGRESS: === Extracted 7574 precursors and 78117 fragments ===
4:49:46.935178 INFO: === FDR correction performed with classifier version 9 ===
4:49:46.935920 PROGRESS: ============================= Precursor FDR =============================
4:49:46.936010 PROGRESS: Total precursors accumulated: 1,374
4:49:46.936070 PROGRESS: Target precursors: 794 (57.79%)
4:49:46.936119 PROGRESS: Decoy precursors: 580 (42.21%)
4:49:46.936163 PROGRESS: 
4:49:46.936205 PROGRESS: Precursor Summary:
4:49:46.937231 PROGRESS: Channel   0:	 0.050 FDR:   447; 0.010 FDR:   447; 0.001 FDR:   447
4:49:46.937329 PROGRESS: 
4:49:46.937387 PROGRESS: Protein Summary:
4:49:46.938593 PROGRESS: Channel   0:	 0.050 FDR:   443; 0.010 FDR:   443; 0.001 FDR:   443
4:49:46.938683 PROGRESS: =========================================================================
4:49:46.938999 INFO: Target number of precursors reached.
4:49:46.948103 INFO: fragments_df: keeping 2119 of 78117 [sum(precursor_idx_mask)=12978 sum(mass_error_mask)=78117 stop_rank=2119
4:49:47.068261 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:49:47.254371 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:49:47.469849 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:49:47.603932 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:49:47.916767 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:49:47.917197 INFO: Using score_cutoff 30.80264063529968 (fac=0.99, q=1)
4:49:47.917524 INFO: Updating optimization_manager: fwhm_rt             : 2.868030071258545 -> 2.886918783187866
4:49:47.917602 INFO: Updating optimization_manager: fwhm_mobility       : 0.005583030171692371 -> 0.005612944718450308
4:49:47.917656 INFO: Updating optimization_manager: score_cutoff        : 30.593681501770018 -> 30.80264063529968
4:49:47.917717 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:49:47.918983 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:49:47.921291 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:49:47.922265 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:49:47.926867 INFO: === checking if optimization conditions were reached ===
4:49:47.926990 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
4:49:47.928393 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.09392934837228928
4:49:47.928491 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0939.
4:49:47.928555 INFO: ==============================================
4:49:47.928620 INFO: Starting optimization step 1.
4:49:47.928674 PROGRESS: === Extracting elution groups 0 to 1400 ===
4:49:47.928728 INFO: Using classic extraction backend
4:49:47.928838 PROGRESS: Extracting batch of 2749 precursors
4:49:47.928901 INFO: === Search parameters used ===
4:49:47.928947 INFO: rt_error       : 849.0278031192261
4:49:47.928989 INFO: mobility_error : 0.09392934837228928
4:49:47.929030 INFO: num_candidates : 3
4:49:47.929070 INFO: ms1_error      : 15.0
4:49:47.929108 INFO: ms2_error      : 15.0
4:49:47.929148 INFO: fwhm_rt        : 2.886918783187866
4:49:47.929189 INFO: quant_window   : 3
4:49:47.929226 INFO: ==============================================
4:49:47.930480 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:49:47.930527 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:49:47.930561 INFO: FWHM in RT is 2.89 seconds, sigma is 0.63
4:49:47.930583 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.60
4:49:47.931478 INFO: Starting candidate selection
4:50:02.665584 INFO: Starting candidate scoring
4:50:03.055588 INFO: Finished candidate processing
4:50:03.055774 INFO: Collecting candidate features
4:50:03.099394 INFO: Collecting fragment features
4:50:03.112823 INFO: Finished candidate scoring
4:50:03.119707 INFO: performing precursor FDR with 47 features
4:50:03.119814 INFO: Decoy channel: -1
4:50:03.119856 INFO: Competetive: True
4:50:03.126516 INFO: Setting torch num_threads to 2 for FDR classification task
4:50:03.131334 INFO: Using random state 111459 for train-test-split
4:50:03.153282 INFO: Test AUC: 0.484
4:50:03.153381 INFO: Train AUC: 0.500
4:50:03.153415 INFO: AUC difference: 3.05%
4:50:03.434532 INFO: Resetting torch num_threads to 80
4:50:03.435871 PROGRESS: === Extracted 7545 precursors and 77757 fragments ===
4:50:03.436768 INFO: === FDR correction performed with classifier version 9 ===
4:50:03.438188 PROGRESS: ============================= Precursor FDR =============================
4:50:03.438427 PROGRESS: Total precursors accumulated: 1,366
4:50:03.438634 PROGRESS: Target precursors: 769 (56.30%)
4:50:03.438835 PROGRESS: Decoy precursors: 597 (43.70%)
4:50:03.439038 PROGRESS: 
4:50:03.439234 PROGRESS: Precursor Summary:
4:50:03.440846 PROGRESS: Channel   0:	 0.050 FDR:   445; 0.010 FDR:   445; 0.001 FDR:   445
4:50:03.441108 PROGRESS: 
4:50:03.441307 PROGRESS: Protein Summary:
4:50:03.443042 PROGRESS: Channel   0:	 0.050 FDR:   441; 0.010 FDR:   441; 0.001 FDR:   441
4:50:03.443301 PROGRESS: =========================================================================
4:50:03.443753 INFO: Target number of precursors reached.
4:50:03.466214 INFO: fragments_df: keeping 2125 of 77757 [sum(precursor_idx_mask)=12923 sum(mass_error_mask)=77757 stop_rank=2125
4:50:03.634464 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:50:03.895570 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:50:04.081003 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:50:04.267820 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:50:04.573493 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:50:04.574092 INFO: Using score_cutoff 31.190967176055906 (fac=0.99, q=1)
4:50:04.574471 INFO: Updating optimization_manager: fwhm_rt             : 2.886918783187866 -> 2.940244674682617
4:50:04.575340 INFO: Updating optimization_manager: fwhm_mobility       : 0.005612944718450308 -> 0.005706725642085075
4:50:04.575410 INFO: Updating optimization_manager: score_cutoff        : 30.80264063529968 -> 31.190967176055906
4:50:04.575468 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:50:04.577115 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:50:04.579423 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:50:04.580408 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:50:04.585373 INFO: === checking if optimization conditions were reached ===
4:50:04.585497 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
4:50:04.587157 INFO: Updating optimization_manager: mobility_error      : 0.09392934837228928 -> 0.08948467796187723
4:50:04.587261 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0895.
4:50:04.587328 INFO: ==============================================
4:50:04.587400 INFO: Starting optimization step 2.
4:50:04.587461 PROGRESS: === Extracting elution groups 0 to 1400 ===
4:50:04.587521 INFO: Using classic extraction backend
4:50:04.587657 PROGRESS: Extracting batch of 2749 precursors
4:50:04.587724 INFO: === Search parameters used ===
4:50:04.587771 INFO: rt_error       : 849.0278031192261
4:50:04.587815 INFO: mobility_error : 0.08948467796187723
4:50:04.587858 INFO: num_candidates : 3
4:50:04.587909 INFO: ms1_error      : 15.0
4:50:04.587953 INFO: ms2_error      : 15.0
4:50:04.587993 INFO: fwhm_rt        : 2.940244674682617
4:50:04.588033 INFO: quant_window   : 3
4:50:04.588072 INFO: ==============================================
4:50:04.589468 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:50:04.589517 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:50:04.589554 INFO: FWHM in RT is 2.94 seconds, sigma is 0.65
4:50:04.589576 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.65
4:50:04.590386 INFO: Starting candidate selection
4:50:12.966822 INFO: Starting candidate scoring
4:50:13.394548 INFO: Finished candidate processing
4:50:13.394703 INFO: Collecting candidate features
4:50:13.421163 INFO: Collecting fragment features
4:50:13.429985 INFO: Finished candidate scoring
4:50:13.434530 INFO: performing precursor FDR with 47 features
4:50:13.434607 INFO: Decoy channel: -1
4:50:13.434638 INFO: Competetive: True
4:50:13.440120 INFO: Setting torch num_threads to 2 for FDR classification task
4:50:13.443681 INFO: Using random state 111459 for train-test-split
4:50:13.464384 INFO: Test AUC: 0.479
4:50:13.464481 INFO: Train AUC: 0.501
4:50:13.464518 INFO: AUC difference: 4.30%
4:50:13.701461 INFO: Resetting torch num_threads to 80
4:50:13.702334 PROGRESS: === Extracted 7550 precursors and 77753 fragments ===
4:50:13.702871 INFO: === FDR correction performed with classifier version 9 ===
4:50:13.703793 PROGRESS: ============================= Precursor FDR =============================
4:50:13.703911 PROGRESS: Total precursors accumulated: 1,370
4:50:13.703985 PROGRESS: Target precursors: 808 (58.98%)
4:50:13.704046 PROGRESS: Decoy precursors: 562 (41.02%)
4:50:13.704098 PROGRESS: 
4:50:13.704150 PROGRESS: Precursor Summary:
4:50:13.705363 PROGRESS: Channel   0:	 0.050 FDR:   453; 0.010 FDR:   453; 0.001 FDR:   453
4:50:13.705471 PROGRESS: 
4:50:13.705536 PROGRESS: Protein Summary:
4:50:13.706969 PROGRESS: Channel   0:	 0.050 FDR:   449; 0.010 FDR:   449; 0.001 FDR:   449
4:50:13.707083 PROGRESS: =========================================================================
4:50:13.707516 INFO: Target number of precursors reached.
4:50:13.717926 INFO: fragments_df: keeping 2094 of 77753 [sum(precursor_idx_mask)=13271 sum(mass_error_mask)=77753 stop_rank=2094
4:50:13.839392 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
4:50:13.963889 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:50:14.078539 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
4:50:14.188049 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:50:14.423037 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:50:14.423478 INFO: Using score_cutoff 29.336953573608398 (fac=0.99, q=1)
4:50:14.423821 INFO: Updating optimization_manager: fwhm_rt             : 2.940244674682617 -> 2.9277498722076416
4:50:14.423903 INFO: Updating optimization_manager: fwhm_mobility       : 0.005706725642085075 -> 0.005798607133328915
4:50:14.423959 INFO: Updating optimization_manager: score_cutoff        : 31.190967176055906 -> 29.336953573608398
4:50:14.424017 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:50:14.425273 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:50:14.427508 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:50:14.428454 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:50:14.433188 INFO: === checking if optimization conditions were reached ===
4:50:14.433313 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
4:50:14.434159 INFO: Updating optimization_manager: mobility_error      : 0.08948467796187723 -> 0.08948467796187723
4:50:14.434286 INFO: Updating optimization_manager: classifier_version  : 9 -> 12
4:50:14.434383 INFO: Updating optimization_manager: score_cutoff        : 29.336953573608398 -> 29.336953573608398
4:50:14.434471 INFO: Updating optimization_manager: fwhm_rt             : 2.9277498722076416 -> 2.9277498722076416
4:50:14.434566 INFO: Updating optimization_manager: fwhm_mobility       : 0.005798607133328915 -> 0.005798607133328915
4:50:14.434667 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0895 found after 3 searches.
4:50:14.434736 INFO: ==============================================
4:50:14.434821 PROGRESS: Optimization finished for mobility_error.
4:50:14.552173 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:50:14.553469 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:50:14.555690 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:50:14.556619 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:50:14.586838 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
4:50:14.586982 PROGRESS: ==============================================
4:50:14.587051 PROGRESS: ms2_error      : 15.0000
4:50:14.587112 PROGRESS: ms1_error      : 15.0000
4:50:14.587169 PROGRESS: rt_error       : 849.0278
4:50:14.587216 PROGRESS: mobility_error : 0.0895
4:50:14.587260 PROGRESS: ==============================================
4:50:14.588539 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
4:50:16.347263 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:50:24.229519 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
4:50:25.936593 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:50:45.102806 INFO: Using classic extraction backend
4:50:45.103585 PROGRESS: Extracting batch of 12073114 precursors
4:50:45.103714 INFO: === Search parameters used ===
4:50:45.103773 INFO: rt_error       : 849.0278031192261
4:50:45.103822 INFO: mobility_error : 0.08948467796187723
4:50:45.103867 INFO: num_candidates : 3
4:50:45.103912 INFO: ms1_error      : 15.0
4:50:45.103959 INFO: ms2_error      : 15.0
4:50:45.104005 INFO: fwhm_rt        : 2.9277498722076416
4:50:45.104047 INFO: quant_window   : 3
4:50:45.104088 INFO: ==============================================
4:50:48.607182 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
4:50:48.607430 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
4:50:48.607495 INFO: FWHM in RT is 2.93 seconds, sigma is 0.64
4:50:48.607522 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.69
4:50:48.632352 INFO: Starting candidate selection
13:09:11.519493 INFO: Removed 1417251 precursors with score below cutoff 29.336953573608398
13:09:15.049293 INFO: Starting candidate scoring
13:32:43.670068 INFO: Finished candidate processing
13:32:43.670674 INFO: Collecting candidate features
13:34:08.236703 WARNING: intensity_correlation has 10 NaNs ( 0.00 % out of 32225595)
13:34:08.266072 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 32225595)
13:34:09.383553 INFO: Collecting fragment features
13:34:35.184148 INFO: Finished candidate scoring
13:35:13.454486 INFO: === Performing FDR correction with classifier version 12 ===
13:35:13.456984 INFO: performing precursor FDR with 47 features
13:35:13.457036 INFO: Decoy channel: -1
13:35:13.457063 INFO: Competetive: True
13:35:21.673240 INFO: Setting torch num_threads to 2 for FDR classification task
13:35:26.604651 WARNING: dropped 7 target PSMs due to missing features
13:35:26.605121 WARNING: dropped 3 decoy PSMs due to missing features
13:35:42.237286 INFO: Using random state 724073 for train-test-split
13:47:42.315998 INFO: Test AUC: 0.578
13:47:42.318382 INFO: Train AUC: 0.578
13:47:42.318478 INFO: AUC difference: 0.09%
13:47:48.009140 INFO: Resetting torch num_threads to 80
13:47:48.955929 INFO: Removing fragments below FDR threshold
13:47:53.437786 PROGRESS: ============================= Precursor FDR =============================
13:47:53.438347 PROGRESS: Total precursors accumulated: 55,685
13:47:53.438432 PROGRESS: Target precursors: 55,134 (99.01%)
13:47:53.438486 PROGRESS: Decoy precursors: 551 (0.99%)
13:47:53.438533 PROGRESS: 
13:47:53.438578 PROGRESS: Precursor Summary:
13:47:53.486488 PROGRESS: Channel   0:	 0.050 FDR: 55,134; 0.010 FDR: 55,134; 0.001 FDR: 35,034
13:47:53.489175 PROGRESS: 
13:47:53.489441 PROGRESS: Protein Summary:
13:47:53.570354 PROGRESS: Channel   0:	 0.050 FDR: 9,519; 0.010 FDR: 9,519; 0.001 FDR: 7,318
13:47:53.571071 PROGRESS: =========================================================================
13:47:54.301869 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/psm.parquet
13:47:54.739794 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/frag.parquet
13:47:54.971103 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
13:47:55.734636 PROGRESS: 
13:47:55.734884 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark/quant
13:47:55.735031 INFO: Initializing TimingManager
13:47:55.735695 INFO: Initializing RawFileManager
13:47:55.735830 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
13:47:55.735929 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
13:47:55.735985 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
13:47:56.098413 INFO: Reading 39,128 frames with 2,897,842,446 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
13:48:06.975754 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d...
13:48:06.981428 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
13:48:06.985010 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
13:48:06.985423 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
13:48:06.986074 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
13:48:06.987744 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
13:48:07.011312 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
13:48:07.011860 INFO: Indexing quadrupole dimension
13:48:07.756274 INFO: Transposing detector events
13:48:18.738510 INFO: Finished transposing data
13:48:18.783964 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
13:48:18.786350 INFO: RT (min)            : 0.0 - 70.0
13:48:18.786443 INFO: RT duration (sec)   : 4199.8
13:48:18.786499 INFO: RT duration (min)   : 70.0
13:48:18.786548 INFO: Cycle len (scans)   : 9
13:48:18.786595 INFO: Cycle len (sec)     : 0.97
13:48:18.786638 INFO: Number of cycles    : 4347
13:48:18.786685 INFO: MS2 range (m/z)     : 400.0 - 1000.0
13:48:18.786891 INFO: Creating DIA data object took: 23.05104684829712
13:48:21.183749 INFO: Initializing CalibrationManager
13:48:21.185580 INFO: Setting up calibration estimators ..
13:48:21.185670 INFO: Found 1 estimator(s) in calibration group 'fragment'
13:48:21.185791 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'}' ..
13:48:21.185914 INFO: Found 3 estimator(s) in calibration group 'precursor'
13:48:21.185993 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
13:48:21.186070 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}}' ..
13:48:21.186158 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
13:48:21.186220 INFO: Done setting up calibration estimators.
13:48:21.186387 INFO: Initializing OptimizationManager
13:48:21.186513 INFO: initial parameter: ms1_error = 30
13:48:21.186576 INFO: initial parameter: ms2_error = 30
13:48:21.186630 INFO: initial parameter: rt_error = 2099.8992935
13:48:21.186675 INFO: initial parameter: mobility_error = 0.1
13:48:21.186715 INFO: initial parameter: num_candidates = 1
13:48:21.186756 INFO: initial parameter: fwhm_rt = 5
13:48:21.186812 INFO: initial parameter: fwhm_mobility = 0.01
13:48:21.186857 INFO: initial parameter: score_cutoff = 0
13:48:21.186898 INFO: initial parameter: classifier_version = -1
13:48:21.186993 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
13:48:21.187514 INFO: FDRManager: loading saved state not requested, will be initialized.
13:48:21.187557 INFO: Initializing FDRManager
13:48:21.187616 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
13:48:22.675204 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
13:48:23.989401 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
13:48:23.990087 INFO: Updating optimization_manager: rt_error            : 2099.8992935 -> 2099.8992935
13:48:23.990214 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
13:48:23.990419 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
13:48:23.990547 PROGRESS: Starting initial search for precursors.
13:48:23.990650 INFO: Starting optimization step 0.
13:48:23.990714 PROGRESS: === Extracting elution groups 0 to 200 ===
13:48:23.990800 INFO: Using classic extraction backend
13:48:23.991268 PROGRESS: Extracting batch of 390 precursors
13:48:23.991350 INFO: === Search parameters used ===
13:48:23.991400 INFO: rt_error       : 2099.8992935
13:48:23.991442 INFO: mobility_error : 0.1
13:48:23.991484 INFO: num_candidates : 1
13:48:23.991524 INFO: ms1_error      : 30
13:48:23.991565 INFO: ms2_error      : 30
13:48:23.991604 INFO: fwhm_rt        : 5
13:48:23.991642 INFO: quant_window   : 3
13:48:23.991680 INFO: ==============================================
13:48:23.992967 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:48:23.993034 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:48:23.993077 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
13:48:23.993103 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
13:48:23.997749 INFO: Starting candidate selection
13:48:28.286678 INFO: Starting candidate scoring
13:48:28.357035 INFO: Finished candidate processing
13:48:28.357760 INFO: Collecting candidate features
13:48:28.367455 INFO: Collecting fragment features
13:48:28.369622 INFO: Finished candidate scoring
13:48:28.370391 INFO: performing precursor FDR with 47 features
13:48:28.370432 INFO: Decoy channel: -1
13:48:28.370457 INFO: Competetive: True
13:48:28.371609 INFO: Setting torch num_threads to 2 for FDR classification task
13:48:28.374613 INFO: Using random state 386019 for train-test-split
13:48:28.383805 INFO: Test AUC: 0.493
13:48:28.383873 INFO: Train AUC: 0.519
13:48:28.383904 INFO: AUC difference: 5.03%
13:48:28.383925 WARNING: AUC difference > 5%. This may indicate overfitting.
13:48:28.609816 INFO: Resetting torch num_threads to 80
13:48:28.610273 PROGRESS: === Extracted 363 precursors and 3936 fragments ===
13:48:28.610697 INFO: === FDR correction performed with classifier version -1 ===
13:48:28.611228 PROGRESS: ============================= Precursor FDR =============================
13:48:28.611320 PROGRESS: Total precursors accumulated: 188
13:48:28.611382 PROGRESS: Target precursors: 164 (87.23%)
13:48:28.611434 PROGRESS: Decoy precursors: 24 (12.77%)
13:48:28.611480 PROGRESS: 
13:48:28.611523 PROGRESS: Precursor Summary:
13:48:28.612508 PROGRESS: Channel   0:	 0.050 FDR:   157; 0.010 FDR:   157; 0.001 FDR:   157
13:48:28.612642 PROGRESS: 
13:48:28.612721 PROGRESS: Protein Summary:
13:48:28.614016 PROGRESS: Channel   0:	 0.050 FDR:   157; 0.010 FDR:   157; 0.001 FDR:   157
13:48:28.614120 PROGRESS: =========================================================================
13:48:28.614243 INFO: Target number of precursors not reached yet.
13:48:28.729673 INFO: Starting optimization step 1.
13:48:28.729939 PROGRESS: === Extracting elution groups 200 to 600 ===
13:48:28.730024 INFO: Using classic extraction backend
13:48:28.730152 PROGRESS: Extracting batch of 783 precursors
13:48:28.730228 INFO: === Search parameters used ===
13:48:28.730281 INFO: rt_error       : 2099.8992935
13:48:28.730325 INFO: mobility_error : 0.1
13:48:28.730373 INFO: num_candidates : 1
13:48:28.730415 INFO: ms1_error      : 30
13:48:28.730458 INFO: ms2_error      : 30
13:48:28.730497 INFO: fwhm_rt        : 5
13:48:28.730537 INFO: quant_window   : 3
13:48:28.730576 INFO: ==============================================
13:48:28.731498 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:48:28.731546 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:48:28.731575 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
13:48:28.731595 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
13:48:28.732301 INFO: Starting candidate selection
13:48:35.036211 INFO: Starting candidate scoring
13:48:35.182648 INFO: Finished candidate processing
13:48:35.182828 INFO: Collecting candidate features
13:48:35.195421 INFO: Collecting fragment features
13:48:35.198502 INFO: Finished candidate scoring
13:48:35.201649 INFO: performing precursor FDR with 47 features
13:48:35.201704 INFO: Decoy channel: -1
13:48:35.201728 INFO: Competetive: True
13:48:35.205784 INFO: Setting torch num_threads to 2 for FDR classification task
13:48:35.208780 INFO: Using random state 730445 for train-test-split
13:48:35.219243 INFO: Test AUC: 0.549
13:48:35.219304 INFO: Train AUC: 0.491
13:48:35.219338 INFO: AUC difference: 11.77%
13:48:35.219361 WARNING: AUC difference > 5%. This may indicate overfitting.
13:48:35.439805 INFO: Resetting torch num_threads to 80
13:48:35.441238 PROGRESS: === Extracted 1117 precursors and 12174 fragments ===
13:48:35.441721 INFO: === FDR correction performed with classifier version -1 ===
13:48:35.442317 PROGRESS: ============================= Precursor FDR =============================
13:48:35.442410 PROGRESS: Total precursors accumulated: 576
13:48:35.442477 PROGRESS: Target precursors: 497 (86.28%)
13:48:35.442534 PROGRESS: Decoy precursors: 79 (13.72%)
13:48:35.442580 PROGRESS: 
13:48:35.442621 PROGRESS: Precursor Summary:
13:48:35.443652 PROGRESS: Channel   0:	 0.050 FDR:   473; 0.010 FDR:   473; 0.001 FDR:   473
13:48:35.443742 PROGRESS: 
13:48:35.443797 PROGRESS: Protein Summary:
13:48:35.445020 PROGRESS: Channel   0:	 0.050 FDR:   465; 0.010 FDR:   465; 0.001 FDR:   465
13:48:35.445107 PROGRESS: =========================================================================
13:48:35.445414 INFO: Target number of precursors reached.
13:48:35.448873 INFO: fragments_df: keeping 1017 of 12174 [sum(precursor_idx_mask)=5275 sum(mass_error_mask)=12174 stop_rank=1017
13:48:35.553545 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
13:48:35.696058 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
13:48:35.833519 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
13:48:35.969936 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
13:48:36.142304 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
13:48:36.142791 INFO: Using score_cutoff 29.566817763519285 (fac=0.99, q=1)
13:48:36.143167 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.2251949310302734
13:48:36.143250 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007908967323601246
13:48:36.143304 INFO: Updating optimization_manager: score_cutoff        : 0 -> 29.566817763519285
13:48:36.143364 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:48:36.144542 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:48:36.145872 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:48:36.146653 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:48:36.148902 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
13:48:36.149008 PROGRESS: Required number of precursors found. Starting search parameter optimization.
13:48:36.149132 INFO: Starting optimization step 2.
13:48:36.149206 PROGRESS: === Extracting elution groups 0 to 600 ===
13:48:36.149293 INFO: Using classic extraction backend
13:48:36.149542 PROGRESS: Extracting batch of 1173 precursors
13:48:36.149629 INFO: === Search parameters used ===
13:48:36.149692 INFO: rt_error       : 2099.8992935
13:48:36.149743 INFO: mobility_error : 0.1
13:48:36.149784 INFO: num_candidates : 3
13:48:36.149826 INFO: ms1_error      : 30
13:48:36.149866 INFO: ms2_error      : 30
13:48:36.149905 INFO: fwhm_rt        : 3.2251949310302734
13:48:36.149943 INFO: quant_window   : 3
13:48:36.149981 INFO: ==============================================
13:48:36.151498 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:48:36.151547 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:48:36.151613 INFO: FWHM in RT is 3.23 seconds, sigma is 0.71
13:48:36.151642 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.67
13:48:36.177029 INFO: Starting candidate selection
13:48:46.659663 INFO: Starting candidate scoring
13:48:47.051303 INFO: Finished candidate processing
13:48:47.051432 INFO: Collecting candidate features
13:48:47.066337 INFO: Collecting fragment features
13:48:47.070893 INFO: Finished candidate scoring
13:48:47.073705 INFO: performing precursor FDR with 47 features
13:48:47.073767 INFO: Decoy channel: -1
13:48:47.073796 INFO: Competetive: True
13:48:47.077517 INFO: Setting torch num_threads to 2 for FDR classification task
13:48:47.079855 INFO: Using random state 728132 for train-test-split
13:48:47.091105 INFO: Test AUC: 0.499
13:48:47.091223 INFO: Train AUC: 0.498
13:48:47.091251 INFO: AUC difference: 0.22%
13:48:47.311776 INFO: Resetting torch num_threads to 80
13:48:47.312471 PROGRESS: === Extracted 3225 precursors and 35298 fragments ===
13:48:47.313473 INFO: === FDR correction performed with classifier version 1 ===
13:48:47.314254 PROGRESS: ============================= Precursor FDR =============================
13:48:47.314371 PROGRESS: Total precursors accumulated: 587
13:48:47.314432 PROGRESS: Target precursors: 543 (92.50%)
13:48:47.314480 PROGRESS: Decoy precursors: 44 (7.50%)
13:48:47.314526 PROGRESS: 
13:48:47.314569 PROGRESS: Precursor Summary:
13:48:47.315726 PROGRESS: Channel   0:	 0.050 FDR:   538; 0.010 FDR:   538; 0.001 FDR:   538
13:48:47.315830 PROGRESS: 
13:48:47.315887 PROGRESS: Protein Summary:
13:48:47.317168 PROGRESS: Channel   0:	 0.050 FDR:   527; 0.010 FDR:   527; 0.001 FDR:   527
13:48:47.317261 PROGRESS: =========================================================================
13:48:47.317418 INFO: Target number of precursors reached.
13:48:47.324597 INFO: fragments_df: keeping 3324 of 35298 [sum(precursor_idx_mask)=16750 sum(mass_error_mask)=35298 stop_rank=3324
13:48:47.425342 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
13:48:47.615272 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
13:48:47.761282 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
13:48:47.910420 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
13:48:48.357362 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
13:48:48.357903 INFO: Using score_cutoff 34.51098016090393 (fac=0.99, q=1)
13:48:48.358253 INFO: Updating optimization_manager: fwhm_rt             : 3.2251949310302734 -> 3.186673641204834
13:48:48.358348 INFO: Updating optimization_manager: fwhm_mobility       : 0.007908967323601246 -> 0.007981179282069206
13:48:48.358404 INFO: Updating optimization_manager: score_cutoff        : 29.566817763519285 -> 34.51098016090393
13:48:48.358459 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:48:48.359723 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:48:48.361098 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:48:48.361867 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:48:48.364041 INFO: === checking if optimization conditions were reached ===
13:48:48.365479 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.209626768968214
13:48:48.365581 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
13:48:48.365669 PROGRESS: ❌ ms2_error      : 17.2096 > 15.0000 or insufficient steps taken.
13:48:48.366657 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
13:48:48.366751 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
13:48:48.366825 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
13:48:48.366883 INFO: ==============================================
13:48:48.366949 INFO: Starting optimization step 3.
13:48:48.367007 PROGRESS: === Extracting elution groups 0 to 600 ===
13:48:48.367060 INFO: Using classic extraction backend
13:48:48.367175 PROGRESS: Extracting batch of 1173 precursors
13:48:48.367239 INFO: === Search parameters used ===
13:48:48.367295 INFO: rt_error       : 2099.8992935
13:48:48.367340 INFO: mobility_error : 0.1
13:48:48.367381 INFO: num_candidates : 3
13:48:48.367421 INFO: ms1_error      : 15.0
13:48:48.367460 INFO: ms2_error      : 17.209626768968214
13:48:48.367500 INFO: fwhm_rt        : 3.186673641204834
13:48:48.367540 INFO: quant_window   : 3
13:48:48.367579 INFO: ==============================================
13:48:48.368733 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:48:48.368784 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:48:48.368820 INFO: FWHM in RT is 3.19 seconds, sigma is 0.70
13:48:48.368843 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.70
13:48:48.370298 INFO: Starting candidate selection
13:49:00.566473 INFO: Starting candidate scoring
13:49:00.766900 INFO: Finished candidate processing
13:49:00.767009 INFO: Collecting candidate features
13:49:00.779899 INFO: Collecting fragment features
13:49:00.783965 INFO: Finished candidate scoring
13:49:00.785790 INFO: performing precursor FDR with 47 features
13:49:00.785835 INFO: Decoy channel: -1
13:49:00.785871 INFO: Competetive: True
13:49:00.789018 INFO: Setting torch num_threads to 2 for FDR classification task
13:49:00.791075 INFO: Using random state 436899 for train-test-split
13:49:00.801361 INFO: Test AUC: 0.514
13:49:00.801420 INFO: Train AUC: 0.503
13:49:00.801448 INFO: AUC difference: 2.27%
13:49:01.014817 INFO: Resetting torch num_threads to 80
13:49:01.015452 PROGRESS: === Extracted 3222 precursors and 33985 fragments ===
13:49:01.017411 INFO: === FDR correction performed with classifier version 2 ===
13:49:01.018080 PROGRESS: ============================= Precursor FDR =============================
13:49:01.018173 PROGRESS: Total precursors accumulated: 587
13:49:01.018233 PROGRESS: Target precursors: 523 (89.10%)
13:49:01.018282 PROGRESS: Decoy precursors: 64 (10.90%)
13:49:01.018330 PROGRESS: 
13:49:01.018373 PROGRESS: Precursor Summary:
13:49:01.019423 PROGRESS: Channel   0:	 0.050 FDR:   507; 0.010 FDR:   507; 0.001 FDR:   507
13:49:01.019520 PROGRESS: 
13:49:01.019576 PROGRESS: Protein Summary:
13:49:01.020792 PROGRESS: Channel   0:	 0.050 FDR:   499; 0.010 FDR:   499; 0.001 FDR:   499
13:49:01.020886 PROGRESS: =========================================================================
13:49:01.021068 INFO: Target number of precursors reached.
13:49:01.027617 INFO: fragments_df: keeping 2707 of 33985 [sum(precursor_idx_mask)=15400 sum(mass_error_mask)=33985 stop_rank=2707
13:49:01.157454 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
13:49:01.335037 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
13:49:01.475846 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
13:49:01.598830 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
13:49:01.903558 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
13:49:01.904033 INFO: Using score_cutoff 31.334044842910767 (fac=0.99, q=1)
13:49:01.904361 INFO: Updating optimization_manager: fwhm_rt             : 3.186673641204834 -> 2.9015183448791504
13:49:01.904439 INFO: Updating optimization_manager: fwhm_mobility       : 0.007981179282069206 -> 0.006024629343301058
13:49:01.904492 INFO: Updating optimization_manager: score_cutoff        : 34.51098016090393 -> 31.334044842910767
13:49:01.904546 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:49:01.905691 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:49:01.907028 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:49:01.907784 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:49:01.909798 INFO: === checking if optimization conditions were reached ===
13:49:01.911062 INFO: Updating optimization_manager: ms2_error           : 17.209626768968214 -> 15.0
13:49:01.911164 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
13:49:01.911227 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
13:49:01.912172 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
13:49:01.912265 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
13:49:01.912324 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
13:49:01.912374 INFO: ==============================================
13:49:01.912436 PROGRESS: Optimization finished for ms2_error, ms1_error.
13:49:02.015227 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:49:02.016455 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:49:02.017867 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:49:02.018666 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:49:02.020770 INFO: Starting optimization step 0.
13:49:02.020875 PROGRESS: === Extracting elution groups 0 to 600 ===
13:49:02.020943 INFO: Using classic extraction backend
13:49:02.021062 PROGRESS: Extracting batch of 1173 precursors
13:49:02.021132 INFO: === Search parameters used ===
13:49:02.021183 INFO: rt_error       : 2099.8992935
13:49:02.021229 INFO: mobility_error : 0.1
13:49:02.021270 INFO: num_candidates : 3
13:49:02.021310 INFO: ms1_error      : 15.0
13:49:02.021362 INFO: ms2_error      : 15.0
13:49:02.021404 INFO: fwhm_rt        : 2.9015183448791504
13:49:02.021445 INFO: quant_window   : 3
13:49:02.021490 INFO: ==============================================
13:49:02.022390 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:49:02.022437 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:49:02.022472 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
13:49:02.022494 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.79
13:49:02.051316 INFO: Starting candidate selection
13:49:11.514072 INFO: Starting candidate scoring
13:49:11.764617 INFO: Finished candidate processing
13:49:11.764735 INFO: Collecting candidate features
13:49:11.779098 INFO: Collecting fragment features
13:49:11.783237 INFO: Finished candidate scoring
13:49:11.785139 INFO: performing precursor FDR with 47 features
13:49:11.785185 INFO: Decoy channel: -1
13:49:11.785210 INFO: Competetive: True
13:49:11.789740 INFO: Setting torch num_threads to 2 for FDR classification task
13:49:11.792519 INFO: Using random state 369367 for train-test-split
13:49:11.809459 INFO: Test AUC: 0.514
13:49:11.809542 INFO: Train AUC: 0.504
13:49:11.809574 INFO: AUC difference: 2.09%
13:49:12.030627 INFO: Resetting torch num_threads to 80
13:49:12.031258 PROGRESS: === Extracted 3210 precursors and 33298 fragments ===
13:49:12.031791 INFO: === FDR correction performed with classifier version 3 ===
13:49:12.032381 PROGRESS: ============================= Precursor FDR =============================
13:49:12.032471 PROGRESS: Total precursors accumulated: 587
13:49:12.032535 PROGRESS: Target precursors: 527 (89.78%)
13:49:12.032588 PROGRESS: Decoy precursors: 60 (10.22%)
13:49:12.032634 PROGRESS: 
13:49:12.032678 PROGRESS: Precursor Summary:
13:49:12.033691 PROGRESS: Channel   0:	 0.050 FDR:   507; 0.010 FDR:   507; 0.001 FDR:   507
13:49:12.033781 PROGRESS: 
13:49:12.033837 PROGRESS: Protein Summary:
13:49:12.035067 PROGRESS: Channel   0:	 0.050 FDR:   497; 0.010 FDR:   497; 0.001 FDR:   497
13:49:12.035161 PROGRESS: =========================================================================
13:49:12.035432 INFO: Target number of precursors reached.
13:49:12.041665 INFO: fragments_df: keeping 2733 of 33298 [sum(precursor_idx_mask)=15046 sum(mass_error_mask)=33298 stop_rank=2733
13:49:12.150979 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
13:49:12.502128 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
13:49:12.651094 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
13:49:13.781469 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
13:49:14.187658 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
13:49:14.188140 INFO: Using score_cutoff 30.657892751312254 (fac=0.99, q=1)
13:49:14.188467 INFO: Updating optimization_manager: fwhm_rt             : 2.9015183448791504 -> 2.7357800006866455
13:49:14.188548 INFO: Updating optimization_manager: fwhm_mobility       : 0.006024629343301058 -> 0.00560347456485033
13:49:14.188604 INFO: Updating optimization_manager: score_cutoff        : 31.334044842910767 -> 30.657892751312254
13:49:14.188657 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:49:14.189790 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:49:14.191144 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:49:14.191912 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:49:14.193981 INFO: === checking if optimization conditions were reached ===
13:49:14.194089 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
13:49:14.195712 INFO: Updating optimization_manager: rt_error            : 2099.8992935 -> 1385.989966833027
13:49:14.195813 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1385.9900.
13:49:14.195879 INFO: ==============================================
13:49:14.195945 INFO: Starting optimization step 1.
13:49:14.196016 PROGRESS: === Extracting elution groups 0 to 600 ===
13:49:14.196076 INFO: Using classic extraction backend
13:49:14.196199 PROGRESS: Extracting batch of 1173 precursors
13:49:14.196266 INFO: === Search parameters used ===
13:49:14.196325 INFO: rt_error       : 1385.989966833027
13:49:14.196372 INFO: mobility_error : 0.1
13:49:14.196412 INFO: num_candidates : 3
13:49:14.196453 INFO: ms1_error      : 15.0
13:49:14.196493 INFO: ms2_error      : 15.0
13:49:14.196532 INFO: fwhm_rt        : 2.7357800006866455
13:49:14.196571 INFO: quant_window   : 3
13:49:14.196610 INFO: ==============================================
13:49:14.197604 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:49:14.197650 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:49:14.197686 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
13:49:14.197710 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.60
13:49:14.210268 INFO: Starting candidate selection
13:49:20.828720 INFO: Starting candidate scoring
13:49:21.074475 INFO: Finished candidate processing
13:49:21.074628 INFO: Collecting candidate features
13:49:21.089104 INFO: Collecting fragment features
13:49:21.093243 INFO: Finished candidate scoring
13:49:21.096267 INFO: performing precursor FDR with 47 features
13:49:21.096375 INFO: Decoy channel: -1
13:49:21.096436 INFO: Competetive: True
13:49:21.101976 INFO: Setting torch num_threads to 2 for FDR classification task
13:49:21.105407 INFO: Using random state 369367 for train-test-split
13:49:21.121814 INFO: Test AUC: 0.537
13:49:21.121912 INFO: Train AUC: 0.501
13:49:21.121962 INFO: AUC difference: 7.08%
13:49:21.122000 WARNING: AUC difference > 5%. This may indicate overfitting.
13:49:21.342063 INFO: Resetting torch num_threads to 80
13:49:21.342726 PROGRESS: === Extracted 3209 precursors and 33242 fragments ===
13:49:21.343740 INFO: === FDR correction performed with classifier version 3 ===
13:49:21.344398 PROGRESS: ============================= Precursor FDR =============================
13:49:21.344490 PROGRESS: Total precursors accumulated: 586
13:49:21.344553 PROGRESS: Target precursors: 522 (89.08%)
13:49:21.344605 PROGRESS: Decoy precursors: 64 (10.92%)
13:49:21.344654 PROGRESS: 
13:49:21.344700 PROGRESS: Precursor Summary:
13:49:21.345751 PROGRESS: Channel   0:	 0.050 FDR:   505; 0.010 FDR:   505; 0.001 FDR:   505
13:49:21.345841 PROGRESS: 
13:49:21.345899 PROGRESS: Protein Summary:
13:49:21.347178 PROGRESS: Channel   0:	 0.050 FDR:   495; 0.010 FDR:   495; 0.001 FDR:   495
13:49:21.347272 PROGRESS: =========================================================================
13:49:21.347426 INFO: Target number of precursors reached.
13:49:21.353948 INFO: fragments_df: keeping 2774 of 33242 [sum(precursor_idx_mask)=14962 sum(mass_error_mask)=33242 stop_rank=2774
13:49:21.454584 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
13:49:21.599301 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
13:49:21.745021 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
13:49:21.890639 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
13:49:22.268424 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
13:49:22.268890 INFO: Using score_cutoff 30.2031043258667 (fac=0.99, q=1)
13:49:22.269213 INFO: Updating optimization_manager: fwhm_rt             : 2.7357800006866455 -> 2.6916708946228027
13:49:22.269296 INFO: Updating optimization_manager: fwhm_mobility       : 0.00560347456485033 -> 0.005548864137381315
13:49:22.269349 INFO: Updating optimization_manager: score_cutoff        : 30.657892751312254 -> 30.2031043258667
13:49:22.269402 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:49:22.270526 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:49:22.271934 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:49:22.272703 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:49:22.274895 INFO: === checking if optimization conditions were reached ===
13:49:22.275002 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
13:49:22.276730 INFO: Updating optimization_manager: rt_error            : 1385.989966833027 -> 859.9394174447588
13:49:22.276840 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 859.9394.
13:49:22.276937 INFO: ==============================================
13:49:22.277006 INFO: Starting optimization step 2.
13:49:22.277064 PROGRESS: === Extracting elution groups 0 to 600 ===
13:49:22.277118 INFO: Using classic extraction backend
13:49:22.277230 PROGRESS: Extracting batch of 1173 precursors
13:49:22.277294 INFO: === Search parameters used ===
13:49:22.277342 INFO: rt_error       : 859.9394174447588
13:49:22.277385 INFO: mobility_error : 0.1
13:49:22.277426 INFO: num_candidates : 3
13:49:22.277465 INFO: ms1_error      : 15.0
13:49:22.277506 INFO: ms2_error      : 15.0
13:49:22.277543 INFO: fwhm_rt        : 2.6916708946228027
13:49:22.277582 INFO: quant_window   : 3
13:49:22.277619 INFO: ==============================================
13:49:22.278488 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:49:22.278531 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:49:22.278565 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
13:49:22.278586 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.57
13:49:22.279475 INFO: Starting candidate selection
13:49:26.161607 INFO: Starting candidate scoring
13:49:26.385489 INFO: Finished candidate processing
13:49:26.385602 INFO: Collecting candidate features
13:49:26.398171 INFO: Collecting fragment features
13:49:26.401858 INFO: Finished candidate scoring
13:49:26.404171 INFO: performing precursor FDR with 47 features
13:49:26.404218 INFO: Decoy channel: -1
13:49:26.404242 INFO: Competetive: True
13:49:26.407966 INFO: Setting torch num_threads to 2 for FDR classification task
13:49:26.410089 INFO: Using random state 369367 for train-test-split
13:49:26.420692 INFO: Test AUC: 0.516
13:49:26.420755 INFO: Train AUC: 0.506
13:49:26.420783 INFO: AUC difference: 1.96%
13:49:26.652731 INFO: Resetting torch num_threads to 80
13:49:26.653449 PROGRESS: === Extracted 3208 precursors and 33229 fragments ===
13:49:26.653942 INFO: === FDR correction performed with classifier version 3 ===
13:49:26.654543 PROGRESS: ============================= Precursor FDR =============================
13:49:26.654630 PROGRESS: Total precursors accumulated: 586
13:49:26.654689 PROGRESS: Target precursors: 522 (89.08%)
13:49:26.654738 PROGRESS: Decoy precursors: 64 (10.92%)
13:49:26.654789 PROGRESS: 
13:49:26.654836 PROGRESS: Precursor Summary:
13:49:26.655874 PROGRESS: Channel   0:	 0.050 FDR:   501; 0.010 FDR:   501; 0.001 FDR:   501
13:49:26.655961 PROGRESS: 
13:49:26.656017 PROGRESS: Protein Summary:
13:49:26.657248 PROGRESS: Channel   0:	 0.050 FDR:   491; 0.010 FDR:   491; 0.001 FDR:   491
13:49:26.657341 PROGRESS: =========================================================================
13:49:26.657528 INFO: Target number of precursors reached.
13:49:26.663944 INFO: fragments_df: keeping 2707 of 33229 [sum(precursor_idx_mask)=14908 sum(mass_error_mask)=33229 stop_rank=2707
13:49:26.851885 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
13:49:27.022953 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
13:49:27.162983 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
13:49:27.306978 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
13:49:27.691928 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
13:49:27.692455 INFO: Using score_cutoff 31.0549658203125 (fac=0.99, q=1)
13:49:27.692842 INFO: Updating optimization_manager: fwhm_rt             : 2.6916708946228027 -> 2.7421817779541016
13:49:27.692930 INFO: Updating optimization_manager: fwhm_mobility       : 0.005548864137381315 -> 0.0055651613511145115
13:49:27.692986 INFO: Updating optimization_manager: score_cutoff        : 30.2031043258667 -> 31.0549658203125
13:49:27.693041 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:49:27.694247 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:49:27.695728 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:49:27.697142 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:49:27.699482 INFO: === checking if optimization conditions were reached ===
13:49:27.699591 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
13:49:27.701470 INFO: Updating optimization_manager: rt_error            : 859.9394174447588 -> 823.9679038501481
13:49:27.701571 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 823.9679.
13:49:27.701636 INFO: ==============================================
13:49:27.701703 INFO: Starting optimization step 3.
13:49:27.701759 PROGRESS: === Extracting elution groups 0 to 600 ===
13:49:27.701813 INFO: Using classic extraction backend
13:49:27.701925 PROGRESS: Extracting batch of 1173 precursors
13:49:27.701989 INFO: === Search parameters used ===
13:49:27.702035 INFO: rt_error       : 823.9679038501481
13:49:27.702075 INFO: mobility_error : 0.1
13:49:27.702115 INFO: num_candidates : 3
13:49:27.702155 INFO: ms1_error      : 15.0
13:49:27.702193 INFO: ms2_error      : 15.0
13:49:27.702229 INFO: fwhm_rt        : 2.7421817779541016
13:49:27.702267 INFO: quant_window   : 3
13:49:27.702305 INFO: ==============================================
13:49:27.703285 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:49:27.703333 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:49:27.703366 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
13:49:27.703386 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.58
13:49:27.734859 INFO: Starting candidate selection
13:49:32.396019 INFO: Starting candidate scoring
13:49:32.618182 INFO: Finished candidate processing
13:49:32.618307 INFO: Collecting candidate features
13:49:32.631398 INFO: Collecting fragment features
13:49:32.635258 INFO: Finished candidate scoring
13:49:32.637281 INFO: performing precursor FDR with 47 features
13:49:32.637323 INFO: Decoy channel: -1
13:49:32.637346 INFO: Competetive: True
13:49:32.640500 INFO: Setting torch num_threads to 2 for FDR classification task
13:49:32.642593 INFO: Using random state 369367 for train-test-split
13:49:32.652550 INFO: Test AUC: 0.501
13:49:32.652613 INFO: Train AUC: 0.501
13:49:32.652646 INFO: AUC difference: 0.03%
13:49:32.874201 INFO: Resetting torch num_threads to 80
13:49:32.874823 PROGRESS: === Extracted 3218 precursors and 33375 fragments ===
13:49:32.875273 INFO: === FDR correction performed with classifier version 3 ===
13:49:32.875859 PROGRESS: ============================= Precursor FDR =============================
13:49:32.875947 PROGRESS: Total precursors accumulated: 586
13:49:32.876005 PROGRESS: Target precursors: 518 (88.40%)
13:49:32.876054 PROGRESS: Decoy precursors: 68 (11.60%)
13:49:32.876100 PROGRESS: 
13:49:32.876143 PROGRESS: Precursor Summary:
13:49:32.877160 PROGRESS: Channel   0:	 0.050 FDR:   500; 0.010 FDR:   500; 0.001 FDR:   500
13:49:32.877248 PROGRESS: 
13:49:32.877304 PROGRESS: Protein Summary:
13:49:32.878512 PROGRESS: Channel   0:	 0.050 FDR:   490; 0.010 FDR:   490; 0.001 FDR:   490
13:49:32.878599 PROGRESS: =========================================================================
13:49:32.878739 INFO: Target number of precursors reached.
13:49:32.884990 INFO: fragments_df: keeping 2684 of 33375 [sum(precursor_idx_mask)=14907 sum(mass_error_mask)=33375 stop_rank=2684
13:49:32.985775 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
13:49:33.127869 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
13:49:33.268752 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
13:49:33.409726 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
13:49:33.766315 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
13:49:33.766803 INFO: Using score_cutoff 31.112545523071287 (fac=0.99, q=1)
13:49:33.767148 INFO: Updating optimization_manager: fwhm_rt             : 2.7421817779541016 -> 2.7482032775878906
13:49:33.767228 INFO: Updating optimization_manager: fwhm_mobility       : 0.0055651613511145115 -> 0.005549396853893995
13:49:33.767284 INFO: Updating optimization_manager: score_cutoff        : 31.0549658203125 -> 31.112545523071287
13:49:33.767337 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:49:33.768477 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:49:33.769823 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:49:33.770583 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:49:33.772670 INFO: === checking if optimization conditions were reached ===
13:49:33.772775 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
13:49:33.773864 INFO: Updating optimization_manager: rt_error            : 823.9679038501481 -> 823.9679038501481
13:49:33.773990 INFO: Updating optimization_manager: classifier_version  : 3 -> 7
13:49:33.774087 INFO: Updating optimization_manager: score_cutoff        : 31.112545523071287 -> 31.112545523071287
13:49:33.774174 INFO: Updating optimization_manager: fwhm_rt             : 2.7482032775878906 -> 2.7482032775878906
13:49:33.774258 INFO: Updating optimization_manager: fwhm_mobility       : 0.005549396853893995 -> 0.005549396853893995
13:49:33.774344 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 823.9679 found after 4 searches.
13:49:33.774407 INFO: ==============================================
13:49:33.774474 PROGRESS: Optimization finished for rt_error.
13:49:33.878376 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:49:33.879593 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:49:33.881047 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:49:33.881866 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:49:33.908752 INFO: Starting optimization step 0.
13:49:33.908907 PROGRESS: === Extracting elution groups 0 to 600 ===
13:49:33.908990 INFO: Using classic extraction backend
13:49:33.909117 PROGRESS: Extracting batch of 1173 precursors
13:49:33.909190 INFO: === Search parameters used ===
13:49:33.909239 INFO: rt_error       : 823.9679038501481
13:49:33.909283 INFO: mobility_error : 0.1
13:49:33.909326 INFO: num_candidates : 3
13:49:33.909368 INFO: ms1_error      : 15.0
13:49:33.909410 INFO: ms2_error      : 15.0
13:49:33.909451 INFO: fwhm_rt        : 2.7482032775878906
13:49:33.909493 INFO: quant_window   : 3
13:49:33.909533 INFO: ==============================================
13:49:33.910368 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:49:33.910414 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:49:33.910450 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
13:49:33.910472 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.57
13:49:33.911214 INFO: Starting candidate selection
13:49:39.508314 INFO: Starting candidate scoring
13:49:39.705016 INFO: Finished candidate processing
13:49:39.705162 INFO: Collecting candidate features
13:49:39.722558 INFO: Collecting fragment features
13:49:39.726994 INFO: Finished candidate scoring
13:49:39.729899 INFO: performing precursor FDR with 47 features
13:49:39.729982 INFO: Decoy channel: -1
13:49:39.730039 INFO: Competetive: True
13:49:39.736761 INFO: Setting torch num_threads to 2 for FDR classification task
13:49:39.741673 INFO: Using random state 594965 for train-test-split
13:49:39.759028 INFO: Test AUC: 0.474
13:49:39.759166 INFO: Train AUC: 0.514
13:49:39.759197 INFO: AUC difference: 7.80%
13:49:39.759220 WARNING: AUC difference > 5%. This may indicate overfitting.
13:49:39.992949 INFO: Resetting torch num_threads to 80
13:49:39.993853 PROGRESS: === Extracted 3225 precursors and 33473 fragments ===
13:49:39.994821 INFO: === FDR correction performed with classifier version 7 ===
13:49:39.995800 PROGRESS: ============================= Precursor FDR =============================
13:49:39.995927 PROGRESS: Total precursors accumulated: 587
13:49:39.995991 PROGRESS: Target precursors: 521 (88.76%)
13:49:39.996063 PROGRESS: Decoy precursors: 66 (11.24%)
13:49:39.996112 PROGRESS: 
13:49:39.996157 PROGRESS: Precursor Summary:
13:49:39.997391 PROGRESS: Channel   0:	 0.050 FDR:   503; 0.010 FDR:   503; 0.001 FDR:   503
13:49:39.997489 PROGRESS: 
13:49:39.997545 PROGRESS: Protein Summary:
13:49:39.998913 PROGRESS: Channel   0:	 0.050 FDR:   492; 0.010 FDR:   492; 0.001 FDR:   492
13:49:39.999011 PROGRESS: =========================================================================
13:49:39.999500 INFO: Target number of precursors reached.
13:49:40.006446 INFO: fragments_df: keeping 2669 of 33473 [sum(precursor_idx_mask)=14964 sum(mass_error_mask)=33473 stop_rank=2669
13:49:40.108310 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
13:49:40.266711 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
13:49:40.409196 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
13:49:40.553715 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
13:49:40.913236 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
13:49:40.913808 INFO: Using score_cutoff 31.01933289756775 (fac=0.99, q=1)
13:49:40.914268 INFO: Updating optimization_manager: fwhm_rt             : 2.7482032775878906 -> 2.7026968002319336
13:49:40.914359 INFO: Updating optimization_manager: fwhm_mobility       : 0.005549396853893995 -> 0.005445933435112238
13:49:40.914413 INFO: Updating optimization_manager: score_cutoff        : 31.112545523071287 -> 31.01933289756775
13:49:40.914482 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:49:40.915779 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:49:40.917301 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:49:40.918165 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:49:40.920345 INFO: === checking if optimization conditions were reached ===
13:49:40.920487 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
13:49:40.922147 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.09882285618881125
13:49:40.922253 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0988.
13:49:40.922320 INFO: ==============================================
13:49:40.922396 INFO: Starting optimization step 1.
13:49:40.922455 PROGRESS: === Extracting elution groups 0 to 600 ===
13:49:40.922516 INFO: Using classic extraction backend
13:49:40.922667 PROGRESS: Extracting batch of 1173 precursors
13:49:40.922736 INFO: === Search parameters used ===
13:49:40.922796 INFO: rt_error       : 823.9679038501481
13:49:40.922841 INFO: mobility_error : 0.09882285618881125
13:49:40.922882 INFO: num_candidates : 3
13:49:40.922921 INFO: ms1_error      : 15.0
13:49:40.922961 INFO: ms2_error      : 15.0
13:49:40.923000 INFO: fwhm_rt        : 2.7026968002319336
13:49:40.923040 INFO: quant_window   : 3
13:49:40.923086 INFO: ==============================================
13:49:40.924457 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:49:40.924505 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:49:40.924559 INFO: FWHM in RT is 2.70 seconds, sigma is 0.59
13:49:40.924581 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.53
13:49:40.925530 INFO: Starting candidate selection
13:50:02.583570 INFO: Starting candidate scoring
13:50:02.818239 INFO: Finished candidate processing
13:50:02.818334 INFO: Collecting candidate features
13:50:02.830941 INFO: Collecting fragment features
13:50:02.834460 INFO: Finished candidate scoring
13:50:02.836221 INFO: performing precursor FDR with 47 features
13:50:02.836267 INFO: Decoy channel: -1
13:50:02.836291 INFO: Competetive: True
13:50:02.839164 INFO: Setting torch num_threads to 2 for FDR classification task
13:50:02.841185 INFO: Using random state 594965 for train-test-split
13:50:02.850732 INFO: Test AUC: 0.489
13:50:02.850814 INFO: Train AUC: 0.502
13:50:02.850848 INFO: AUC difference: 2.58%
13:50:03.064365 INFO: Resetting torch num_threads to 80
13:50:03.064869 PROGRESS: === Extracted 3222 precursors and 33406 fragments ===
13:50:03.065279 INFO: === FDR correction performed with classifier version 7 ===
13:50:03.065840 PROGRESS: ============================= Precursor FDR =============================
13:50:03.065930 PROGRESS: Total precursors accumulated: 587
13:50:03.065989 PROGRESS: Target precursors: 514 (87.56%)
13:50:03.066038 PROGRESS: Decoy precursors: 73 (12.44%)
13:50:03.066086 PROGRESS: 
13:50:03.066128 PROGRESS: Precursor Summary:
13:50:03.067140 PROGRESS: Channel   0:	 0.050 FDR:   498; 0.010 FDR:   498; 0.001 FDR:   498
13:50:03.067232 PROGRESS: 
13:50:03.067287 PROGRESS: Protein Summary:
13:50:03.068487 PROGRESS: Channel   0:	 0.050 FDR:   488; 0.010 FDR:   488; 0.001 FDR:   488
13:50:03.068577 PROGRESS: =========================================================================
13:50:03.068722 INFO: Target number of precursors reached.
13:50:03.074746 INFO: fragments_df: keeping 2575 of 33406 [sum(precursor_idx_mask)=14692 sum(mass_error_mask)=33406 stop_rank=2575
13:50:03.173431 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
13:50:03.309958 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
13:50:03.449074 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
13:50:03.586517 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
13:50:03.924549 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
13:50:03.924969 INFO: Using score_cutoff 30.7565762008667 (fac=0.99, q=1)
13:50:03.925273 INFO: Updating optimization_manager: fwhm_rt             : 2.7026968002319336 -> 2.6675305366516113
13:50:03.925354 INFO: Updating optimization_manager: fwhm_mobility       : 0.005445933435112238 -> 0.005352110601961613
13:50:03.925410 INFO: Updating optimization_manager: score_cutoff        : 31.01933289756775 -> 30.7565762008667
13:50:03.925463 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:50:03.926528 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:50:03.927855 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:50:03.928607 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:50:03.930665 INFO: === checking if optimization conditions were reached ===
13:50:03.930768 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
13:50:03.932199 INFO: Updating optimization_manager: mobility_error      : 0.09882285618881125 -> 0.09969828562041703
13:50:03.932300 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0997.
13:50:03.932365 INFO: ==============================================
13:50:03.932432 INFO: Starting optimization step 2.
13:50:03.932489 PROGRESS: === Extracting elution groups 0 to 600 ===
13:50:03.932546 INFO: Using classic extraction backend
13:50:03.932658 PROGRESS: Extracting batch of 1173 precursors
13:50:03.932722 INFO: === Search parameters used ===
13:50:03.932779 INFO: rt_error       : 823.9679038501481
13:50:03.932826 INFO: mobility_error : 0.09969828562041703
13:50:03.932868 INFO: num_candidates : 3
13:50:03.932910 INFO: ms1_error      : 15.0
13:50:03.932949 INFO: ms2_error      : 15.0
13:50:03.932988 INFO: fwhm_rt        : 2.6675305366516113
13:50:03.933030 INFO: quant_window   : 3
13:50:03.933069 INFO: ==============================================
13:50:03.933849 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:50:03.933896 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:50:03.933931 INFO: FWHM in RT is 2.67 seconds, sigma is 0.59
13:50:03.933954 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.48
13:50:03.934675 INFO: Starting candidate selection
13:50:08.783813 INFO: Starting candidate scoring
13:50:08.986692 INFO: Finished candidate processing
13:50:08.986841 INFO: Collecting candidate features
13:50:09.000637 INFO: Collecting fragment features
13:50:09.004345 INFO: Finished candidate scoring
13:50:09.006117 INFO: performing precursor FDR with 47 features
13:50:09.006160 INFO: Decoy channel: -1
13:50:09.006183 INFO: Competetive: True
13:50:09.009077 INFO: Setting torch num_threads to 2 for FDR classification task
13:50:09.011182 INFO: Using random state 594965 for train-test-split
13:50:09.021366 INFO: Test AUC: 0.509
13:50:09.021423 INFO: Train AUC: 0.498
13:50:09.021452 INFO: AUC difference: 2.40%
13:50:09.236344 INFO: Resetting torch num_threads to 80
13:50:09.236861 PROGRESS: === Extracted 3220 precursors and 33405 fragments ===
13:50:09.237271 INFO: === FDR correction performed with classifier version 7 ===
13:50:09.237851 PROGRESS: ============================= Precursor FDR =============================
13:50:09.237941 PROGRESS: Total precursors accumulated: 587
13:50:09.237999 PROGRESS: Target precursors: 517 (88.07%)
13:50:09.238047 PROGRESS: Decoy precursors: 70 (11.93%)
13:50:09.238093 PROGRESS: 
13:50:09.238134 PROGRESS: Precursor Summary:
13:50:09.239134 PROGRESS: Channel   0:	 0.050 FDR:   502; 0.010 FDR:   502; 0.001 FDR:   502
13:50:09.239225 PROGRESS: 
13:50:09.239280 PROGRESS: Protein Summary:
13:50:09.240470 PROGRESS: Channel   0:	 0.050 FDR:   491; 0.010 FDR:   491; 0.001 FDR:   491
13:50:09.240562 PROGRESS: =========================================================================
13:50:09.240704 INFO: Target number of precursors reached.
13:50:09.246918 INFO: fragments_df: keeping 2615 of 33405 [sum(precursor_idx_mask)=14875 sum(mass_error_mask)=33405 stop_rank=2615
13:50:09.345495 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
13:50:09.455941 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
13:50:09.572082 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
13:50:09.689098 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
13:50:09.971732 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
13:50:09.972145 INFO: Using score_cutoff 30.789273573303223 (fac=0.99, q=1)
13:50:09.972452 INFO: Updating optimization_manager: fwhm_rt             : 2.6675305366516113 -> 2.701327323913574
13:50:09.972531 INFO: Updating optimization_manager: fwhm_mobility       : 0.005352110601961613 -> 0.005396375432610512
13:50:09.972584 INFO: Updating optimization_manager: score_cutoff        : 30.7565762008667 -> 30.789273573303223
13:50:09.972635 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:50:09.973700 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:50:09.975020 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:50:09.975785 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:50:09.978087 INFO: === checking if optimization conditions were reached ===
13:50:09.978187 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
13:50:09.978916 INFO: Updating optimization_manager: mobility_error      : 0.09969828562041703 -> 0.1
13:50:09.979059 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
13:50:09.979151 INFO: Updating optimization_manager: score_cutoff        : 30.789273573303223 -> 31.01933289756775
13:50:09.979236 INFO: Updating optimization_manager: fwhm_rt             : 2.701327323913574 -> 2.7026968002319336
13:50:09.979318 INFO: Updating optimization_manager: fwhm_mobility       : 0.005396375432610512 -> 0.005445933435112238
13:50:09.979401 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
13:50:09.979461 INFO: ==============================================
13:50:09.979525 PROGRESS: Optimization finished for mobility_error.
13:50:10.079386 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:50:10.080515 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:50:10.081895 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:50:10.082681 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:50:10.109902 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
13:50:10.110034 PROGRESS: ==============================================
13:50:10.110121 PROGRESS: ms2_error      : 15.0000
13:50:10.110188 PROGRESS: ms1_error      : 15.0000
13:50:10.110244 PROGRESS: rt_error       : 823.9679
13:50:10.110293 PROGRESS: mobility_error : 0.1000
13:50:10.110334 PROGRESS: ==============================================
13:50:10.110962 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
13:50:11.654511 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
13:50:19.061481 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
13:50:20.534060 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
13:50:38.181596 INFO: Using classic extraction backend
13:50:38.182531 PROGRESS: Extracting batch of 12073114 precursors
13:50:38.182684 INFO: === Search parameters used ===
13:50:38.182747 INFO: rt_error       : 823.9679038501481
13:50:38.182811 INFO: mobility_error : 0.1
13:50:38.182861 INFO: num_candidates : 3
13:50:38.182904 INFO: ms1_error      : 15.0
13:50:38.182949 INFO: ms2_error      : 15.0
13:50:38.182993 INFO: fwhm_rt        : 2.7026968002319336
13:50:38.183039 INFO: quant_window   : 3
13:50:38.183084 INFO: ==============================================
13:50:42.445671 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
13:50:42.445798 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
13:50:42.445869 INFO: FWHM in RT is 2.70 seconds, sigma is 0.59
13:50:42.445903 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.53
13:50:42.482945 INFO: Starting candidate selection
23:44:19.645123 INFO: Removed 1703877 precursors with score below cutoff 31.01933289756775
23:44:22.836153 INFO: Starting candidate scoring
1 day, 0:04:36.041023 INFO: Finished candidate processing
1 day, 0:04:36.041451 INFO: Collecting candidate features
1 day, 0:05:22.298178 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 32170472)
1 day, 0:05:23.389070 INFO: Collecting fragment features
1 day, 0:05:48.352898 INFO: Finished candidate scoring
1 day, 0:06:23.826296 INFO: === Performing FDR correction with classifier version 8 ===
1 day, 0:06:23.830965 INFO: performing precursor FDR with 47 features
1 day, 0:06:23.831034 INFO: Decoy channel: -1
1 day, 0:06:23.831064 INFO: Competetive: True
1 day, 0:06:31.563828 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:06:35.498481 WARNING: dropped 2 target PSMs due to missing features
1 day, 0:06:49.693605 INFO: Using random state 422979 for train-test-split
1 day, 0:19:01.470017 INFO: Test AUC: 0.577
1 day, 0:19:01.470249 INFO: Train AUC: 0.577
1 day, 0:19:01.470295 INFO: AUC difference: 0.08%
1 day, 0:19:07.456058 INFO: Resetting torch num_threads to 80
1 day, 0:19:07.849635 INFO: Removing fragments below FDR threshold
1 day, 0:19:10.533285 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:19:10.533519 PROGRESS: Total precursors accumulated: 53,985
1 day, 0:19:10.533591 PROGRESS: Target precursors: 53,451 (99.01%)
1 day, 0:19:10.533642 PROGRESS: Decoy precursors: 534 (0.99%)
1 day, 0:19:10.533700 PROGRESS: 
1 day, 0:19:10.533744 PROGRESS: Precursor Summary:
1 day, 0:19:10.550814 PROGRESS: Channel   0:	 0.050 FDR: 53,451; 0.010 FDR: 53,451; 0.001 FDR: 32,366
1 day, 0:19:10.551038 PROGRESS: 
1 day, 0:19:10.551097 PROGRESS: Protein Summary:
1 day, 0:19:10.573346 PROGRESS: Channel   0:	 0.050 FDR: 9,453; 0.010 FDR: 9,453; 0.001 FDR: 7,080
1 day, 0:19:10.573559 PROGRESS: =========================================================================
1 day, 0:19:10.872329 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/psm.parquet
1 day, 0:19:11.249704 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/frag.parquet
1 day, 0:19:11.471748 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 0:19:11.955515 PROGRESS: 
1 day, 0:19:11.955654 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark/quant
1 day, 0:19:11.955761 INFO: Initializing TimingManager
1 day, 0:19:11.956338 INFO: Initializing RawFileManager
1 day, 0:19:11.956463 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 0:19:11.956543 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 0:19:11.956593 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 0:19:12.280167 INFO: Reading 39,128 frames with 2,751,035,867 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 0:19:23.244258 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d...
1 day, 0:19:23.245201 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 0:19:23.247726 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 0:19:23.247932 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 0:19:23.248286 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 0:19:23.249606 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 0:19:23.267857 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 0:19:23.268021 INFO: Indexing quadrupole dimension
1 day, 0:19:23.708298 INFO: Transposing detector events
1 day, 0:19:32.138829 INFO: Finished transposing data
1 day, 0:19:32.163970 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 0:19:32.164443 INFO: RT (min)            : 0.0 - 70.0
1 day, 0:19:32.164484 INFO: RT duration (sec)   : 4199.8
1 day, 0:19:32.164509 INFO: RT duration (min)   : 70.0
1 day, 0:19:32.164531 INFO: Cycle len (scans)   : 9
1 day, 0:19:32.164551 INFO: Cycle len (sec)     : 0.97
1 day, 0:19:32.164569 INFO: Number of cycles    : 4347
1 day, 0:19:32.164587 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 0:19:32.164616 INFO: Creating DIA data object took: 20.208180904388428
1 day, 0:19:33.433190 INFO: Initializing CalibrationManager
1 day, 0:19:33.433457 INFO: Setting up calibration estimators ..
1 day, 0:19:33.433521 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 0:19:33.433602 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1 day, 0:19:33.433688 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 0:19:33.433751 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1 day, 0:19:33.433811 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
1 day, 0:19:33.433872 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
1 day, 0:19:33.433923 INFO: Done setting up calibration estimators.
1 day, 0:19:33.434032 INFO: Initializing OptimizationManager
1 day, 0:19:33.434138 INFO: initial parameter: ms1_error = 30
1 day, 0:19:33.434188 INFO: initial parameter: ms2_error = 30
1 day, 0:19:33.434234 INFO: initial parameter: rt_error = 2099.891532
1 day, 0:19:33.434284 INFO: initial parameter: mobility_error = 0.1
1 day, 0:19:33.434327 INFO: initial parameter: num_candidates = 1
1 day, 0:19:33.434366 INFO: initial parameter: fwhm_rt = 5
1 day, 0:19:33.434408 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 0:19:33.434448 INFO: initial parameter: score_cutoff = 0
1 day, 0:19:33.434488 INFO: initial parameter: classifier_version = -1
1 day, 0:19:33.434553 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 0:19:33.434758 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 0:19:33.434804 INFO: Initializing FDRManager
1 day, 0:19:33.434841 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 0:19:34.629218 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
1 day, 0:19:35.357807 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 0:19:35.358200 INFO: Updating optimization_manager: rt_error            : 2099.891532 -> 2099.891532
1 day, 0:19:35.358312 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 0:19:35.358488 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 0:19:35.358579 PROGRESS: Starting initial search for precursors.
1 day, 0:19:35.358667 INFO: Starting optimization step 0.
1 day, 0:19:35.358732 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 0:19:35.358824 INFO: Using classic extraction backend
1 day, 0:19:35.359078 PROGRESS: Extracting batch of 390 precursors
1 day, 0:19:35.359151 INFO: === Search parameters used ===
1 day, 0:19:35.359201 INFO: rt_error       : 2099.891532
1 day, 0:19:35.359246 INFO: mobility_error : 0.1
1 day, 0:19:35.359288 INFO: num_candidates : 1
1 day, 0:19:35.359329 INFO: ms1_error      : 30
1 day, 0:19:35.359369 INFO: ms2_error      : 30
1 day, 0:19:35.359406 INFO: fwhm_rt        : 5
1 day, 0:19:35.359446 INFO: quant_window   : 3
1 day, 0:19:35.359485 INFO: ==============================================
1 day, 0:19:35.360369 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:19:35.360413 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:19:35.360456 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 0:19:35.360477 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 0:19:35.361366 INFO: Starting candidate selection
1 day, 0:19:39.119367 INFO: Starting candidate scoring
1 day, 0:19:39.182909 INFO: Finished candidate processing
1 day, 0:19:39.183043 INFO: Collecting candidate features
1 day, 0:19:39.193190 INFO: Collecting fragment features
1 day, 0:19:39.195699 INFO: Finished candidate scoring
1 day, 0:19:39.196607 INFO: performing precursor FDR with 47 features
1 day, 0:19:39.196650 INFO: Decoy channel: -1
1 day, 0:19:39.196674 INFO: Competetive: True
1 day, 0:19:39.197800 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:19:39.200407 INFO: Using random state 705341 for train-test-split
1 day, 0:19:39.209141 INFO: Test AUC: 0.467
1 day, 0:19:39.209209 INFO: Train AUC: 0.537
1 day, 0:19:39.209246 INFO: AUC difference: 13.10%
1 day, 0:19:39.209276 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 0:19:39.430960 INFO: Resetting torch num_threads to 80
1 day, 0:19:39.431366 PROGRESS: === Extracted 364 precursors and 3956 fragments ===
1 day, 0:19:39.431760 INFO: === FDR correction performed with classifier version -1 ===
1 day, 0:19:39.432250 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:19:39.432338 PROGRESS: Total precursors accumulated: 187
1 day, 0:19:39.432396 PROGRESS: Target precursors: 135 (72.19%)
1 day, 0:19:39.432444 PROGRESS: Decoy precursors: 52 (27.81%)
1 day, 0:19:39.432492 PROGRESS: 
1 day, 0:19:39.432535 PROGRESS: Precursor Summary:
1 day, 0:19:39.433347 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
1 day, 0:19:39.433434 PROGRESS: 
1 day, 0:19:39.433502 PROGRESS: Protein Summary:
1 day, 0:19:39.434408 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
1 day, 0:19:39.434497 PROGRESS: =========================================================================
1 day, 0:19:39.434601 INFO: Target number of precursors not reached yet.
1 day, 0:19:39.499556 INFO: Starting optimization step 1.
1 day, 0:19:39.499748 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 0:19:39.499822 INFO: Using classic extraction backend
1 day, 0:19:39.499933 PROGRESS: Extracting batch of 783 precursors
1 day, 0:19:39.500002 INFO: === Search parameters used ===
1 day, 0:19:39.500051 INFO: rt_error       : 2099.891532
1 day, 0:19:39.500093 INFO: mobility_error : 0.1
1 day, 0:19:39.500137 INFO: num_candidates : 1
1 day, 0:19:39.500177 INFO: ms1_error      : 30
1 day, 0:19:39.500216 INFO: ms2_error      : 30
1 day, 0:19:39.500254 INFO: fwhm_rt        : 5
1 day, 0:19:39.500293 INFO: quant_window   : 3
1 day, 0:19:39.500332 INFO: ==============================================
1 day, 0:19:39.500949 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:19:39.500992 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:19:39.501021 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 0:19:39.501042 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 0:19:39.501689 INFO: Starting candidate selection
1 day, 0:19:45.566745 INFO: Starting candidate scoring
1 day, 0:19:45.682469 INFO: Finished candidate processing
1 day, 0:19:45.682563 INFO: Collecting candidate features
1 day, 0:19:45.691562 INFO: Collecting fragment features
1 day, 0:19:45.693895 INFO: Finished candidate scoring
1 day, 0:19:45.695643 INFO: performing precursor FDR with 47 features
1 day, 0:19:45.695691 INFO: Decoy channel: -1
1 day, 0:19:45.695714 INFO: Competetive: True
1 day, 0:19:45.698298 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:19:45.699904 INFO: Using random state 918449 for train-test-split
1 day, 0:19:45.707930 INFO: Test AUC: 0.537
1 day, 0:19:45.707988 INFO: Train AUC: 0.503
1 day, 0:19:45.708017 INFO: AUC difference: 6.75%
1 day, 0:19:45.708039 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 0:19:45.918512 INFO: Resetting torch num_threads to 80
1 day, 0:19:45.919639 PROGRESS: === Extracted 1117 precursors and 12152 fragments ===
1 day, 0:19:45.920018 INFO: === FDR correction performed with classifier version -1 ===
1 day, 0:19:45.920555 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:19:45.920646 PROGRESS: Total precursors accumulated: 575
1 day, 0:19:45.920707 PROGRESS: Target precursors: 411 (71.48%)
1 day, 0:19:45.920763 PROGRESS: Decoy precursors: 164 (28.52%)
1 day, 0:19:45.920814 PROGRESS: 
1 day, 0:19:45.920864 PROGRESS: Precursor Summary:
1 day, 0:19:45.921703 PROGRESS: Channel   0:	 0.050 FDR:    23; 0.010 FDR:    23; 0.001 FDR:    23
1 day, 0:19:45.921792 PROGRESS: 
1 day, 0:19:45.921847 PROGRESS: Protein Summary:
1 day, 0:19:45.922762 PROGRESS: Channel   0:	 0.050 FDR:    23; 0.010 FDR:    23; 0.001 FDR:    23
1 day, 0:19:45.922861 PROGRESS: =========================================================================
1 day, 0:19:45.922990 INFO: Target number of precursors not reached yet.
1 day, 0:19:45.990438 INFO: Starting optimization step 2.
1 day, 0:19:45.990637 PROGRESS: === Extracting elution groups 600 to 1400 ===
1 day, 0:19:45.990709 INFO: Using classic extraction backend
1 day, 0:19:45.990829 PROGRESS: Extracting batch of 1576 precursors
1 day, 0:19:45.990902 INFO: === Search parameters used ===
1 day, 0:19:45.990952 INFO: rt_error       : 2099.891532
1 day, 0:19:45.990997 INFO: mobility_error : 0.1
1 day, 0:19:45.991047 INFO: num_candidates : 1
1 day, 0:19:45.991091 INFO: ms1_error      : 30
1 day, 0:19:45.991131 INFO: ms2_error      : 30
1 day, 0:19:45.991171 INFO: fwhm_rt        : 5
1 day, 0:19:45.991211 INFO: quant_window   : 3
1 day, 0:19:45.991251 INFO: ==============================================
1 day, 0:19:45.992019 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:19:45.992064 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:19:45.992091 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 0:19:45.992112 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 0:19:45.992736 INFO: Starting candidate selection
1 day, 0:19:57.503751 INFO: Starting candidate scoring
1 day, 0:19:57.683331 INFO: Finished candidate processing
1 day, 0:19:57.683468 INFO: Collecting candidate features
1 day, 0:19:57.695575 INFO: Collecting fragment features
1 day, 0:19:57.698853 INFO: Finished candidate scoring
1 day, 0:19:57.701468 INFO: performing precursor FDR with 47 features
1 day, 0:19:57.701518 INFO: Decoy channel: -1
1 day, 0:19:57.701543 INFO: Competetive: True
1 day, 0:19:57.704652 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:19:57.706534 INFO: Using random state 576274 for train-test-split
1 day, 0:19:57.717076 INFO: Test AUC: 0.532
1 day, 0:19:57.717136 INFO: Train AUC: 0.495
1 day, 0:19:57.717164 INFO: AUC difference: 7.55%
1 day, 0:19:57.717187 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 0:19:57.927578 INFO: Resetting torch num_threads to 80
1 day, 0:19:57.929093 PROGRESS: === Extracted 2639 precursors and 28566 fragments ===
1 day, 0:19:57.929646 INFO: === FDR correction performed with classifier version -1 ===
1 day, 0:19:57.930265 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:19:57.930366 PROGRESS: Total precursors accumulated: 1,354
1 day, 0:19:57.930427 PROGRESS: Target precursors: 968 (71.49%)
1 day, 0:19:57.930478 PROGRESS: Decoy precursors: 386 (28.51%)
1 day, 0:19:57.930528 PROGRESS: 
1 day, 0:19:57.930573 PROGRESS: Precursor Summary:
1 day, 0:19:57.931428 PROGRESS: Channel   0:	 0.050 FDR:    42; 0.010 FDR:    42; 0.001 FDR:    42
1 day, 0:19:57.931519 PROGRESS: 
1 day, 0:19:57.931574 PROGRESS: Protein Summary:
1 day, 0:19:57.932515 PROGRESS: Channel   0:	 0.050 FDR:    42; 0.010 FDR:    42; 0.001 FDR:    42
1 day, 0:19:57.932605 PROGRESS: =========================================================================
1 day, 0:19:57.932742 INFO: Target number of precursors not reached yet.
1 day, 0:19:58.002280 INFO: Starting optimization step 3.
1 day, 0:19:58.002481 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1 day, 0:19:58.002555 INFO: Using classic extraction backend
1 day, 0:19:58.002668 PROGRESS: Extracting batch of 3162 precursors
1 day, 0:19:58.002739 INFO: === Search parameters used ===
1 day, 0:19:58.002801 INFO: rt_error       : 2099.891532
1 day, 0:19:58.002849 INFO: mobility_error : 0.1
1 day, 0:19:58.002912 INFO: num_candidates : 1
1 day, 0:19:58.002958 INFO: ms1_error      : 30
1 day, 0:19:58.003000 INFO: ms2_error      : 30
1 day, 0:19:58.003041 INFO: fwhm_rt        : 5
1 day, 0:19:58.003082 INFO: quant_window   : 3
1 day, 0:19:58.003121 INFO: ==============================================
1 day, 0:19:58.004031 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:19:58.004076 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:19:58.004104 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 0:19:58.004126 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 0:19:58.004780 INFO: Starting candidate selection
1 day, 0:20:23.020302 INFO: Starting candidate scoring
1 day, 0:20:23.291311 INFO: Finished candidate processing
1 day, 0:20:23.291440 INFO: Collecting candidate features
1 day, 0:20:23.303323 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3028)
1 day, 0:20:23.306483 INFO: Collecting fragment features
1 day, 0:20:23.310506 INFO: Finished candidate scoring
1 day, 0:20:23.314485 INFO: performing precursor FDR with 47 features
1 day, 0:20:23.314538 INFO: Decoy channel: -1
1 day, 0:20:23.314563 INFO: Competetive: True
1 day, 0:20:23.318940 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:20:23.320513 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 0:20:23.321673 INFO: Using random state 726473 for train-test-split
1 day, 0:20:23.337929 INFO: Test AUC: 0.537
1 day, 0:20:23.338016 INFO: Train AUC: 0.491
1 day, 0:20:23.338045 INFO: AUC difference: 9.32%
1 day, 0:20:23.338066 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 0:20:23.548557 INFO: Resetting torch num_threads to 80
1 day, 0:20:23.550610 PROGRESS: === Extracted 5667 precursors and 61145 fragments ===
1 day, 0:20:23.551001 INFO: === FDR correction performed with classifier version -1 ===
1 day, 0:20:23.551815 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:20:23.551907 PROGRESS: Total precursors accumulated: 2,900
1 day, 0:20:23.551970 PROGRESS: Target precursors: 2,021 (69.69%)
1 day, 0:20:23.552019 PROGRESS: Decoy precursors: 879 (30.31%)
1 day, 0:20:23.552069 PROGRESS: 
1 day, 0:20:23.552115 PROGRESS: Precursor Summary:
1 day, 0:20:23.552997 PROGRESS: Channel   0:	 0.050 FDR:   102; 0.010 FDR:   102; 0.001 FDR:   102
1 day, 0:20:23.553090 PROGRESS: 
1 day, 0:20:23.553148 PROGRESS: Protein Summary:
1 day, 0:20:23.554116 PROGRESS: Channel   0:	 0.050 FDR:   102; 0.010 FDR:   102; 0.001 FDR:   102
1 day, 0:20:23.554206 PROGRESS: =========================================================================
1 day, 0:20:23.554357 INFO: Target number of precursors not reached yet.
1 day, 0:20:23.628285 INFO: Starting optimization step 4.
1 day, 0:20:23.628514 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1 day, 0:20:23.628591 INFO: Using classic extraction backend
1 day, 0:20:23.628705 PROGRESS: Extracting batch of 6312 precursors
1 day, 0:20:23.628778 INFO: === Search parameters used ===
1 day, 0:20:23.628828 INFO: rt_error       : 2099.891532
1 day, 0:20:23.628874 INFO: mobility_error : 0.1
1 day, 0:20:23.628917 INFO: num_candidates : 1
1 day, 0:20:23.628957 INFO: ms1_error      : 30
1 day, 0:20:23.629002 INFO: ms2_error      : 30
1 day, 0:20:23.629044 INFO: fwhm_rt        : 5
1 day, 0:20:23.629084 INFO: quant_window   : 3
1 day, 0:20:23.629123 INFO: ==============================================
1 day, 0:20:23.630443 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:20:23.630488 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:20:23.630516 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 0:20:23.630537 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 0:20:23.631257 INFO: Starting candidate selection
1 day, 0:21:05.021271 INFO: Starting candidate scoring
1 day, 0:21:05.491019 INFO: Finished candidate processing
1 day, 0:21:05.491113 INFO: Collecting candidate features
1 day, 0:21:05.508142 INFO: Collecting fragment features
1 day, 0:21:05.513508 INFO: Finished candidate scoring
1 day, 0:21:05.520675 INFO: performing precursor FDR with 47 features
1 day, 0:21:05.520757 INFO: Decoy channel: -1
1 day, 0:21:05.520782 INFO: Competetive: True
1 day, 0:21:06.437305 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:21:06.440702 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 0:21:06.442655 INFO: Using random state 649534 for train-test-split
1 day, 0:21:06.473810 INFO: Test AUC: 0.493
1 day, 0:21:06.473914 INFO: Train AUC: 0.499
1 day, 0:21:06.473943 INFO: AUC difference: 1.05%
1 day, 0:21:06.680340 INFO: Resetting torch num_threads to 80
1 day, 0:21:06.683523 PROGRESS: === Extracted 11688 precursors and 125854 fragments ===
1 day, 0:21:06.683955 INFO: === FDR correction performed with classifier version -1 ===
1 day, 0:21:06.685114 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:21:06.685212 PROGRESS: Total precursors accumulated: 5,980
1 day, 0:21:06.685272 PROGRESS: Target precursors: 4,153 (69.45%)
1 day, 0:21:06.685320 PROGRESS: Decoy precursors: 1,827 (30.55%)
1 day, 0:21:06.685368 PROGRESS: 
1 day, 0:21:06.685410 PROGRESS: Precursor Summary:
1 day, 0:21:06.686384 PROGRESS: Channel   0:	 0.050 FDR:   224; 0.010 FDR:   224; 0.001 FDR:   224
1 day, 0:21:06.686476 PROGRESS: 
1 day, 0:21:06.686541 PROGRESS: Protein Summary:
1 day, 0:21:06.687673 PROGRESS: Channel   0:	 0.050 FDR:   223; 0.010 FDR:   223; 0.001 FDR:   223
1 day, 0:21:06.687767 PROGRESS: =========================================================================
1 day, 0:21:06.687951 INFO: Target number of precursors reached.
1 day, 0:21:06.697996 INFO: fragments_df: keeping 435 of 125854 [sum(precursor_idx_mask)=2543 sum(mass_error_mask)=125854 stop_rank=435
1 day, 0:21:06.878171 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:21:06.979811 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:21:07.077050 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:21:07.179096 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:21:07.285352 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 0:21:07.285739 INFO: Using score_cutoff 42.57972899780273 (fac=0.99, q=1)
1 day, 0:21:07.286026 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.7450196743011475
1 day, 0:21:07.286108 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.008079000748693943
1 day, 0:21:07.286164 INFO: Updating optimization_manager: score_cutoff        : 0 -> 42.57972899780273
1 day, 0:21:07.286217 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:21:07.288733 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:21:07.296523 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:21:07.298746 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:21:07.313931 INFO: Updating optimization_manager: classifier_version  : -1 -> 4
1 day, 0:21:07.314080 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 0:21:07.314166 INFO: Starting optimization step 5.
1 day, 0:21:07.314227 PROGRESS: === Extracting elution groups 0 to 6200 ===
1 day, 0:21:07.314285 INFO: Using classic extraction backend
1 day, 0:21:07.314387 PROGRESS: Extracting batch of 12223 precursors
1 day, 0:21:07.314453 INFO: === Search parameters used ===
1 day, 0:21:07.314503 INFO: rt_error       : 2099.891532
1 day, 0:21:07.314547 INFO: mobility_error : 0.1
1 day, 0:21:07.314590 INFO: num_candidates : 3
1 day, 0:21:07.314632 INFO: ms1_error      : 30
1 day, 0:21:07.314672 INFO: ms2_error      : 30
1 day, 0:21:07.314713 INFO: fwhm_rt        : 3.7450196743011475
1 day, 0:21:07.314753 INFO: quant_window   : 3
1 day, 0:21:07.314803 INFO: ==============================================
1 day, 0:21:07.318298 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:21:07.318361 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:21:07.318398 INFO: FWHM in RT is 3.75 seconds, sigma is 0.82
1 day, 0:21:07.318423 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.75
1 day, 0:21:07.319043 INFO: Starting candidate selection
1 day, 0:22:51.249263 INFO: Starting candidate scoring
1 day, 0:22:53.917221 INFO: Finished candidate processing
1 day, 0:22:53.918340 INFO: Collecting candidate features
1 day, 0:22:53.970817 INFO: Collecting fragment features
1 day, 0:22:53.991101 INFO: Finished candidate scoring
1 day, 0:22:54.006922 INFO: performing precursor FDR with 47 features
1 day, 0:22:54.007034 INFO: Decoy channel: -1
1 day, 0:22:54.007060 INFO: Competetive: True
1 day, 0:22:54.019176 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:22:54.029038 INFO: Using random state 106063 for train-test-split
1 day, 0:22:54.490303 INFO: Test AUC: 0.553
1 day, 0:22:54.490417 INFO: Train AUC: 0.557
1 day, 0:22:54.490449 INFO: AUC difference: 0.77%
1 day, 0:22:54.721448 INFO: Resetting torch num_threads to 80
1 day, 0:22:54.722739 PROGRESS: === Extracted 33847 precursors and 368287 fragments ===
1 day, 0:22:54.723874 INFO: === FDR correction performed with classifier version 4 ===
1 day, 0:22:54.725176 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:22:54.725277 PROGRESS: Total precursors accumulated: 6,090
1 day, 0:22:54.725349 PROGRESS: Target precursors: 3,663 (60.15%)
1 day, 0:22:54.725401 PROGRESS: Decoy precursors: 2,427 (39.85%)
1 day, 0:22:54.725448 PROGRESS: 
1 day, 0:22:54.725497 PROGRESS: Precursor Summary:
1 day, 0:22:54.726384 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 0:22:54.726471 PROGRESS: 
1 day, 0:22:54.726526 PROGRESS: Protein Summary:
1 day, 0:22:54.727498 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 0:22:54.727587 PROGRESS: =========================================================================
1 day, 0:22:54.727980 INFO: Target number of precursors not reached yet.
1 day, 0:22:54.869880 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:22:54.873122 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:22:54.881308 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:22:54.883644 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:22:54.899667 INFO: === skipping optimization until target number of precursors are found ===
1 day, 0:22:54.899832 INFO: Starting optimization step 6.
1 day, 0:22:54.899904 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1 day, 0:22:54.899977 INFO: Using classic extraction backend
1 day, 0:22:54.900118 PROGRESS: Extracting batch of 12615 precursors
1 day, 0:22:54.900194 INFO: === Search parameters used ===
1 day, 0:22:54.900243 INFO: rt_error       : 2099.891532
1 day, 0:22:54.900288 INFO: mobility_error : 0.1
1 day, 0:22:54.900329 INFO: num_candidates : 3
1 day, 0:22:54.900370 INFO: ms1_error      : 30
1 day, 0:22:54.900419 INFO: ms2_error      : 30
1 day, 0:22:54.900464 INFO: fwhm_rt        : 3.7450196743011475
1 day, 0:22:54.900502 INFO: quant_window   : 3
1 day, 0:22:54.900546 INFO: ==============================================
1 day, 0:22:54.903940 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:22:54.903998 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:22:54.904043 INFO: FWHM in RT is 3.75 seconds, sigma is 0.82
1 day, 0:22:54.904068 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.75
1 day, 0:22:54.904778 INFO: Starting candidate selection
1 day, 0:24:38.937358 INFO: Starting candidate scoring
1 day, 0:24:41.762329 INFO: Finished candidate processing
1 day, 0:24:41.762542 INFO: Collecting candidate features
1 day, 0:24:41.851791 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 34816)
1 day, 0:24:41.856679 INFO: Collecting fragment features
1 day, 0:24:41.883894 INFO: Finished candidate scoring
1 day, 0:24:41.946133 INFO: performing precursor FDR with 47 features
1 day, 0:24:41.946317 INFO: Decoy channel: -1
1 day, 0:24:41.946346 INFO: Competetive: True
1 day, 0:24:41.985427 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:24:41.999755 WARNING: dropped 1 target PSMs due to missing features
1 day, 0:24:42.012429 INFO: Using random state 106063 for train-test-split
1 day, 0:24:43.218230 INFO: Test AUC: 0.559
1 day, 0:24:43.218390 INFO: Train AUC: 0.577
1 day, 0:24:43.218429 INFO: AUC difference: 3.21%
1 day, 0:24:43.485495 INFO: Resetting torch num_threads to 80
1 day, 0:24:43.497895 PROGRESS: === Extracted 68663 precursors and 746948 fragments ===
1 day, 0:24:43.498909 INFO: === FDR correction performed with classifier version 4 ===
1 day, 0:24:43.502439 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:24:43.502554 PROGRESS: Total precursors accumulated: 12,383
1 day, 0:24:43.502620 PROGRESS: Target precursors: 7,687 (62.08%)
1 day, 0:24:43.502673 PROGRESS: Decoy precursors: 4,696 (37.92%)
1 day, 0:24:43.502721 PROGRESS: 
1 day, 0:24:43.502766 PROGRESS: Precursor Summary:
1 day, 0:24:43.503759 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 0:24:43.503850 PROGRESS: 
1 day, 0:24:43.503905 PROGRESS: Protein Summary:
1 day, 0:24:43.504960 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 0:24:43.505059 PROGRESS: =========================================================================
1 day, 0:24:43.505660 INFO: Target number of precursors not reached yet.
1 day, 0:24:43.965311 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:24:43.970285 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:24:43.984971 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:24:43.989101 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:24:44.022124 INFO: === skipping optimization until target number of precursors are found ===
1 day, 0:24:44.022408 INFO: Starting optimization step 7.
1 day, 0:24:44.022491 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1 day, 0:24:44.022578 INFO: Using classic extraction backend
1 day, 0:24:44.022756 PROGRESS: Extracting batch of 25223 precursors
1 day, 0:24:44.022865 INFO: === Search parameters used ===
1 day, 0:24:44.022926 INFO: rt_error       : 2099.891532
1 day, 0:24:44.022978 INFO: mobility_error : 0.1
1 day, 0:24:44.023029 INFO: num_candidates : 3
1 day, 0:24:44.023080 INFO: ms1_error      : 30
1 day, 0:24:44.023128 INFO: ms2_error      : 30
1 day, 0:24:44.023177 INFO: fwhm_rt        : 3.7450196743011475
1 day, 0:24:44.023229 INFO: quant_window   : 3
1 day, 0:24:44.023277 INFO: ==============================================
1 day, 0:24:44.032806 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:24:44.032900 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:24:44.032957 INFO: FWHM in RT is 3.75 seconds, sigma is 0.82
1 day, 0:24:44.032986 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.75
1 day, 0:24:44.034430 INFO: Starting candidate selection
1 day, 0:28:22.123173 INFO: Starting candidate scoring
1 day, 0:28:26.957771 INFO: Finished candidate processing
1 day, 0:28:26.957979 INFO: Collecting candidate features
1 day, 0:28:27.173307 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 69762)
1 day, 0:28:27.180217 INFO: Collecting fragment features
1 day, 0:28:27.225334 INFO: Finished candidate scoring
1 day, 0:28:27.440747 INFO: performing precursor FDR with 47 features
1 day, 0:28:27.440933 INFO: Decoy channel: -1
1 day, 0:28:27.440962 INFO: Competetive: True
1 day, 0:28:27.505462 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:28:27.559160 WARNING: dropped 1 target PSMs due to missing features
1 day, 0:28:27.559334 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 0:28:27.579511 INFO: Using random state 106063 for train-test-split
1 day, 0:28:30.363067 INFO: Test AUC: 0.564
1 day, 0:28:30.363677 INFO: Train AUC: 0.582
1 day, 0:28:30.363715 INFO: AUC difference: 3.15%
1 day, 0:28:30.643215 INFO: Resetting torch num_threads to 80
1 day, 0:28:30.670932 PROGRESS: === Extracted 138425 precursors and 1505971 fragments ===
1 day, 0:28:30.671681 INFO: === FDR correction performed with classifier version 4 ===
1 day, 0:28:30.677481 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:28:30.677612 PROGRESS: Total precursors accumulated: 24,963
1 day, 0:28:30.677675 PROGRESS: Target precursors: 15,508 (62.12%)
1 day, 0:28:30.677739 PROGRESS: Decoy precursors: 9,455 (37.88%)
1 day, 0:28:30.677785 PROGRESS: 
1 day, 0:28:30.677833 PROGRESS: Precursor Summary:
1 day, 0:28:30.678866 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 0:28:30.678957 PROGRESS: 
1 day, 0:28:30.679013 PROGRESS: Protein Summary:
1 day, 0:28:30.680088 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1 day, 0:28:30.680177 PROGRESS: =========================================================================
1 day, 0:28:30.680994 INFO: Target number of precursors not reached yet.
1 day, 0:28:30.961111 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:28:30.970032 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:28:30.998546 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:28:31.006119 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:28:31.073523 INFO: === skipping optimization until target number of precursors are found ===
1 day, 0:28:31.073839 INFO: Starting optimization step 8.
1 day, 0:28:31.073912 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1 day, 0:28:31.074006 INFO: Using classic extraction backend
1 day, 0:28:31.074182 PROGRESS: Extracting batch of 50469 precursors
1 day, 0:28:31.074265 INFO: === Search parameters used ===
1 day, 0:28:31.074315 INFO: rt_error       : 2099.891532
1 day, 0:28:31.074359 INFO: mobility_error : 0.1
1 day, 0:28:31.074413 INFO: num_candidates : 3
1 day, 0:28:31.074456 INFO: ms1_error      : 30
1 day, 0:28:31.074496 INFO: ms2_error      : 30
1 day, 0:28:31.074535 INFO: fwhm_rt        : 3.7450196743011475
1 day, 0:28:31.074575 INFO: quant_window   : 3
1 day, 0:28:31.074614 INFO: ==============================================
1 day, 0:28:31.089566 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:28:31.089672 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:28:31.089727 INFO: FWHM in RT is 3.75 seconds, sigma is 0.82
1 day, 0:28:31.089753 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.75
1 day, 0:28:31.090851 INFO: Starting candidate selection
1 day, 0:35:21.675601 INFO: Starting candidate scoring
1 day, 0:35:31.105208 INFO: Finished candidate processing
1 day, 0:35:31.105417 INFO: Collecting candidate features
1 day, 0:35:31.373585 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 139679)
1 day, 0:35:31.388034 INFO: Collecting fragment features
1 day, 0:35:31.483394 INFO: Finished candidate scoring
1 day, 0:35:31.724860 INFO: performing precursor FDR with 47 features
1 day, 0:35:31.725049 INFO: Decoy channel: -1
1 day, 0:35:31.725078 INFO: Competetive: True
1 day, 0:35:31.851074 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:35:31.907740 WARNING: dropped 1 target PSMs due to missing features
1 day, 0:35:31.907903 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 0:35:31.989974 INFO: Using random state 106063 for train-test-split
1 day, 0:35:37.896050 INFO: Test AUC: 0.566
1 day, 0:35:37.896220 INFO: Train AUC: 0.585
1 day, 0:35:37.896259 INFO: AUC difference: 3.25%
1 day, 0:35:38.236364 INFO: Resetting torch num_threads to 80
1 day, 0:35:38.297068 PROGRESS: === Extracted 278104 precursors and 3026152 fragments ===
1 day, 0:35:38.297885 INFO: === FDR correction performed with classifier version 4 ===
1 day, 0:35:38.313195 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:35:38.313560 PROGRESS: Total precursors accumulated: 50,098
1 day, 0:35:38.313658 PROGRESS: Target precursors: 31,513 (62.90%)
1 day, 0:35:38.313716 PROGRESS: Decoy precursors: 18,585 (37.10%)
1 day, 0:35:38.313763 PROGRESS: 
1 day, 0:35:38.313808 PROGRESS: Precursor Summary:
1 day, 0:35:38.315700 PROGRESS: Channel   0:	 0.050 FDR:   283; 0.010 FDR:   175; 0.001 FDR:   133
1 day, 0:35:38.315810 PROGRESS: 
1 day, 0:35:38.315872 PROGRESS: Protein Summary:
1 day, 0:35:38.317327 PROGRESS: Channel   0:	 0.050 FDR:   272; 0.010 FDR:   172; 0.001 FDR:   131
1 day, 0:35:38.317426 PROGRESS: =========================================================================
1 day, 0:35:38.319156 INFO: Target number of precursors not reached yet.
1 day, 0:35:39.110652 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:35:39.133212 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:35:39.190824 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:35:39.206415 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:35:39.357736 INFO: === skipping optimization until target number of precursors are found ===
1 day, 0:35:39.358193 INFO: Starting optimization step 9.
1 day, 0:35:39.358288 PROGRESS: === Extracting elution groups 51000 to 102200 ===
1 day, 0:35:39.358389 INFO: Using classic extraction backend
1 day, 0:35:39.358619 PROGRESS: Extracting batch of 100931 precursors
1 day, 0:35:39.358724 INFO: === Search parameters used ===
1 day, 0:35:39.358806 INFO: rt_error       : 2099.891532
1 day, 0:35:39.358864 INFO: mobility_error : 0.1
1 day, 0:35:39.358920 INFO: num_candidates : 3
1 day, 0:35:39.358975 INFO: ms1_error      : 30
1 day, 0:35:39.359029 INFO: ms2_error      : 30
1 day, 0:35:39.359081 INFO: fwhm_rt        : 3.7450196743011475
1 day, 0:35:39.359131 INFO: quant_window   : 3
1 day, 0:35:39.359183 INFO: ==============================================
1 day, 0:35:39.403963 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:35:39.404735 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:35:39.404824 INFO: FWHM in RT is 3.75 seconds, sigma is 0.82
1 day, 0:35:39.404851 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.75
1 day, 0:35:39.405830 INFO: Starting candidate selection
1 day, 0:48:42.139048 INFO: Starting candidate scoring
1 day, 0:49:00.385878 INFO: Finished candidate processing
1 day, 0:49:00.386324 INFO: Collecting candidate features
1 day, 0:49:00.987414 WARNING: intensity_correlation has 8 NaNs ( 0.00 % out of 279375)
1 day, 0:49:01.000937 INFO: Collecting fragment features
1 day, 0:49:01.185513 INFO: Finished candidate scoring
1 day, 0:49:01.921000 INFO: performing precursor FDR with 47 features
1 day, 0:49:01.921218 INFO: Decoy channel: -1
1 day, 0:49:01.921248 INFO: Competetive: True
1 day, 0:49:02.237966 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:49:02.387797 WARNING: dropped 5 target PSMs due to missing features
1 day, 0:49:02.387941 WARNING: dropped 11 decoy PSMs due to missing features
1 day, 0:49:02.599158 INFO: Using random state 106063 for train-test-split
1 day, 0:49:14.041198 INFO: Test AUC: 0.575
1 day, 0:49:14.041738 INFO: Train AUC: 0.586
1 day, 0:49:14.041778 INFO: AUC difference: 1.89%
1 day, 0:49:14.455760 INFO: Resetting torch num_threads to 80
1 day, 0:49:14.563804 PROGRESS: === Extracted 557479 precursors and 6063429 fragments ===
1 day, 0:49:14.565234 INFO: === FDR correction performed with classifier version 4 ===
1 day, 0:49:14.583773 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:49:14.584026 PROGRESS: Total precursors accumulated: 100,364
1 day, 0:49:14.584107 PROGRESS: Target precursors: 63,151 (62.92%)
1 day, 0:49:14.584165 PROGRESS: Decoy precursors: 37,213 (37.08%)
1 day, 0:49:14.584213 PROGRESS: 
1 day, 0:49:14.584261 PROGRESS: Precursor Summary:
1 day, 0:49:14.586019 PROGRESS: Channel   0:	 0.050 FDR:   605; 0.010 FDR:   423; 0.001 FDR:   150
1 day, 0:49:14.586116 PROGRESS: 
1 day, 0:49:14.586171 PROGRESS: Protein Summary:
1 day, 0:49:14.587853 PROGRESS: Channel   0:	 0.050 FDR:   559; 0.010 FDR:   402; 0.001 FDR:   149
1 day, 0:49:14.587948 PROGRESS: =========================================================================
1 day, 0:49:14.589768 INFO: Target number of precursors reached.
1 day, 0:49:15.013333 INFO: fragments_df: keeping 5000 of 6063429 [sum(precursor_idx_mask)=13894 sum(mass_error_mask)=6063429 stop_rank=5000
1 day, 0:49:15.641789 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:49:15.770640 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:49:15.896375 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:49:15.999631 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:49:16.615349 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 0:49:16.615766 INFO: Using score_cutoff 56.600724922943115 (fac=0.99, q=1)
1 day, 0:49:16.616113 INFO: Updating optimization_manager: fwhm_rt             : 3.7450196743011475 -> 3.0682005882263184
1 day, 0:49:16.616194 INFO: Updating optimization_manager: fwhm_mobility       : 0.008079000748693943 -> 0.011256670579314232
1 day, 0:49:16.616248 INFO: Updating optimization_manager: score_cutoff        : 42.57972899780273 -> 56.600724922943115
1 day, 0:49:16.616315 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:49:16.629819 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:49:16.689353 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:49:16.706573 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:49:16.849092 INFO: === checking if optimization conditions were reached ===
1 day, 0:49:16.851264 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 0:49:16.851373 INFO: Updating optimization_manager: classifier_version  : 4 -> 9
1 day, 0:49:16.851442 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 0:49:16.852409 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 0:49:16.852503 INFO: Updating optimization_manager: classifier_version  : 9 -> 9
1 day, 0:49:16.852568 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 0:49:16.852624 INFO: ==============================================
1 day, 0:49:16.852695 INFO: Starting optimization step 10.
1 day, 0:49:16.852752 PROGRESS: === Extracting elution groups 0 to 51000 ===
1 day, 0:49:16.852818 INFO: Using classic extraction backend
1 day, 0:49:16.852966 PROGRESS: Extracting batch of 100530 precursors
1 day, 0:49:16.853034 INFO: === Search parameters used ===
1 day, 0:49:16.853084 INFO: rt_error       : 2099.891532
1 day, 0:49:16.853128 INFO: mobility_error : 0.1
1 day, 0:49:16.853169 INFO: num_candidates : 3
1 day, 0:49:16.853220 INFO: ms1_error      : 15.0
1 day, 0:49:16.853262 INFO: ms2_error      : 15.0
1 day, 0:49:16.853301 INFO: fwhm_rt        : 3.0682005882263184
1 day, 0:49:16.853340 INFO: quant_window   : 3
1 day, 0:49:16.853379 INFO: ==============================================
1 day, 0:49:16.881039 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:49:16.881154 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:49:16.881202 INFO: FWHM in RT is 3.07 seconds, sigma is 0.67
1 day, 0:49:16.881225 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.22
1 day, 0:49:16.890113 INFO: Starting candidate selection
1 day, 0:59:15.339514 INFO: Starting candidate scoring
1 day, 0:59:27.681031 INFO: Finished candidate processing
1 day, 0:59:27.681223 INFO: Collecting candidate features
1 day, 0:59:28.116829 WARNING: intensity_correlation has 10 NaNs ( 0.00 % out of 279287)
1 day, 0:59:28.130091 INFO: Collecting fragment features
1 day, 0:59:28.314726 INFO: Finished candidate scoring
1 day, 0:59:28.470380 INFO: performing precursor FDR with 47 features
1 day, 0:59:28.470505 INFO: Decoy channel: -1
1 day, 0:59:28.470531 INFO: Competetive: True
1 day, 0:59:28.574796 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 0:59:28.630299 WARNING: dropped 5 target PSMs due to missing features
1 day, 0:59:28.630434 WARNING: dropped 5 decoy PSMs due to missing features
1 day, 0:59:28.717596 INFO: Using random state 229432 for train-test-split
1 day, 0:59:34.452092 INFO: Test AUC: 0.572
1 day, 0:59:34.452224 INFO: Train AUC: 0.590
1 day, 0:59:34.452262 INFO: AUC difference: 3.05%
1 day, 0:59:34.769735 INFO: Resetting torch num_threads to 80
1 day, 0:59:34.777636 PROGRESS: === Extracted 279287 precursors and 2889677 fragments ===
1 day, 0:59:34.779397 INFO: === FDR correction performed with classifier version 9 ===
1 day, 0:59:34.789505 PROGRESS: ============================= Precursor FDR =============================
1 day, 0:59:34.789782 PROGRESS: Total precursors accumulated: 50,032
1 day, 0:59:34.789871 PROGRESS: Target precursors: 31,465 (62.89%)
1 day, 0:59:34.789945 PROGRESS: Decoy precursors: 18,567 (37.11%)
1 day, 0:59:34.790010 PROGRESS: 
1 day, 0:59:34.790073 PROGRESS: Precursor Summary:
1 day, 0:59:34.791723 PROGRESS: Channel   0:	 0.050 FDR:   575; 0.010 FDR:   429; 0.001 FDR:   214
1 day, 0:59:34.791836 PROGRESS: 
1 day, 0:59:34.791909 PROGRESS: Protein Summary:
1 day, 0:59:34.793446 PROGRESS: Channel   0:	 0.050 FDR:   546; 0.010 FDR:   409; 0.001 FDR:   204
1 day, 0:59:34.793710 PROGRESS: =========================================================================
1 day, 0:59:34.835242 INFO: Target number of precursors reached.
1 day, 0:59:35.023016 INFO: fragments_df: keeping 5000 of 2889677 [sum(precursor_idx_mask)=13725 sum(mass_error_mask)=2889675 stop_rank=5000
1 day, 0:59:35.573633 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:59:35.684351 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:59:35.796750 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:59:35.903188 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:59:36.509721 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 0:59:36.510179 INFO: Using score_cutoff 45.150997796630854 (fac=0.99, q=1)
1 day, 0:59:36.510508 INFO: Updating optimization_manager: fwhm_rt             : 3.0682005882263184 -> 2.752497911453247
1 day, 0:59:36.510592 INFO: Updating optimization_manager: fwhm_mobility       : 0.011256670579314232 -> 0.008729173801839352
1 day, 0:59:36.510657 INFO: Updating optimization_manager: score_cutoff        : 56.600724922943115 -> 45.150997796630854
1 day, 0:59:36.510717 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:59:36.518116 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:59:36.548256 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:59:36.555513 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:59:36.619832 INFO: === checking if optimization conditions were reached ===
1 day, 0:59:36.621984 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 0:59:36.622087 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1 day, 0:59:36.622158 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 0:59:36.623146 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 0:59:36.623243 INFO: Updating optimization_manager: classifier_version  : 10 -> 10
1 day, 0:59:36.623316 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 0:59:36.623372 INFO: ==============================================
1 day, 0:59:36.623455 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 0:59:36.760839 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 0:59:36.768622 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 0:59:36.798868 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 0:59:36.806154 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 0:59:36.869617 INFO: Starting optimization step 0.
1 day, 0:59:36.869866 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 0:59:36.869948 INFO: Using classic extraction backend
1 day, 0:59:36.870105 PROGRESS: Extracting batch of 50061 precursors
1 day, 0:59:36.870185 INFO: === Search parameters used ===
1 day, 0:59:36.870239 INFO: rt_error       : 2099.891532
1 day, 0:59:36.870284 INFO: mobility_error : 0.1
1 day, 0:59:36.870328 INFO: num_candidates : 3
1 day, 0:59:36.870372 INFO: ms1_error      : 15.0
1 day, 0:59:36.870413 INFO: ms2_error      : 15.0
1 day, 0:59:36.870455 INFO: fwhm_rt        : 2.752497911453247
1 day, 0:59:36.870495 INFO: quant_window   : 3
1 day, 0:59:36.870534 INFO: ==============================================
1 day, 0:59:36.885917 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 0:59:36.886037 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 0:59:36.886085 INFO: FWHM in RT is 2.75 seconds, sigma is 0.61
1 day, 0:59:36.886109 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.05
1 day, 0:59:36.894935 INFO: Starting candidate selection
1 day, 1:04:38.680931 INFO: Starting candidate scoring
1 day, 1:04:44.437265 INFO: Finished candidate processing
1 day, 1:04:44.438540 INFO: Collecting candidate features
1 day, 1:04:44.674404 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 138714)
1 day, 1:04:44.683167 INFO: Collecting fragment features
1 day, 1:04:44.766976 INFO: Finished candidate scoring
1 day, 1:04:44.826670 INFO: performing precursor FDR with 47 features
1 day, 1:04:44.826800 INFO: Decoy channel: -1
1 day, 1:04:44.826826 INFO: Competetive: True
1 day, 1:04:44.873936 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:04:44.899630 WARNING: dropped 2 target PSMs due to missing features
1 day, 1:04:44.899761 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 1:04:44.923687 INFO: Using random state 488372 for train-test-split
1 day, 1:04:47.680446 INFO: Test AUC: 0.568
1 day, 1:04:47.680579 INFO: Train AUC: 0.608
1 day, 1:04:47.680611 INFO: AUC difference: 6.59%
1 day, 1:04:47.680633 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 1:04:47.941242 INFO: Resetting torch num_threads to 80
1 day, 1:04:47.944834 PROGRESS: === Extracted 138714 precursors and 1432714 fragments ===
1 day, 1:04:47.945399 INFO: === FDR correction performed with classifier version 10 ===
1 day, 1:04:47.949758 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:04:47.949891 PROGRESS: Total precursors accumulated: 24,894
1 day, 1:04:47.949953 PROGRESS: Target precursors: 15,912 (63.92%)
1 day, 1:04:47.950005 PROGRESS: Decoy precursors: 8,982 (36.08%)
1 day, 1:04:47.950051 PROGRESS: 
1 day, 1:04:47.950095 PROGRESS: Precursor Summary:
1 day, 1:04:47.951206 PROGRESS: Channel   0:	 0.050 FDR:   306; 0.010 FDR:   242; 0.001 FDR:    87
1 day, 1:04:47.951300 PROGRESS: 
1 day, 1:04:47.951358 PROGRESS: Protein Summary:
1 day, 1:04:47.952541 PROGRESS: Channel   0:	 0.050 FDR:   301; 0.010 FDR:   238; 0.001 FDR:    85
1 day, 1:04:47.952639 PROGRESS: =========================================================================
1 day, 1:04:47.981176 INFO: Target number of precursors reached.
1 day, 1:04:48.077260 INFO: fragments_df: keeping 3354 of 1432714 [sum(precursor_idx_mask)=7719 sum(mass_error_mask)=1432714 stop_rank=3354
1 day, 1:04:48.288597 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:04:48.400857 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:04:48.501619 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:04:48.596200 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:04:48.990301 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 1:04:48.990902 INFO: Using score_cutoff 43.93073034667969 (fac=0.99, q=1)
1 day, 1:04:48.991325 INFO: Updating optimization_manager: fwhm_rt             : 2.752497911453247 -> 2.617743492126465
1 day, 1:04:48.991426 INFO: Updating optimization_manager: fwhm_mobility       : 0.008729173801839352 -> 0.008579516783356667
1 day, 1:04:48.991502 INFO: Updating optimization_manager: score_cutoff        : 45.150997796630854 -> 43.93073034667969
1 day, 1:04:48.991578 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:04:49.000427 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:04:49.032540 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:04:49.040957 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:04:49.125252 INFO: === checking if optimization conditions were reached ===
1 day, 1:04:49.126725 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 1:04:49.129210 INFO: Updating optimization_manager: rt_error            : 2099.891532 -> 411.1561188933912
1 day, 1:04:49.129333 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 411.1561.
1 day, 1:04:49.129434 INFO: ==============================================
1 day, 1:04:49.129548 INFO: Starting optimization step 1.
1 day, 1:04:49.129632 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 1:04:49.129716 INFO: Using classic extraction backend
1 day, 1:04:49.129900 PROGRESS: Extracting batch of 50061 precursors
1 day, 1:04:49.129989 INFO: === Search parameters used ===
1 day, 1:04:49.130073 INFO: rt_error       : 411.1561188933912
1 day, 1:04:49.130134 INFO: mobility_error : 0.1
1 day, 1:04:49.130200 INFO: num_candidates : 3
1 day, 1:04:49.130261 INFO: ms1_error      : 15.0
1 day, 1:04:49.130318 INFO: ms2_error      : 15.0
1 day, 1:04:49.130373 INFO: fwhm_rt        : 2.617743492126465
1 day, 1:04:49.130428 INFO: quant_window   : 3
1 day, 1:04:49.130484 INFO: ==============================================
1 day, 1:04:49.155147 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:04:49.155309 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:04:49.155371 INFO: FWHM in RT is 2.62 seconds, sigma is 0.58
1 day, 1:04:49.155403 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.98
1 day, 1:04:49.174947 INFO: Starting candidate selection
1 day, 1:05:48.747485 INFO: Starting candidate scoring
1 day, 1:05:54.393081 INFO: Finished candidate processing
1 day, 1:05:54.393907 INFO: Collecting candidate features
1 day, 1:05:54.601696 WARNING: intensity_correlation has 34 NaNs ( 0.03 % out of 133480)
1 day, 1:05:54.602029 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 133480)
1 day, 1:05:54.609775 INFO: Collecting fragment features
1 day, 1:05:54.695271 INFO: Finished candidate scoring
1 day, 1:05:54.753442 INFO: performing precursor FDR with 47 features
1 day, 1:05:54.753553 INFO: Decoy channel: -1
1 day, 1:05:54.753577 INFO: Competetive: True
1 day, 1:05:54.791897 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:05:54.813965 WARNING: dropped 21 target PSMs due to missing features
1 day, 1:05:54.814086 WARNING: dropped 16 decoy PSMs due to missing features
1 day, 1:05:54.836441 INFO: Using random state 488372 for train-test-split
1 day, 1:05:57.390124 INFO: Test AUC: 0.565
1 day, 1:05:57.390259 INFO: Train AUC: 0.582
1 day, 1:05:57.390295 INFO: AUC difference: 2.97%
1 day, 1:05:57.650875 INFO: Resetting torch num_threads to 80
1 day, 1:05:57.654721 PROGRESS: === Extracted 133480 precursors and 1344841 fragments ===
1 day, 1:05:57.655386 INFO: === FDR correction performed with classifier version 10 ===
1 day, 1:05:57.660610 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:05:57.660789 PROGRESS: Total precursors accumulated: 24,323
1 day, 1:05:57.660862 PROGRESS: Target precursors: 15,000 (61.67%)
1 day, 1:05:57.660922 PROGRESS: Decoy precursors: 9,323 (38.33%)
1 day, 1:05:57.660977 PROGRESS: 
1 day, 1:05:57.661027 PROGRESS: Precursor Summary:
1 day, 1:05:57.662212 PROGRESS: Channel   0:	 0.050 FDR:   298; 0.010 FDR:   204; 0.001 FDR:   187
1 day, 1:05:57.662310 PROGRESS: 
1 day, 1:05:57.662374 PROGRESS: Protein Summary:
1 day, 1:05:57.663602 PROGRESS: Channel   0:	 0.050 FDR:   294; 0.010 FDR:   200; 0.001 FDR:   183
1 day, 1:05:57.663698 PROGRESS: =========================================================================
1 day, 1:05:57.665035 INFO: Target number of precursors reached.
1 day, 1:05:57.753863 INFO: fragments_df: keeping 2946 of 1344841 [sum(precursor_idx_mask)=6576 sum(mass_error_mask)=1344838 stop_rank=2946
1 day, 1:05:57.978914 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:05:58.153346 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:05:58.254074 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:05:58.352560 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:05:58.677277 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 1:05:58.677836 INFO: Using score_cutoff 44.7525684928894 (fac=0.99, q=1)
1 day, 1:05:58.678204 INFO: Updating optimization_manager: fwhm_rt             : 2.617743492126465 -> 2.607682228088379
1 day, 1:05:58.678288 INFO: Updating optimization_manager: fwhm_mobility       : 0.008579516783356667 -> 0.00862718652933836
1 day, 1:05:58.678344 INFO: Updating optimization_manager: score_cutoff        : 43.93073034667969 -> 44.7525684928894
1 day, 1:05:58.678417 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:05:58.686621 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:05:58.717115 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:05:58.725420 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:05:58.790786 INFO: === checking if optimization conditions were reached ===
1 day, 1:05:58.791159 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 1:05:58.793537 INFO: Updating optimization_manager: rt_error            : 411.1561188933912 -> 346.8541187160484
1 day, 1:05:58.793642 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 346.8541.
1 day, 1:05:58.793711 INFO: ==============================================
1 day, 1:05:58.793824 INFO: Starting optimization step 2.
1 day, 1:05:58.793894 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 1:05:58.793973 INFO: Using classic extraction backend
1 day, 1:05:58.794219 PROGRESS: Extracting batch of 50061 precursors
1 day, 1:05:58.794301 INFO: === Search parameters used ===
1 day, 1:05:58.794354 INFO: rt_error       : 346.8541187160484
1 day, 1:05:58.794399 INFO: mobility_error : 0.1
1 day, 1:05:58.794441 INFO: num_candidates : 3
1 day, 1:05:58.794483 INFO: ms1_error      : 15.0
1 day, 1:05:58.794524 INFO: ms2_error      : 15.0
1 day, 1:05:58.794564 INFO: fwhm_rt        : 2.607682228088379
1 day, 1:05:58.794603 INFO: quant_window   : 3
1 day, 1:05:58.794656 INFO: ==============================================
1 day, 1:05:58.813462 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:05:58.813622 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:05:58.813701 INFO: FWHM in RT is 2.61 seconds, sigma is 0.57
1 day, 1:05:58.813728 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.00
1 day, 1:05:58.827362 INFO: Starting candidate selection
1 day, 1:06:47.950544 INFO: Starting candidate scoring
1 day, 1:06:53.041943 INFO: Finished candidate processing
1 day, 1:06:53.044011 INFO: Collecting candidate features
1 day, 1:06:53.381958 WARNING: intensity_correlation has 42 NaNs ( 0.03 % out of 133108)
1 day, 1:06:53.382351 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 133108)
1 day, 1:06:53.390411 INFO: Collecting fragment features
1 day, 1:06:53.478328 INFO: Finished candidate scoring
1 day, 1:06:53.667512 INFO: performing precursor FDR with 47 features
1 day, 1:06:53.667668 INFO: Decoy channel: -1
1 day, 1:06:53.667694 INFO: Competetive: True
1 day, 1:06:53.715261 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:06:53.743077 WARNING: dropped 23 target PSMs due to missing features
1 day, 1:06:53.743248 WARNING: dropped 20 decoy PSMs due to missing features
1 day, 1:06:53.769595 INFO: Using random state 488372 for train-test-split
1 day, 1:06:56.389509 INFO: Test AUC: 0.563
1 day, 1:06:56.389695 INFO: Train AUC: 0.580
1 day, 1:06:56.389732 INFO: AUC difference: 2.98%
1 day, 1:06:56.664491 INFO: Resetting torch num_threads to 80
1 day, 1:06:56.668787 PROGRESS: === Extracted 133108 precursors and 1331235 fragments ===
1 day, 1:06:56.669850 INFO: === FDR correction performed with classifier version 10 ===
1 day, 1:06:56.674682 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:06:56.674838 PROGRESS: Total precursors accumulated: 24,271
1 day, 1:06:56.674904 PROGRESS: Target precursors: 14,870 (61.27%)
1 day, 1:06:56.674956 PROGRESS: Decoy precursors: 9,401 (38.73%)
1 day, 1:06:56.675017 PROGRESS: 
1 day, 1:06:56.675065 PROGRESS: Precursor Summary:
1 day, 1:06:56.676248 PROGRESS: Channel   0:	 0.050 FDR:   361; 0.010 FDR:   251; 0.001 FDR:   205
1 day, 1:06:56.676354 PROGRESS: 
1 day, 1:06:56.676412 PROGRESS: Protein Summary:
1 day, 1:06:56.677634 PROGRESS: Channel   0:	 0.050 FDR:   356; 0.010 FDR:   247; 0.001 FDR:   201
1 day, 1:06:56.677727 PROGRESS: =========================================================================
1 day, 1:06:56.678897 INFO: Target number of precursors reached.
1 day, 1:06:56.768398 INFO: fragments_df: keeping 3442 of 1331235 [sum(precursor_idx_mask)=7973 sum(mass_error_mask)=1331232 stop_rank=3442
1 day, 1:06:57.109440 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:06:57.213533 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:06:57.316468 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:06:57.414002 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:06:57.798705 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 1:06:57.799284 INFO: Using score_cutoff 39.6466498374939 (fac=0.99, q=1)
1 day, 1:06:57.799687 INFO: Updating optimization_manager: fwhm_rt             : 2.607682228088379 -> 2.6701467037200928
1 day, 1:06:57.799773 INFO: Updating optimization_manager: fwhm_mobility       : 0.00862718652933836 -> 0.008403375744819641
1 day, 1:06:57.799832 INFO: Updating optimization_manager: score_cutoff        : 44.7525684928894 -> 39.6466498374939
1 day, 1:06:57.799895 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:06:57.807893 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:06:57.839313 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:06:57.847963 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:06:57.966210 INFO: === checking if optimization conditions were reached ===
1 day, 1:06:57.966571 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 1:06:57.969040 INFO: Updating optimization_manager: rt_error            : 346.8541187160484 -> 204.48369539112738
1 day, 1:06:57.969151 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 204.4837.
1 day, 1:06:57.969219 INFO: ==============================================
1 day, 1:06:57.969302 INFO: Starting optimization step 3.
1 day, 1:06:57.969364 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 1:06:57.969452 INFO: Using classic extraction backend
1 day, 1:06:57.969673 PROGRESS: Extracting batch of 50061 precursors
1 day, 1:06:57.969748 INFO: === Search parameters used ===
1 day, 1:06:57.969798 INFO: rt_error       : 204.48369539112738
1 day, 1:06:57.969859 INFO: mobility_error : 0.1
1 day, 1:06:57.969906 INFO: num_candidates : 3
1 day, 1:06:57.969946 INFO: ms1_error      : 15.0
1 day, 1:06:57.969985 INFO: ms2_error      : 15.0
1 day, 1:06:57.970024 INFO: fwhm_rt        : 2.6701467037200928
1 day, 1:06:57.970062 INFO: quant_window   : 3
1 day, 1:06:57.970101 INFO: ==============================================
1 day, 1:06:57.987571 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:06:57.987719 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:06:57.987772 INFO: FWHM in RT is 2.67 seconds, sigma is 0.59
1 day, 1:06:57.987794 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.90
1 day, 1:06:57.988620 INFO: Starting candidate selection
1 day, 1:07:28.670601 INFO: Starting candidate scoring
1 day, 1:07:34.545782 INFO: Finished candidate processing
1 day, 1:07:34.545930 INFO: Collecting candidate features
1 day, 1:07:34.784770 WARNING: intensity_correlation has 55 NaNs ( 0.04 % out of 133026)
1 day, 1:07:34.785174 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 133026)
1 day, 1:07:34.792964 INFO: Collecting fragment features
1 day, 1:07:34.878843 INFO: Finished candidate scoring
1 day, 1:07:34.950141 INFO: performing precursor FDR with 47 features
1 day, 1:07:34.950294 INFO: Decoy channel: -1
1 day, 1:07:34.950320 INFO: Competetive: True
1 day, 1:07:35.003650 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:07:35.031518 WARNING: dropped 31 target PSMs due to missing features
1 day, 1:07:35.031684 WARNING: dropped 28 decoy PSMs due to missing features
1 day, 1:07:35.064112 INFO: Using random state 488372 for train-test-split
1 day, 1:07:37.332444 INFO: Test AUC: 0.557
1 day, 1:07:37.332566 INFO: Train AUC: 0.580
1 day, 1:07:37.332612 INFO: AUC difference: 3.99%
1 day, 1:07:37.601355 INFO: Resetting torch num_threads to 80
1 day, 1:07:37.604969 PROGRESS: === Extracted 133026 precursors and 1314732 fragments ===
1 day, 1:07:37.605686 INFO: === FDR correction performed with classifier version 10 ===
1 day, 1:07:37.609917 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:07:37.610049 PROGRESS: Total precursors accumulated: 24,320
1 day, 1:07:37.610111 PROGRESS: Target precursors: 14,823 (60.95%)
1 day, 1:07:37.610161 PROGRESS: Decoy precursors: 9,497 (39.05%)
1 day, 1:07:37.610206 PROGRESS: 
1 day, 1:07:37.610250 PROGRESS: Precursor Summary:
1 day, 1:07:37.611400 PROGRESS: Channel   0:	 0.050 FDR:   389; 0.010 FDR:   294; 0.001 FDR:   240
1 day, 1:07:37.611493 PROGRESS: 
1 day, 1:07:37.611549 PROGRESS: Protein Summary:
1 day, 1:07:37.612766 PROGRESS: Channel   0:	 0.050 FDR:   383; 0.010 FDR:   289; 0.001 FDR:   236
1 day, 1:07:37.612858 PROGRESS: =========================================================================
1 day, 1:07:37.613745 INFO: Target number of precursors reached.
1 day, 1:07:37.702507 INFO: fragments_df: keeping 3876 of 1314732 [sum(precursor_idx_mask)=9155 sum(mass_error_mask)=1314730 stop_rank=3876
1 day, 1:07:37.921012 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:07:38.039693 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:07:38.166908 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:07:38.285678 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:07:38.788652 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 1:07:38.789126 INFO: Using score_cutoff 38.13521817741394 (fac=0.99, q=1)
1 day, 1:07:38.789473 INFO: Updating optimization_manager: fwhm_rt             : 2.6701467037200928 -> 2.652470827102661
1 day, 1:07:38.789562 INFO: Updating optimization_manager: fwhm_mobility       : 0.008403375744819641 -> 0.008087556809186935
1 day, 1:07:38.789619 INFO: Updating optimization_manager: score_cutoff        : 39.6466498374939 -> 38.13521817741394
1 day, 1:07:38.789677 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:07:38.798401 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:07:38.828545 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:07:38.836239 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:07:38.898767 INFO: === checking if optimization conditions were reached ===
1 day, 1:07:38.899042 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 1:07:38.901294 INFO: Updating optimization_manager: rt_error            : 204.48369539112738 -> 176.32798081720387
1 day, 1:07:38.901395 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 176.3280.
1 day, 1:07:38.901461 INFO: ==============================================
1 day, 1:07:38.901542 INFO: Starting optimization step 4.
1 day, 1:07:38.901605 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 1:07:38.901666 INFO: Using classic extraction backend
1 day, 1:07:38.901819 PROGRESS: Extracting batch of 50061 precursors
1 day, 1:07:38.901886 INFO: === Search parameters used ===
1 day, 1:07:38.901935 INFO: rt_error       : 176.32798081720387
1 day, 1:07:38.901977 INFO: mobility_error : 0.1
1 day, 1:07:38.902017 INFO: num_candidates : 3
1 day, 1:07:38.902071 INFO: ms1_error      : 15.0
1 day, 1:07:38.902112 INFO: ms2_error      : 15.0
1 day, 1:07:38.902150 INFO: fwhm_rt        : 2.652470827102661
1 day, 1:07:38.902188 INFO: quant_window   : 3
1 day, 1:07:38.902233 INFO: ==============================================
1 day, 1:07:38.917780 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:07:38.917906 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:07:38.917959 INFO: FWHM in RT is 2.65 seconds, sigma is 0.58
1 day, 1:07:38.917992 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.75
1 day, 1:07:38.926608 INFO: Starting candidate selection
1 day, 1:08:05.985306 INFO: Starting candidate scoring
1 day, 1:08:10.847422 INFO: Finished candidate processing
1 day, 1:08:10.847590 INFO: Collecting candidate features
1 day, 1:08:11.068867 WARNING: intensity_correlation has 45 NaNs ( 0.03 % out of 132637)
1 day, 1:08:11.069218 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 132637)
1 day, 1:08:11.077223 INFO: Collecting fragment features
1 day, 1:08:11.160414 INFO: Finished candidate scoring
1 day, 1:08:11.222384 INFO: performing precursor FDR with 47 features
1 day, 1:08:11.222503 INFO: Decoy channel: -1
1 day, 1:08:11.222527 INFO: Competetive: True
1 day, 1:08:11.264288 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:08:11.288004 WARNING: dropped 25 target PSMs due to missing features
1 day, 1:08:11.288132 WARNING: dropped 21 decoy PSMs due to missing features
1 day, 1:08:11.320646 INFO: Using random state 488372 for train-test-split
1 day, 1:08:13.652418 INFO: Test AUC: 0.563
1 day, 1:08:13.652558 INFO: Train AUC: 0.586
1 day, 1:08:13.652596 INFO: AUC difference: 3.88%
1 day, 1:08:13.920816 INFO: Resetting torch num_threads to 80
1 day, 1:08:13.923955 PROGRESS: === Extracted 132637 precursors and 1305734 fragments ===
1 day, 1:08:13.924567 INFO: === FDR correction performed with classifier version 10 ===
1 day, 1:08:13.928717 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:08:13.928844 PROGRESS: Total precursors accumulated: 24,285
1 day, 1:08:13.928915 PROGRESS: Target precursors: 14,913 (61.41%)
1 day, 1:08:13.928971 PROGRESS: Decoy precursors: 9,372 (38.59%)
1 day, 1:08:13.929019 PROGRESS: 
1 day, 1:08:13.929065 PROGRESS: Precursor Summary:
1 day, 1:08:13.930174 PROGRESS: Channel   0:	 0.050 FDR:   373; 0.010 FDR:   301; 0.001 FDR:   259
1 day, 1:08:13.930266 PROGRESS: 
1 day, 1:08:13.930324 PROGRESS: Protein Summary:
1 day, 1:08:13.931542 PROGRESS: Channel   0:	 0.050 FDR:   368; 0.010 FDR:   297; 0.001 FDR:   255
1 day, 1:08:13.931636 PROGRESS: =========================================================================
1 day, 1:08:13.932455 INFO: Target number of precursors reached.
1 day, 1:08:14.019707 INFO: fragments_df: keeping 3883 of 1305734 [sum(precursor_idx_mask)=9294 sum(mass_error_mask)=1305734 stop_rank=3883
1 day, 1:08:14.306262 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:08:14.426821 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:08:14.551209 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:08:14.673607 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:08:15.176626 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 1:08:15.177098 INFO: Using score_cutoff 39.56603370666504 (fac=0.99, q=1)
1 day, 1:08:15.177488 INFO: Updating optimization_manager: fwhm_rt             : 2.652470827102661 -> 2.7265207767486572
1 day, 1:08:15.177573 INFO: Updating optimization_manager: fwhm_mobility       : 0.008087556809186935 -> 0.00847170501947403
1 day, 1:08:15.177631 INFO: Updating optimization_manager: score_cutoff        : 38.13521817741394 -> 39.56603370666504
1 day, 1:08:15.177698 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:08:15.185092 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:08:15.215105 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:08:15.222621 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:08:15.286416 INFO: === checking if optimization conditions were reached ===
1 day, 1:08:15.287462 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 1:08:15.291783 INFO: Updating optimization_manager: rt_error            : 176.32798081720387 -> 143.59841682065695
1 day, 1:08:15.291894 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 143.5984.
1 day, 1:08:15.291973 INFO: ==============================================
1 day, 1:08:15.292083 INFO: Starting optimization step 5.
1 day, 1:08:15.292156 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 1:08:15.292229 INFO: Using classic extraction backend
1 day, 1:08:15.292460 PROGRESS: Extracting batch of 50061 precursors
1 day, 1:08:15.292536 INFO: === Search parameters used ===
1 day, 1:08:15.292588 INFO: rt_error       : 143.59841682065695
1 day, 1:08:15.292632 INFO: mobility_error : 0.1
1 day, 1:08:15.292672 INFO: num_candidates : 3
1 day, 1:08:15.292713 INFO: ms1_error      : 15.0
1 day, 1:08:15.292751 INFO: ms2_error      : 15.0
1 day, 1:08:15.292788 INFO: fwhm_rt        : 2.7265207767486572
1 day, 1:08:15.292826 INFO: quant_window   : 3
1 day, 1:08:15.292866 INFO: ==============================================
1 day, 1:08:15.306609 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:08:15.306724 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:08:15.306811 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
1 day, 1:08:15.306837 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 1:08:15.315610 INFO: Starting candidate selection
1 day, 1:08:39.515590 INFO: Starting candidate scoring
1 day, 1:08:45.221451 INFO: Finished candidate processing
1 day, 1:08:45.221553 INFO: Collecting candidate features
1 day, 1:08:45.409708 WARNING: intensity_correlation has 48 NaNs ( 0.04 % out of 132453)
1 day, 1:08:45.410060 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 132453)
1 day, 1:08:45.417762 INFO: Collecting fragment features
1 day, 1:08:45.505574 INFO: Finished candidate scoring
1 day, 1:08:45.564214 INFO: performing precursor FDR with 47 features
1 day, 1:08:45.564326 INFO: Decoy channel: -1
1 day, 1:08:45.564350 INFO: Competetive: True
1 day, 1:08:45.608789 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:08:45.630391 WARNING: dropped 31 target PSMs due to missing features
1 day, 1:08:45.630515 WARNING: dropped 17 decoy PSMs due to missing features
1 day, 1:08:45.649637 INFO: Using random state 488372 for train-test-split
1 day, 1:08:47.783438 INFO: Test AUC: 0.554
1 day, 1:08:47.783559 INFO: Train AUC: 0.587
1 day, 1:08:47.783591 INFO: AUC difference: 5.68%
1 day, 1:08:47.783613 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 1:08:48.043774 INFO: Resetting torch num_threads to 80
1 day, 1:08:48.046844 PROGRESS: === Extracted 132453 precursors and 1299449 fragments ===
1 day, 1:08:48.047337 INFO: === FDR correction performed with classifier version 10 ===
1 day, 1:08:48.051161 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:08:48.051296 PROGRESS: Total precursors accumulated: 24,269
1 day, 1:08:48.051357 PROGRESS: Target precursors: 14,812 (61.03%)
1 day, 1:08:48.051407 PROGRESS: Decoy precursors: 9,457 (38.97%)
1 day, 1:08:48.051460 PROGRESS: 
1 day, 1:08:48.051502 PROGRESS: Precursor Summary:
1 day, 1:08:48.052602 PROGRESS: Channel   0:	 0.050 FDR:   345; 0.010 FDR:   277; 0.001 FDR:   246
1 day, 1:08:48.052691 PROGRESS: 
1 day, 1:08:48.052757 PROGRESS: Protein Summary:
1 day, 1:08:48.053956 PROGRESS: Channel   0:	 0.050 FDR:   339; 0.010 FDR:   273; 0.001 FDR:   242
1 day, 1:08:48.054046 PROGRESS: =========================================================================
1 day, 1:08:48.054825 INFO: Target number of precursors reached.
1 day, 1:08:48.141325 INFO: fragments_df: keeping 3699 of 1299449 [sum(precursor_idx_mask)=8718 sum(mass_error_mask)=1299449 stop_rank=3699
1 day, 1:08:48.346352 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:08:48.468588 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:08:48.587684 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:08:48.706290 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:08:49.184522 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 1:08:49.184940 INFO: Using score_cutoff 40.722923693847655 (fac=0.99, q=1)
1 day, 1:08:49.185256 INFO: Updating optimization_manager: fwhm_rt             : 2.7265207767486572 -> 2.6442692279815674
1 day, 1:08:49.185336 INFO: Updating optimization_manager: fwhm_mobility       : 0.00847170501947403 -> 0.008306932635605335
1 day, 1:08:49.185390 INFO: Updating optimization_manager: score_cutoff        : 39.56603370666504 -> 40.722923693847655
1 day, 1:08:49.185447 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:08:49.192909 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:08:49.223037 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:08:49.230397 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:08:49.290393 INFO: === checking if optimization conditions were reached ===
1 day, 1:08:49.290629 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 1:08:49.292702 INFO: Updating optimization_manager: rt_error            : 143.59841682065695 -> 124.10330449821922
1 day, 1:08:49.292812 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 124.1033.
1 day, 1:08:49.292881 INFO: ==============================================
1 day, 1:08:49.292957 INFO: Starting optimization step 6.
1 day, 1:08:49.293018 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 1:08:49.293077 INFO: Using classic extraction backend
1 day, 1:08:49.293211 PROGRESS: Extracting batch of 50061 precursors
1 day, 1:08:49.293280 INFO: === Search parameters used ===
1 day, 1:08:49.293330 INFO: rt_error       : 124.10330449821922
1 day, 1:08:49.293373 INFO: mobility_error : 0.1
1 day, 1:08:49.293415 INFO: num_candidates : 3
1 day, 1:08:49.293458 INFO: ms1_error      : 15.0
1 day, 1:08:49.293497 INFO: ms2_error      : 15.0
1 day, 1:08:49.293536 INFO: fwhm_rt        : 2.6442692279815674
1 day, 1:08:49.293576 INFO: quant_window   : 3
1 day, 1:08:49.293625 INFO: ==============================================
1 day, 1:08:49.306674 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:08:49.306797 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:08:49.306848 INFO: FWHM in RT is 2.64 seconds, sigma is 0.58
1 day, 1:08:49.306871 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.85
1 day, 1:08:49.315451 INFO: Starting candidate selection
1 day, 1:09:09.201682 INFO: Starting candidate scoring
1 day, 1:09:14.584091 INFO: Finished candidate processing
1 day, 1:09:14.584296 INFO: Collecting candidate features
1 day, 1:09:14.821147 WARNING: intensity_correlation has 42 NaNs ( 0.03 % out of 132402)
1 day, 1:09:14.821537 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 132402)
1 day, 1:09:14.829755 INFO: Collecting fragment features
1 day, 1:09:14.921286 INFO: Finished candidate scoring
1 day, 1:09:14.997808 INFO: performing precursor FDR with 47 features
1 day, 1:09:14.997961 INFO: Decoy channel: -1
1 day, 1:09:14.997988 INFO: Competetive: True
1 day, 1:09:15.052670 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:09:15.083110 WARNING: dropped 25 target PSMs due to missing features
1 day, 1:09:15.083276 WARNING: dropped 20 decoy PSMs due to missing features
1 day, 1:09:15.111496 INFO: Using random state 488372 for train-test-split
1 day, 1:09:18.048135 INFO: Test AUC: 0.560
1 day, 1:09:18.048334 INFO: Train AUC: 0.584
1 day, 1:09:18.048380 INFO: AUC difference: 4.21%
1 day, 1:09:18.322507 INFO: Resetting torch num_threads to 80
1 day, 1:09:18.327187 PROGRESS: === Extracted 132402 precursors and 1295274 fragments ===
1 day, 1:09:18.327921 INFO: === FDR correction performed with classifier version 10 ===
1 day, 1:09:18.333317 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:09:18.333483 PROGRESS: Total precursors accumulated: 24,246
1 day, 1:09:18.333555 PROGRESS: Target precursors: 14,813 (61.09%)
1 day, 1:09:18.333611 PROGRESS: Decoy precursors: 9,433 (38.91%)
1 day, 1:09:18.333666 PROGRESS: 
1 day, 1:09:18.333713 PROGRESS: Precursor Summary:
1 day, 1:09:18.334932 PROGRESS: Channel   0:	 0.050 FDR:   394; 0.010 FDR:   316; 0.001 FDR:   234
1 day, 1:09:18.335027 PROGRESS: 
1 day, 1:09:18.335085 PROGRESS: Protein Summary:
1 day, 1:09:18.336370 PROGRESS: Channel   0:	 0.050 FDR:   389; 0.010 FDR:   311; 0.001 FDR:   230
1 day, 1:09:18.336461 PROGRESS: =========================================================================
1 day, 1:09:18.337658 INFO: Target number of precursors reached.
1 day, 1:09:18.426965 INFO: fragments_df: keeping 3980 of 1295274 [sum(precursor_idx_mask)=9807 sum(mass_error_mask)=1295273 stop_rank=3980
1 day, 1:09:19.191012 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:09:20.814944 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:09:20.924700 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:09:21.027550 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:09:21.514547 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 1:09:21.514987 INFO: Using score_cutoff 40.64998049354553 (fac=0.99, q=1)
1 day, 1:09:21.515295 INFO: Updating optimization_manager: fwhm_rt             : 2.6442692279815674 -> 2.725472927093506
1 day, 1:09:21.515377 INFO: Updating optimization_manager: fwhm_mobility       : 0.008306932635605335 -> 0.008275044150650501
1 day, 1:09:21.515444 INFO: Updating optimization_manager: score_cutoff        : 40.722923693847655 -> 40.64998049354553
1 day, 1:09:21.515500 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:09:21.522742 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:09:21.552641 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:09:21.560189 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:09:21.624858 INFO: === checking if optimization conditions were reached ===
1 day, 1:09:21.625338 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 1:09:21.627901 INFO: Updating optimization_manager: rt_error            : 124.10330449821922 -> 123.82769342485916
1 day, 1:09:21.628025 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 123.8277.
1 day, 1:09:21.628108 INFO: ==============================================
1 day, 1:09:21.628195 INFO: Starting optimization step 7.
1 day, 1:09:21.628266 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 1:09:21.628336 INFO: Using classic extraction backend
1 day, 1:09:21.628508 PROGRESS: Extracting batch of 50061 precursors
1 day, 1:09:21.628603 INFO: === Search parameters used ===
1 day, 1:09:21.628678 INFO: rt_error       : 123.82769342485916
1 day, 1:09:21.628750 INFO: mobility_error : 0.1
1 day, 1:09:21.628817 INFO: num_candidates : 3
1 day, 1:09:21.628882 INFO: ms1_error      : 15.0
1 day, 1:09:21.628947 INFO: ms2_error      : 15.0
1 day, 1:09:21.629022 INFO: fwhm_rt        : 2.725472927093506
1 day, 1:09:21.629090 INFO: quant_window   : 3
1 day, 1:09:21.629154 INFO: ==============================================
1 day, 1:09:21.643810 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:09:21.643931 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:09:21.643986 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
1 day, 1:09:21.644017 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1 day, 1:09:21.659873 INFO: Starting candidate selection
1 day, 1:09:41.318507 INFO: Starting candidate scoring
1 day, 1:09:47.586597 INFO: Finished candidate processing
1 day, 1:09:47.587834 INFO: Collecting candidate features
1 day, 1:09:47.815105 WARNING: intensity_correlation has 51 NaNs ( 0.04 % out of 132270)
1 day, 1:09:47.815531 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 132270)
1 day, 1:09:47.823471 INFO: Collecting fragment features
1 day, 1:09:47.915651 INFO: Finished candidate scoring
1 day, 1:09:47.993090 INFO: performing precursor FDR with 47 features
1 day, 1:09:47.993272 INFO: Decoy channel: -1
1 day, 1:09:47.993297 INFO: Competetive: True
1 day, 1:09:48.051264 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:09:48.080963 WARNING: dropped 24 target PSMs due to missing features
1 day, 1:09:48.081145 WARNING: dropped 28 decoy PSMs due to missing features
1 day, 1:09:48.107899 INFO: Using random state 488372 for train-test-split
1 day, 1:09:50.599847 INFO: Test AUC: 0.558
1 day, 1:09:50.600033 INFO: Train AUC: 0.584
1 day, 1:09:50.600072 INFO: AUC difference: 4.54%
1 day, 1:09:50.875083 INFO: Resetting torch num_threads to 80
1 day, 1:09:50.879512 PROGRESS: === Extracted 132270 precursors and 1293761 fragments ===
1 day, 1:09:50.880200 INFO: === FDR correction performed with classifier version 10 ===
1 day, 1:09:50.884953 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:09:50.885109 PROGRESS: Total precursors accumulated: 24,239
1 day, 1:09:50.885173 PROGRESS: Target precursors: 14,810 (61.10%)
1 day, 1:09:50.885226 PROGRESS: Decoy precursors: 9,429 (38.90%)
1 day, 1:09:50.885274 PROGRESS: 
1 day, 1:09:50.885322 PROGRESS: Precursor Summary:
1 day, 1:09:50.886498 PROGRESS: Channel   0:	 0.050 FDR:   362; 0.010 FDR:   267; 0.001 FDR:   256
1 day, 1:09:50.886595 PROGRESS: 
1 day, 1:09:50.886654 PROGRESS: Protein Summary:
1 day, 1:09:50.887911 PROGRESS: Channel   0:	 0.050 FDR:   354; 0.010 FDR:   263; 0.001 FDR:   252
1 day, 1:09:50.888006 PROGRESS: =========================================================================
1 day, 1:09:50.888966 INFO: Target number of precursors reached.
1 day, 1:09:50.974751 INFO: fragments_df: keeping 3526 of 1293761 [sum(precursor_idx_mask)=8376 sum(mass_error_mask)=1293761 stop_rank=3526
1 day, 1:09:51.269984 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:09:51.369771 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:09:51.469725 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:09:51.568093 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:09:51.972016 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 1:09:51.972552 INFO: Using score_cutoff 40.685185910797124 (fac=0.99, q=1)
1 day, 1:09:51.972960 INFO: Updating optimization_manager: fwhm_rt             : 2.725472927093506 -> 2.7183258533477783
1 day, 1:09:51.973051 INFO: Updating optimization_manager: fwhm_mobility       : 0.008275044150650501 -> 0.008537402376532555
1 day, 1:09:51.973107 INFO: Updating optimization_manager: score_cutoff        : 40.64998049354553 -> 40.685185910797124
1 day, 1:09:51.973172 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:09:51.981090 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:09:52.011500 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:09:52.019169 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:09:52.082956 INFO: === checking if optimization conditions were reached ===
1 day, 1:09:52.083353 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1 day, 1:09:52.085175 INFO: Updating optimization_manager: rt_error            : 123.82769342485916 -> 124.10330449821922
1 day, 1:09:52.085333 INFO: Updating optimization_manager: classifier_version  : 10 -> 17
1 day, 1:09:52.085448 INFO: Updating optimization_manager: score_cutoff        : 40.685185910797124 -> 40.64998049354553
1 day, 1:09:52.085552 INFO: Updating optimization_manager: fwhm_rt             : 2.7183258533477783 -> 2.725472927093506
1 day, 1:09:52.085660 INFO: Updating optimization_manager: fwhm_mobility       : 0.008537402376532555 -> 0.008275044150650501
1 day, 1:09:52.085796 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 124.1033 found after 8 searches.
1 day, 1:09:52.085880 INFO: ==============================================
1 day, 1:09:52.085979 PROGRESS: Optimization finished for rt_error.
1 day, 1:09:52.242823 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:09:52.251074 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:09:52.281239 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:09:52.289041 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:09:52.384439 INFO: Starting optimization step 0.
1 day, 1:09:52.384752 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 1:09:52.384860 INFO: Using classic extraction backend
1 day, 1:09:52.385113 PROGRESS: Extracting batch of 50061 precursors
1 day, 1:09:52.385222 INFO: === Search parameters used ===
1 day, 1:09:52.385293 INFO: rt_error       : 124.10330449821922
1 day, 1:09:52.385367 INFO: mobility_error : 0.1
1 day, 1:09:52.385422 INFO: num_candidates : 3
1 day, 1:09:52.385476 INFO: ms1_error      : 15.0
1 day, 1:09:52.385526 INFO: ms2_error      : 15.0
1 day, 1:09:52.385578 INFO: fwhm_rt        : 2.725472927093506
1 day, 1:09:52.385628 INFO: quant_window   : 3
1 day, 1:09:52.385677 INFO: ==============================================
1 day, 1:09:52.411467 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:09:52.411652 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:09:52.411733 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
1 day, 1:09:52.411765 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1 day, 1:09:52.420690 INFO: Starting candidate selection
1 day, 1:10:12.609611 INFO: Starting candidate scoring
1 day, 1:10:17.889008 INFO: Finished candidate processing
1 day, 1:10:17.890065 INFO: Collecting candidate features
1 day, 1:10:18.378307 WARNING: intensity_correlation has 41 NaNs ( 0.03 % out of 132310)
1 day, 1:10:18.387560 INFO: Collecting fragment features
1 day, 1:10:18.465969 INFO: Finished candidate scoring
1 day, 1:10:18.678463 INFO: performing precursor FDR with 47 features
1 day, 1:10:18.678648 INFO: Decoy channel: -1
1 day, 1:10:18.678677 INFO: Competetive: True
1 day, 1:10:18.734154 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:10:18.766000 WARNING: dropped 22 target PSMs due to missing features
1 day, 1:10:18.766183 WARNING: dropped 19 decoy PSMs due to missing features
1 day, 1:10:18.793270 INFO: Using random state 853619 for train-test-split
1 day, 1:10:21.160026 INFO: Test AUC: 0.559
1 day, 1:10:21.160185 INFO: Train AUC: 0.603
1 day, 1:10:21.160219 INFO: AUC difference: 7.27%
1 day, 1:10:21.160244 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 1:10:21.424236 INFO: Resetting torch num_threads to 80
1 day, 1:10:21.428475 PROGRESS: === Extracted 132310 precursors and 1294697 fragments ===
1 day, 1:10:21.429106 INFO: === FDR correction performed with classifier version 17 ===
1 day, 1:10:21.433991 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:10:21.434132 PROGRESS: Total precursors accumulated: 24,225
1 day, 1:10:21.434197 PROGRESS: Target precursors: 15,098 (62.32%)
1 day, 1:10:21.434250 PROGRESS: Decoy precursors: 9,127 (37.68%)
1 day, 1:10:21.434295 PROGRESS: 
1 day, 1:10:21.434338 PROGRESS: Precursor Summary:
1 day, 1:10:21.435589 PROGRESS: Channel   0:	 0.050 FDR:   441; 0.010 FDR:   313; 0.001 FDR:   183
1 day, 1:10:21.435702 PROGRESS: 
1 day, 1:10:21.435760 PROGRESS: Protein Summary:
1 day, 1:10:21.437043 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   308; 0.001 FDR:   179
1 day, 1:10:21.437132 PROGRESS: =========================================================================
1 day, 1:10:21.438359 INFO: Target number of precursors reached.
1 day, 1:10:21.526286 INFO: fragments_df: keeping 3949 of 1294697 [sum(precursor_idx_mask)=9717 sum(mass_error_mask)=1294695 stop_rank=3949
1 day, 1:10:21.742118 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:10:21.869561 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:10:21.993617 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:10:22.115241 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:10:22.638902 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 1:10:22.639418 INFO: Using score_cutoff 39.03163748931885 (fac=0.99, q=1)
1 day, 1:10:22.639769 INFO: Updating optimization_manager: fwhm_rt             : 2.725472927093506 -> 2.758636236190796
1 day, 1:10:22.639847 INFO: Updating optimization_manager: fwhm_mobility       : 0.008275044150650501 -> 0.008466213010251522
1 day, 1:10:22.639901 INFO: Updating optimization_manager: score_cutoff        : 40.64998049354553 -> 39.03163748931885
1 day, 1:10:22.639960 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:10:22.647336 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:10:22.677907 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:10:22.685503 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:10:22.748184 INFO: === checking if optimization conditions were reached ===
1 day, 1:10:22.748526 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 1:10:22.750587 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07738166472467163
1 day, 1:10:22.750694 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0774.
1 day, 1:10:22.750761 INFO: ==============================================
1 day, 1:10:22.750860 INFO: Starting optimization step 1.
1 day, 1:10:22.750922 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 1:10:22.751012 INFO: Using classic extraction backend
1 day, 1:10:22.751200 PROGRESS: Extracting batch of 50061 precursors
1 day, 1:10:22.751274 INFO: === Search parameters used ===
1 day, 1:10:22.751321 INFO: rt_error       : 124.10330449821922
1 day, 1:10:22.751364 INFO: mobility_error : 0.07738166472467163
1 day, 1:10:22.751421 INFO: num_candidates : 3
1 day, 1:10:22.751463 INFO: ms1_error      : 15.0
1 day, 1:10:22.751503 INFO: ms2_error      : 15.0
1 day, 1:10:22.751556 INFO: fwhm_rt        : 2.758636236190796
1 day, 1:10:22.751598 INFO: quant_window   : 3
1 day, 1:10:22.751637 INFO: ==============================================
1 day, 1:10:22.768495 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:10:22.768627 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:10:22.768685 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 1:10:22.768709 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 1:10:22.777631 INFO: Starting candidate selection
1 day, 1:10:39.480646 INFO: Starting candidate scoring
1 day, 1:10:46.200161 INFO: Finished candidate processing
1 day, 1:10:46.200275 INFO: Collecting candidate features
1 day, 1:10:46.494366 WARNING: intensity_correlation has 58 NaNs ( 0.04 % out of 129972)
1 day, 1:10:46.495125 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 129972)
1 day, 1:10:46.512475 INFO: Collecting fragment features
1 day, 1:10:46.615431 INFO: Finished candidate scoring
1 day, 1:10:46.767195 INFO: performing precursor FDR with 47 features
1 day, 1:10:46.767348 INFO: Decoy channel: -1
1 day, 1:10:46.767378 INFO: Competetive: True
1 day, 1:10:46.828567 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:10:46.856155 WARNING: dropped 29 target PSMs due to missing features
1 day, 1:10:46.856294 WARNING: dropped 29 decoy PSMs due to missing features
1 day, 1:10:46.884946 INFO: Using random state 853619 for train-test-split
1 day, 1:10:49.411451 INFO: Test AUC: 0.562
1 day, 1:10:49.411604 INFO: Train AUC: 0.586
1 day, 1:10:49.411635 INFO: AUC difference: 4.07%
1 day, 1:10:49.670679 INFO: Resetting torch num_threads to 80
1 day, 1:10:49.674640 PROGRESS: === Extracted 129972 precursors and 1265342 fragments ===
1 day, 1:10:49.675181 INFO: === FDR correction performed with classifier version 17 ===
1 day, 1:10:49.679499 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:10:49.679658 PROGRESS: Total precursors accumulated: 23,848
1 day, 1:10:49.679725 PROGRESS: Target precursors: 14,502 (60.81%)
1 day, 1:10:49.679780 PROGRESS: Decoy precursors: 9,346 (39.19%)
1 day, 1:10:49.679826 PROGRESS: 
1 day, 1:10:49.679871 PROGRESS: Precursor Summary:
1 day, 1:10:49.681029 PROGRESS: Channel   0:	 0.050 FDR:   406; 0.010 FDR:   315; 0.001 FDR:   277
1 day, 1:10:49.681121 PROGRESS: 
1 day, 1:10:49.681178 PROGRESS: Protein Summary:
1 day, 1:10:49.682420 PROGRESS: Channel   0:	 0.050 FDR:   398; 0.010 FDR:   310; 0.001 FDR:   272
1 day, 1:10:49.682522 PROGRESS: =========================================================================
1 day, 1:10:49.683355 INFO: Target number of precursors reached.
1 day, 1:10:49.769272 INFO: fragments_df: keeping 3878 of 1265342 [sum(precursor_idx_mask)=9711 sum(mass_error_mask)=1265337 stop_rank=3878
1 day, 1:10:49.911951 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:10:50.034631 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:10:50.158357 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:10:50.267914 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:10:50.716955 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 1:10:50.717476 INFO: Using score_cutoff 38.881400804901126 (fac=0.99, q=1)
1 day, 1:10:50.717805 INFO: Updating optimization_manager: fwhm_rt             : 2.758636236190796 -> 2.8380579948425293
1 day, 1:10:50.717887 INFO: Updating optimization_manager: fwhm_mobility       : 0.008466213010251522 -> 0.008388558402657509
1 day, 1:10:50.717942 INFO: Updating optimization_manager: score_cutoff        : 39.03163748931885 -> 38.881400804901126
1 day, 1:10:50.717998 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:10:50.725183 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:10:50.755673 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:10:50.762978 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:10:50.826051 INFO: === checking if optimization conditions were reached ===
1 day, 1:10:50.826369 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 1:10:50.828474 INFO: Updating optimization_manager: mobility_error      : 0.07738166472467163 -> 0.06371041984712059
1 day, 1:10:50.828582 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0637.
1 day, 1:10:50.828652 INFO: ==============================================
1 day, 1:10:50.828741 INFO: Starting optimization step 2.
1 day, 1:10:50.828804 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 1:10:50.828867 INFO: Using classic extraction backend
1 day, 1:10:50.828988 PROGRESS: Extracting batch of 50061 precursors
1 day, 1:10:50.829055 INFO: === Search parameters used ===
1 day, 1:10:50.829103 INFO: rt_error       : 124.10330449821922
1 day, 1:10:50.829147 INFO: mobility_error : 0.06371041984712059
1 day, 1:10:50.829191 INFO: num_candidates : 3
1 day, 1:10:50.829233 INFO: ms1_error      : 15.0
1 day, 1:10:50.829273 INFO: ms2_error      : 15.0
1 day, 1:10:50.829315 INFO: fwhm_rt        : 2.8380579948425293
1 day, 1:10:50.829355 INFO: quant_window   : 3
1 day, 1:10:50.829394 INFO: ==============================================
1 day, 1:10:50.848462 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:10:50.848612 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:10:50.848660 INFO: FWHM in RT is 2.84 seconds, sigma is 0.62
1 day, 1:10:50.848684 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.89
1 day, 1:10:50.857449 INFO: Starting candidate selection
1 day, 1:11:04.883223 INFO: Starting candidate scoring
1 day, 1:11:10.790827 INFO: Finished candidate processing
1 day, 1:11:10.791013 INFO: Collecting candidate features
1 day, 1:11:11.005305 WARNING: intensity_correlation has 67 NaNs ( 0.05 % out of 128033)
1 day, 1:11:11.005760 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 128033)
1 day, 1:11:11.016702 INFO: Collecting fragment features
1 day, 1:11:11.097863 INFO: Finished candidate scoring
1 day, 1:11:11.164109 INFO: performing precursor FDR with 47 features
1 day, 1:11:11.164237 INFO: Decoy channel: -1
1 day, 1:11:11.164269 INFO: Competetive: True
1 day, 1:11:11.213700 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 1:11:11.239872 WARNING: dropped 40 target PSMs due to missing features
1 day, 1:11:11.240010 WARNING: dropped 29 decoy PSMs due to missing features
1 day, 1:11:11.266805 INFO: Using random state 853619 for train-test-split
1 day, 1:11:13.777073 INFO: Test AUC: 0.558
1 day, 1:11:13.777226 INFO: Train AUC: 0.589
1 day, 1:11:13.777258 INFO: AUC difference: 5.19%
1 day, 1:11:13.777282 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 1:11:14.040072 INFO: Resetting torch num_threads to 80
1 day, 1:11:14.043962 PROGRESS: === Extracted 128033 precursors and 1236897 fragments ===
1 day, 1:11:14.044539 INFO: === FDR correction performed with classifier version 17 ===
1 day, 1:11:14.048978 PROGRESS: ============================= Precursor FDR =============================
1 day, 1:11:14.049133 PROGRESS: Total precursors accumulated: 23,550
1 day, 1:11:14.049198 PROGRESS: Target precursors: 14,388 (61.10%)
1 day, 1:11:14.049250 PROGRESS: Decoy precursors: 9,162 (38.90%)
1 day, 1:11:14.049301 PROGRESS: 
1 day, 1:11:14.049345 PROGRESS: Precursor Summary:
1 day, 1:11:14.050505 PROGRESS: Channel   0:	 0.050 FDR:   392; 0.010 FDR:   245; 0.001 FDR:   192
1 day, 1:11:14.050604 PROGRESS: 
1 day, 1:11:14.050660 PROGRESS: Protein Summary:
1 day, 1:11:14.051898 PROGRESS: Channel   0:	 0.050 FDR:   385; 0.010 FDR:   240; 0.001 FDR:   188
1 day, 1:11:14.051996 PROGRESS: =========================================================================
1 day, 1:11:14.052761 INFO: Target number of precursors reached.
1 day, 1:11:14.136051 INFO: fragments_df: keeping 3221 of 1236897 [sum(precursor_idx_mask)=7595 sum(mass_error_mask)=1236894 stop_rank=3221
1 day, 1:11:14.351650 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:11:14.470468 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:11:14.587900 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:11:14.707672 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:11:15.129825 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 1:11:15.130346 INFO: Using score_cutoff 39.44400596466064 (fac=0.99, q=1)
1 day, 1:11:15.130671 INFO: Updating optimization_manager: fwhm_rt             : 2.8380579948425293 -> 2.7765839099884033
1 day, 1:11:15.130754 INFO: Updating optimization_manager: fwhm_mobility       : 0.008388558402657509 -> 0.00847170501947403
1 day, 1:11:15.130821 INFO: Updating optimization_manager: score_cutoff        : 38.881400804901126 -> 39.44400596466064
1 day, 1:11:15.130878 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:11:15.138742 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:11:15.169523 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:11:15.177269 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:11:15.242464 INFO: === checking if optimization conditions were reached ===
1 day, 1:11:15.242774 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 1:11:15.243852 INFO: Updating optimization_manager: mobility_error      : 0.06371041984712059 -> 0.07738166472467163
1 day, 1:11:15.243976 INFO: Updating optimization_manager: classifier_version  : 17 -> 20
1 day, 1:11:15.244071 INFO: Updating optimization_manager: score_cutoff        : 39.44400596466064 -> 38.881400804901126
1 day, 1:11:15.244158 INFO: Updating optimization_manager: fwhm_rt             : 2.7765839099884033 -> 2.8380579948425293
1 day, 1:11:15.244244 INFO: Updating optimization_manager: fwhm_mobility       : 0.00847170501947403 -> 0.008388558402657509
1 day, 1:11:15.244350 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0774 found after 3 searches.
1 day, 1:11:15.244417 INFO: ==============================================
1 day, 1:11:15.244489 PROGRESS: Optimization finished for mobility_error.
1 day, 1:11:15.383614 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:11:15.391935 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:11:15.422757 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:11:15.430663 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:11:15.519617 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 1:11:15.519869 PROGRESS: ==============================================
1 day, 1:11:15.519954 PROGRESS: ms2_error      : 15.0000
1 day, 1:11:15.520037 PROGRESS: ms1_error      : 15.0000
1 day, 1:11:15.520099 PROGRESS: rt_error       : 124.1033
1 day, 1:11:15.520150 PROGRESS: mobility_error : 0.0774
1 day, 1:11:15.520194 PROGRESS: ==============================================
1 day, 1:11:15.522532 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 1:11:17.172817 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 1:11:24.799742 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 1:11:26.533997 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 1:11:42.830696 INFO: Using classic extraction backend
1 day, 1:11:42.831675 PROGRESS: Extracting batch of 12073114 precursors
1 day, 1:11:42.832061 INFO: === Search parameters used ===
1 day, 1:11:42.832134 INFO: rt_error       : 124.10330449821922
1 day, 1:11:42.832192 INFO: mobility_error : 0.07738166472467163
1 day, 1:11:42.832243 INFO: num_candidates : 3
1 day, 1:11:42.832287 INFO: ms1_error      : 15.0
1 day, 1:11:42.832333 INFO: ms2_error      : 15.0
1 day, 1:11:42.832375 INFO: fwhm_rt        : 2.8380579948425293
1 day, 1:11:42.832416 INFO: quant_window   : 3
1 day, 1:11:42.832458 INFO: ==============================================
1 day, 1:11:46.082175 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 1:11:46.082333 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 1:11:46.082388 INFO: FWHM in RT is 2.84 seconds, sigma is 0.62
1 day, 1:11:46.082422 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.89
1 day, 1:11:46.083526 INFO: Starting candidate selection
1 day, 2:09:02.700133 INFO: Removed 17401390 precursors with score below cutoff 38.881400804901126
1 day, 2:09:06.681990 INFO: Starting candidate scoring
1 day, 2:19:54.049089 INFO: Finished candidate processing
1 day, 2:19:54.051457 INFO: Collecting candidate features
1 day, 2:20:19.923415 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 15853552)
1 day, 2:20:20.463525 INFO: Collecting fragment features
1 day, 2:20:32.079593 INFO: Finished candidate scoring
1 day, 2:20:49.753567 INFO: === Performing FDR correction with classifier version 20 ===
1 day, 2:20:49.758346 INFO: performing precursor FDR with 47 features
1 day, 2:20:49.758399 INFO: Decoy channel: -1
1 day, 2:20:49.758424 INFO: Competetive: True
1 day, 2:20:53.592029 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 2:20:56.015938 WARNING: dropped 3 target PSMs due to missing features
1 day, 2:20:56.016073 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 2:21:03.119164 INFO: Using random state 713905 for train-test-split
1 day, 2:25:57.712790 INFO: Test AUC: 0.566
1 day, 2:25:57.713012 INFO: Train AUC: 0.567
1 day, 2:25:57.713051 INFO: AUC difference: 0.10%
1 day, 2:26:01.464618 INFO: Resetting torch num_threads to 80
1 day, 2:26:01.744817 INFO: Removing fragments below FDR threshold
1 day, 2:26:03.298314 PROGRESS: ============================= Precursor FDR =============================
1 day, 2:26:03.298564 PROGRESS: Total precursors accumulated: 70,967
1 day, 2:26:03.298644 PROGRESS: Target precursors: 70,265 (99.01%)
1 day, 2:26:03.298711 PROGRESS: Decoy precursors: 702 (0.99%)
1 day, 2:26:03.298758 PROGRESS: 
1 day, 2:26:03.298822 PROGRESS: Precursor Summary:
1 day, 2:26:03.324503 PROGRESS: Channel   0:	 0.050 FDR: 70,265; 0.010 FDR: 70,265; 0.001 FDR: 48,229
1 day, 2:26:03.324748 PROGRESS: 
1 day, 2:26:03.324811 PROGRESS: Protein Summary:
1 day, 2:26:03.356203 PROGRESS: Channel   0:	 0.050 FDR: 11,189; 0.010 FDR: 11,189; 0.001 FDR: 8,717
1 day, 2:26:03.356431 PROGRESS: =========================================================================
1 day, 2:26:03.409819 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/psm.parquet
1 day, 2:26:03.767773 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/frag.parquet
1 day, 2:26:04.055133 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 2:26:04.654183 PROGRESS: 
1 day, 2:26:04.654322 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark/quant
1 day, 2:26:04.654429 INFO: Initializing TimingManager
1 day, 2:26:04.655020 INFO: Initializing RawFileManager
1 day, 2:26:04.655157 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 2:26:04.655221 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 2:26:04.655267 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 2:26:04.981654 INFO: Reading 39,128 frames with 2,766,418,119 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 2:26:14.885046 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d...
1 day, 2:26:14.886339 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 2:26:14.889179 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 2:26:14.889455 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 2:26:14.889835 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 2:26:14.891567 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 2:26:14.906427 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 2:26:14.906660 INFO: Indexing quadrupole dimension
1 day, 2:26:15.380211 INFO: Transposing detector events
1 day, 2:26:24.881777 INFO: Finished transposing data
1 day, 2:26:24.911053 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 2:26:24.911719 INFO: RT (min)            : 0.0 - 70.0
1 day, 2:26:24.911785 INFO: RT duration (sec)   : 4199.9
1 day, 2:26:24.911823 INFO: RT duration (min)   : 70.0
1 day, 2:26:24.911856 INFO: Cycle len (scans)   : 9
1 day, 2:26:24.911885 INFO: Cycle len (sec)     : 0.97
1 day, 2:26:24.911915 INFO: Number of cycles    : 4347
1 day, 2:26:24.911946 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 2:26:24.911985 INFO: Creating DIA data object took: 20.256864309310913
1 day, 2:26:26.527774 INFO: Initializing CalibrationManager
1 day, 2:26:26.528036 INFO: Setting up calibration estimators ..
1 day, 2:26:26.528093 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 2:26:26.528165 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1 day, 2:26:26.528236 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 2:26:26.528293 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1 day, 2:26:26.528361 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
1 day, 2:26:26.528423 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
1 day, 2:26:26.528474 INFO: Done setting up calibration estimators.
1 day, 2:26:26.528578 INFO: Initializing OptimizationManager
1 day, 2:26:26.528688 INFO: initial parameter: ms1_error = 30
1 day, 2:26:26.528738 INFO: initial parameter: ms2_error = 30
1 day, 2:26:26.528786 INFO: initial parameter: rt_error = 2099.9331315
1 day, 2:26:26.528828 INFO: initial parameter: mobility_error = 0.1
1 day, 2:26:26.528870 INFO: initial parameter: num_candidates = 1
1 day, 2:26:26.528911 INFO: initial parameter: fwhm_rt = 5
1 day, 2:26:26.528952 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 2:26:26.528995 INFO: initial parameter: score_cutoff = 0
1 day, 2:26:26.529035 INFO: initial parameter: classifier_version = -1
1 day, 2:26:26.529102 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 2:26:26.529378 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 2:26:26.529413 INFO: Initializing FDRManager
1 day, 2:26:26.529450 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 2:26:27.705435 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
1 day, 2:26:28.427888 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 2:26:28.428281 INFO: Updating optimization_manager: rt_error            : 2099.9331315 -> 2099.9331315
1 day, 2:26:28.428383 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 2:26:28.428554 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 2:26:28.428651 PROGRESS: Starting initial search for precursors.
1 day, 2:26:28.428738 INFO: Starting optimization step 0.
1 day, 2:26:28.428801 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 2:26:28.429238 INFO: Using classic extraction backend
1 day, 2:26:28.429452 PROGRESS: Extracting batch of 390 precursors
1 day, 2:26:28.429531 INFO: === Search parameters used ===
1 day, 2:26:28.429583 INFO: rt_error       : 2099.9331315
1 day, 2:26:28.429627 INFO: mobility_error : 0.1
1 day, 2:26:28.429674 INFO: num_candidates : 1
1 day, 2:26:28.429715 INFO: ms1_error      : 30
1 day, 2:26:28.429758 INFO: ms2_error      : 30
1 day, 2:26:28.429798 INFO: fwhm_rt        : 5
1 day, 2:26:28.429838 INFO: quant_window   : 3
1 day, 2:26:28.429877 INFO: ==============================================
1 day, 2:26:28.430710 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 2:26:28.430755 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 2:26:28.430802 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 2:26:28.430825 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 2:26:28.431783 INFO: Starting candidate selection
1 day, 2:26:32.247674 INFO: Starting candidate scoring
1 day, 2:26:32.315274 INFO: Finished candidate processing
1 day, 2:26:32.315371 INFO: Collecting candidate features
1 day, 2:26:32.324491 INFO: Collecting fragment features
1 day, 2:26:32.326751 INFO: Finished candidate scoring
1 day, 2:26:32.327593 INFO: performing precursor FDR with 47 features
1 day, 2:26:32.327637 INFO: Decoy channel: -1
1 day, 2:26:32.327662 INFO: Competetive: True
1 day, 2:26:32.328748 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 2:26:32.331385 INFO: Using random state 374675 for train-test-split
1 day, 2:26:32.338748 INFO: Test AUC: 0.504
1 day, 2:26:32.338831 INFO: Train AUC: 0.502
1 day, 2:26:32.338862 INFO: AUC difference: 0.50%
1 day, 2:26:32.544559 INFO: Resetting torch num_threads to 80
1 day, 2:26:32.544984 PROGRESS: === Extracted 364 precursors and 3938 fragments ===
1 day, 2:26:32.545370 INFO: === FDR correction performed with classifier version -1 ===
1 day, 2:26:32.545873 PROGRESS: ============================= Precursor FDR =============================
1 day, 2:26:32.545960 PROGRESS: Total precursors accumulated: 187
1 day, 2:26:32.546020 PROGRESS: Target precursors: 113 (60.43%)
1 day, 2:26:32.546068 PROGRESS: Decoy precursors: 74 (39.57%)
1 day, 2:26:32.546114 PROGRESS: 
1 day, 2:26:32.546156 PROGRESS: Precursor Summary:
1 day, 2:26:32.546994 PROGRESS: Channel   0:	 0.050 FDR:    23; 0.010 FDR:    23; 0.001 FDR:    23
1 day, 2:26:32.547085 PROGRESS: 
1 day, 2:26:32.547148 PROGRESS: Protein Summary:
1 day, 2:26:32.548067 PROGRESS: Channel   0:	 0.050 FDR:    23; 0.010 FDR:    23; 0.001 FDR:    23
1 day, 2:26:32.548155 PROGRESS: =========================================================================
1 day, 2:26:32.548267 INFO: Target number of precursors not reached yet.
1 day, 2:26:32.613151 INFO: Starting optimization step 1.
1 day, 2:26:32.613357 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 2:26:32.613433 INFO: Using classic extraction backend
1 day, 2:26:32.613549 PROGRESS: Extracting batch of 783 precursors
1 day, 2:26:32.613623 INFO: === Search parameters used ===
1 day, 2:26:32.613672 INFO: rt_error       : 2099.9331315
1 day, 2:26:32.613716 INFO: mobility_error : 0.1
1 day, 2:26:32.613762 INFO: num_candidates : 1
1 day, 2:26:32.613803 INFO: ms1_error      : 30
1 day, 2:26:32.613844 INFO: ms2_error      : 30
1 day, 2:26:32.613884 INFO: fwhm_rt        : 5
1 day, 2:26:32.613931 INFO: quant_window   : 3
1 day, 2:26:32.613971 INFO: ==============================================
1 day, 2:26:32.614604 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 2:26:32.614650 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 2:26:32.614681 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 2:26:32.614703 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 2:26:32.615438 INFO: Starting candidate selection
1 day, 2:26:38.591032 INFO: Starting candidate scoring
1 day, 2:26:38.711747 INFO: Finished candidate processing
1 day, 2:26:38.711884 INFO: Collecting candidate features
1 day, 2:26:38.721711 INFO: Collecting fragment features
1 day, 2:26:38.724225 INFO: Finished candidate scoring
1 day, 2:26:38.726454 INFO: performing precursor FDR with 47 features
1 day, 2:26:38.726503 INFO: Decoy channel: -1
1 day, 2:26:38.726530 INFO: Competetive: True
1 day, 2:26:38.729418 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 2:26:38.731206 INFO: Using random state 740776 for train-test-split
1 day, 2:26:38.739418 INFO: Test AUC: 0.526
1 day, 2:26:38.739484 INFO: Train AUC: 0.508
1 day, 2:26:38.739513 INFO: AUC difference: 3.40%
1 day, 2:26:38.952894 INFO: Resetting torch num_threads to 80
1 day, 2:26:38.954364 PROGRESS: === Extracted 1114 precursors and 12160 fragments ===
1 day, 2:26:38.954848 INFO: === FDR correction performed with classifier version -1 ===
1 day, 2:26:38.955450 PROGRESS: ============================= Precursor FDR =============================
1 day, 2:26:38.955540 PROGRESS: Total precursors accumulated: 574
1 day, 2:26:38.955600 PROGRESS: Target precursors: 349 (60.80%)
1 day, 2:26:38.955656 PROGRESS: Decoy precursors: 225 (39.20%)
1 day, 2:26:38.955704 PROGRESS: 
1 day, 2:26:38.955748 PROGRESS: Precursor Summary:
1 day, 2:26:38.956626 PROGRESS: Channel   0:	 0.050 FDR:    78; 0.010 FDR:    78; 0.001 FDR:    78
1 day, 2:26:38.956714 PROGRESS: 
1 day, 2:26:38.956768 PROGRESS: Protein Summary:
1 day, 2:26:38.957735 PROGRESS: Channel   0:	 0.050 FDR:    78; 0.010 FDR:    78; 0.001 FDR:    78
1 day, 2:26:38.957823 PROGRESS: =========================================================================
1 day, 2:26:38.957989 INFO: Target number of precursors not reached yet.
1 day, 2:26:39.026958 INFO: Starting optimization step 2.
1 day, 2:26:39.027232 PROGRESS: === Extracting elution groups 600 to 1400 ===
1 day, 2:26:39.027316 INFO: Using classic extraction backend
1 day, 2:26:39.027452 PROGRESS: Extracting batch of 1576 precursors
1 day, 2:26:39.027530 INFO: === Search parameters used ===
1 day, 2:26:39.027582 INFO: rt_error       : 2099.9331315
1 day, 2:26:39.027628 INFO: mobility_error : 0.1
1 day, 2:26:39.027671 INFO: num_candidates : 1
1 day, 2:26:39.027714 INFO: ms1_error      : 30
1 day, 2:26:39.027755 INFO: ms2_error      : 30
1 day, 2:26:39.027798 INFO: fwhm_rt        : 5
1 day, 2:26:39.027838 INFO: quant_window   : 3
1 day, 2:26:39.027879 INFO: ==============================================
1 day, 2:26:39.028782 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 2:26:39.028828 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 2:26:39.028857 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 2:26:39.028878 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 2:26:39.029653 INFO: Starting candidate selection
1 day, 2:26:50.553643 INFO: Starting candidate scoring
1 day, 2:26:50.744344 INFO: Finished candidate processing
1 day, 2:26:50.744476 INFO: Collecting candidate features
1 day, 2:26:50.752820 WARNING: height_correlation has 1 NaNs ( 0.07 % out of 1518)
1 day, 2:26:50.755739 INFO: Collecting fragment features
1 day, 2:26:50.759160 INFO: Finished candidate scoring
1 day, 2:26:50.762085 INFO: performing precursor FDR with 47 features
1 day, 2:26:50.762136 INFO: Decoy channel: -1
1 day, 2:26:50.762160 INFO: Competetive: True
1 day, 2:26:50.765354 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 2:26:50.766622 WARNING: dropped 1 target PSMs due to missing features
1 day, 2:26:50.767628 INFO: Using random state 208709 for train-test-split
1 day, 2:26:50.778742 INFO: Test AUC: 0.508
1 day, 2:26:50.778822 INFO: Train AUC: 0.514
1 day, 2:26:50.778853 INFO: AUC difference: 1.15%
1 day, 2:26:50.992548 INFO: Resetting torch num_threads to 80
1 day, 2:26:50.994094 PROGRESS: === Extracted 2632 precursors and 28525 fragments ===
1 day, 2:26:50.994483 INFO: === FDR correction performed with classifier version -1 ===
1 day, 2:26:50.995211 PROGRESS: ============================= Precursor FDR =============================
1 day, 2:26:50.995308 PROGRESS: Total precursors accumulated: 1,351
1 day, 2:26:50.995370 PROGRESS: Target precursors: 836 (61.88%)
1 day, 2:26:50.995422 PROGRESS: Decoy precursors: 515 (38.12%)
1 day, 2:26:50.995468 PROGRESS: 
1 day, 2:26:50.995513 PROGRESS: Precursor Summary:
1 day, 2:26:50.996412 PROGRESS: Channel   0:	 0.050 FDR:   182; 0.010 FDR:   182; 0.001 FDR:   182
1 day, 2:26:50.996503 PROGRESS: 
1 day, 2:26:50.996563 PROGRESS: Protein Summary:
1 day, 2:26:50.997583 PROGRESS: Channel   0:	 0.050 FDR:   181; 0.010 FDR:   181; 0.001 FDR:   181
1 day, 2:26:50.997673 PROGRESS: =========================================================================
1 day, 2:26:50.997822 INFO: Target number of precursors not reached yet.
1 day, 2:26:51.069591 INFO: Starting optimization step 3.
1 day, 2:26:51.069804 PROGRESS: === Extracting elution groups 1400 to 3000 ===
1 day, 2:26:51.069883 INFO: Using classic extraction backend
1 day, 2:26:51.070004 PROGRESS: Extracting batch of 3162 precursors
1 day, 2:26:51.070080 INFO: === Search parameters used ===
1 day, 2:26:51.070133 INFO: rt_error       : 2099.9331315
1 day, 2:26:51.070180 INFO: mobility_error : 0.1
1 day, 2:26:51.070238 INFO: num_candidates : 1
1 day, 2:26:51.070284 INFO: ms1_error      : 30
1 day, 2:26:51.070327 INFO: ms2_error      : 30
1 day, 2:26:51.070369 INFO: fwhm_rt        : 5
1 day, 2:26:51.070412 INFO: quant_window   : 3
1 day, 2:26:51.070451 INFO: ==============================================
1 day, 2:26:51.071410 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 2:26:51.071459 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 2:26:51.071488 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 2:26:51.071519 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 2:26:51.072249 INFO: Starting candidate selection
1 day, 2:27:13.918118 INFO: Starting candidate scoring
1 day, 2:27:14.220405 INFO: Finished candidate processing
1 day, 2:27:14.222434 INFO: Collecting candidate features
1 day, 2:27:14.246500 WARNING: intensity_correlation has 1 NaNs ( 0.03 % out of 3022)
1 day, 2:27:14.254262 INFO: Collecting fragment features
1 day, 2:27:14.263453 INFO: Finished candidate scoring
1 day, 2:27:14.270902 INFO: performing precursor FDR with 47 features
1 day, 2:27:14.271024 INFO: Decoy channel: -1
1 day, 2:27:14.271067 INFO: Competetive: True
1 day, 2:27:14.277323 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 2:27:14.279936 WARNING: dropped 2 target PSMs due to missing features
1 day, 2:27:14.281964 INFO: Using random state 582685 for train-test-split
1 day, 2:27:14.301270 INFO: Test AUC: 0.503
1 day, 2:27:14.301354 INFO: Train AUC: 0.514
1 day, 2:27:14.301384 INFO: AUC difference: 2.09%
1 day, 2:27:14.517954 INFO: Resetting torch num_threads to 80
1 day, 2:27:14.520249 PROGRESS: === Extracted 5654 precursors and 61068 fragments ===
1 day, 2:27:14.520669 INFO: === FDR correction performed with classifier version -1 ===
1 day, 2:27:14.521522 PROGRESS: ============================= Precursor FDR =============================
1 day, 2:27:14.521624 PROGRESS: Total precursors accumulated: 2,893
1 day, 2:27:14.521700 PROGRESS: Target precursors: 1,778 (61.46%)
1 day, 2:27:14.521767 PROGRESS: Decoy precursors: 1,115 (38.54%)
1 day, 2:27:14.521830 PROGRESS: 
1 day, 2:27:14.521895 PROGRESS: Precursor Summary:
1 day, 2:27:14.522938 PROGRESS: Channel   0:	 0.050 FDR:   386; 0.010 FDR:   386; 0.001 FDR:   386
1 day, 2:27:14.523044 PROGRESS: 
1 day, 2:27:14.523125 PROGRESS: Protein Summary:
1 day, 2:27:14.524380 PROGRESS: Channel   0:	 0.050 FDR:   383; 0.010 FDR:   383; 0.001 FDR:   383
1 day, 2:27:14.524481 PROGRESS: =========================================================================
1 day, 2:27:14.524704 INFO: Target number of precursors reached.
1 day, 2:27:14.531192 INFO: fragments_df: keeping 796 of 61068 [sum(precursor_idx_mask)=4335 sum(mass_error_mask)=61068 stop_rank=796
1 day, 2:27:14.688058 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:27:14.801563 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:27:14.934051 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:27:15.065635 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:27:15.218041 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 2:27:15.218896 INFO: Using score_cutoff 36.46001105117798 (fac=0.99, q=1)
1 day, 2:27:15.219226 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.4790749549865723
1 day, 2:27:15.219304 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.008478345349431038
1 day, 2:27:15.219357 INFO: Updating optimization_manager: score_cutoff        : 0 -> 36.46001105117798
1 day, 2:27:15.219415 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:27:15.221148 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:27:15.225687 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:27:15.227047 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:27:15.235205 INFO: Updating optimization_manager: classifier_version  : -1 -> 3
1 day, 2:27:15.235320 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 2:27:15.235400 INFO: Starting optimization step 4.
1 day, 2:27:15.235461 PROGRESS: === Extracting elution groups 0 to 3000 ===
1 day, 2:27:15.235517 INFO: Using classic extraction backend
1 day, 2:27:15.235624 PROGRESS: Extracting batch of 5911 precursors
1 day, 2:27:15.235697 INFO: === Search parameters used ===
1 day, 2:27:15.235744 INFO: rt_error       : 2099.9331315
1 day, 2:27:15.235785 INFO: mobility_error : 0.1
1 day, 2:27:15.235831 INFO: num_candidates : 3
1 day, 2:27:15.235870 INFO: ms1_error      : 30
1 day, 2:27:15.235909 INFO: ms2_error      : 30
1 day, 2:27:15.235946 INFO: fwhm_rt        : 3.4790749549865723
1 day, 2:27:15.235984 INFO: quant_window   : 3
1 day, 2:27:15.236022 INFO: ==============================================
1 day, 2:27:15.237798 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 2:27:15.237845 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 2:27:15.237881 INFO: FWHM in RT is 3.48 seconds, sigma is 0.76
1 day, 2:27:15.237903 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 2:27:15.238908 INFO: Starting candidate selection
1 day, 2:28:03.395125 INFO: Starting candidate scoring
1 day, 2:28:04.802551 INFO: Finished candidate processing
1 day, 2:28:04.802721 INFO: Collecting candidate features
1 day, 2:28:04.869390 INFO: Collecting fragment features
1 day, 2:28:04.889189 INFO: Finished candidate scoring
1 day, 2:28:04.897026 INFO: performing precursor FDR with 47 features
1 day, 2:28:04.897119 INFO: Decoy channel: -1
1 day, 2:28:04.897145 INFO: Competetive: True
1 day, 2:28:04.904348 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 2:28:04.909210 INFO: Using random state 727608 for train-test-split
1 day, 2:28:05.005951 INFO: Test AUC: 0.524
1 day, 2:28:05.006053 INFO: Train AUC: 0.520
1 day, 2:28:05.006089 INFO: AUC difference: 0.84%
1 day, 2:28:05.237348 INFO: Resetting torch num_threads to 80
1 day, 2:28:05.238312 PROGRESS: === Extracted 16440 precursors and 179206 fragments ===
1 day, 2:28:05.238849 INFO: === FDR correction performed with classifier version 3 ===
1 day, 2:28:05.240044 PROGRESS: ============================= Precursor FDR =============================
1 day, 2:28:05.240132 PROGRESS: Total precursors accumulated: 2,955
1 day, 2:28:05.240202 PROGRESS: Target precursors: 1,581 (53.50%)
1 day, 2:28:05.240254 PROGRESS: Decoy precursors: 1,374 (46.50%)
1 day, 2:28:05.240299 PROGRESS: 
1 day, 2:28:05.240342 PROGRESS: Precursor Summary:
1 day, 2:28:05.241184 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 2:28:05.241281 PROGRESS: 
1 day, 2:28:05.241336 PROGRESS: Protein Summary:
1 day, 2:28:05.242226 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 2:28:05.242309 PROGRESS: =========================================================================
1 day, 2:28:05.242711 INFO: Target number of precursors not reached yet.
1 day, 2:28:05.344918 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:28:05.347272 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:28:05.352205 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:28:05.353671 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:28:05.362608 INFO: === skipping optimization until target number of precursors are found ===
1 day, 2:28:05.362787 INFO: Starting optimization step 5.
1 day, 2:28:05.362863 PROGRESS: === Extracting elution groups 3000 to 6200 ===
1 day, 2:28:05.362950 INFO: Using classic extraction backend
1 day, 2:28:05.363169 PROGRESS: Extracting batch of 6312 precursors
1 day, 2:28:05.363253 INFO: === Search parameters used ===
1 day, 2:28:05.363305 INFO: rt_error       : 2099.9331315
1 day, 2:28:05.363348 INFO: mobility_error : 0.1
1 day, 2:28:05.363390 INFO: num_candidates : 3
1 day, 2:28:05.363431 INFO: ms1_error      : 30
1 day, 2:28:05.363471 INFO: ms2_error      : 30
1 day, 2:28:05.363511 INFO: fwhm_rt        : 3.4790749549865723
1 day, 2:28:05.363552 INFO: quant_window   : 3
1 day, 2:28:05.363594 INFO: ==============================================
1 day, 2:28:05.365751 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 2:28:05.365806 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 2:28:05.365877 INFO: FWHM in RT is 3.48 seconds, sigma is 0.76
1 day, 2:28:05.365902 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 2:28:05.370417 INFO: Starting candidate selection
1 day, 2:28:59.223278 INFO: Starting candidate scoring
1 day, 2:29:00.697404 INFO: Finished candidate processing
1 day, 2:29:00.697540 INFO: Collecting candidate features
1 day, 2:29:00.732417 INFO: Collecting fragment features
1 day, 2:29:00.747789 INFO: Finished candidate scoring
1 day, 2:29:00.776956 INFO: performing precursor FDR with 47 features
1 day, 2:29:00.777112 INFO: Decoy channel: -1
1 day, 2:29:00.777138 INFO: Competetive: True
1 day, 2:29:00.794224 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 2:29:00.804849 INFO: Using random state 727608 for train-test-split
1 day, 2:29:01.334715 INFO: Test AUC: 0.548
1 day, 2:29:01.334860 INFO: Train AUC: 0.565
1 day, 2:29:01.334892 INFO: AUC difference: 3.10%
1 day, 2:29:01.570526 INFO: Resetting torch num_threads to 80
1 day, 2:29:01.577580 PROGRESS: === Extracted 33998 precursors and 369854 fragments ===
1 day, 2:29:01.578481 INFO: === FDR correction performed with classifier version 3 ===
1 day, 2:29:01.580085 PROGRESS: ============================= Precursor FDR =============================
1 day, 2:29:01.580198 PROGRESS: Total precursors accumulated: 6,107
1 day, 2:29:01.580261 PROGRESS: Target precursors: 3,667 (60.05%)
1 day, 2:29:01.580313 PROGRESS: Decoy precursors: 2,440 (39.95%)
1 day, 2:29:01.580360 PROGRESS: 
1 day, 2:29:01.580408 PROGRESS: Precursor Summary:
1 day, 2:29:01.581367 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 2:29:01.581457 PROGRESS: 
1 day, 2:29:01.581514 PROGRESS: Protein Summary:
1 day, 2:29:01.582502 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1 day, 2:29:01.582591 PROGRESS: =========================================================================
1 day, 2:29:01.583136 INFO: Target number of precursors not reached yet.
1 day, 2:29:02.029257 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:29:02.031955 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:29:02.040125 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:29:02.042256 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:29:02.060561 INFO: === skipping optimization until target number of precursors are found ===
1 day, 2:29:02.061113 INFO: Starting optimization step 6.
1 day, 2:29:02.061283 PROGRESS: === Extracting elution groups 6200 to 12600 ===
1 day, 2:29:02.061446 INFO: Using classic extraction backend
1 day, 2:29:02.061802 PROGRESS: Extracting batch of 12615 precursors
1 day, 2:29:02.061986 INFO: === Search parameters used ===
1 day, 2:29:02.062105 INFO: rt_error       : 2099.9331315
1 day, 2:29:02.062210 INFO: mobility_error : 0.1
1 day, 2:29:02.062308 INFO: num_candidates : 3
1 day, 2:29:02.062405 INFO: ms1_error      : 30
1 day, 2:29:02.062498 INFO: ms2_error      : 30
1 day, 2:29:02.062591 INFO: fwhm_rt        : 3.4790749549865723
1 day, 2:29:02.062685 INFO: quant_window   : 3
1 day, 2:29:02.062819 INFO: ==============================================
1 day, 2:29:02.068820 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 2:29:02.068883 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 2:29:02.068936 INFO: FWHM in RT is 3.48 seconds, sigma is 0.76
1 day, 2:29:02.068960 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 2:29:02.069878 INFO: Starting candidate selection
1 day, 2:30:46.371162 INFO: Starting candidate scoring
1 day, 2:30:49.209328 INFO: Finished candidate processing
1 day, 2:30:49.209479 INFO: Collecting candidate features
1 day, 2:30:49.267095 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 35153)
1 day, 2:30:49.271963 INFO: Collecting fragment features
1 day, 2:30:49.296511 INFO: Finished candidate scoring
1 day, 2:30:49.380086 INFO: performing precursor FDR with 47 features
1 day, 2:30:49.380274 INFO: Decoy channel: -1
1 day, 2:30:49.380300 INFO: Competetive: True
1 day, 2:30:49.420272 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 2:30:49.434510 WARNING: dropped 1 target PSMs due to missing features
1 day, 2:30:49.449076 INFO: Using random state 727608 for train-test-split
1 day, 2:30:50.798939 INFO: Test AUC: 0.570
1 day, 2:30:50.799097 INFO: Train AUC: 0.571
1 day, 2:30:50.799134 INFO: AUC difference: 0.32%
1 day, 2:30:51.056871 INFO: Resetting torch num_threads to 80
1 day, 2:30:51.070302 PROGRESS: === Extracted 69151 precursors and 751924 fragments ===
1 day, 2:30:51.071387 INFO: === FDR correction performed with classifier version 3 ===
1 day, 2:30:51.074916 PROGRESS: ============================= Precursor FDR =============================
1 day, 2:30:51.075054 PROGRESS: Total precursors accumulated: 12,425
1 day, 2:30:51.075125 PROGRESS: Target precursors: 7,572 (60.94%)
1 day, 2:30:51.075180 PROGRESS: Decoy precursors: 4,853 (39.06%)
1 day, 2:30:51.075227 PROGRESS: 
1 day, 2:30:51.075270 PROGRESS: Precursor Summary:
1 day, 2:30:51.076250 PROGRESS: Channel   0:	 0.050 FDR:     8; 0.010 FDR:     8; 0.001 FDR:     8
1 day, 2:30:51.076343 PROGRESS: 
1 day, 2:30:51.076399 PROGRESS: Protein Summary:
1 day, 2:30:51.077439 PROGRESS: Channel   0:	 0.050 FDR:     8; 0.010 FDR:     8; 0.001 FDR:     8
1 day, 2:30:51.077531 PROGRESS: =========================================================================
1 day, 2:30:51.078013 INFO: Target number of precursors not reached yet.
1 day, 2:30:51.592743 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:30:51.598059 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:30:51.612781 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:30:51.616526 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:30:51.648709 INFO: === skipping optimization until target number of precursors are found ===
1 day, 2:30:51.649055 INFO: Starting optimization step 7.
1 day, 2:30:51.649147 PROGRESS: === Extracting elution groups 12600 to 25400 ===
1 day, 2:30:51.649281 INFO: Using classic extraction backend
1 day, 2:30:51.649610 PROGRESS: Extracting batch of 25223 precursors
1 day, 2:30:51.649728 INFO: === Search parameters used ===
1 day, 2:30:51.649794 INFO: rt_error       : 2099.9331315
1 day, 2:30:51.649851 INFO: mobility_error : 0.1
1 day, 2:30:51.649903 INFO: num_candidates : 3
1 day, 2:30:51.649955 INFO: ms1_error      : 30
1 day, 2:30:51.650005 INFO: ms2_error      : 30
1 day, 2:30:51.650057 INFO: fwhm_rt        : 3.4790749549865723
1 day, 2:30:51.650107 INFO: quant_window   : 3
1 day, 2:30:51.650158 INFO: ==============================================
1 day, 2:30:51.663217 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 2:30:51.663329 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 2:30:51.663430 INFO: FWHM in RT is 3.48 seconds, sigma is 0.76
1 day, 2:30:51.663462 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 2:30:51.667770 INFO: Starting candidate selection
1 day, 2:34:21.466191 INFO: Starting candidate scoring
1 day, 2:34:26.770720 INFO: Finished candidate processing
1 day, 2:34:26.770865 INFO: Collecting candidate features
1 day, 2:34:26.870675 WARNING: intensity_correlation has 4 NaNs ( 0.01 % out of 70276)
1 day, 2:34:26.879018 INFO: Collecting fragment features
1 day, 2:34:26.923910 INFO: Finished candidate scoring
1 day, 2:34:27.109081 INFO: performing precursor FDR with 47 features
1 day, 2:34:27.109264 INFO: Decoy channel: -1
1 day, 2:34:27.109290 INFO: Competetive: True
1 day, 2:34:27.172365 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 2:34:27.201556 WARNING: dropped 2 target PSMs due to missing features
1 day, 2:34:27.201731 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 2:34:27.228603 INFO: Using random state 727608 for train-test-split
1 day, 2:34:30.294166 INFO: Test AUC: 0.557
1 day, 2:34:30.294356 INFO: Train AUC: 0.585
1 day, 2:34:30.294394 INFO: AUC difference: 4.78%
1 day, 2:34:30.560639 INFO: Resetting torch num_threads to 80
1 day, 2:34:30.587903 PROGRESS: === Extracted 139427 precursors and 1515556 fragments ===
1 day, 2:34:30.588888 INFO: === FDR correction performed with classifier version 3 ===
1 day, 2:34:30.594864 PROGRESS: ============================= Precursor FDR =============================
1 day, 2:34:30.595000 PROGRESS: Total precursors accumulated: 25,040
1 day, 2:34:30.595064 PROGRESS: Target precursors: 15,719 (62.78%)
1 day, 2:34:30.595117 PROGRESS: Decoy precursors: 9,321 (37.22%)
1 day, 2:34:30.595170 PROGRESS: 
1 day, 2:34:30.595215 PROGRESS: Precursor Summary:
1 day, 2:34:30.596313 PROGRESS: Channel   0:	 0.050 FDR:    93; 0.010 FDR:    20; 0.001 FDR:    20
1 day, 2:34:30.596408 PROGRESS: 
1 day, 2:34:30.596463 PROGRESS: Protein Summary:
1 day, 2:34:30.597555 PROGRESS: Channel   0:	 0.050 FDR:    92; 0.010 FDR:    20; 0.001 FDR:    20
1 day, 2:34:30.597655 PROGRESS: =========================================================================
1 day, 2:34:30.598364 INFO: Target number of precursors not reached yet.
1 day, 2:34:30.930991 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:34:30.940499 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:34:30.969633 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:34:30.976992 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:34:31.053897 INFO: === skipping optimization until target number of precursors are found ===
1 day, 2:34:31.054272 INFO: Starting optimization step 8.
1 day, 2:34:31.054377 PROGRESS: === Extracting elution groups 25400 to 51000 ===
1 day, 2:34:31.054474 INFO: Using classic extraction backend
1 day, 2:34:31.054673 PROGRESS: Extracting batch of 50469 precursors
1 day, 2:34:31.054771 INFO: === Search parameters used ===
1 day, 2:34:31.054851 INFO: rt_error       : 2099.9331315
1 day, 2:34:31.054909 INFO: mobility_error : 0.1
1 day, 2:34:31.054962 INFO: num_candidates : 3
1 day, 2:34:31.055012 INFO: ms1_error      : 30
1 day, 2:34:31.055062 INFO: ms2_error      : 30
1 day, 2:34:31.055111 INFO: fwhm_rt        : 3.4790749549865723
1 day, 2:34:31.055160 INFO: quant_window   : 3
1 day, 2:34:31.055210 INFO: ==============================================
1 day, 2:34:31.074812 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 2:34:31.074987 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 2:34:31.075044 INFO: FWHM in RT is 3.48 seconds, sigma is 0.76
1 day, 2:34:31.075068 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 2:34:31.076780 INFO: Starting candidate selection
1 day, 2:41:14.105072 INFO: Starting candidate scoring
1 day, 2:41:24.310498 INFO: Finished candidate processing
1 day, 2:41:24.310669 INFO: Collecting candidate features
1 day, 2:41:24.536452 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 140572)
1 day, 2:41:24.545033 INFO: Collecting fragment features
1 day, 2:41:24.631586 INFO: Finished candidate scoring
1 day, 2:41:24.829760 INFO: performing precursor FDR with 47 features
1 day, 2:41:24.829924 INFO: Decoy channel: -1
1 day, 2:41:24.829951 INFO: Competetive: True
1 day, 2:41:24.932652 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 2:41:24.980392 WARNING: dropped 2 target PSMs due to missing features
1 day, 2:41:24.980549 WARNING: dropped 5 decoy PSMs due to missing features
1 day, 2:41:25.050572 INFO: Using random state 727608 for train-test-split
1 day, 2:41:29.695387 INFO: Test AUC: 0.562
1 day, 2:41:29.695535 INFO: Train AUC: 0.585
1 day, 2:41:29.695570 INFO: AUC difference: 4.00%
1 day, 2:41:30.004982 INFO: Resetting torch num_threads to 80
1 day, 2:41:30.054395 PROGRESS: === Extracted 279999 precursors and 3043496 fragments ===
1 day, 2:41:30.055265 INFO: === FDR correction performed with classifier version 3 ===
1 day, 2:41:30.065284 PROGRESS: ============================= Precursor FDR =============================
1 day, 2:41:30.065520 PROGRESS: Total precursors accumulated: 50,293
1 day, 2:41:30.065588 PROGRESS: Target precursors: 31,207 (62.05%)
1 day, 2:41:30.065639 PROGRESS: Decoy precursors: 19,086 (37.95%)
1 day, 2:41:30.065705 PROGRESS: 
1 day, 2:41:30.065753 PROGRESS: Precursor Summary:
1 day, 2:41:30.067099 PROGRESS: Channel   0:	 0.050 FDR:   256; 0.010 FDR:   154; 0.001 FDR:   148
1 day, 2:41:30.067197 PROGRESS: 
1 day, 2:41:30.067262 PROGRESS: Protein Summary:
1 day, 2:41:30.068588 PROGRESS: Channel   0:	 0.050 FDR:   246; 0.010 FDR:   151; 0.001 FDR:   145
1 day, 2:41:30.068681 PROGRESS: =========================================================================
1 day, 2:41:30.069541 INFO: Target number of precursors not reached yet.
1 day, 2:41:30.576170 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:41:30.591259 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:41:30.648784 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:41:30.664887 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:41:30.818984 INFO: === skipping optimization until target number of precursors are found ===
1 day, 2:41:30.819361 INFO: Starting optimization step 9.
1 day, 2:41:30.819447 PROGRESS: === Extracting elution groups 51000 to 102200 ===
1 day, 2:41:30.819537 INFO: Using classic extraction backend
1 day, 2:41:30.819721 PROGRESS: Extracting batch of 100931 precursors
1 day, 2:41:30.819819 INFO: === Search parameters used ===
1 day, 2:41:30.819888 INFO: rt_error       : 2099.9331315
1 day, 2:41:30.819944 INFO: mobility_error : 0.1
1 day, 2:41:30.820000 INFO: num_candidates : 3
1 day, 2:41:30.820055 INFO: ms1_error      : 30
1 day, 2:41:30.820104 INFO: ms2_error      : 30
1 day, 2:41:30.820155 INFO: fwhm_rt        : 3.4790749549865723
1 day, 2:41:30.820205 INFO: quant_window   : 3
1 day, 2:41:30.820272 INFO: ==============================================
1 day, 2:41:30.869319 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 2:41:30.869477 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 2:41:30.869531 INFO: FWHM in RT is 3.48 seconds, sigma is 0.76
1 day, 2:41:30.869554 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 2:41:30.870363 INFO: Starting candidate selection
1 day, 2:54:57.927734 INFO: Starting candidate scoring
1 day, 2:55:16.964001 INFO: Finished candidate processing
1 day, 2:55:16.964185 INFO: Collecting candidate features
1 day, 2:55:17.425859 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 280849)
1 day, 2:55:17.441045 INFO: Collecting fragment features
1 day, 2:55:17.622257 INFO: Finished candidate scoring
1 day, 2:55:18.005382 INFO: performing precursor FDR with 47 features
1 day, 2:55:18.005545 INFO: Decoy channel: -1
1 day, 2:55:18.005572 INFO: Competetive: True
1 day, 2:55:18.239780 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 2:55:18.352347 WARNING: dropped 4 target PSMs due to missing features
1 day, 2:55:18.352509 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 2:55:18.528778 INFO: Using random state 727608 for train-test-split
1 day, 2:55:29.959740 INFO: Test AUC: 0.572
1 day, 2:55:29.959944 INFO: Train AUC: 0.586
1 day, 2:55:29.959981 INFO: AUC difference: 2.41%
1 day, 2:55:30.372791 INFO: Resetting torch num_threads to 80
1 day, 2:55:30.496796 PROGRESS: === Extracted 560848 precursors and 6094370 fragments ===
1 day, 2:55:30.498026 INFO: === FDR correction performed with classifier version 3 ===
1 day, 2:55:30.528569 PROGRESS: ============================= Precursor FDR =============================
1 day, 2:55:30.529109 PROGRESS: Total precursors accumulated: 100,718
1 day, 2:55:30.529177 PROGRESS: Target precursors: 62,701 (62.25%)
1 day, 2:55:30.529228 PROGRESS: Decoy precursors: 38,017 (37.75%)
1 day, 2:55:30.529273 PROGRESS: 
1 day, 2:55:30.529320 PROGRESS: Precursor Summary:
1 day, 2:55:30.531494 PROGRESS: Channel   0:	 0.050 FDR:   746; 0.010 FDR:   563; 0.001 FDR:   375
1 day, 2:55:30.531599 PROGRESS: 
1 day, 2:55:30.531667 PROGRESS: Protein Summary:
1 day, 2:55:30.533505 PROGRESS: Channel   0:	 0.050 FDR:   681; 0.010 FDR:   521; 0.001 FDR:   355
1 day, 2:55:30.533603 PROGRESS: =========================================================================
1 day, 2:55:30.536334 INFO: Target number of precursors reached.
1 day, 2:55:30.976164 INFO: fragments_df: keeping 5000 of 6094370 [sum(precursor_idx_mask)=18366 sum(mass_error_mask)=6094369 stop_rank=5000
1 day, 2:55:31.454306 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:55:31.581190 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:55:31.699858 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:55:31.824587 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:55:32.427716 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 2:55:32.428180 INFO: Using score_cutoff 50.763483798980715 (fac=0.99, q=1)
1 day, 2:55:32.428512 INFO: Updating optimization_manager: fwhm_rt             : 3.4790749549865723 -> 3.0595405101776123
1 day, 2:55:32.428596 INFO: Updating optimization_manager: fwhm_mobility       : 0.008478345349431038 -> 0.01075291633605957
1 day, 2:55:32.428655 INFO: Updating optimization_manager: score_cutoff        : 36.46001105117798 -> 50.763483798980715
1 day, 2:55:32.428715 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 2:55:32.442478 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 2:55:32.503259 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 2:55:32.519343 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 2:55:32.660202 INFO: === checking if optimization conditions were reached ===
1 day, 2:55:32.662853 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 2:55:32.662976 INFO: Updating optimization_manager: classifier_version  : 3 -> 9
1 day, 2:55:32.663059 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 2:55:32.664246 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 2:55:32.664354 INFO: Updating optimization_manager: classifier_version  : 9 -> 9
1 day, 2:55:32.664428 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 2:55:32.664494 INFO: ==============================================
1 day, 2:55:32.664581 INFO: Starting optimization step 10.
1 day, 2:55:32.664665 PROGRESS: === Extracting elution groups 0 to 51000 ===
1 day, 2:55:32.664760 INFO: Using classic extraction backend
1 day, 2:55:32.664934 PROGRESS: Extracting batch of 100530 precursors
1 day, 2:55:32.665020 INFO: === Search parameters used ===
1 day, 2:55:32.665082 INFO: rt_error       : 2099.9331315
1 day, 2:55:32.665136 INFO: mobility_error : 0.1
1 day, 2:55:32.665186 INFO: num_candidates : 3
1 day, 2:55:32.665236 INFO: ms1_error      : 15.0
1 day, 2:55:32.665286 INFO: ms2_error      : 15.0
1 day, 2:55:32.665335 INFO: fwhm_rt        : 3.0595405101776123
1 day, 2:55:32.665385 INFO: quant_window   : 3
1 day, 2:55:32.665433 INFO: ==============================================
1 day, 2:55:32.703569 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 2:55:32.703737 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 2:55:32.703797 INFO: FWHM in RT is 3.06 seconds, sigma is 0.67
1 day, 2:55:32.703824 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.99
1 day, 2:55:32.709392 INFO: Starting candidate selection
1 day, 3:05:38.878546 INFO: Starting candidate scoring
1 day, 3:05:51.003495 INFO: Finished candidate processing
1 day, 3:05:51.003646 INFO: Collecting candidate features
1 day, 3:05:51.444018 WARNING: intensity_correlation has 10 NaNs ( 0.00 % out of 278910)
1 day, 3:05:51.444507 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 278910)
1 day, 3:05:51.456791 INFO: Collecting fragment features
1 day, 3:05:51.624506 INFO: Finished candidate scoring
1 day, 3:05:51.787401 INFO: performing precursor FDR with 47 features
1 day, 3:05:51.787549 INFO: Decoy channel: -1
1 day, 3:05:51.787575 INFO: Competetive: True
1 day, 3:05:51.868380 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:05:51.915009 WARNING: dropped 5 target PSMs due to missing features
1 day, 3:05:51.915173 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 3:05:51.984026 INFO: Using random state 432080 for train-test-split
1 day, 3:05:56.592699 INFO: Test AUC: 0.569
1 day, 3:05:56.592854 INFO: Train AUC: 0.596
1 day, 3:05:56.592888 INFO: AUC difference: 4.59%
1 day, 3:05:58.758757 INFO: Resetting torch num_threads to 80
1 day, 3:05:58.764629 PROGRESS: === Extracted 278910 precursors and 2885776 fragments ===
1 day, 3:05:58.765178 INFO: === FDR correction performed with classifier version 9 ===
1 day, 3:05:58.774312 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:05:58.774598 PROGRESS: Total precursors accumulated: 50,012
1 day, 3:05:58.774663 PROGRESS: Target precursors: 31,582 (63.15%)
1 day, 3:05:58.774714 PROGRESS: Decoy precursors: 18,430 (36.85%)
1 day, 3:05:58.774760 PROGRESS: 
1 day, 3:05:58.774814 PROGRESS: Precursor Summary:
1 day, 3:05:58.776237 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   421; 0.001 FDR:   323
1 day, 3:05:58.776344 PROGRESS: 
1 day, 3:05:58.776638 PROGRESS: Protein Summary:
1 day, 3:05:58.778100 PROGRESS: Channel   0:	 0.050 FDR:   553; 0.010 FDR:   400; 0.001 FDR:   310
1 day, 3:05:58.778197 PROGRESS: =========================================================================
1 day, 3:05:58.781373 INFO: Target number of precursors reached.
1 day, 3:05:58.970150 INFO: fragments_df: keeping 5000 of 2885776 [sum(precursor_idx_mask)=13445 sum(mass_error_mask)=2885776 stop_rank=5000
1 day, 3:05:59.190327 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:05:59.323745 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:05:59.458261 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:05:59.591984 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:06:00.276869 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:06:00.277331 INFO: Using score_cutoff 44.356880058288574 (fac=0.99, q=1)
1 day, 3:06:00.277638 INFO: Updating optimization_manager: fwhm_rt             : 3.0595405101776123 -> 2.7472779750823975
1 day, 3:06:00.277721 INFO: Updating optimization_manager: fwhm_mobility       : 0.01075291633605957 -> 0.008622842840850353
1 day, 3:06:00.277774 INFO: Updating optimization_manager: score_cutoff        : 50.763483798980715 -> 44.356880058288574
1 day, 3:06:00.277827 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:06:00.285128 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:06:00.315510 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:06:00.322442 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:06:00.383378 INFO: === checking if optimization conditions were reached ===
1 day, 3:06:00.385710 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 3:06:00.385830 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1 day, 3:06:00.385911 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 3:06:00.386940 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 3:06:00.387060 INFO: Updating optimization_manager: classifier_version  : 10 -> 10
1 day, 3:06:00.387139 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 3:06:00.387212 INFO: ==============================================
1 day, 3:06:00.387299 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 3:06:00.521182 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:06:00.528838 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:06:00.559360 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:06:00.566267 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:06:00.627690 INFO: Starting optimization step 0.
1 day, 3:06:00.627966 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 3:06:00.628059 INFO: Using classic extraction backend
1 day, 3:06:00.628197 PROGRESS: Extracting batch of 50061 precursors
1 day, 3:06:00.628274 INFO: === Search parameters used ===
1 day, 3:06:00.628325 INFO: rt_error       : 2099.9331315
1 day, 3:06:00.628381 INFO: mobility_error : 0.1
1 day, 3:06:00.628435 INFO: num_candidates : 3
1 day, 3:06:00.628487 INFO: ms1_error      : 15.0
1 day, 3:06:00.628531 INFO: ms2_error      : 15.0
1 day, 3:06:00.628570 INFO: fwhm_rt        : 2.7472779750823975
1 day, 3:06:00.628609 INFO: quant_window   : 3
1 day, 3:06:00.628650 INFO: ==============================================
1 day, 3:06:00.642868 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:06:00.643005 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:06:00.643054 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 3:06:00.643076 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.00
1 day, 3:06:00.649216 INFO: Starting candidate selection
1 day, 3:11:09.230923 INFO: Starting candidate scoring
1 day, 3:11:15.279971 INFO: Finished candidate processing
1 day, 3:11:15.280177 INFO: Collecting candidate features
1 day, 3:11:15.551758 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 138699)
1 day, 3:11:15.560524 INFO: Collecting fragment features
1 day, 3:11:15.647895 INFO: Finished candidate scoring
1 day, 3:11:15.720250 INFO: performing precursor FDR with 47 features
1 day, 3:11:15.720378 INFO: Decoy channel: -1
1 day, 3:11:15.720406 INFO: Competetive: True
1 day, 3:11:15.761916 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:11:15.785578 WARNING: dropped 2 target PSMs due to missing features
1 day, 3:11:15.785731 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 3:11:15.811790 INFO: Using random state 826007 for train-test-split
1 day, 3:11:18.189136 INFO: Test AUC: 0.579
1 day, 3:11:18.189276 INFO: Train AUC: 0.617
1 day, 3:11:18.189310 INFO: AUC difference: 6.22%
1 day, 3:11:18.189333 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:11:18.467882 INFO: Resetting torch num_threads to 80
1 day, 3:11:18.471209 PROGRESS: === Extracted 138699 precursors and 1429422 fragments ===
1 day, 3:11:18.471724 INFO: === FDR correction performed with classifier version 10 ===
1 day, 3:11:18.475832 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:11:18.475977 PROGRESS: Total precursors accumulated: 24,915
1 day, 3:11:18.476041 PROGRESS: Target precursors: 16,221 (65.11%)
1 day, 3:11:18.476093 PROGRESS: Decoy precursors: 8,694 (34.89%)
1 day, 3:11:18.476142 PROGRESS: 
1 day, 3:11:18.476187 PROGRESS: Precursor Summary:
1 day, 3:11:18.477325 PROGRESS: Channel   0:	 0.050 FDR:   343; 0.010 FDR:   218; 0.001 FDR:   170
1 day, 3:11:18.477420 PROGRESS: 
1 day, 3:11:18.477477 PROGRESS: Protein Summary:
1 day, 3:11:18.478711 PROGRESS: Channel   0:	 0.050 FDR:   338; 0.010 FDR:   213; 0.001 FDR:   165
1 day, 3:11:18.478812 PROGRESS: =========================================================================
1 day, 3:11:18.507715 INFO: Target number of precursors reached.
1 day, 3:11:18.600999 INFO: fragments_df: keeping 3089 of 1429422 [sum(precursor_idx_mask)=6943 sum(mass_error_mask)=1429419 stop_rank=3089
1 day, 3:11:18.813450 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:11:18.915378 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:11:19.014727 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:11:19.130868 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:11:19.479728 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:11:19.480189 INFO: Using score_cutoff 40.400232766342164 (fac=0.99, q=1)
1 day, 3:11:19.480519 INFO: Updating optimization_manager: fwhm_rt             : 2.7472779750823975 -> 2.738624095916748
1 day, 3:11:19.480602 INFO: Updating optimization_manager: fwhm_mobility       : 0.008622842840850353 -> 0.008571689948439598
1 day, 3:11:19.480660 INFO: Updating optimization_manager: score_cutoff        : 44.356880058288574 -> 40.400232766342164
1 day, 3:11:19.480729 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:11:19.488256 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:11:19.518215 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:11:19.525807 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:11:19.588567 INFO: === checking if optimization conditions were reached ===
1 day, 3:11:19.588935 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 3:11:19.591235 INFO: Updating optimization_manager: rt_error            : 2099.9331315 -> 401.42929825706256
1 day, 3:11:19.591358 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 401.4293.
1 day, 3:11:19.591435 INFO: ==============================================
1 day, 3:11:19.591521 INFO: Starting optimization step 1.
1 day, 3:11:19.591606 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 3:11:19.591681 INFO: Using classic extraction backend
1 day, 3:11:19.591851 PROGRESS: Extracting batch of 50061 precursors
1 day, 3:11:19.591937 INFO: === Search parameters used ===
1 day, 3:11:19.591993 INFO: rt_error       : 401.42929825706256
1 day, 3:11:19.592046 INFO: mobility_error : 0.1
1 day, 3:11:19.592097 INFO: num_candidates : 3
1 day, 3:11:19.592146 INFO: ms1_error      : 15.0
1 day, 3:11:19.592198 INFO: ms2_error      : 15.0
1 day, 3:11:19.592247 INFO: fwhm_rt        : 2.738624095916748
1 day, 3:11:19.592295 INFO: quant_window   : 3
1 day, 3:11:19.592345 INFO: ==============================================
1 day, 3:11:19.612221 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:11:19.612379 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:11:19.612443 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
1 day, 3:11:19.612505 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.98
1 day, 3:11:19.621215 INFO: Starting candidate selection
1 day, 3:12:18.032969 INFO: Starting candidate scoring
1 day, 3:12:24.014021 INFO: Finished candidate processing
1 day, 3:12:24.014208 INFO: Collecting candidate features
1 day, 3:12:24.269557 WARNING: intensity_correlation has 41 NaNs ( 0.03 % out of 133179)
1 day, 3:12:24.269919 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 133179)
1 day, 3:12:24.284138 INFO: Collecting fragment features
1 day, 3:12:24.369350 INFO: Finished candidate scoring
1 day, 3:12:24.448967 INFO: performing precursor FDR with 47 features
1 day, 3:12:24.449104 INFO: Decoy channel: -1
1 day, 3:12:24.449134 INFO: Competetive: True
1 day, 3:12:24.494634 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:12:24.517351 WARNING: dropped 22 target PSMs due to missing features
1 day, 3:12:24.517513 WARNING: dropped 19 decoy PSMs due to missing features
1 day, 3:12:24.540575 INFO: Using random state 826007 for train-test-split
1 day, 3:12:26.658923 INFO: Test AUC: 0.558
1 day, 3:12:26.659073 INFO: Train AUC: 0.594
1 day, 3:12:26.659106 INFO: AUC difference: 6.07%
1 day, 3:12:26.659129 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:12:26.926850 INFO: Resetting torch num_threads to 80
1 day, 3:12:26.930114 PROGRESS: === Extracted 133179 precursors and 1337931 fragments ===
1 day, 3:12:26.930656 INFO: === FDR correction performed with classifier version 10 ===
1 day, 3:12:26.934797 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:12:26.934937 PROGRESS: Total precursors accumulated: 24,299
1 day, 3:12:26.935001 PROGRESS: Target precursors: 15,029 (61.85%)
1 day, 3:12:26.935054 PROGRESS: Decoy precursors: 9,270 (38.15%)
1 day, 3:12:26.935101 PROGRESS: 
1 day, 3:12:26.935145 PROGRESS: Precursor Summary:
1 day, 3:12:26.936310 PROGRESS: Channel   0:	 0.050 FDR:   343; 0.010 FDR:   217; 0.001 FDR:   209
1 day, 3:12:26.936407 PROGRESS: 
1 day, 3:12:26.936474 PROGRESS: Protein Summary:
1 day, 3:12:26.937727 PROGRESS: Channel   0:	 0.050 FDR:   337; 0.010 FDR:   213; 0.001 FDR:   205
1 day, 3:12:26.937822 PROGRESS: =========================================================================
1 day, 3:12:26.938723 INFO: Target number of precursors reached.
1 day, 3:12:27.062716 INFO: fragments_df: keeping 3168 of 1337931 [sum(precursor_idx_mask)=7013 sum(mass_error_mask)=1337928 stop_rank=3168
1 day, 3:12:27.273423 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:12:27.393774 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:12:27.516944 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:12:27.629751 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:12:27.981247 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:12:27.981728 INFO: Using score_cutoff 40.4372821975708 (fac=0.99, q=1)
1 day, 3:12:27.982059 INFO: Updating optimization_manager: fwhm_rt             : 2.738624095916748 -> 2.6522927284240723
1 day, 3:12:27.982139 INFO: Updating optimization_manager: fwhm_mobility       : 0.008571689948439598 -> 0.008464006707072258
1 day, 3:12:27.982196 INFO: Updating optimization_manager: score_cutoff        : 40.400232766342164 -> 40.4372821975708
1 day, 3:12:27.982256 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:12:27.990144 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:12:28.020818 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:12:28.028931 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:12:28.092795 INFO: === checking if optimization conditions were reached ===
1 day, 3:12:28.093151 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 3:12:28.095588 INFO: Updating optimization_manager: rt_error            : 401.42929825706256 -> 301.3579891854295
1 day, 3:12:28.095725 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 301.3580.
1 day, 3:12:28.095806 INFO: ==============================================
1 day, 3:12:28.095897 INFO: Starting optimization step 2.
1 day, 3:12:28.095967 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 3:12:28.096041 INFO: Using classic extraction backend
1 day, 3:12:28.096219 PROGRESS: Extracting batch of 50061 precursors
1 day, 3:12:28.096302 INFO: === Search parameters used ===
1 day, 3:12:28.096363 INFO: rt_error       : 301.3579891854295
1 day, 3:12:28.096416 INFO: mobility_error : 0.1
1 day, 3:12:28.096469 INFO: num_candidates : 3
1 day, 3:12:28.096520 INFO: ms1_error      : 15.0
1 day, 3:12:28.096570 INFO: ms2_error      : 15.0
1 day, 3:12:28.096619 INFO: fwhm_rt        : 2.6522927284240723
1 day, 3:12:28.096668 INFO: quant_window   : 3
1 day, 3:12:28.096718 INFO: ==============================================
1 day, 3:12:28.113664 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:12:28.113812 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:12:28.113864 INFO: FWHM in RT is 2.65 seconds, sigma is 0.58
1 day, 3:12:28.113889 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 3:12:28.122568 INFO: Starting candidate selection
1 day, 3:13:11.580174 INFO: Starting candidate scoring
1 day, 3:13:16.993939 INFO: Finished candidate processing
1 day, 3:13:16.994062 INFO: Collecting candidate features
1 day, 3:13:17.178799 WARNING: intensity_correlation has 44 NaNs ( 0.03 % out of 132380)
1 day, 3:13:17.179177 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 132380)
1 day, 3:13:17.187383 INFO: Collecting fragment features
1 day, 3:13:17.266498 INFO: Finished candidate scoring
1 day, 3:13:17.340908 INFO: performing precursor FDR with 47 features
1 day, 3:13:17.341048 INFO: Decoy channel: -1
1 day, 3:13:17.341075 INFO: Competetive: True
1 day, 3:13:17.381341 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:13:17.404159 WARNING: dropped 25 target PSMs due to missing features
1 day, 3:13:17.404337 WARNING: dropped 20 decoy PSMs due to missing features
1 day, 3:13:17.429445 INFO: Using random state 826007 for train-test-split
1 day, 3:13:19.781644 INFO: Test AUC: 0.553
1 day, 3:13:19.781784 INFO: Train AUC: 0.591
1 day, 3:13:19.781817 INFO: AUC difference: 6.34%
1 day, 3:13:19.781839 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:13:20.046396 INFO: Resetting torch num_threads to 80
1 day, 3:13:20.049692 PROGRESS: === Extracted 132380 precursors and 1319138 fragments ===
1 day, 3:13:20.050241 INFO: === FDR correction performed with classifier version 10 ===
1 day, 3:13:20.054184 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:13:20.054330 PROGRESS: Total precursors accumulated: 24,194
1 day, 3:13:20.054394 PROGRESS: Target precursors: 14,841 (61.34%)
1 day, 3:13:20.054446 PROGRESS: Decoy precursors: 9,353 (38.66%)
1 day, 3:13:20.054496 PROGRESS: 
1 day, 3:13:20.054543 PROGRESS: Precursor Summary:
1 day, 3:13:20.055694 PROGRESS: Channel   0:	 0.050 FDR:   310; 0.010 FDR:   246; 0.001 FDR:   197
1 day, 3:13:20.055792 PROGRESS: 
1 day, 3:13:20.055848 PROGRESS: Protein Summary:
1 day, 3:13:20.057057 PROGRESS: Channel   0:	 0.050 FDR:   305; 0.010 FDR:   241; 0.001 FDR:   194
1 day, 3:13:20.057149 PROGRESS: =========================================================================
1 day, 3:13:20.057999 INFO: Target number of precursors reached.
1 day, 3:13:20.145532 INFO: fragments_df: keeping 3417 of 1319138 [sum(precursor_idx_mask)=7884 sum(mass_error_mask)=1319135 stop_rank=3417
1 day, 3:13:20.360624 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:13:20.463253 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:13:20.562681 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:13:20.664458 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:13:21.047414 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:13:21.047925 INFO: Using score_cutoff 43.908399793624874 (fac=0.99, q=1)
1 day, 3:13:21.048265 INFO: Updating optimization_manager: fwhm_rt             : 2.6522927284240723 -> 2.7286553382873535
1 day, 3:13:21.048348 INFO: Updating optimization_manager: fwhm_mobility       : 0.008464006707072258 -> 0.008497819304466248
1 day, 3:13:21.048412 INFO: Updating optimization_manager: score_cutoff        : 40.4372821975708 -> 43.908399793624874
1 day, 3:13:21.048473 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:13:21.056171 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:13:21.086480 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:13:21.094341 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:13:21.157695 INFO: === checking if optimization conditions were reached ===
1 day, 3:13:21.158043 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 3:13:21.160548 INFO: Updating optimization_manager: rt_error            : 301.3579891854295 -> 348.49095122983437
1 day, 3:13:21.160674 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 348.4910.
1 day, 3:13:21.160759 INFO: ==============================================
1 day, 3:13:21.160858 INFO: Starting optimization step 3.
1 day, 3:13:21.160930 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 3:13:21.161004 INFO: Using classic extraction backend
1 day, 3:13:21.161182 PROGRESS: Extracting batch of 50061 precursors
1 day, 3:13:21.161267 INFO: === Search parameters used ===
1 day, 3:13:21.161330 INFO: rt_error       : 348.49095122983437
1 day, 3:13:21.161384 INFO: mobility_error : 0.1
1 day, 3:13:21.161436 INFO: num_candidates : 3
1 day, 3:13:21.161490 INFO: ms1_error      : 15.0
1 day, 3:13:21.162288 INFO: ms2_error      : 15.0
1 day, 3:13:21.162355 INFO: fwhm_rt        : 2.7286553382873535
1 day, 3:13:21.162407 INFO: quant_window   : 3
1 day, 3:13:21.162466 INFO: ==============================================
1 day, 3:13:21.179603 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:13:21.179741 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:13:21.179792 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
1 day, 3:13:21.179816 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.94
1 day, 3:13:21.188651 INFO: Starting candidate selection
1 day, 3:14:13.359096 INFO: Starting candidate scoring
1 day, 3:14:19.572289 INFO: Finished candidate processing
1 day, 3:14:19.572423 INFO: Collecting candidate features
1 day, 3:14:19.788321 WARNING: intensity_correlation has 48 NaNs ( 0.04 % out of 133206)
1 day, 3:14:19.788738 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 133206)
1 day, 3:14:19.796868 INFO: Collecting fragment features
1 day, 3:14:19.872534 INFO: Finished candidate scoring
1 day, 3:14:20.036027 INFO: performing precursor FDR with 47 features
1 day, 3:14:20.036176 INFO: Decoy channel: -1
1 day, 3:14:20.036202 INFO: Competetive: True
1 day, 3:14:20.077505 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:14:20.101223 WARNING: dropped 24 target PSMs due to missing features
1 day, 3:14:20.101379 WARNING: dropped 25 decoy PSMs due to missing features
1 day, 3:14:20.128365 INFO: Using random state 826007 for train-test-split
1 day, 3:14:22.520235 INFO: Test AUC: 0.556
1 day, 3:14:22.520377 INFO: Train AUC: 0.603
1 day, 3:14:22.520409 INFO: AUC difference: 7.75%
1 day, 3:14:22.520431 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:14:22.792489 INFO: Resetting torch num_threads to 80
1 day, 3:14:22.795769 PROGRESS: === Extracted 133206 precursors and 1334938 fragments ===
1 day, 3:14:22.796281 INFO: === FDR correction performed with classifier version 10 ===
1 day, 3:14:22.800300 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:14:22.800428 PROGRESS: Total precursors accumulated: 24,331
1 day, 3:14:22.800492 PROGRESS: Target precursors: 15,266 (62.74%)
1 day, 3:14:22.800548 PROGRESS: Decoy precursors: 9,065 (37.26%)
1 day, 3:14:22.800598 PROGRESS: 
1 day, 3:14:22.800643 PROGRESS: Precursor Summary:
1 day, 3:14:22.801754 PROGRESS: Channel   0:	 0.050 FDR:   326; 0.010 FDR:   235; 0.001 FDR:   154
1 day, 3:14:22.801848 PROGRESS: 
1 day, 3:14:22.801906 PROGRESS: Protein Summary:
1 day, 3:14:22.803125 PROGRESS: Channel   0:	 0.050 FDR:   321; 0.010 FDR:   230; 0.001 FDR:   151
1 day, 3:14:22.803220 PROGRESS: =========================================================================
1 day, 3:14:22.804059 INFO: Target number of precursors reached.
1 day, 3:14:22.894683 INFO: fragments_df: keeping 3334 of 1334938 [sum(precursor_idx_mask)=7482 sum(mass_error_mask)=1334935 stop_rank=3334
1 day, 3:14:23.112088 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:14:23.231657 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:14:23.353558 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:14:23.478319 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:14:23.911269 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:14:23.911742 INFO: Using score_cutoff 41.251811208343504 (fac=0.99, q=1)
1 day, 3:14:23.912072 INFO: Updating optimization_manager: fwhm_rt             : 2.7286553382873535 -> 2.7884035110473633
1 day, 3:14:23.912156 INFO: Updating optimization_manager: fwhm_mobility       : 0.008497819304466248 -> 0.008645701222121716
1 day, 3:14:23.912214 INFO: Updating optimization_manager: score_cutoff        : 43.908399793624874 -> 41.251811208343504
1 day, 3:14:23.912274 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:14:23.920025 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:14:23.950576 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:14:23.958326 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:14:24.021523 INFO: === checking if optimization conditions were reached ===
1 day, 3:14:24.021821 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 3:14:24.023918 INFO: Updating optimization_manager: rt_error            : 348.49095122983437 -> 207.23586116352942
1 day, 3:14:24.024025 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 207.2359.
1 day, 3:14:24.024097 INFO: ==============================================
1 day, 3:14:24.024177 INFO: Starting optimization step 4.
1 day, 3:14:24.024240 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 3:14:24.024319 INFO: Using classic extraction backend
1 day, 3:14:24.024470 PROGRESS: Extracting batch of 50061 precursors
1 day, 3:14:24.024539 INFO: === Search parameters used ===
1 day, 3:14:24.024591 INFO: rt_error       : 207.23586116352942
1 day, 3:14:24.024636 INFO: mobility_error : 0.1
1 day, 3:14:24.024680 INFO: num_candidates : 3
1 day, 3:14:24.024723 INFO: ms1_error      : 15.0
1 day, 3:14:24.024764 INFO: ms2_error      : 15.0
1 day, 3:14:24.024803 INFO: fwhm_rt        : 2.7884035110473633
1 day, 3:14:24.024843 INFO: quant_window   : 3
1 day, 3:14:24.024882 INFO: ==============================================
1 day, 3:14:24.039135 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:14:24.039277 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:14:24.039333 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1 day, 3:14:24.039360 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.01
1 day, 3:14:24.048053 INFO: Starting candidate selection
1 day, 3:14:53.818603 INFO: Starting candidate scoring
1 day, 3:14:59.755702 INFO: Finished candidate processing
1 day, 3:14:59.755870 INFO: Collecting candidate features
1 day, 3:14:59.989775 WARNING: intensity_correlation has 45 NaNs ( 0.03 % out of 133151)
1 day, 3:14:59.990184 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 133151)
1 day, 3:15:00.005246 INFO: Collecting fragment features
1 day, 3:15:00.104544 INFO: Finished candidate scoring
1 day, 3:15:00.173579 INFO: performing precursor FDR with 47 features
1 day, 3:15:00.173716 INFO: Decoy channel: -1
1 day, 3:15:00.173743 INFO: Competetive: True
1 day, 3:15:00.225563 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:15:00.254236 WARNING: dropped 29 target PSMs due to missing features
1 day, 3:15:00.254385 WARNING: dropped 18 decoy PSMs due to missing features
1 day, 3:15:00.282197 INFO: Using random state 826007 for train-test-split
1 day, 3:15:02.837182 INFO: Test AUC: 0.546
1 day, 3:15:02.837336 INFO: Train AUC: 0.592
1 day, 3:15:02.837372 INFO: AUC difference: 7.76%
1 day, 3:15:02.837395 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:15:03.129757 INFO: Resetting torch num_threads to 80
1 day, 3:15:03.133994 PROGRESS: === Extracted 133151 precursors and 1315100 fragments ===
1 day, 3:15:03.134597 INFO: === FDR correction performed with classifier version 10 ===
1 day, 3:15:03.139173 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:15:03.139314 PROGRESS: Total precursors accumulated: 24,379
1 day, 3:15:03.139401 PROGRESS: Target precursors: 14,915 (61.18%)
1 day, 3:15:03.139467 PROGRESS: Decoy precursors: 9,464 (38.82%)
1 day, 3:15:03.139514 PROGRESS: 
1 day, 3:15:03.139558 PROGRESS: Precursor Summary:
1 day, 3:15:03.140760 PROGRESS: Channel   0:	 0.050 FDR:   368; 0.010 FDR:   262; 0.001 FDR:   189
1 day, 3:15:03.140855 PROGRESS: 
1 day, 3:15:03.140916 PROGRESS: Protein Summary:
1 day, 3:15:03.142164 PROGRESS: Channel   0:	 0.050 FDR:   359; 0.010 FDR:   257; 0.001 FDR:   186
1 day, 3:15:03.142256 PROGRESS: =========================================================================
1 day, 3:15:03.144014 INFO: Target number of precursors reached.
1 day, 3:15:03.231523 INFO: fragments_df: keeping 3420 of 1315100 [sum(precursor_idx_mask)=8125 sum(mass_error_mask)=1315097 stop_rank=3420
1 day, 3:15:03.634421 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:15:03.739366 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:15:03.845693 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:15:03.946826 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:15:04.327459 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:15:04.327973 INFO: Using score_cutoff 38.03430577011108 (fac=0.99, q=1)
1 day, 3:15:04.328365 INFO: Updating optimization_manager: fwhm_rt             : 2.7884035110473633 -> 2.789369583129883
1 day, 3:15:04.328446 INFO: Updating optimization_manager: fwhm_mobility       : 0.008645701222121716 -> 0.008504614233970642
1 day, 3:15:04.328501 INFO: Updating optimization_manager: score_cutoff        : 41.251811208343504 -> 38.03430577011108
1 day, 3:15:04.328558 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:15:04.336459 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:15:04.366634 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:15:04.374040 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:15:04.445060 INFO: === checking if optimization conditions were reached ===
1 day, 3:15:04.445401 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 3:15:04.447930 INFO: Updating optimization_manager: rt_error            : 207.23586116352942 -> 163.9564206186506
1 day, 3:15:04.448054 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 163.9564.
1 day, 3:15:04.448132 INFO: ==============================================
1 day, 3:15:04.448222 INFO: Starting optimization step 5.
1 day, 3:15:04.448292 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 3:15:04.448366 INFO: Using classic extraction backend
1 day, 3:15:04.448540 PROGRESS: Extracting batch of 50061 precursors
1 day, 3:15:04.448620 INFO: === Search parameters used ===
1 day, 3:15:04.448678 INFO: rt_error       : 163.9564206186506
1 day, 3:15:04.448732 INFO: mobility_error : 0.1
1 day, 3:15:04.448783 INFO: num_candidates : 3
1 day, 3:15:04.448833 INFO: ms1_error      : 15.0
1 day, 3:15:04.448882 INFO: ms2_error      : 15.0
1 day, 3:15:04.448932 INFO: fwhm_rt        : 2.789369583129883
1 day, 3:15:04.448980 INFO: quant_window   : 3
1 day, 3:15:04.449027 INFO: ==============================================
1 day, 3:15:04.469126 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:15:04.469267 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:15:04.469325 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1 day, 3:15:04.469354 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.94
1 day, 3:15:04.485159 INFO: Starting candidate selection
1 day, 3:15:31.364050 INFO: Starting candidate scoring
1 day, 3:15:37.315652 INFO: Finished candidate processing
1 day, 3:15:37.315847 INFO: Collecting candidate features
1 day, 3:15:37.548134 WARNING: intensity_correlation has 67 NaNs ( 0.05 % out of 132543)
1 day, 3:15:37.548504 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 132543)
1 day, 3:15:37.556312 INFO: Collecting fragment features
1 day, 3:15:37.640357 INFO: Finished candidate scoring
1 day, 3:15:37.711457 INFO: performing precursor FDR with 47 features
1 day, 3:15:37.711596 INFO: Decoy channel: -1
1 day, 3:15:37.711623 INFO: Competetive: True
1 day, 3:15:37.755345 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:15:37.779374 WARNING: dropped 39 target PSMs due to missing features
1 day, 3:15:37.779532 WARNING: dropped 28 decoy PSMs due to missing features
1 day, 3:15:37.804664 INFO: Using random state 826007 for train-test-split
1 day, 3:15:40.154346 INFO: Test AUC: 0.556
1 day, 3:15:40.154494 INFO: Train AUC: 0.590
1 day, 3:15:40.154527 INFO: AUC difference: 5.90%
1 day, 3:15:40.154550 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:15:40.416807 INFO: Resetting torch num_threads to 80
1 day, 3:15:40.420276 PROGRESS: === Extracted 132543 precursors and 1302547 fragments ===
1 day, 3:15:40.420821 INFO: === FDR correction performed with classifier version 10 ===
1 day, 3:15:40.425442 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:15:40.425579 PROGRESS: Total precursors accumulated: 24,288
1 day, 3:15:40.425656 PROGRESS: Target precursors: 14,801 (60.94%)
1 day, 3:15:40.425709 PROGRESS: Decoy precursors: 9,487 (39.06%)
1 day, 3:15:40.425758 PROGRESS: 
1 day, 3:15:40.425802 PROGRESS: Precursor Summary:
1 day, 3:15:40.426920 PROGRESS: Channel   0:	 0.050 FDR:   340; 0.010 FDR:   220; 0.001 FDR:   160
1 day, 3:15:40.427011 PROGRESS: 
1 day, 3:15:40.427065 PROGRESS: Protein Summary:
1 day, 3:15:40.428248 PROGRESS: Channel   0:	 0.050 FDR:   332; 0.010 FDR:   215; 0.001 FDR:   157
1 day, 3:15:40.428336 PROGRESS: =========================================================================
1 day, 3:15:40.429373 INFO: Target number of precursors reached.
1 day, 3:15:40.515513 INFO: fragments_df: keeping 3038 of 1302547 [sum(precursor_idx_mask)=6915 sum(mass_error_mask)=1302544 stop_rank=3038
1 day, 3:15:40.664078 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:15:40.815840 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:15:40.934900 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:15:41.072532 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:15:41.477288 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:15:41.477766 INFO: Using score_cutoff 40.69516008224487 (fac=0.99, q=1)
1 day, 3:15:41.478104 INFO: Updating optimization_manager: fwhm_rt             : 2.789369583129883 -> 2.7388358116149902
1 day, 3:15:41.478184 INFO: Updating optimization_manager: fwhm_mobility       : 0.008504614233970642 -> 0.008507242426276207
1 day, 3:15:41.478238 INFO: Updating optimization_manager: score_cutoff        : 38.03430577011108 -> 40.69516008224487
1 day, 3:15:41.478306 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:15:41.486507 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:15:41.518266 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:15:41.526169 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:15:41.656091 INFO: === checking if optimization conditions were reached ===
1 day, 3:15:41.656449 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 3:15:41.659016 INFO: Updating optimization_manager: rt_error            : 163.9564206186506 -> 110.25216442611664
1 day, 3:15:41.659142 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 110.2522.
1 day, 3:15:41.659221 INFO: ==============================================
1 day, 3:15:41.659310 INFO: Starting optimization step 6.
1 day, 3:15:41.659383 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 3:15:41.659456 INFO: Using classic extraction backend
1 day, 3:15:41.659630 PROGRESS: Extracting batch of 50061 precursors
1 day, 3:15:41.659708 INFO: === Search parameters used ===
1 day, 3:15:41.659764 INFO: rt_error       : 110.25216442611664
1 day, 3:15:41.659817 INFO: mobility_error : 0.1
1 day, 3:15:41.659867 INFO: num_candidates : 3
1 day, 3:15:41.659917 INFO: ms1_error      : 15.0
1 day, 3:15:41.659966 INFO: ms2_error      : 15.0
1 day, 3:15:41.660033 INFO: fwhm_rt        : 2.7388358116149902
1 day, 3:15:41.660085 INFO: quant_window   : 3
1 day, 3:15:41.660134 INFO: ==============================================
1 day, 3:15:41.680688 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:15:41.680856 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:15:41.680917 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
1 day, 3:15:41.680946 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.95
1 day, 3:15:41.683608 INFO: Starting candidate selection
1 day, 3:15:59.940069 INFO: Starting candidate scoring
1 day, 3:16:05.540467 INFO: Finished candidate processing
1 day, 3:16:05.541377 INFO: Collecting candidate features
1 day, 3:16:05.807176 WARNING: intensity_correlation has 69 NaNs ( 0.05 % out of 131760)
1 day, 3:16:05.807566 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 131760)
1 day, 3:16:05.815420 INFO: Collecting fragment features
1 day, 3:16:05.900439 INFO: Finished candidate scoring
1 day, 3:16:05.975165 INFO: performing precursor FDR with 47 features
1 day, 3:16:05.975327 INFO: Decoy channel: -1
1 day, 3:16:05.975352 INFO: Competetive: True
1 day, 3:16:06.027694 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:16:06.057465 WARNING: dropped 41 target PSMs due to missing features
1 day, 3:16:06.057647 WARNING: dropped 29 decoy PSMs due to missing features
1 day, 3:16:06.083684 INFO: Using random state 826007 for train-test-split
1 day, 3:16:08.823593 INFO: Test AUC: 0.554
1 day, 3:16:08.823766 INFO: Train AUC: 0.583
1 day, 3:16:08.823801 INFO: AUC difference: 5.09%
1 day, 3:16:08.823824 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:16:09.099667 INFO: Resetting torch num_threads to 80
1 day, 3:16:09.104392 PROGRESS: === Extracted 131760 precursors and 1284399 fragments ===
1 day, 3:16:09.104994 INFO: === FDR correction performed with classifier version 10 ===
1 day, 3:16:09.110190 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:16:09.110339 PROGRESS: Total precursors accumulated: 24,157
1 day, 3:16:09.110405 PROGRESS: Target precursors: 14,690 (60.81%)
1 day, 3:16:09.110455 PROGRESS: Decoy precursors: 9,467 (39.19%)
1 day, 3:16:09.110502 PROGRESS: 
1 day, 3:16:09.110545 PROGRESS: Precursor Summary:
1 day, 3:16:09.111715 PROGRESS: Channel   0:	 0.050 FDR:   377; 0.010 FDR:   267; 0.001 FDR:   162
1 day, 3:16:09.111810 PROGRESS: 
1 day, 3:16:09.111867 PROGRESS: Protein Summary:
1 day, 3:16:09.113091 PROGRESS: Channel   0:	 0.050 FDR:   370; 0.010 FDR:   262; 0.001 FDR:   159
1 day, 3:16:09.113181 PROGRESS: =========================================================================
1 day, 3:16:09.114225 INFO: Target number of precursors reached.
1 day, 3:16:09.200955 INFO: fragments_df: keeping 3475 of 1284399 [sum(precursor_idx_mask)=8280 sum(mass_error_mask)=1284393 stop_rank=3475
1 day, 3:16:09.427427 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:16:09.707471 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:16:09.829576 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:16:09.959338 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:16:10.411182 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:16:10.411727 INFO: Using score_cutoff 38.65452922897339 (fac=0.99, q=1)
1 day, 3:16:10.412134 INFO: Updating optimization_manager: fwhm_rt             : 2.7388358116149902 -> 2.732227087020874
1 day, 3:16:10.412220 INFO: Updating optimization_manager: fwhm_mobility       : 0.008507242426276207 -> 0.008269079029560089
1 day, 3:16:10.412278 INFO: Updating optimization_manager: score_cutoff        : 40.69516008224487 -> 38.65452922897339
1 day, 3:16:10.412337 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:16:10.419939 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:16:10.450251 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:16:10.457806 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:16:10.525287 INFO: === checking if optimization conditions were reached ===
1 day, 3:16:10.525669 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 3:16:10.528490 INFO: Updating optimization_manager: rt_error            : 110.25216442611664 -> 102.42365084640448
1 day, 3:16:10.528615 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 102.4237.
1 day, 3:16:10.528715 INFO: ==============================================
1 day, 3:16:10.528814 INFO: Starting optimization step 7.
1 day, 3:16:10.528884 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 3:16:10.528961 INFO: Using classic extraction backend
1 day, 3:16:10.529157 PROGRESS: Extracting batch of 50061 precursors
1 day, 3:16:10.529270 INFO: === Search parameters used ===
1 day, 3:16:10.529331 INFO: rt_error       : 102.42365084640448
1 day, 3:16:10.529385 INFO: mobility_error : 0.1
1 day, 3:16:10.529436 INFO: num_candidates : 3
1 day, 3:16:10.529487 INFO: ms1_error      : 15.0
1 day, 3:16:10.529539 INFO: ms2_error      : 15.0
1 day, 3:16:10.529588 INFO: fwhm_rt        : 2.732227087020874
1 day, 3:16:10.529637 INFO: quant_window   : 3
1 day, 3:16:10.529686 INFO: ==============================================
1 day, 3:16:10.556825 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:16:10.557002 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:16:10.557068 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
1 day, 3:16:10.557099 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1 day, 3:16:10.569921 INFO: Starting candidate selection
1 day, 3:16:27.408574 INFO: Starting candidate scoring
1 day, 3:16:32.513152 INFO: Finished candidate processing
1 day, 3:16:32.513413 INFO: Collecting candidate features
1 day, 3:16:32.775997 WARNING: intensity_correlation has 66 NaNs ( 0.05 % out of 131747)
1 day, 3:16:32.776409 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 131747)
1 day, 3:16:32.784297 INFO: Collecting fragment features
1 day, 3:16:32.878249 INFO: Finished candidate scoring
1 day, 3:16:32.986978 INFO: performing precursor FDR with 47 features
1 day, 3:16:32.987135 INFO: Decoy channel: -1
1 day, 3:16:32.987160 INFO: Competetive: True
1 day, 3:16:33.032324 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:16:33.061097 WARNING: dropped 39 target PSMs due to missing features
1 day, 3:16:33.061266 WARNING: dropped 29 decoy PSMs due to missing features
1 day, 3:16:33.083954 INFO: Using random state 826007 for train-test-split
1 day, 3:16:35.458773 INFO: Test AUC: 0.553
1 day, 3:16:35.458933 INFO: Train AUC: 0.586
1 day, 3:16:35.458966 INFO: AUC difference: 5.58%
1 day, 3:16:35.458989 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:16:35.726861 INFO: Resetting torch num_threads to 80
1 day, 3:16:35.731265 PROGRESS: === Extracted 131747 precursors and 1284138 fragments ===
1 day, 3:16:35.731850 INFO: === FDR correction performed with classifier version 10 ===
1 day, 3:16:35.736356 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:16:35.736492 PROGRESS: Total precursors accumulated: 24,147
1 day, 3:16:35.736557 PROGRESS: Target precursors: 14,642 (60.64%)
1 day, 3:16:35.736609 PROGRESS: Decoy precursors: 9,505 (39.36%)
1 day, 3:16:35.736661 PROGRESS: 
1 day, 3:16:35.736705 PROGRESS: Precursor Summary:
1 day, 3:16:35.737846 PROGRESS: Channel   0:	 0.050 FDR:   385; 0.010 FDR:   293; 0.001 FDR:   150
1 day, 3:16:35.737942 PROGRESS: 
1 day, 3:16:35.738002 PROGRESS: Protein Summary:
1 day, 3:16:35.739272 PROGRESS: Channel   0:	 0.050 FDR:   377; 0.010 FDR:   288; 0.001 FDR:   148
1 day, 3:16:35.739382 PROGRESS: =========================================================================
1 day, 3:16:35.740371 INFO: Target number of precursors reached.
1 day, 3:16:35.826238 INFO: fragments_df: keeping 3793 of 1284138 [sum(precursor_idx_mask)=9034 sum(mass_error_mask)=1284132 stop_rank=3793
1 day, 3:16:36.209859 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:16:36.338589 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:16:36.464778 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:16:36.588222 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:16:37.082172 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:16:37.082716 INFO: Using score_cutoff 37.14169144592285 (fac=0.99, q=1)
1 day, 3:16:37.083103 INFO: Updating optimization_manager: fwhm_rt             : 2.732227087020874 -> 2.6870460510253906
1 day, 3:16:37.083192 INFO: Updating optimization_manager: fwhm_mobility       : 0.008269079029560089 -> 0.008097738958895206
1 day, 3:16:37.083251 INFO: Updating optimization_manager: score_cutoff        : 38.65452922897339 -> 37.14169144592285
1 day, 3:16:37.083310 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:16:37.090483 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:16:37.120489 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:16:37.127672 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:16:37.188093 INFO: === checking if optimization conditions were reached ===
1 day, 3:16:37.188471 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1 day, 3:16:37.191356 INFO: Updating optimization_manager: rt_error            : 102.42365084640448 -> 101.86967045668027
1 day, 3:16:37.191478 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 101.8697.
1 day, 3:16:37.191556 INFO: ==============================================
1 day, 3:16:37.191648 INFO: Starting optimization step 8.
1 day, 3:16:37.191722 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 3:16:37.191808 INFO: Using classic extraction backend
1 day, 3:16:37.192028 PROGRESS: Extracting batch of 50061 precursors
1 day, 3:16:37.192114 INFO: === Search parameters used ===
1 day, 3:16:37.192173 INFO: rt_error       : 101.86967045668027
1 day, 3:16:37.192226 INFO: mobility_error : 0.1
1 day, 3:16:37.192279 INFO: num_candidates : 3
1 day, 3:16:37.192329 INFO: ms1_error      : 15.0
1 day, 3:16:37.192380 INFO: ms2_error      : 15.0
1 day, 3:16:37.192428 INFO: fwhm_rt        : 2.6870460510253906
1 day, 3:16:37.192478 INFO: quant_window   : 3
1 day, 3:16:37.192527 INFO: ==============================================
1 day, 3:16:37.219745 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:16:37.219932 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:16:37.219995 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
1 day, 3:16:37.220025 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.76
1 day, 3:16:37.235305 INFO: Starting candidate selection
1 day, 3:16:54.731733 INFO: Starting candidate scoring
1 day, 3:17:00.589971 INFO: Finished candidate processing
1 day, 3:17:00.591271 INFO: Collecting candidate features
1 day, 3:17:00.868770 WARNING: intensity_correlation has 58 NaNs ( 0.04 % out of 131793)
1 day, 3:17:00.869123 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 131793)
1 day, 3:17:00.879261 INFO: Collecting fragment features
1 day, 3:17:00.965578 INFO: Finished candidate scoring
1 day, 3:17:01.064770 INFO: performing precursor FDR with 47 features
1 day, 3:17:01.064888 INFO: Decoy channel: -1
1 day, 3:17:01.064913 INFO: Competetive: True
1 day, 3:17:01.108197 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:17:01.155995 WARNING: dropped 36 target PSMs due to missing features
1 day, 3:17:01.156180 WARNING: dropped 24 decoy PSMs due to missing features
1 day, 3:17:01.211906 INFO: Using random state 826007 for train-test-split
1 day, 3:17:04.545989 INFO: Test AUC: 0.550
1 day, 3:17:04.548490 INFO: Train AUC: 0.584
1 day, 3:17:04.548596 INFO: AUC difference: 5.75%
1 day, 3:17:04.548645 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:17:04.851795 INFO: Resetting torch num_threads to 80
1 day, 3:17:04.857518 PROGRESS: === Extracted 131793 precursors and 1283290 fragments ===
1 day, 3:17:04.858218 INFO: === FDR correction performed with classifier version 10 ===
1 day, 3:17:04.863737 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:17:04.863872 PROGRESS: Total precursors accumulated: 24,158
1 day, 3:17:04.863939 PROGRESS: Target precursors: 14,687 (60.80%)
1 day, 3:17:04.864008 PROGRESS: Decoy precursors: 9,471 (39.20%)
1 day, 3:17:04.864063 PROGRESS: 
1 day, 3:17:04.864109 PROGRESS: Precursor Summary:
1 day, 3:17:04.865278 PROGRESS: Channel   0:	 0.050 FDR:   383; 0.010 FDR:   274; 0.001 FDR:   172
1 day, 3:17:04.865372 PROGRESS: 
1 day, 3:17:04.865429 PROGRESS: Protein Summary:
1 day, 3:17:04.866662 PROGRESS: Channel   0:	 0.050 FDR:   376; 0.010 FDR:   268; 0.001 FDR:   169
1 day, 3:17:04.866753 PROGRESS: =========================================================================
1 day, 3:17:04.867819 INFO: Target number of precursors reached.
1 day, 3:17:04.956040 INFO: fragments_df: keeping 3559 of 1283290 [sum(precursor_idx_mask)=8471 sum(mass_error_mask)=1283283 stop_rank=3559
1 day, 3:17:05.177454 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:17:05.298246 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:17:05.421253 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:17:05.546848 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:17:06.007484 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:17:06.007979 INFO: Using score_cutoff 38.43491659812927 (fac=0.99, q=1)
1 day, 3:17:06.008313 INFO: Updating optimization_manager: fwhm_rt             : 2.6870460510253906 -> 2.7727065086364746
1 day, 3:17:06.008394 INFO: Updating optimization_manager: fwhm_mobility       : 0.008097738958895206 -> 0.008218152448534966
1 day, 3:17:06.008450 INFO: Updating optimization_manager: score_cutoff        : 37.14169144592285 -> 38.43491659812927
1 day, 3:17:06.008520 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:17:06.015730 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:17:06.045913 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:17:06.053314 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:17:06.116978 INFO: === checking if optimization conditions were reached ===
1 day, 3:17:06.117277 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
1 day, 3:17:06.118659 INFO: Updating optimization_manager: rt_error            : 101.86967045668027 -> 101.86967045668027
1 day, 3:17:06.118798 INFO: Updating optimization_manager: classifier_version  : 10 -> 19
1 day, 3:17:06.118899 INFO: Updating optimization_manager: score_cutoff        : 38.43491659812927 -> 38.43491659812927
1 day, 3:17:06.118986 INFO: Updating optimization_manager: fwhm_rt             : 2.7727065086364746 -> 2.7727065086364746
1 day, 3:17:06.119072 INFO: Updating optimization_manager: fwhm_mobility       : 0.008218152448534966 -> 0.008218152448534966
1 day, 3:17:06.119158 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 101.8697 found after 9 searches.
1 day, 3:17:06.119222 INFO: ==============================================
1 day, 3:17:06.119304 PROGRESS: Optimization finished for rt_error.
1 day, 3:17:06.260863 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:17:06.268565 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:17:06.298949 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:17:06.306393 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:17:06.396583 INFO: Starting optimization step 0.
1 day, 3:17:06.396871 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 3:17:06.396986 INFO: Using classic extraction backend
1 day, 3:17:06.397207 PROGRESS: Extracting batch of 50061 precursors
1 day, 3:17:06.397290 INFO: === Search parameters used ===
1 day, 3:17:06.397343 INFO: rt_error       : 101.86967045668027
1 day, 3:17:06.397394 INFO: mobility_error : 0.1
1 day, 3:17:06.397440 INFO: num_candidates : 3
1 day, 3:17:06.397483 INFO: ms1_error      : 15.0
1 day, 3:17:06.397524 INFO: ms2_error      : 15.0
1 day, 3:17:06.397566 INFO: fwhm_rt        : 2.7727065086364746
1 day, 3:17:06.397606 INFO: quant_window   : 3
1 day, 3:17:06.397654 INFO: ==============================================
1 day, 3:17:06.417984 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:17:06.418150 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:17:06.418208 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 3:17:06.418232 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.81
1 day, 3:17:06.427119 INFO: Starting candidate selection
1 day, 3:17:24.057180 INFO: Starting candidate scoring
1 day, 3:17:29.978376 INFO: Finished candidate processing
1 day, 3:17:29.978565 INFO: Collecting candidate features
1 day, 3:17:30.195974 WARNING: intensity_correlation has 65 NaNs ( 0.05 % out of 131683)
1 day, 3:17:30.196324 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 131683)
1 day, 3:17:30.204113 INFO: Collecting fragment features
1 day, 3:17:30.288806 INFO: Finished candidate scoring
1 day, 3:17:30.353496 INFO: performing precursor FDR with 47 features
1 day, 3:17:30.353643 INFO: Decoy channel: -1
1 day, 3:17:30.353670 INFO: Competetive: True
1 day, 3:17:30.399651 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:17:30.427606 WARNING: dropped 40 target PSMs due to missing features
1 day, 3:17:30.427770 WARNING: dropped 27 decoy PSMs due to missing features
1 day, 3:17:30.447476 INFO: Using random state 693195 for train-test-split
1 day, 3:17:32.893042 INFO: Test AUC: 0.566
1 day, 3:17:32.893177 INFO: Train AUC: 0.604
1 day, 3:17:32.893209 INFO: AUC difference: 6.37%
1 day, 3:17:32.893234 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:17:33.147270 INFO: Resetting torch num_threads to 80
1 day, 3:17:33.151526 PROGRESS: === Extracted 131683 precursors and 1283113 fragments ===
1 day, 3:17:33.152040 INFO: === FDR correction performed with classifier version 19 ===
1 day, 3:17:33.156247 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:17:33.156374 PROGRESS: Total precursors accumulated: 24,148
1 day, 3:17:33.156438 PROGRESS: Target precursors: 15,190 (62.90%)
1 day, 3:17:33.156491 PROGRESS: Decoy precursors: 8,958 (37.10%)
1 day, 3:17:33.156546 PROGRESS: 
1 day, 3:17:33.156592 PROGRESS: Precursor Summary:
1 day, 3:17:33.157678 PROGRESS: Channel   0:	 0.050 FDR:   415; 0.010 FDR:   211; 0.001 FDR:     0
1 day, 3:17:33.157782 PROGRESS: 
1 day, 3:17:33.157839 PROGRESS: Protein Summary:
1 day, 3:17:33.159028 PROGRESS: Channel   0:	 0.050 FDR:   407; 0.010 FDR:   207; 0.001 FDR:     0
1 day, 3:17:33.159125 PROGRESS: =========================================================================
1 day, 3:17:33.159925 INFO: Target number of precursors reached.
1 day, 3:17:33.244081 INFO: fragments_df: keeping 2952 of 1283113 [sum(precursor_idx_mask)=6594 sum(mass_error_mask)=1283107 stop_rank=2952
1 day, 3:17:33.393794 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:17:33.489793 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:17:33.588442 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:17:33.685736 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:17:34.006581 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:17:34.007083 INFO: Using score_cutoff 40.04098249053955 (fac=0.99, q=1)
1 day, 3:17:34.007395 INFO: Updating optimization_manager: fwhm_rt             : 2.7727065086364746 -> 2.7316975593566895
1 day, 3:17:34.007478 INFO: Updating optimization_manager: fwhm_mobility       : 0.008218152448534966 -> 0.008464006707072258
1 day, 3:17:34.007535 INFO: Updating optimization_manager: score_cutoff        : 38.43491659812927 -> 40.04098249053955
1 day, 3:17:34.007590 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:17:34.015760 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:17:34.045749 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:17:34.053351 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:17:34.111772 INFO: === checking if optimization conditions were reached ===
1 day, 3:17:34.112096 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 3:17:34.113936 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.06415201145619238
1 day, 3:17:34.114040 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0642.
1 day, 3:17:34.114108 INFO: ==============================================
1 day, 3:17:34.114176 INFO: Starting optimization step 1.
1 day, 3:17:34.114236 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 3:17:34.114292 INFO: Using classic extraction backend
1 day, 3:17:34.114408 PROGRESS: Extracting batch of 50061 precursors
1 day, 3:17:34.114473 INFO: === Search parameters used ===
1 day, 3:17:34.114523 INFO: rt_error       : 101.86967045668027
1 day, 3:17:34.114567 INFO: mobility_error : 0.06415201145619238
1 day, 3:17:34.114610 INFO: num_candidates : 3
1 day, 3:17:34.114653 INFO: ms1_error      : 15.0
1 day, 3:17:34.114695 INFO: ms2_error      : 15.0
1 day, 3:17:34.114735 INFO: fwhm_rt        : 2.7316975593566895
1 day, 3:17:34.114775 INFO: quant_window   : 3
1 day, 3:17:34.114835 INFO: ==============================================
1 day, 3:17:34.132133 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:17:34.132280 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:17:34.132322 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
1 day, 3:17:34.132345 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
1 day, 3:17:34.133313 INFO: Starting candidate selection
1 day, 3:17:45.715861 INFO: Starting candidate scoring
1 day, 3:17:51.555461 INFO: Finished candidate processing
1 day, 3:17:51.555655 INFO: Collecting candidate features
1 day, 3:17:51.807926 WARNING: intensity_correlation has 61 NaNs ( 0.05 % out of 127727)
1 day, 3:17:51.808455 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 127727)
1 day, 3:17:51.823692 INFO: Collecting fragment features
1 day, 3:17:51.909887 INFO: Finished candidate scoring
1 day, 3:17:52.001991 INFO: performing precursor FDR with 47 features
1 day, 3:17:52.002124 INFO: Decoy channel: -1
1 day, 3:17:52.002149 INFO: Competetive: True
1 day, 3:17:52.038926 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:17:52.059984 WARNING: dropped 41 target PSMs due to missing features
1 day, 3:17:52.060125 WARNING: dropped 26 decoy PSMs due to missing features
1 day, 3:17:52.083674 INFO: Using random state 693195 for train-test-split
1 day, 3:17:54.800763 INFO: Test AUC: 0.563
1 day, 3:17:54.801151 INFO: Train AUC: 0.595
1 day, 3:17:54.801187 INFO: AUC difference: 5.35%
1 day, 3:17:54.801211 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:17:55.061710 INFO: Resetting torch num_threads to 80
1 day, 3:17:55.066031 PROGRESS: === Extracted 127727 precursors and 1225869 fragments ===
1 day, 3:17:55.066617 INFO: === FDR correction performed with classifier version 19 ===
1 day, 3:17:55.070899 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:17:55.071026 PROGRESS: Total precursors accumulated: 23,451
1 day, 3:17:55.071090 PROGRESS: Target precursors: 14,599 (62.25%)
1 day, 3:17:55.071140 PROGRESS: Decoy precursors: 8,852 (37.75%)
1 day, 3:17:55.071184 PROGRESS: 
1 day, 3:17:55.071229 PROGRESS: Precursor Summary:
1 day, 3:17:55.072355 PROGRESS: Channel   0:	 0.050 FDR:   365; 0.010 FDR:   310; 0.001 FDR:   180
1 day, 3:17:55.072446 PROGRESS: 
1 day, 3:17:55.072500 PROGRESS: Protein Summary:
1 day, 3:17:55.073754 PROGRESS: Channel   0:	 0.050 FDR:   358; 0.010 FDR:   305; 0.001 FDR:   178
1 day, 3:17:55.073843 PROGRESS: =========================================================================
1 day, 3:17:55.076938 INFO: Target number of precursors reached.
1 day, 3:17:55.161658 INFO: fragments_df: keeping 3891 of 1225869 [sum(precursor_idx_mask)=9543 sum(mass_error_mask)=1225861 stop_rank=3891
1 day, 3:17:55.467333 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:17:55.586457 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:17:55.710663 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:17:55.832384 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:17:56.341096 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:17:56.341667 INFO: Using score_cutoff 35.522071854400636 (fac=0.99, q=1)
1 day, 3:17:56.342029 INFO: Updating optimization_manager: fwhm_rt             : 2.7316975593566895 -> 2.750082492828369
1 day, 3:17:56.342135 INFO: Updating optimization_manager: fwhm_mobility       : 0.008464006707072258 -> 0.007932594045996666
1 day, 3:17:56.342191 INFO: Updating optimization_manager: score_cutoff        : 40.04098249053955 -> 35.522071854400636
1 day, 3:17:56.342256 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:17:56.349910 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:17:56.380239 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:17:56.387632 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:17:56.453261 INFO: === checking if optimization conditions were reached ===
1 day, 3:17:56.453641 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 3:17:56.455811 INFO: Updating optimization_manager: mobility_error      : 0.06415201145619238 -> 0.05741404268073602
1 day, 3:17:56.455935 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0574.
1 day, 3:17:56.456004 INFO: ==============================================
1 day, 3:17:56.456084 INFO: Starting optimization step 2.
1 day, 3:17:56.456144 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 3:17:56.456213 INFO: Using classic extraction backend
1 day, 3:17:56.456445 PROGRESS: Extracting batch of 50061 precursors
1 day, 3:17:56.456523 INFO: === Search parameters used ===
1 day, 3:17:56.456576 INFO: rt_error       : 101.86967045668027
1 day, 3:17:56.456620 INFO: mobility_error : 0.05741404268073602
1 day, 3:17:56.456661 INFO: num_candidates : 3
1 day, 3:17:56.456717 INFO: ms1_error      : 15.0
1 day, 3:17:56.456759 INFO: ms2_error      : 15.0
1 day, 3:17:56.456797 INFO: fwhm_rt        : 2.750082492828369
1 day, 3:17:56.456836 INFO: quant_window   : 3
1 day, 3:17:56.456876 INFO: ==============================================
1 day, 3:17:56.482421 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:17:56.482602 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:17:56.482667 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 3:17:56.482692 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.68
1 day, 3:17:56.521549 INFO: Starting candidate selection
1 day, 3:18:07.425939 INFO: Starting candidate scoring
1 day, 3:18:12.861263 INFO: Finished candidate processing
1 day, 3:18:12.861446 INFO: Collecting candidate features
1 day, 3:18:13.074326 WARNING: intensity_correlation has 81 NaNs ( 0.06 % out of 126603)
1 day, 3:18:13.074768 WARNING: height_correlation has 10 NaNs ( 0.01 % out of 126603)
1 day, 3:18:13.085271 INFO: Collecting fragment features
1 day, 3:18:13.158315 INFO: Finished candidate scoring
1 day, 3:18:13.304996 INFO: performing precursor FDR with 47 features
1 day, 3:18:13.305144 INFO: Decoy channel: -1
1 day, 3:18:13.305172 INFO: Competetive: True
1 day, 3:18:13.352983 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:18:13.380583 WARNING: dropped 51 target PSMs due to missing features
1 day, 3:18:13.380751 WARNING: dropped 39 decoy PSMs due to missing features
1 day, 3:18:13.400527 INFO: Using random state 693195 for train-test-split
1 day, 3:18:15.681818 INFO: Test AUC: 0.563
1 day, 3:18:15.681965 INFO: Train AUC: 0.598
1 day, 3:18:15.681997 INFO: AUC difference: 5.95%
1 day, 3:18:15.682019 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:18:15.933072 INFO: Resetting torch num_threads to 80
1 day, 3:18:15.937230 PROGRESS: === Extracted 126603 precursors and 1207294 fragments ===
1 day, 3:18:15.937733 INFO: === FDR correction performed with classifier version 19 ===
1 day, 3:18:15.941941 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:18:15.942063 PROGRESS: Total precursors accumulated: 23,290
1 day, 3:18:15.942123 PROGRESS: Target precursors: 14,588 (62.64%)
1 day, 3:18:15.942180 PROGRESS: Decoy precursors: 8,702 (37.36%)
1 day, 3:18:15.942237 PROGRESS: 
1 day, 3:18:15.942288 PROGRESS: Precursor Summary:
1 day, 3:18:15.943448 PROGRESS: Channel   0:	 0.050 FDR:   424; 0.010 FDR:   301; 0.001 FDR:   233
1 day, 3:18:15.943556 PROGRESS: 
1 day, 3:18:15.943620 PROGRESS: Protein Summary:
1 day, 3:18:15.944884 PROGRESS: Channel   0:	 0.050 FDR:   414; 0.010 FDR:   295; 0.001 FDR:   229
1 day, 3:18:15.944983 PROGRESS: =========================================================================
1 day, 3:18:15.945784 INFO: Target number of precursors reached.
1 day, 3:18:16.026711 INFO: fragments_df: keeping 3892 of 1207294 [sum(precursor_idx_mask)=9338 sum(mass_error_mask)=1207284 stop_rank=3892
1 day, 3:18:16.170878 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:18:16.288733 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:18:16.417330 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:18:16.535899 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:18:17.042727 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:18:17.043230 INFO: Using score_cutoff 36.2471484375 (fac=0.99, q=1)
1 day, 3:18:17.043544 INFO: Updating optimization_manager: fwhm_rt             : 2.750082492828369 -> 2.6885228157043457
1 day, 3:18:17.043628 INFO: Updating optimization_manager: fwhm_mobility       : 0.007932594045996666 -> 0.008112340234220028
1 day, 3:18:17.043689 INFO: Updating optimization_manager: score_cutoff        : 35.522071854400636 -> 36.2471484375
1 day, 3:18:17.043748 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:18:17.051181 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:18:17.081796 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:18:17.088891 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:18:17.151739 INFO: === checking if optimization conditions were reached ===
1 day, 3:18:17.152068 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 3:18:17.154430 INFO: Updating optimization_manager: mobility_error      : 0.05741404268073602 -> 0.052898615643436106
1 day, 3:18:17.154545 PROGRESS: ❌ mobility_error : optimization incomplete after 3 search(es). Will search with parameter 0.0529.
1 day, 3:18:17.154623 INFO: ==============================================
1 day, 3:18:17.154702 INFO: Starting optimization step 3.
1 day, 3:18:17.154797 PROGRESS: === Extracting elution groups 0 to 25400 ===
1 day, 3:18:17.154870 INFO: Using classic extraction backend
1 day, 3:18:17.155005 PROGRESS: Extracting batch of 50061 precursors
1 day, 3:18:17.155081 INFO: === Search parameters used ===
1 day, 3:18:17.155136 INFO: rt_error       : 101.86967045668027
1 day, 3:18:17.155188 INFO: mobility_error : 0.052898615643436106
1 day, 3:18:17.155240 INFO: num_candidates : 3
1 day, 3:18:17.155288 INFO: ms1_error      : 15.0
1 day, 3:18:17.155337 INFO: ms2_error      : 15.0
1 day, 3:18:17.155384 INFO: fwhm_rt        : 2.6885228157043457
1 day, 3:18:17.155432 INFO: quant_window   : 3
1 day, 3:18:17.155479 INFO: ==============================================
1 day, 3:18:17.180128 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:18:17.180283 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:18:17.180333 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
1 day, 3:18:17.180359 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.76
1 day, 3:18:17.192263 INFO: Starting candidate selection
1 day, 3:18:27.203021 INFO: Starting candidate scoring
1 day, 3:18:32.373052 INFO: Finished candidate processing
1 day, 3:18:32.373329 INFO: Collecting candidate features
1 day, 3:18:32.628056 WARNING: intensity_correlation has 86 NaNs ( 0.07 % out of 126813)
1 day, 3:18:32.628600 WARNING: height_correlation has 9 NaNs ( 0.01 % out of 126813)
1 day, 3:18:32.643642 INFO: Collecting fragment features
1 day, 3:18:32.720187 INFO: Finished candidate scoring
1 day, 3:18:32.790548 INFO: performing precursor FDR with 47 features
1 day, 3:18:32.790665 INFO: Decoy channel: -1
1 day, 3:18:32.790691 INFO: Competetive: True
1 day, 3:18:32.844265 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 3:18:32.872112 WARNING: dropped 54 target PSMs due to missing features
1 day, 3:18:32.872263 WARNING: dropped 38 decoy PSMs due to missing features
1 day, 3:18:32.908640 INFO: Using random state 693195 for train-test-split
1 day, 3:18:35.216886 INFO: Test AUC: 0.565
1 day, 3:18:35.217033 INFO: Train AUC: 0.595
1 day, 3:18:35.217066 INFO: AUC difference: 5.15%
1 day, 3:18:35.217091 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 3:18:35.476358 INFO: Resetting torch num_threads to 80
1 day, 3:18:35.479605 PROGRESS: === Extracted 126813 precursors and 1208749 fragments ===
1 day, 3:18:35.480156 INFO: === FDR correction performed with classifier version 19 ===
1 day, 3:18:35.484239 PROGRESS: ============================= Precursor FDR =============================
1 day, 3:18:35.484359 PROGRESS: Total precursors accumulated: 23,310
1 day, 3:18:35.484422 PROGRESS: Target precursors: 14,477 (62.11%)
1 day, 3:18:35.484471 PROGRESS: Decoy precursors: 8,833 (37.89%)
1 day, 3:18:35.484515 PROGRESS: 
1 day, 3:18:35.484558 PROGRESS: Precursor Summary:
1 day, 3:18:35.485671 PROGRESS: Channel   0:	 0.050 FDR:   414; 0.010 FDR:   314; 0.001 FDR:   212
1 day, 3:18:35.485760 PROGRESS: 
1 day, 3:18:35.485825 PROGRESS: Protein Summary:
1 day, 3:18:35.487086 PROGRESS: Channel   0:	 0.050 FDR:   406; 0.010 FDR:   310; 0.001 FDR:   209
1 day, 3:18:35.487175 PROGRESS: =========================================================================
1 day, 3:18:35.488144 INFO: Target number of precursors reached.
1 day, 3:18:35.571713 INFO: fragments_df: keeping 3928 of 1208749 [sum(precursor_idx_mask)=9700 sum(mass_error_mask)=1208737 stop_rank=3928
1 day, 3:18:35.785839 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:18:35.905456 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:18:36.034637 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:18:36.153767 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:18:36.664560 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 3:18:36.665051 INFO: Using score_cutoff 36.35666299552918 (fac=0.99, q=1)
1 day, 3:18:36.665384 INFO: Updating optimization_manager: fwhm_rt             : 2.6885228157043457 -> 2.702253580093384
1 day, 3:18:36.665465 INFO: Updating optimization_manager: fwhm_mobility       : 0.008112340234220028 -> 0.007916592061519623
1 day, 3:18:36.665523 INFO: Updating optimization_manager: score_cutoff        : 36.2471484375 -> 36.35666299552918
1 day, 3:18:36.665581 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:18:36.672851 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:18:36.703074 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:18:36.710140 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:18:36.774401 INFO: === checking if optimization conditions were reached ===
1 day, 3:18:36.774766 PROGRESS: === Optimization of mobility_error has been performed 4 time(s); minimum number is 2 ===
1 day, 3:18:36.775784 INFO: Updating optimization_manager: mobility_error      : 0.052898615643436106 -> 0.052898615643436106
1 day, 3:18:36.775927 INFO: Updating optimization_manager: classifier_version  : 19 -> 23
1 day, 3:18:36.776046 INFO: Updating optimization_manager: score_cutoff        : 36.35666299552918 -> 36.35666299552918
1 day, 3:18:36.776169 INFO: Updating optimization_manager: fwhm_rt             : 2.702253580093384 -> 2.702253580093384
1 day, 3:18:36.776284 INFO: Updating optimization_manager: fwhm_mobility       : 0.007916592061519623 -> 0.007916592061519623
1 day, 3:18:36.776395 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0529 found after 4 searches.
1 day, 3:18:36.776481 INFO: ==============================================
1 day, 3:18:36.776576 PROGRESS: Optimization finished for mobility_error.
1 day, 3:18:36.911524 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:18:36.919217 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:18:36.949651 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:18:36.956662 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:18:37.044769 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 3:18:37.045027 PROGRESS: ==============================================
1 day, 3:18:37.045122 PROGRESS: ms2_error      : 15.0000
1 day, 3:18:37.045208 PROGRESS: ms1_error      : 15.0000
1 day, 3:18:37.045285 PROGRESS: rt_error       : 101.8697
1 day, 3:18:37.045370 PROGRESS: mobility_error : 0.0529
1 day, 3:18:37.045438 PROGRESS: ==============================================
1 day, 3:18:37.047765 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 3:18:38.532456 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 3:18:46.025008 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 3:18:47.577135 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 3:19:03.614893 INFO: Using classic extraction backend
1 day, 3:19:03.616059 PROGRESS: Extracting batch of 12073114 precursors
1 day, 3:19:03.616160 INFO: === Search parameters used ===
1 day, 3:19:03.616217 INFO: rt_error       : 101.86967045668027
1 day, 3:19:03.616263 INFO: mobility_error : 0.052898615643436106
1 day, 3:19:03.616308 INFO: num_candidates : 3
1 day, 3:19:03.616350 INFO: ms1_error      : 15.0
1 day, 3:19:03.616392 INFO: ms2_error      : 15.0
1 day, 3:19:03.616432 INFO: fwhm_rt        : 2.702253580093384
1 day, 3:19:03.616472 INFO: quant_window   : 3
1 day, 3:19:03.616511 INFO: ==============================================
1 day, 3:19:06.498216 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 3:19:06.498376 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 3:19:06.498432 INFO: FWHM in RT is 2.70 seconds, sigma is 0.59
1 day, 3:19:06.498459 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.67
1 day, 3:19:06.499320 INFO: Starting candidate selection
1 day, 3:53:57.550520 INFO: Removed 15733605 precursors with score below cutoff 36.35666299552918
1 day, 3:54:00.291415 INFO: Starting candidate scoring
1 day, 4:05:27.872058 INFO: Finished candidate processing
1 day, 4:05:27.875338 INFO: Collecting candidate features
1 day, 4:05:58.455000 WARNING: intensity_correlation has 10 NaNs ( 0.00 % out of 16893576)
1 day, 4:05:59.037609 INFO: Collecting fragment features
1 day, 4:06:13.086148 INFO: Finished candidate scoring
1 day, 4:06:41.499630 INFO: === Performing FDR correction with classifier version 23 ===
1 day, 4:06:41.556549 INFO: performing precursor FDR with 47 features
1 day, 4:06:41.556695 INFO: Decoy channel: -1
1 day, 4:06:41.556723 INFO: Competetive: True
1 day, 4:06:45.756148 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:06:48.354050 WARNING: dropped 6 target PSMs due to missing features
1 day, 4:06:48.354494 WARNING: dropped 4 decoy PSMs due to missing features
1 day, 4:06:55.367293 INFO: Using random state 355540 for train-test-split
1 day, 4:12:52.374407 INFO: Test AUC: 0.569
1 day, 4:12:52.374675 INFO: Train AUC: 0.570
1 day, 4:12:52.374717 INFO: AUC difference: 0.17%
1 day, 4:12:57.815353 INFO: Resetting torch num_threads to 80
1 day, 4:12:58.106457 INFO: Removing fragments below FDR threshold
1 day, 4:12:59.710765 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:12:59.711084 PROGRESS: Total precursors accumulated: 68,913
1 day, 4:12:59.711147 PROGRESS: Target precursors: 68,231 (99.01%)
1 day, 4:12:59.711199 PROGRESS: Decoy precursors: 682 (0.99%)
1 day, 4:12:59.711244 PROGRESS: 
1 day, 4:12:59.711286 PROGRESS: Precursor Summary:
1 day, 4:12:59.736569 PROGRESS: Channel   0:	 0.050 FDR: 68,231; 0.010 FDR: 68,231; 0.001 FDR: 47,827
1 day, 4:12:59.736868 PROGRESS: 
1 day, 4:12:59.736928 PROGRESS: Protein Summary:
1 day, 4:12:59.767523 PROGRESS: Channel   0:	 0.050 FDR: 11,073; 0.010 FDR: 11,073; 0.001 FDR: 8,699
1 day, 4:12:59.767779 PROGRESS: =========================================================================
1 day, 4:12:59.962987 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/psm.parquet
1 day, 4:13:00.383890 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/frag.parquet
1 day, 4:13:00.661971 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 4:13:01.239005 PROGRESS: 
1 day, 4:13:01.239164 INFO: Quantification results path: run_output/alphadia_1.12.1_rs_benchmark/quant
1 day, 4:13:01.239246 INFO: Initializing TimingManager
1 day, 4:13:01.239890 INFO: Initializing RawFileManager
1 day, 4:13:01.239987 INFO: Importing data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:13:01.240039 INFO: Using .d import for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:13:01.240068 INFO: Reading frame metadata for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:13:01.564619 INFO: Reading 39,129 frames with 2,804,178,635 detector events for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:13:13.072838 INFO: Indexing ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d...
1 day, 4:13:13.076263 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:13:13.082096 INFO: Fetching mobility values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:13:13.082539 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:13:13.083069 INFO: Opening handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:13:13.086451 INFO: Fetching mz values from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:13:13.101860 INFO: Closing handle for ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:13:13.102134 INFO: Indexing quadrupole dimension
1 day, 4:13:13.667476 INFO: Transposing detector events
1 day, 4:13:22.500341 INFO: Finished transposing data
1 day, 4:13:22.537319 INFO: Successfully imported data from ./raw_diapasef_2025/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 4:13:22.538453 INFO: RT (min)            : 0.0 - 70.0
1 day, 4:13:22.538544 INFO: RT duration (sec)   : 4199.8
1 day, 4:13:22.538601 INFO: RT duration (min)   : 70.0
1 day, 4:13:22.538650 INFO: Cycle len (scans)   : 9
1 day, 4:13:22.538695 INFO: Cycle len (sec)     : 0.97
1 day, 4:13:22.538739 INFO: Number of cycles    : 4347
1 day, 4:13:22.538798 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 4:13:22.538916 INFO: Creating DIA data object took: 21.298920154571533
1 day, 4:13:24.217354 INFO: Initializing CalibrationManager
1 day, 4:13:24.217684 INFO: Setting up calibration estimators ..
1 day, 4:13:24.217749 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 4:13:24.217832 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1 day, 4:13:24.218094 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 4:13:24.218155 INFO: Initializing estimator 'mz' in group 'precursor' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1 day, 4:13:24.218211 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
1 day, 4:13:24.218272 INFO: Initializing estimator 'mobility' in group 'precursor' with '{'input_columns': ['mobility_library'], 'target_columns': ['mobility_observed'], 'output_columns': ['mobility_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}}' ..
1 day, 4:13:24.218338 INFO: Done setting up calibration estimators.
1 day, 4:13:24.218481 INFO: Initializing OptimizationManager
1 day, 4:13:24.218574 INFO: initial parameter: ms1_error = 30
1 day, 4:13:24.218620 INFO: initial parameter: ms2_error = 30
1 day, 4:13:24.218663 INFO: initial parameter: rt_error = 2099.9231665
1 day, 4:13:24.218704 INFO: initial parameter: mobility_error = 0.1
1 day, 4:13:24.218743 INFO: initial parameter: num_candidates = 1
1 day, 4:13:24.218788 INFO: initial parameter: fwhm_rt = 5
1 day, 4:13:24.218831 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 4:13:24.218870 INFO: initial parameter: score_cutoff = 0
1 day, 4:13:24.218907 INFO: initial parameter: classifier_version = -1
1 day, 4:13:24.218979 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 4:13:24.219266 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 4:13:24.219299 INFO: Initializing FDRManager
1 day, 4:13:24.219337 INFO: Loading classifier store from /home/robbe/.pyenv/versions/alphadia/lib/python3.11/site-packages/alphadia/constants/classifier
1 day, 4:13:25.445421 PROGRESS: Initializing spectral library: 6,124,046 target precursors potentially observable (0 removed)
1 day, 4:13:26.177736 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 4:13:26.178189 INFO: Updating optimization_manager: rt_error            : 2099.9231665 -> 2099.9231665
1 day, 4:13:26.178301 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 4:13:26.178469 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 4:13:26.178553 PROGRESS: Starting initial search for precursors.
1 day, 4:13:26.178633 INFO: Starting optimization step 0.
1 day, 4:13:26.178692 PROGRESS: === Extracting elution groups 0 to 200 ===
1 day, 4:13:26.178762 INFO: Using classic extraction backend
1 day, 4:13:26.178983 PROGRESS: Extracting batch of 390 precursors
1 day, 4:13:26.179063 INFO: === Search parameters used ===
1 day, 4:13:26.179119 INFO: rt_error       : 2099.9231665
1 day, 4:13:26.179173 INFO: mobility_error : 0.1
1 day, 4:13:26.179224 INFO: num_candidates : 1
1 day, 4:13:26.179268 INFO: ms1_error      : 30
1 day, 4:13:26.179317 INFO: ms2_error      : 30
1 day, 4:13:26.179360 INFO: fwhm_rt        : 5
1 day, 4:13:26.179402 INFO: quant_window   : 3
1 day, 4:13:26.179445 INFO: ==============================================
1 day, 4:13:26.180298 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:13:26.180345 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:13:26.180381 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:13:26.180401 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:13:26.181348 INFO: Starting candidate selection
1 day, 4:13:29.948227 INFO: Starting candidate scoring
1 day, 4:13:30.018351 INFO: Finished candidate processing
1 day, 4:13:30.018464 INFO: Collecting candidate features
1 day, 4:13:30.027903 INFO: Collecting fragment features
1 day, 4:13:30.030738 INFO: Finished candidate scoring
1 day, 4:13:30.032040 INFO: performing precursor FDR with 47 features
1 day, 4:13:30.032095 INFO: Decoy channel: -1
1 day, 4:13:30.032121 INFO: Competetive: True
1 day, 4:13:30.033312 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:13:30.036077 INFO: Using random state 182554 for train-test-split
1 day, 4:13:30.045061 INFO: Test AUC: 0.545
1 day, 4:13:30.045123 INFO: Train AUC: 0.510
1 day, 4:13:30.045161 INFO: AUC difference: 6.98%
1 day, 4:13:30.045185 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 4:13:30.286646 INFO: Resetting torch num_threads to 80
1 day, 4:13:30.287201 PROGRESS: === Extracted 363 precursors and 3919 fragments ===
1 day, 4:13:30.287662 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:13:30.288410 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:13:30.288504 PROGRESS: Total precursors accumulated: 188
1 day, 4:13:30.288575 PROGRESS: Target precursors: 163 (86.70%)
1 day, 4:13:30.288640 PROGRESS: Decoy precursors: 25 (13.30%)
1 day, 4:13:30.288691 PROGRESS: 
1 day, 4:13:30.288736 PROGRESS: Precursor Summary:
1 day, 4:13:30.289660 PROGRESS: Channel   0:	 0.050 FDR:   153; 0.010 FDR:   153; 0.001 FDR:   153
1 day, 4:13:30.289755 PROGRESS: 
1 day, 4:13:30.289820 PROGRESS: Protein Summary:
1 day, 4:13:30.290886 PROGRESS: Channel   0:	 0.050 FDR:   153; 0.010 FDR:   153; 0.001 FDR:   153
1 day, 4:13:30.290982 PROGRESS: =========================================================================
1 day, 4:13:30.291096 INFO: Target number of precursors not reached yet.
1 day, 4:13:30.356930 INFO: Starting optimization step 1.
1 day, 4:13:30.357164 PROGRESS: === Extracting elution groups 200 to 600 ===
1 day, 4:13:30.357260 INFO: Using classic extraction backend
1 day, 4:13:30.357405 PROGRESS: Extracting batch of 783 precursors
1 day, 4:13:30.357483 INFO: === Search parameters used ===
1 day, 4:13:30.357534 INFO: rt_error       : 2099.9231665
1 day, 4:13:30.357580 INFO: mobility_error : 0.1
1 day, 4:13:30.357625 INFO: num_candidates : 1
1 day, 4:13:30.357671 INFO: ms1_error      : 30
1 day, 4:13:30.357712 INFO: ms2_error      : 30
1 day, 4:13:30.357753 INFO: fwhm_rt        : 5
1 day, 4:13:30.357795 INFO: quant_window   : 3
1 day, 4:13:30.357835 INFO: ==============================================
1 day, 4:13:30.358595 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:13:30.358642 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:13:30.358671 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 4:13:30.358695 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 4:13:30.359459 INFO: Starting candidate selection
1 day, 4:13:36.935247 INFO: Starting candidate scoring
1 day, 4:13:37.076458 INFO: Finished candidate processing
1 day, 4:13:37.076599 INFO: Collecting candidate features
1 day, 4:13:37.089326 INFO: Collecting fragment features
1 day, 4:13:37.092308 INFO: Finished candidate scoring
1 day, 4:13:37.095499 INFO: performing precursor FDR with 47 features
1 day, 4:13:37.095560 INFO: Decoy channel: -1
1 day, 4:13:37.095590 INFO: Competetive: True
1 day, 4:13:37.099652 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:13:37.102188 INFO: Using random state 235056 for train-test-split
1 day, 4:13:37.110655 INFO: Test AUC: 0.525
1 day, 4:13:37.110729 INFO: Train AUC: 0.508
1 day, 4:13:37.110759 INFO: AUC difference: 3.35%
1 day, 4:13:37.329924 INFO: Resetting torch num_threads to 80
1 day, 4:13:37.331278 PROGRESS: === Extracted 1117 precursors and 12127 fragments ===
1 day, 4:13:37.331712 INFO: === FDR correction performed with classifier version -1 ===
1 day, 4:13:37.332280 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:13:37.332369 PROGRESS: Total precursors accumulated: 576
1 day, 4:13:37.332429 PROGRESS: Target precursors: 509 (88.37%)
1 day, 4:13:37.332487 PROGRESS: Decoy precursors: 67 (11.63%)
1 day, 4:13:37.332534 PROGRESS: 
1 day, 4:13:37.332578 PROGRESS: Precursor Summary:
1 day, 4:13:37.333563 PROGRESS: Channel   0:	 0.050 FDR:   482; 0.010 FDR:   482; 0.001 FDR:   482
1 day, 4:13:37.333662 PROGRESS: 
1 day, 4:13:37.333717 PROGRESS: Protein Summary:
1 day, 4:13:37.334927 PROGRESS: Channel   0:	 0.050 FDR:   472; 0.010 FDR:   472; 0.001 FDR:   472
1 day, 4:13:37.335022 PROGRESS: =========================================================================
1 day, 4:13:37.335159 INFO: Target number of precursors reached.
1 day, 4:13:37.338470 INFO: fragments_df: keeping 981 of 12127 [sum(precursor_idx_mask)=5387 sum(mass_error_mask)=12127 stop_rank=981
1 day, 4:13:37.437582 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:13:37.569926 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:13:37.709992 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:13:37.847445 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:13:38.015356 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 4:13:38.015841 INFO: Using score_cutoff 34.87769735641479 (fac=0.99, q=1)
1 day, 4:13:38.016175 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.126807689666748
1 day, 4:13:38.016257 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.007708919234573841
1 day, 4:13:38.016311 INFO: Updating optimization_manager: score_cutoff        : 0 -> 34.87769735641479
1 day, 4:13:38.016377 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:13:38.017509 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:13:38.018896 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:13:38.019675 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:13:38.021644 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
1 day, 4:13:38.021741 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 4:13:38.021820 INFO: Starting optimization step 2.
1 day, 4:13:38.021882 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:13:38.021939 INFO: Using classic extraction backend
1 day, 4:13:38.022045 PROGRESS: Extracting batch of 1173 precursors
1 day, 4:13:38.022111 INFO: === Search parameters used ===
1 day, 4:13:38.022162 INFO: rt_error       : 2099.9231665
1 day, 4:13:38.022205 INFO: mobility_error : 0.1
1 day, 4:13:38.022247 INFO: num_candidates : 3
1 day, 4:13:38.022289 INFO: ms1_error      : 30
1 day, 4:13:38.022329 INFO: ms2_error      : 30
1 day, 4:13:38.022369 INFO: fwhm_rt        : 3.126807689666748
1 day, 4:13:38.022408 INFO: quant_window   : 3
1 day, 4:13:38.022448 INFO: ==============================================
1 day, 4:13:38.023364 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:13:38.023411 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:13:38.023445 INFO: FWHM in RT is 3.13 seconds, sigma is 0.69
1 day, 4:13:38.023469 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.58
1 day, 4:13:38.024122 INFO: Starting candidate selection
1 day, 4:13:47.311439 INFO: Starting candidate scoring
1 day, 4:13:47.599118 INFO: Finished candidate processing
1 day, 4:13:47.599290 INFO: Collecting candidate features
1 day, 4:13:47.614122 INFO: Collecting fragment features
1 day, 4:13:47.618246 INFO: Finished candidate scoring
1 day, 4:13:47.621056 INFO: performing precursor FDR with 47 features
1 day, 4:13:47.621109 INFO: Decoy channel: -1
1 day, 4:13:47.621133 INFO: Competetive: True
1 day, 4:13:47.625210 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:13:47.627321 INFO: Using random state 135432 for train-test-split
1 day, 4:13:47.637261 INFO: Test AUC: 0.495
1 day, 4:13:47.637331 INFO: Train AUC: 0.497
1 day, 4:13:47.637361 INFO: AUC difference: 0.37%
1 day, 4:13:47.860450 INFO: Resetting torch num_threads to 80
1 day, 4:13:47.861117 PROGRESS: === Extracted 3208 precursors and 35015 fragments ===
1 day, 4:13:47.861558 INFO: === FDR correction performed with classifier version 1 ===
1 day, 4:13:47.862148 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:13:47.863698 PROGRESS: Total precursors accumulated: 588
1 day, 4:13:47.863763 PROGRESS: Target precursors: 548 (93.20%)
1 day, 4:13:47.863813 PROGRESS: Decoy precursors: 40 (6.80%)
1 day, 4:13:47.863858 PROGRESS: 
1 day, 4:13:47.863899 PROGRESS: Precursor Summary:
1 day, 4:13:47.864955 PROGRESS: Channel   0:	 0.050 FDR:   535; 0.010 FDR:   535; 0.001 FDR:   535
1 day, 4:13:47.865047 PROGRESS: 
1 day, 4:13:47.865100 PROGRESS: Protein Summary:
1 day, 4:13:47.866335 PROGRESS: Channel   0:	 0.050 FDR:   525; 0.010 FDR:   525; 0.001 FDR:   525
1 day, 4:13:47.866427 PROGRESS: =========================================================================
1 day, 4:13:47.866569 INFO: Target number of precursors reached.
1 day, 4:13:47.873240 INFO: fragments_df: keeping 3211 of 35015 [sum(precursor_idx_mask)=16611 sum(mass_error_mask)=35015 stop_rank=3211
1 day, 4:13:47.972793 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:13:48.108325 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:13:48.254517 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:13:48.394008 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:13:48.751772 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:13:48.752274 INFO: Using score_cutoff 36.24679857788086 (fac=0.99, q=1)
1 day, 4:13:48.752597 INFO: Updating optimization_manager: fwhm_rt             : 3.126807689666748 -> 3.11285138130188
1 day, 4:13:48.752683 INFO: Updating optimization_manager: fwhm_mobility       : 0.007708919234573841 -> 0.0076975515112280846
1 day, 4:13:48.752743 INFO: Updating optimization_manager: score_cutoff        : 34.87769735641479 -> 36.24679857788086
1 day, 4:13:48.752793 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:13:48.753932 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:13:48.755316 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:13:48.756083 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:13:48.758099 INFO: === checking if optimization conditions were reached ===
1 day, 4:13:48.759483 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.821314515208343
1 day, 4:13:48.759584 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
1 day, 4:13:48.759649 PROGRESS: ❌ ms2_error      : 17.8213 > 15.0000 or insufficient steps taken.
1 day, 4:13:48.760603 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 4:13:48.760697 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
1 day, 4:13:48.760757 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 4:13:48.760810 INFO: ==============================================
1 day, 4:13:48.760872 INFO: Starting optimization step 3.
1 day, 4:13:48.760927 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:13:48.760978 INFO: Using classic extraction backend
1 day, 4:13:48.761085 PROGRESS: Extracting batch of 1173 precursors
1 day, 4:13:48.761147 INFO: === Search parameters used ===
1 day, 4:13:48.761202 INFO: rt_error       : 2099.9231665
1 day, 4:13:48.761248 INFO: mobility_error : 0.1
1 day, 4:13:48.761290 INFO: num_candidates : 3
1 day, 4:13:48.761332 INFO: ms1_error      : 15.0
1 day, 4:13:48.761370 INFO: ms2_error      : 17.821314515208343
1 day, 4:13:48.761410 INFO: fwhm_rt        : 3.11285138130188
1 day, 4:13:48.761450 INFO: quant_window   : 3
1 day, 4:13:48.761490 INFO: ==============================================
1 day, 4:13:48.762381 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:13:48.762429 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:13:48.762461 INFO: FWHM in RT is 3.11 seconds, sigma is 0.68
1 day, 4:13:48.762483 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
1 day, 4:13:48.763174 INFO: Starting candidate selection
1 day, 4:13:57.422372 INFO: Starting candidate scoring
1 day, 4:13:57.640178 INFO: Finished candidate processing
1 day, 4:13:57.640341 INFO: Collecting candidate features
1 day, 4:13:57.668424 INFO: Collecting fragment features
1 day, 4:13:57.676731 INFO: Finished candidate scoring
1 day, 4:13:57.680515 INFO: performing precursor FDR with 47 features
1 day, 4:13:57.680629 INFO: Decoy channel: -1
1 day, 4:13:57.680693 INFO: Competetive: True
1 day, 4:13:57.687044 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:13:57.690368 INFO: Using random state 436533 for train-test-split
1 day, 4:13:57.706377 INFO: Test AUC: 0.510
1 day, 4:13:57.706484 INFO: Train AUC: 0.502
1 day, 4:13:57.706541 INFO: AUC difference: 1.66%
1 day, 4:13:57.931994 INFO: Resetting torch num_threads to 80
1 day, 4:13:57.932668 PROGRESS: === Extracted 3213 precursors and 33898 fragments ===
1 day, 4:13:57.933140 INFO: === FDR correction performed with classifier version 2 ===
1 day, 4:13:57.933735 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:13:57.933826 PROGRESS: Total precursors accumulated: 586
1 day, 4:13:57.933884 PROGRESS: Target precursors: 526 (89.76%)
1 day, 4:13:57.933936 PROGRESS: Decoy precursors: 60 (10.24%)
1 day, 4:13:57.933983 PROGRESS: 
1 day, 4:13:57.934027 PROGRESS: Precursor Summary:
1 day, 4:13:57.935045 PROGRESS: Channel   0:	 0.050 FDR:   500; 0.010 FDR:   500; 0.001 FDR:   500
1 day, 4:13:57.935139 PROGRESS: 
1 day, 4:13:57.935195 PROGRESS: Protein Summary:
1 day, 4:13:57.936392 PROGRESS: Channel   0:	 0.050 FDR:   489; 0.010 FDR:   489; 0.001 FDR:   489
1 day, 4:13:57.936496 PROGRESS: =========================================================================
1 day, 4:13:57.936672 INFO: Target number of precursors reached.
1 day, 4:13:57.942970 INFO: fragments_df: keeping 2532 of 33898 [sum(precursor_idx_mask)=15089 sum(mass_error_mask)=33898 stop_rank=2532
1 day, 4:13:58.043548 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:13:58.205353 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:13:58.350138 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:13:58.494669 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:13:58.855402 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:13:58.855908 INFO: Using score_cutoff 31.580454250717164 (fac=0.99, q=1)
1 day, 4:13:58.856251 INFO: Updating optimization_manager: fwhm_rt             : 3.11285138130188 -> 2.759995460510254
1 day, 4:13:58.856339 INFO: Updating optimization_manager: fwhm_mobility       : 0.0076975515112280846 -> 0.005820855498313904
1 day, 4:13:58.856407 INFO: Updating optimization_manager: score_cutoff        : 36.24679857788086 -> 31.580454250717164
1 day, 4:13:58.856471 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:13:58.857633 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:13:58.859025 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:13:58.859820 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:13:58.861953 INFO: === checking if optimization conditions were reached ===
1 day, 4:13:58.863249 INFO: Updating optimization_manager: ms2_error           : 17.821314515208343 -> 15.0
1 day, 4:13:58.863364 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
1 day, 4:13:58.863444 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 4:13:58.864432 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 4:13:58.864534 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
1 day, 4:13:58.864609 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 4:13:58.864674 INFO: ==============================================
1 day, 4:13:58.864752 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 4:13:58.963487 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:13:58.964667 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:13:58.966057 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:13:58.966859 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:13:58.969013 INFO: Starting optimization step 0.
1 day, 4:13:58.969126 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:13:58.969212 INFO: Using classic extraction backend
1 day, 4:13:58.969350 PROGRESS: Extracting batch of 1173 precursors
1 day, 4:13:58.969443 INFO: === Search parameters used ===
1 day, 4:13:58.969507 INFO: rt_error       : 2099.9231665
1 day, 4:13:58.969564 INFO: mobility_error : 0.1
1 day, 4:13:58.969617 INFO: num_candidates : 3
1 day, 4:13:58.969670 INFO: ms1_error      : 15.0
1 day, 4:13:58.969722 INFO: ms2_error      : 15.0
1 day, 4:13:58.969772 INFO: fwhm_rt        : 2.759995460510254
1 day, 4:13:58.969823 INFO: quant_window   : 3
1 day, 4:13:58.969882 INFO: ==============================================
1 day, 4:13:58.970771 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:13:58.970829 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:13:58.970877 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 4:13:58.970907 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.70
1 day, 4:13:58.971616 INFO: Starting candidate selection
1 day, 4:14:08.760689 INFO: Starting candidate scoring
1 day, 4:14:08.974014 INFO: Finished candidate processing
1 day, 4:14:08.974127 INFO: Collecting candidate features
1 day, 4:14:08.986488 INFO: Collecting fragment features
1 day, 4:14:08.990206 INFO: Finished candidate scoring
1 day, 4:14:08.992438 INFO: performing precursor FDR with 47 features
1 day, 4:14:08.992484 INFO: Decoy channel: -1
1 day, 4:14:08.992507 INFO: Competetive: True
1 day, 4:14:08.995383 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:14:08.997393 INFO: Using random state 196009 for train-test-split
1 day, 4:14:09.007434 INFO: Test AUC: 0.509
1 day, 4:14:09.007492 INFO: Train AUC: 0.498
1 day, 4:14:09.007522 INFO: AUC difference: 2.09%
1 day, 4:14:09.224927 INFO: Resetting torch num_threads to 80
1 day, 4:14:09.225555 PROGRESS: === Extracted 3221 precursors and 33511 fragments ===
1 day, 4:14:09.226011 INFO: === FDR correction performed with classifier version 3 ===
1 day, 4:14:09.226622 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:14:09.226715 PROGRESS: Total precursors accumulated: 588
1 day, 4:14:09.226776 PROGRESS: Target precursors: 518 (88.10%)
1 day, 4:14:09.226843 PROGRESS: Decoy precursors: 70 (11.90%)
1 day, 4:14:09.226890 PROGRESS: 
1 day, 4:14:09.226934 PROGRESS: Precursor Summary:
1 day, 4:14:09.227931 PROGRESS: Channel   0:	 0.050 FDR:   495; 0.010 FDR:   495; 0.001 FDR:   495
1 day, 4:14:09.228021 PROGRESS: 
1 day, 4:14:09.228078 PROGRESS: Protein Summary:
1 day, 4:14:09.229275 PROGRESS: Channel   0:	 0.050 FDR:   486; 0.010 FDR:   486; 0.001 FDR:   486
1 day, 4:14:09.229367 PROGRESS: =========================================================================
1 day, 4:14:09.229503 INFO: Target number of precursors reached.
1 day, 4:14:09.235649 INFO: fragments_df: keeping 2545 of 33511 [sum(precursor_idx_mask)=14714 sum(mass_error_mask)=33511 stop_rank=2545
1 day, 4:14:09.334495 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:09.473299 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:09.613045 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:09.753199 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:10.091560 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:14:10.092048 INFO: Using score_cutoff 31.786232244873045 (fac=0.99, q=1)
1 day, 4:14:10.092366 INFO: Updating optimization_manager: fwhm_rt             : 2.759995460510254 -> 2.686847448348999
1 day, 4:14:10.092455 INFO: Updating optimization_manager: fwhm_mobility       : 0.005820855498313904 -> 0.005389524158090353
1 day, 4:14:10.092511 INFO: Updating optimization_manager: score_cutoff        : 31.580454250717164 -> 31.786232244873045
1 day, 4:14:10.092572 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:10.093683 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:10.095053 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:10.095808 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:10.097897 INFO: === checking if optimization conditions were reached ===
1 day, 4:14:10.098003 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 4:14:10.099610 INFO: Updating optimization_manager: rt_error            : 2099.9231665 -> 1328.5815599039056
1 day, 4:14:10.099714 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1328.5816.
1 day, 4:14:10.099780 INFO: ==============================================
1 day, 4:14:10.099847 INFO: Starting optimization step 1.
1 day, 4:14:10.099906 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:14:10.099964 INFO: Using classic extraction backend
1 day, 4:14:10.100067 PROGRESS: Extracting batch of 1173 precursors
1 day, 4:14:10.100134 INFO: === Search parameters used ===
1 day, 4:14:10.100192 INFO: rt_error       : 1328.5815599039056
1 day, 4:14:10.100239 INFO: mobility_error : 0.1
1 day, 4:14:10.100280 INFO: num_candidates : 3
1 day, 4:14:10.100323 INFO: ms1_error      : 15.0
1 day, 4:14:10.100363 INFO: ms2_error      : 15.0
1 day, 4:14:10.100404 INFO: fwhm_rt        : 2.686847448348999
1 day, 4:14:10.100446 INFO: quant_window   : 3
1 day, 4:14:10.100486 INFO: ==============================================
1 day, 4:14:10.101346 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:14:10.101393 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:14:10.101426 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
1 day, 4:14:10.101450 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.50
1 day, 4:14:10.102139 INFO: Starting candidate selection
1 day, 4:14:16.017838 INFO: Starting candidate scoring
1 day, 4:14:16.220938 INFO: Finished candidate processing
1 day, 4:14:16.221051 INFO: Collecting candidate features
1 day, 4:14:16.235105 INFO: Collecting fragment features
1 day, 4:14:16.239012 INFO: Finished candidate scoring
1 day, 4:14:16.241457 INFO: performing precursor FDR with 47 features
1 day, 4:14:16.241503 INFO: Decoy channel: -1
1 day, 4:14:16.241527 INFO: Competetive: True
1 day, 4:14:16.244590 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:14:16.246724 INFO: Using random state 196009 for train-test-split
1 day, 4:14:16.259923 INFO: Test AUC: 0.516
1 day, 4:14:16.259991 INFO: Train AUC: 0.506
1 day, 4:14:16.260021 INFO: AUC difference: 1.90%
1 day, 4:14:16.486736 INFO: Resetting torch num_threads to 80
1 day, 4:14:16.487377 PROGRESS: === Extracted 3213 precursors and 33299 fragments ===
1 day, 4:14:16.487839 INFO: === FDR correction performed with classifier version 3 ===
1 day, 4:14:16.488443 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:14:16.488533 PROGRESS: Total precursors accumulated: 588
1 day, 4:14:16.488595 PROGRESS: Target precursors: 523 (88.95%)
1 day, 4:14:16.488647 PROGRESS: Decoy precursors: 65 (11.05%)
1 day, 4:14:16.488695 PROGRESS: 
1 day, 4:14:16.488740 PROGRESS: Precursor Summary:
1 day, 4:14:16.489759 PROGRESS: Channel   0:	 0.050 FDR:   500; 0.010 FDR:   500; 0.001 FDR:   500
1 day, 4:14:16.489851 PROGRESS: 
1 day, 4:14:16.489908 PROGRESS: Protein Summary:
1 day, 4:14:16.491130 PROGRESS: Channel   0:	 0.050 FDR:   491; 0.010 FDR:   491; 0.001 FDR:   491
1 day, 4:14:16.491225 PROGRESS: =========================================================================
1 day, 4:14:16.491358 INFO: Target number of precursors reached.
1 day, 4:14:16.497475 INFO: fragments_df: keeping 2583 of 33299 [sum(precursor_idx_mask)=14836 sum(mass_error_mask)=33299 stop_rank=2583
1 day, 4:14:16.596354 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:16.736472 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:16.877943 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:17.019405 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:17.362327 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:14:17.362823 INFO: Using score_cutoff 31.868024015808107 (fac=0.99, q=1)
1 day, 4:14:17.363147 INFO: Updating optimization_manager: fwhm_rt             : 2.686847448348999 -> 2.760643243789673
1 day, 4:14:17.363230 INFO: Updating optimization_manager: fwhm_mobility       : 0.005389524158090353 -> 0.005389689467847347
1 day, 4:14:17.363287 INFO: Updating optimization_manager: score_cutoff        : 31.786232244873045 -> 31.868024015808107
1 day, 4:14:17.363340 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:17.364460 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:17.365817 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:17.366581 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:17.368643 INFO: === checking if optimization conditions were reached ===
1 day, 4:14:17.368747 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 4:14:17.370440 INFO: Updating optimization_manager: rt_error            : 1328.5815599039056 -> 862.0655725946962
1 day, 4:14:17.370542 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 862.0656.
1 day, 4:14:17.370621 INFO: ==============================================
1 day, 4:14:17.370691 INFO: Starting optimization step 2.
1 day, 4:14:17.370750 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:14:17.370815 INFO: Using classic extraction backend
1 day, 4:14:17.370921 PROGRESS: Extracting batch of 1173 precursors
1 day, 4:14:17.370987 INFO: === Search parameters used ===
1 day, 4:14:17.371037 INFO: rt_error       : 862.0655725946962
1 day, 4:14:17.371081 INFO: mobility_error : 0.1
1 day, 4:14:17.371124 INFO: num_candidates : 3
1 day, 4:14:17.371169 INFO: ms1_error      : 15.0
1 day, 4:14:17.371212 INFO: ms2_error      : 15.0
1 day, 4:14:17.371253 INFO: fwhm_rt        : 2.760643243789673
1 day, 4:14:17.371294 INFO: quant_window   : 3
1 day, 4:14:17.371333 INFO: ==============================================
1 day, 4:14:17.372184 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:14:17.372233 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:14:17.372266 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 4:14:17.372289 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.50
1 day, 4:14:17.372997 INFO: Starting candidate selection
1 day, 4:14:20.979731 INFO: Starting candidate scoring
1 day, 4:14:21.204096 INFO: Finished candidate processing
1 day, 4:14:21.204283 INFO: Collecting candidate features
1 day, 4:14:21.236900 INFO: Collecting fragment features
1 day, 4:14:21.246571 INFO: Finished candidate scoring
1 day, 4:14:21.249975 INFO: performing precursor FDR with 47 features
1 day, 4:14:21.250089 INFO: Decoy channel: -1
1 day, 4:14:21.250157 INFO: Competetive: True
1 day, 4:14:21.257515 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:14:21.262546 INFO: Using random state 196009 for train-test-split
1 day, 4:14:21.284625 INFO: Test AUC: 0.500
1 day, 4:14:21.284727 INFO: Train AUC: 0.506
1 day, 4:14:21.284775 INFO: AUC difference: 1.16%
1 day, 4:14:21.511894 INFO: Resetting torch num_threads to 80
1 day, 4:14:21.512511 PROGRESS: === Extracted 3233 precursors and 33497 fragments ===
1 day, 4:14:21.512960 INFO: === FDR correction performed with classifier version 3 ===
1 day, 4:14:21.513573 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:14:21.513667 PROGRESS: Total precursors accumulated: 589
1 day, 4:14:21.513727 PROGRESS: Target precursors: 522 (88.62%)
1 day, 4:14:21.513785 PROGRESS: Decoy precursors: 67 (11.38%)
1 day, 4:14:21.513835 PROGRESS: 
1 day, 4:14:21.513881 PROGRESS: Precursor Summary:
1 day, 4:14:21.514927 PROGRESS: Channel   0:	 0.050 FDR:   497; 0.010 FDR:   497; 0.001 FDR:   497
1 day, 4:14:21.515018 PROGRESS: 
1 day, 4:14:21.515077 PROGRESS: Protein Summary:
1 day, 4:14:21.516280 PROGRESS: Channel   0:	 0.050 FDR:   488; 0.010 FDR:   488; 0.001 FDR:   488
1 day, 4:14:21.516369 PROGRESS: =========================================================================
1 day, 4:14:21.516510 INFO: Target number of precursors reached.
1 day, 4:14:21.522784 INFO: fragments_df: keeping 2585 of 33497 [sum(precursor_idx_mask)=14895 sum(mass_error_mask)=33497 stop_rank=2585
1 day, 4:14:21.621520 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:21.747805 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:21.864551 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:21.983988 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:22.266402 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:14:22.266899 INFO: Using score_cutoff 32.10419481811523 (fac=0.99, q=1)
1 day, 4:14:22.267220 INFO: Updating optimization_manager: fwhm_rt             : 2.760643243789673 -> 2.7446093559265137
1 day, 4:14:22.267303 INFO: Updating optimization_manager: fwhm_mobility       : 0.005389689467847347 -> 0.0053509739227592945
1 day, 4:14:22.267360 INFO: Updating optimization_manager: score_cutoff        : 31.868024015808107 -> 32.10419481811523
1 day, 4:14:22.267413 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:22.268533 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:22.269897 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:22.270673 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:22.272745 INFO: === checking if optimization conditions were reached ===
1 day, 4:14:22.272846 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 4:14:22.274612 INFO: Updating optimization_manager: rt_error            : 862.0655725946962 -> 803.1600877045123
1 day, 4:14:22.274714 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 803.1601.
1 day, 4:14:22.274789 INFO: ==============================================
1 day, 4:14:22.274862 INFO: Starting optimization step 3.
1 day, 4:14:22.274930 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:14:22.274986 INFO: Using classic extraction backend
1 day, 4:14:22.275089 PROGRESS: Extracting batch of 1173 precursors
1 day, 4:14:22.275154 INFO: === Search parameters used ===
1 day, 4:14:22.275203 INFO: rt_error       : 803.1600877045123
1 day, 4:14:22.275246 INFO: mobility_error : 0.1
1 day, 4:14:22.275289 INFO: num_candidates : 3
1 day, 4:14:22.275332 INFO: ms1_error      : 15.0
1 day, 4:14:22.275372 INFO: ms2_error      : 15.0
1 day, 4:14:22.275412 INFO: fwhm_rt        : 2.7446093559265137
1 day, 4:14:22.275453 INFO: quant_window   : 3
1 day, 4:14:22.275495 INFO: ==============================================
1 day, 4:14:22.278368 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:14:22.278421 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:14:22.278457 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
1 day, 4:14:22.278480 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.48
1 day, 4:14:22.279191 INFO: Starting candidate selection
1 day, 4:14:26.170356 INFO: Starting candidate scoring
1 day, 4:14:26.366655 INFO: Finished candidate processing
1 day, 4:14:26.366766 INFO: Collecting candidate features
1 day, 4:14:26.395209 INFO: Collecting fragment features
1 day, 4:14:26.403855 INFO: Finished candidate scoring
1 day, 4:14:26.407254 INFO: performing precursor FDR with 47 features
1 day, 4:14:26.407351 INFO: Decoy channel: -1
1 day, 4:14:26.407410 INFO: Competetive: True
1 day, 4:14:26.413193 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:14:26.416531 INFO: Using random state 196009 for train-test-split
1 day, 4:14:26.433411 INFO: Test AUC: 0.517
1 day, 4:14:26.433511 INFO: Train AUC: 0.499
1 day, 4:14:26.433561 INFO: AUC difference: 3.66%
1 day, 4:14:26.662121 INFO: Resetting torch num_threads to 80
1 day, 4:14:26.662757 PROGRESS: === Extracted 3228 precursors and 33439 fragments ===
1 day, 4:14:26.663215 INFO: === FDR correction performed with classifier version 3 ===
1 day, 4:14:26.663815 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:14:26.663907 PROGRESS: Total precursors accumulated: 589
1 day, 4:14:26.663966 PROGRESS: Target precursors: 515 (87.44%)
1 day, 4:14:26.664015 PROGRESS: Decoy precursors: 74 (12.56%)
1 day, 4:14:26.664062 PROGRESS: 
1 day, 4:14:26.664104 PROGRESS: Precursor Summary:
1 day, 4:14:26.665138 PROGRESS: Channel   0:	 0.050 FDR:   490; 0.010 FDR:   490; 0.001 FDR:   490
1 day, 4:14:26.665231 PROGRESS: 
1 day, 4:14:26.665287 PROGRESS: Protein Summary:
1 day, 4:14:26.666495 PROGRESS: Channel   0:	 0.050 FDR:   481; 0.010 FDR:   481; 0.001 FDR:   481
1 day, 4:14:26.666589 PROGRESS: =========================================================================
1 day, 4:14:26.666743 INFO: Target number of precursors reached.
1 day, 4:14:26.672790 INFO: fragments_df: keeping 2491 of 33439 [sum(precursor_idx_mask)=14679 sum(mass_error_mask)=33439 stop_rank=2491
1 day, 4:14:26.771738 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:26.889384 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:27.007277 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:27.124702 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:27.397887 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:14:27.398372 INFO: Using score_cutoff 32.88487294692993 (fac=0.99, q=1)
1 day, 4:14:27.398697 INFO: Updating optimization_manager: fwhm_rt             : 2.7446093559265137 -> 2.7474470138549805
1 day, 4:14:27.398789 INFO: Updating optimization_manager: fwhm_mobility       : 0.0053509739227592945 -> 0.005293084308505058
1 day, 4:14:27.398848 INFO: Updating optimization_manager: score_cutoff        : 32.10419481811523 -> 32.88487294692993
1 day, 4:14:27.398900 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:27.400019 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:27.401337 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:27.402093 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:27.404162 INFO: === checking if optimization conditions were reached ===
1 day, 4:14:27.404262 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 4:14:27.406079 INFO: Updating optimization_manager: rt_error            : 803.1600877045123 -> 770.7628617682043
1 day, 4:14:27.406182 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 770.7629.
1 day, 4:14:27.406251 INFO: ==============================================
1 day, 4:14:27.406324 INFO: Starting optimization step 4.
1 day, 4:14:27.406387 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:14:27.406444 INFO: Using classic extraction backend
1 day, 4:14:27.406547 PROGRESS: Extracting batch of 1173 precursors
1 day, 4:14:27.406614 INFO: === Search parameters used ===
1 day, 4:14:27.406664 INFO: rt_error       : 770.7628617682043
1 day, 4:14:27.406708 INFO: mobility_error : 0.1
1 day, 4:14:27.406759 INFO: num_candidates : 3
1 day, 4:14:27.406815 INFO: ms1_error      : 15.0
1 day, 4:14:27.406860 INFO: ms2_error      : 15.0
1 day, 4:14:27.406901 INFO: fwhm_rt        : 2.7474470138549805
1 day, 4:14:27.406942 INFO: quant_window   : 3
1 day, 4:14:27.406982 INFO: ==============================================
1 day, 4:14:27.407839 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:14:27.407891 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:14:27.407928 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 4:14:27.407953 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.46
1 day, 4:14:27.408646 INFO: Starting candidate selection
1 day, 4:14:31.164541 INFO: Starting candidate scoring
1 day, 4:14:31.387857 INFO: Finished candidate processing
1 day, 4:14:31.387968 INFO: Collecting candidate features
1 day, 4:14:31.403131 INFO: Collecting fragment features
1 day, 4:14:31.410694 INFO: Finished candidate scoring
1 day, 4:14:31.413763 INFO: performing precursor FDR with 47 features
1 day, 4:14:31.413839 INFO: Decoy channel: -1
1 day, 4:14:31.413880 INFO: Competetive: True
1 day, 4:14:31.419207 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:14:31.421597 INFO: Using random state 196009 for train-test-split
1 day, 4:14:31.433709 INFO: Test AUC: 0.519
1 day, 4:14:31.433776 INFO: Train AUC: 0.499
1 day, 4:14:31.433806 INFO: AUC difference: 4.04%
1 day, 4:14:31.650866 INFO: Resetting torch num_threads to 80
1 day, 4:14:31.651481 PROGRESS: === Extracted 3213 precursors and 33260 fragments ===
1 day, 4:14:31.651929 INFO: === FDR correction performed with classifier version 3 ===
1 day, 4:14:31.652506 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:14:31.652599 PROGRESS: Total precursors accumulated: 589
1 day, 4:14:31.652658 PROGRESS: Target precursors: 516 (87.61%)
1 day, 4:14:31.652706 PROGRESS: Decoy precursors: 73 (12.39%)
1 day, 4:14:31.652755 PROGRESS: 
1 day, 4:14:31.652799 PROGRESS: Precursor Summary:
1 day, 4:14:31.653808 PROGRESS: Channel   0:	 0.050 FDR:   490; 0.010 FDR:   490; 0.001 FDR:   490
1 day, 4:14:31.653900 PROGRESS: 
1 day, 4:14:31.653957 PROGRESS: Protein Summary:
1 day, 4:14:31.655162 PROGRESS: Channel   0:	 0.050 FDR:   481; 0.010 FDR:   481; 0.001 FDR:   481
1 day, 4:14:31.655257 PROGRESS: =========================================================================
1 day, 4:14:31.655415 INFO: Target number of precursors reached.
1 day, 4:14:31.661610 INFO: fragments_df: keeping 2460 of 33260 [sum(precursor_idx_mask)=14612 sum(mass_error_mask)=33260 stop_rank=2460
1 day, 4:14:31.842360 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:31.981187 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:32.119938 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:32.262214 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:32.591856 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:14:32.592336 INFO: Using score_cutoff 30.930784273910522 (fac=0.99, q=1)
1 day, 4:14:32.592666 INFO: Updating optimization_manager: fwhm_rt             : 2.7474470138549805 -> 2.7272191047668457
1 day, 4:14:32.592745 INFO: Updating optimization_manager: fwhm_mobility       : 0.005293084308505058 -> 0.005349918268620968
1 day, 4:14:32.592799 INFO: Updating optimization_manager: score_cutoff        : 32.88487294692993 -> 30.930784273910522
1 day, 4:14:32.592853 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:32.594006 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:32.595357 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:32.596127 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:32.598220 INFO: === checking if optimization conditions were reached ===
1 day, 4:14:32.598325 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 4:14:32.599458 INFO: Updating optimization_manager: rt_error            : 770.7628617682043 -> 770.7628617682043
1 day, 4:14:32.599584 INFO: Updating optimization_manager: classifier_version  : 3 -> 8
1 day, 4:14:32.599685 INFO: Updating optimization_manager: score_cutoff        : 30.930784273910522 -> 30.930784273910522
1 day, 4:14:32.599784 INFO: Updating optimization_manager: fwhm_rt             : 2.7272191047668457 -> 2.7272191047668457
1 day, 4:14:32.599877 INFO: Updating optimization_manager: fwhm_mobility       : 0.005349918268620968 -> 0.005349918268620968
1 day, 4:14:32.599967 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 770.7629 found after 5 searches.
1 day, 4:14:32.600036 INFO: ==============================================
1 day, 4:14:32.600104 PROGRESS: Optimization finished for rt_error.
1 day, 4:14:32.699689 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:32.701004 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:32.702339 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:32.703115 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:32.731340 INFO: Starting optimization step 0.
1 day, 4:14:32.731618 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:14:32.731701 INFO: Using classic extraction backend
1 day, 4:14:32.731844 PROGRESS: Extracting batch of 1173 precursors
1 day, 4:14:32.731920 INFO: === Search parameters used ===
1 day, 4:14:32.731970 INFO: rt_error       : 770.7628617682043
1 day, 4:14:32.732016 INFO: mobility_error : 0.1
1 day, 4:14:32.732060 INFO: num_candidates : 3
1 day, 4:14:32.732103 INFO: ms1_error      : 15.0
1 day, 4:14:32.732144 INFO: ms2_error      : 15.0
1 day, 4:14:32.732187 INFO: fwhm_rt        : 2.7272191047668457
1 day, 4:14:32.732230 INFO: quant_window   : 3
1 day, 4:14:32.732282 INFO: ==============================================
1 day, 4:14:32.733496 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:14:32.733554 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:14:32.733593 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
1 day, 4:14:32.733615 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.48
1 day, 4:14:32.734838 INFO: Starting candidate selection
1 day, 4:14:36.933487 INFO: Starting candidate scoring
1 day, 4:14:37.119490 INFO: Finished candidate processing
1 day, 4:14:37.119605 INFO: Collecting candidate features
1 day, 4:14:37.132787 INFO: Collecting fragment features
1 day, 4:14:37.136714 INFO: Finished candidate scoring
1 day, 4:14:37.138907 INFO: performing precursor FDR with 47 features
1 day, 4:14:37.138957 INFO: Decoy channel: -1
1 day, 4:14:37.138981 INFO: Competetive: True
1 day, 4:14:37.141999 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:14:37.144142 INFO: Using random state 752507 for train-test-split
1 day, 4:14:37.154364 INFO: Test AUC: 0.493
1 day, 4:14:37.154428 INFO: Train AUC: 0.503
1 day, 4:14:37.154459 INFO: AUC difference: 2.07%
1 day, 4:14:37.370502 INFO: Resetting torch num_threads to 80
1 day, 4:14:37.371134 PROGRESS: === Extracted 3220 precursors and 33224 fragments ===
1 day, 4:14:37.371579 INFO: === FDR correction performed with classifier version 8 ===
1 day, 4:14:37.372148 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:14:37.372238 PROGRESS: Total precursors accumulated: 589
1 day, 4:14:37.372299 PROGRESS: Target precursors: 515 (87.44%)
1 day, 4:14:37.372351 PROGRESS: Decoy precursors: 74 (12.56%)
1 day, 4:14:37.372399 PROGRESS: 
1 day, 4:14:37.372445 PROGRESS: Precursor Summary:
1 day, 4:14:37.373438 PROGRESS: Channel   0:	 0.050 FDR:   490; 0.010 FDR:   490; 0.001 FDR:   490
1 day, 4:14:37.373531 PROGRESS: 
1 day, 4:14:37.373589 PROGRESS: Protein Summary:
1 day, 4:14:37.374767 PROGRESS: Channel   0:	 0.050 FDR:   481; 0.010 FDR:   481; 0.001 FDR:   481
1 day, 4:14:37.374871 PROGRESS: =========================================================================
1 day, 4:14:37.375018 INFO: Target number of precursors reached.
1 day, 4:14:37.381085 INFO: fragments_df: keeping 2449 of 33224 [sum(precursor_idx_mask)=14545 sum(mass_error_mask)=33224 stop_rank=2449
1 day, 4:14:37.689787 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:37.806363 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:37.922746 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:38.039262 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:38.307295 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:14:38.307753 INFO: Using score_cutoff 30.889052241325377 (fac=0.99, q=1)
1 day, 4:14:38.308074 INFO: Updating optimization_manager: fwhm_rt             : 2.7272191047668457 -> 2.755573272705078
1 day, 4:14:38.308157 INFO: Updating optimization_manager: fwhm_mobility       : 0.005349918268620968 -> 0.005412509199231863
1 day, 4:14:38.308213 INFO: Updating optimization_manager: score_cutoff        : 30.930784273910522 -> 30.889052241325377
1 day, 4:14:38.308266 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:38.309405 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:38.310720 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:38.311487 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:38.313588 INFO: === checking if optimization conditions were reached ===
1 day, 4:14:38.313697 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 4:14:38.315052 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.10032927285032138
1 day, 4:14:38.315156 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.1003.
1 day, 4:14:38.315223 INFO: ==============================================
1 day, 4:14:38.315290 INFO: Starting optimization step 1.
1 day, 4:14:38.315350 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:14:38.315405 INFO: Using classic extraction backend
1 day, 4:14:38.315528 PROGRESS: Extracting batch of 1173 precursors
1 day, 4:14:38.315595 INFO: === Search parameters used ===
1 day, 4:14:38.315652 INFO: rt_error       : 770.7628617682043
1 day, 4:14:38.315699 INFO: mobility_error : 0.10032927285032138
1 day, 4:14:38.315741 INFO: num_candidates : 3
1 day, 4:14:38.315784 INFO: ms1_error      : 15.0
1 day, 4:14:38.315824 INFO: ms2_error      : 15.0
1 day, 4:14:38.315863 INFO: fwhm_rt        : 2.755573272705078
1 day, 4:14:38.315902 INFO: quant_window   : 3
1 day, 4:14:38.315942 INFO: ==============================================
1 day, 4:14:38.316804 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:14:38.316851 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:14:38.316887 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 4:14:38.316911 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.51
1 day, 4:14:38.317583 INFO: Starting candidate selection
1 day, 4:14:42.084871 INFO: Starting candidate scoring
1 day, 4:14:42.279510 INFO: Finished candidate processing
1 day, 4:14:42.279636 INFO: Collecting candidate features
1 day, 4:14:42.293118 INFO: Collecting fragment features
1 day, 4:14:42.300373 INFO: Finished candidate scoring
1 day, 4:14:42.303459 INFO: performing precursor FDR with 47 features
1 day, 4:14:42.303561 INFO: Decoy channel: -1
1 day, 4:14:42.303633 INFO: Competetive: True
1 day, 4:14:42.309072 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:14:42.312282 INFO: Using random state 752507 for train-test-split
1 day, 4:14:42.328845 INFO: Test AUC: 0.519
1 day, 4:14:42.328986 INFO: Train AUC: 0.498
1 day, 4:14:42.329040 INFO: AUC difference: 4.22%
1 day, 4:14:42.550160 INFO: Resetting torch num_threads to 80
1 day, 4:14:42.550905 PROGRESS: === Extracted 3213 precursors and 33218 fragments ===
1 day, 4:14:42.551436 INFO: === FDR correction performed with classifier version 8 ===
1 day, 4:14:42.552083 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:14:42.552177 PROGRESS: Total precursors accumulated: 589
1 day, 4:14:42.552238 PROGRESS: Target precursors: 512 (86.93%)
1 day, 4:14:42.552287 PROGRESS: Decoy precursors: 77 (13.07%)
1 day, 4:14:42.552343 PROGRESS: 
1 day, 4:14:42.552387 PROGRESS: Precursor Summary:
1 day, 4:14:42.553421 PROGRESS: Channel   0:	 0.050 FDR:   488; 0.010 FDR:   488; 0.001 FDR:   488
1 day, 4:14:42.553510 PROGRESS: 
1 day, 4:14:42.553565 PROGRESS: Protein Summary:
1 day, 4:14:42.554806 PROGRESS: Channel   0:	 0.050 FDR:   480; 0.010 FDR:   480; 0.001 FDR:   480
1 day, 4:14:42.554898 PROGRESS: =========================================================================
1 day, 4:14:42.555069 INFO: Target number of precursors reached.
1 day, 4:14:42.561333 INFO: fragments_df: keeping 2419 of 33218 [sum(precursor_idx_mask)=14444 sum(mass_error_mask)=33218 stop_rank=2419
1 day, 4:14:42.679774 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:42.798510 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:42.937112 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:43.076038 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:43.392821 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:14:43.393316 INFO: Using score_cutoff 32.31369703845978 (fac=0.99, q=1)
1 day, 4:14:43.393636 INFO: Updating optimization_manager: fwhm_rt             : 2.755573272705078 -> 2.7728915214538574
1 day, 4:14:43.393719 INFO: Updating optimization_manager: fwhm_mobility       : 0.005412509199231863 -> 0.005559816956520081
1 day, 4:14:43.393777 INFO: Updating optimization_manager: score_cutoff        : 30.889052241325377 -> 32.31369703845978
1 day, 4:14:43.393831 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:43.394996 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:43.396317 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:43.397071 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:43.399311 INFO: === checking if optimization conditions were reached ===
1 day, 4:14:43.399412 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 4:14:43.400862 INFO: Updating optimization_manager: mobility_error      : 0.10032927285032138 -> 0.10049005934907623
1 day, 4:14:43.400965 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.1005.
1 day, 4:14:43.401042 INFO: ==============================================
1 day, 4:14:43.401113 INFO: Starting optimization step 2.
1 day, 4:14:43.401176 PROGRESS: === Extracting elution groups 0 to 600 ===
1 day, 4:14:43.401237 INFO: Using classic extraction backend
1 day, 4:14:43.401341 PROGRESS: Extracting batch of 1173 precursors
1 day, 4:14:43.401408 INFO: === Search parameters used ===
1 day, 4:14:43.401458 INFO: rt_error       : 770.7628617682043
1 day, 4:14:43.401502 INFO: mobility_error : 0.10049005934907623
1 day, 4:14:43.401546 INFO: num_candidates : 3
1 day, 4:14:43.401590 INFO: ms1_error      : 15.0
1 day, 4:14:43.401631 INFO: ms2_error      : 15.0
1 day, 4:14:43.401672 INFO: fwhm_rt        : 2.7728915214538574
1 day, 4:14:43.401714 INFO: quant_window   : 3
1 day, 4:14:43.401755 INFO: ==============================================
1 day, 4:14:43.402623 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:14:43.402671 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:14:43.402706 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 4:14:43.402731 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.58
1 day, 4:14:43.403426 INFO: Starting candidate selection
1 day, 4:14:47.066772 INFO: Starting candidate scoring
1 day, 4:14:47.258556 INFO: Finished candidate processing
1 day, 4:14:47.258669 INFO: Collecting candidate features
1 day, 4:14:47.272157 INFO: Collecting fragment features
1 day, 4:14:47.275903 INFO: Finished candidate scoring
1 day, 4:14:47.277919 INFO: performing precursor FDR with 47 features
1 day, 4:14:47.277964 INFO: Decoy channel: -1
1 day, 4:14:47.277988 INFO: Competetive: True
1 day, 4:14:47.280852 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 4:14:47.282890 INFO: Using random state 752507 for train-test-split
1 day, 4:14:47.293826 INFO: Test AUC: 0.489
1 day, 4:14:47.293892 INFO: Train AUC: 0.506
1 day, 4:14:47.293922 INFO: AUC difference: 3.37%
1 day, 4:14:47.508056 INFO: Resetting torch num_threads to 80
1 day, 4:14:47.508660 PROGRESS: === Extracted 3229 precursors and 33291 fragments ===
1 day, 4:14:47.509108 INFO: === FDR correction performed with classifier version 8 ===
1 day, 4:14:47.509681 PROGRESS: ============================= Precursor FDR =============================
1 day, 4:14:47.509769 PROGRESS: Total precursors accumulated: 589
1 day, 4:14:47.509827 PROGRESS: Target precursors: 514 (87.27%)
1 day, 4:14:47.509877 PROGRESS: Decoy precursors: 75 (12.73%)
1 day, 4:14:47.509924 PROGRESS: 
1 day, 4:14:47.509973 PROGRESS: Precursor Summary:
1 day, 4:14:47.510994 PROGRESS: Channel   0:	 0.050 FDR:   485; 0.010 FDR:   485; 0.001 FDR:   485
1 day, 4:14:47.511086 PROGRESS: 
1 day, 4:14:47.511141 PROGRESS: Protein Summary:
1 day, 4:14:47.512319 PROGRESS: Channel   0:	 0.050 FDR:   477; 0.010 FDR:   477; 0.001 FDR:   477
1 day, 4:14:47.512411 PROGRESS: =========================================================================
1 day, 4:14:47.512550 INFO: Target number of precursors reached.
1 day, 4:14:47.521614 INFO: fragments_df: keeping 2506 of 33291 [sum(precursor_idx_mask)=14330 sum(mass_error_mask)=33291 stop_rank=2506
1 day, 4:14:47.621133 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:47.754930 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:47.892083 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:48.029830 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:48.361731 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 4:14:48.362195 INFO: Using score_cutoff 32.62667707672119 (fac=0.99, q=1)
1 day, 4:14:48.362504 INFO: Updating optimization_manager: fwhm_rt             : 2.7728915214538574 -> 2.779207944869995
1 day, 4:14:48.362584 INFO: Updating optimization_manager: fwhm_mobility       : 0.005559816956520081 -> 0.005647079087793827
1 day, 4:14:48.362637 INFO: Updating optimization_manager: score_cutoff        : 32.31369703845978 -> 32.62667707672119
1 day, 4:14:48.362688 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:48.363815 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:48.365160 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:48.365915 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:48.368001 INFO: === checking if optimization conditions were reached ===
1 day, 4:14:48.368103 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 4:14:48.368840 INFO: Updating optimization_manager: mobility_error      : 0.10049005934907623 -> 0.1
1 day, 4:14:48.368962 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1 day, 4:14:48.369054 INFO: Updating optimization_manager: score_cutoff        : 32.62667707672119 -> 30.889052241325377
1 day, 4:14:48.369138 INFO: Updating optimization_manager: fwhm_rt             : 2.779207944869995 -> 2.755573272705078
1 day, 4:14:48.369219 INFO: Updating optimization_manager: fwhm_mobility       : 0.005647079087793827 -> 0.005412509199231863
1 day, 4:14:48.369301 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 4:14:48.369360 INFO: ==============================================
1 day, 4:14:48.369424 PROGRESS: Optimization finished for mobility_error.
1 day, 4:14:48.469419 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:48.470606 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:48.471934 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:48.472691 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:14:48.498466 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 4:14:48.498636 PROGRESS: ==============================================
1 day, 4:14:48.498714 PROGRESS: ms2_error      : 15.0000
1 day, 4:14:48.498771 PROGRESS: ms1_error      : 15.0000
1 day, 4:14:48.498835 PROGRESS: rt_error       : 770.7629
1 day, 4:14:48.498882 PROGRESS: mobility_error : 0.1000
1 day, 4:14:48.498925 PROGRESS: ==============================================
1 day, 4:14:48.499676 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 4:14:49.986142 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 4:14:57.473636 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 4:14:58.949666 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 4:15:15.743923 INFO: Using classic extraction backend
1 day, 4:15:15.744598 PROGRESS: Extracting batch of 12073114 precursors
1 day, 4:15:15.744730 INFO: === Search parameters used ===
1 day, 4:15:15.744788 INFO: rt_error       : 770.7628617682043
1 day, 4:15:15.744837 INFO: mobility_error : 0.1
1 day, 4:15:15.744883 INFO: num_candidates : 3
1 day, 4:15:15.744925 INFO: ms1_error      : 15.0
1 day, 4:15:15.744966 INFO: ms2_error      : 15.0
1 day, 4:15:15.745008 INFO: fwhm_rt        : 2.755573272705078
1 day, 4:15:15.745050 INFO: quant_window   : 3
1 day, 4:15:15.745090 INFO: ==============================================
1 day, 4:15:18.477710 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 4:15:18.477860 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 4:15:18.477913 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 4:15:18.477936 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.51
1 day, 4:15:18.478995 INFO: Starting candidate selection
1 day, 11:05:06.003164 INFO: Removed 1781615 precursors with score below cutoff 30.889052241325377
1 day, 11:05:08.767806 INFO: Starting candidate scoring
1 day, 11:24:43.649076 INFO: Finished candidate processing
1 day, 11:24:43.649569 INFO: Collecting candidate features
1 day, 11:26:29.272686 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 32081223)
1 day, 11:26:31.044026 INFO: Collecting fragment features
1 day, 11:28:08.944864 INFO: Finished candidate scoring
1 day, 11:29:00.196263 INFO: === Performing FDR correction with classifier version 9 ===
1 day, 11:29:00.205930 INFO: performing precursor FDR with 47 features
1 day, 11:29:00.206045 INFO: Decoy channel: -1
1 day, 11:29:00.206075 INFO: Competetive: True
1 day, 11:29:09.810525 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 11:29:13.734157 WARNING: dropped 1 target PSMs due to missing features
1 day, 11:29:40.203799 INFO: Using random state 862963 for train-test-split
1 day, 11:42:59.491313 INFO: Test AUC: 0.576
1 day, 11:42:59.491596 INFO: Train AUC: 0.576
1 day, 11:42:59.491642 INFO: AUC difference: 0.08%
1 day, 11:43:08.758904 INFO: Resetting torch num_threads to 80
1 day, 11:43:09.274421 INFO: Removing fragments below FDR threshold
1 day, 11:43:11.966291 PROGRESS: ============================= Precursor FDR =============================
1 day, 11:43:11.966587 PROGRESS: Total precursors accumulated: 50,518
1 day, 11:43:11.966671 PROGRESS: Target precursors: 50,018 (99.01%)
1 day, 11:43:11.966727 PROGRESS: Decoy precursors: 500 (0.99%)
1 day, 11:43:11.966774 PROGRESS: 
1 day, 11:43:11.966828 PROGRESS: Precursor Summary:
1 day, 11:43:11.982452 PROGRESS: Channel   0:	 0.050 FDR: 50,018; 0.010 FDR: 50,018; 0.001 FDR: 31,125
1 day, 11:43:11.982743 PROGRESS: 
1 day, 11:43:11.982813 PROGRESS: Protein Summary:
1 day, 11:43:12.005215 PROGRESS: Channel   0:	 0.050 FDR: 9,101; 0.010 FDR: 9,101; 0.001 FDR: 6,909
1 day, 11:43:12.005478 PROGRESS: =========================================================================
1 day, 11:43:12.422602 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/psm.parquet
1 day, 11:43:12.783024 INFO: Saving results to run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/frag.parquet
1 day, 11:43:12.992761 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 11:43:50.771450 PROGRESS: Processing search outputs
1 day, 11:43:50.771616 PROGRESS: Performing protein grouping and FDR
1 day, 11:43:50.771654 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 11:43:50.836529 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 11:43:50.865328 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 11:43:50.900132 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 11:43:50.938928 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 11:43:50.969764 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 11:43:51.003578 INFO: Building combined output
1 day, 11:43:51.027716 INFO: Performing protein inference
1 day, 11:43:51.422689 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
1 day, 11:44:15.932316 INFO: Performing protein FDR
1 day, 11:44:21.035444 INFO: Normalizing q-values using 13,868 targets and 2,669 decoys
1 day, 11:44:21.039378 INFO: Test AUC: 0.878
1 day, 11:44:21.039603 INFO: Train AUC: 0.878
1 day, 11:44:21.039693 INFO: AUC difference: 0.04%
1 day, 11:44:21.595243 PROGRESS: ================ Protein FDR =================
1 day, 11:44:21.595417 PROGRESS: Unique protein groups in output
1 day, 11:44:21.595449 PROGRESS:   1% protein FDR: 8,672
1 day, 11:44:21.595471 PROGRESS: 
1 day, 11:44:21.595492 PROGRESS: Unique precursor in output
1 day, 11:44:21.595510 PROGRESS:   1% protein FDR: 86,992
1 day, 11:44:21.595527 PROGRESS: ================================================
1 day, 11:44:21.645130 PROGRESS: Building search statistics
1 day, 11:44:21.741308 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/optimization_manager.pkl
1 day, 11:44:21.741549 INFO: Initializing OptimizationManager
1 day, 11:44:21.741912 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/calibration_manager.pkl
1 day, 11:44:21.741990 INFO: Initializing CalibrationManager
1 day, 11:44:21.742471 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/raw_file_manager.pkl
1 day, 11:44:21.742553 INFO: Initializing RawFileManager
1 day, 11:44:21.767416 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/optimization_manager.pkl
1 day, 11:44:21.769013 INFO: Initializing OptimizationManager
1 day, 11:44:21.769376 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/calibration_manager.pkl
1 day, 11:44:21.769477 INFO: Initializing CalibrationManager
1 day, 11:44:21.769690 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/raw_file_manager.pkl
1 day, 11:44:21.769763 INFO: Initializing RawFileManager
1 day, 11:44:21.795124 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/optimization_manager.pkl
1 day, 11:44:21.795373 INFO: Initializing OptimizationManager
1 day, 11:44:21.795597 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/calibration_manager.pkl
1 day, 11:44:21.795666 INFO: Initializing CalibrationManager
1 day, 11:44:21.795869 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/raw_file_manager.pkl
1 day, 11:44:21.795943 INFO: Initializing RawFileManager
1 day, 11:44:21.823774 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/optimization_manager.pkl
1 day, 11:44:21.824014 INFO: Initializing OptimizationManager
1 day, 11:44:21.824229 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/calibration_manager.pkl
1 day, 11:44:21.824315 INFO: Initializing CalibrationManager
1 day, 11:44:21.824515 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/raw_file_manager.pkl
1 day, 11:44:21.824584 INFO: Initializing RawFileManager
1 day, 11:44:21.852735 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/optimization_manager.pkl
1 day, 11:44:21.852955 INFO: Initializing OptimizationManager
1 day, 11:44:21.853177 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/calibration_manager.pkl
1 day, 11:44:21.853246 INFO: Initializing CalibrationManager
1 day, 11:44:21.853459 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/raw_file_manager.pkl
1 day, 11:44:21.853528 INFO: Initializing RawFileManager
1 day, 11:44:21.878085 INFO: Loaded OptimizationManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/optimization_manager.pkl
1 day, 11:44:21.878304 INFO: Initializing OptimizationManager
1 day, 11:44:21.878530 INFO: Loaded CalibrationManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/calibration_manager.pkl
1 day, 11:44:21.878599 INFO: Initializing CalibrationManager
1 day, 11:44:21.878789 INFO: Loaded RawFileManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/raw_file_manager.pkl
1 day, 11:44:21.878862 INFO: Initializing RawFileManager
1 day, 11:44:21.881902 INFO: Writing stat output to disk
1 day, 11:44:21.881968 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark/stat.tsv to disk
1 day, 11:44:21.889284 PROGRESS: Building internal statistics
1 day, 11:44:21.889583 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/timing_manager.pkl
1 day, 11:44:21.889633 INFO: Initializing TimingManager
1 day, 11:44:21.890021 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/timing_manager.pkl
1 day, 11:44:21.890061 INFO: Initializing TimingManager
1 day, 11:44:21.890249 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/timing_manager.pkl
1 day, 11:44:21.890284 INFO: Initializing TimingManager
1 day, 11:44:21.890456 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/timing_manager.pkl
1 day, 11:44:21.890490 INFO: Initializing TimingManager
1 day, 11:44:21.890660 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/timing_manager.pkl
1 day, 11:44:21.890693 INFO: Initializing TimingManager
1 day, 11:44:21.890869 INFO: Loaded TimingManager from run_output/alphadia_1.12.1_rs_benchmark/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/timing_manager.pkl
1 day, 11:44:21.890904 INFO: Initializing TimingManager
1 day, 11:44:21.891309 INFO: Writing internal output to disk
1 day, 11:44:21.891352 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark/internal.tsv to disk
1 day, 11:44:21.891867 PROGRESS: Performing label free quantification
1 day, 11:44:21.956177 INFO: Accumulating fragment data
1 day, 11:44:21.956380 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 11:44:22.098196 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 11:44:23.019580 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 11:44:24.025437 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 11:44:25.142546 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 11:44:26.239729 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 11:44:27.513208 PROGRESS: Performing label free quantification on the precursor level
1 day, 11:44:27.513361 INFO: Filtering fragments by quality
1 day, 11:44:27.775132 INFO: Performing label-free quantification using directLFQ
1 day, 11:44:29.110595 INFO: 86992 lfq-groups total
1 day, 11:45:56.768635 INFO: using 80 processes
1 day, 11:45:56.991911 INFO: lfq-object 0
1 day, 11:45:57.094234 INFO: lfq-object 300
1 day, 11:45:57.100978 INFO: lfq-object 100
1 day, 11:45:57.200925 INFO: lfq-object 600
1 day, 11:45:57.203167 INFO: lfq-object 400
1 day, 11:45:57.215346 INFO: lfq-object 200
1 day, 11:45:57.292885 INFO: lfq-object 900
1 day, 11:45:57.297740 INFO: lfq-object 1100
1 day, 11:45:57.310258 INFO: lfq-object 700
1 day, 11:45:57.313740 INFO: lfq-object 500
1 day, 11:45:57.401571 INFO: lfq-object 1400
1 day, 11:45:57.404143 INFO: lfq-object 1200
1 day, 11:45:57.406802 INFO: lfq-object 1000
1 day, 11:45:57.419536 INFO: lfq-object 800
1 day, 11:45:57.504817 INFO: lfq-object 1700
1 day, 11:45:57.511392 INFO: lfq-object 1500
1 day, 11:45:57.512966 INFO: lfq-object 1300
1 day, 11:45:57.615233 INFO: lfq-object 1800
1 day, 11:45:57.616287 INFO: lfq-object 1600
1 day, 11:45:57.633661 INFO: lfq-object 2000
1 day, 11:45:57.655682 INFO: lfq-object 2200
1 day, 11:45:57.727361 INFO: lfq-object 1900
1 day, 11:45:57.741716 INFO: lfq-object 2100
1 day, 11:45:57.761613 INFO: lfq-object 2300
1 day, 11:45:57.853750 INFO: lfq-object 2500
1 day, 11:45:57.870395 INFO: lfq-object 2400
1 day, 11:45:57.960743 INFO: lfq-object 2600
1 day, 11:45:57.993802 INFO: lfq-object 2800
1 day, 11:45:58.043489 INFO: lfq-object 3000
1 day, 11:45:58.068492 INFO: lfq-object 2700
1 day, 11:45:58.107427 INFO: lfq-object 2900
1 day, 11:45:58.154498 INFO: lfq-object 3100
1 day, 11:45:58.175669 INFO: lfq-object 3300
1 day, 11:45:58.261589 INFO: lfq-object 3200
1 day, 11:45:58.278418 INFO: lfq-object 3600
1 day, 11:45:58.281484 INFO: lfq-object 3400
1 day, 11:45:58.389925 INFO: lfq-object 3700
1 day, 11:45:58.390126 INFO: lfq-object 3500
1 day, 11:45:58.446206 INFO: lfq-object 3900
1 day, 11:45:58.468221 INFO: lfq-object 4100
1 day, 11:45:58.500256 INFO: lfq-object 3800
1 day, 11:45:58.560885 INFO: lfq-object 4000
1 day, 11:45:58.577507 INFO: lfq-object 4200
1 day, 11:45:58.657995 INFO: lfq-object 4400
1 day, 11:45:58.682647 INFO: lfq-object 4300
1 day, 11:45:58.768975 INFO: lfq-object 4500
1 day, 11:45:58.877712 INFO: lfq-object 4600
1 day, 11:45:58.966771 INFO: lfq-object 4700
1 day, 11:45:59.071793 INFO: lfq-object 4800
1 day, 11:46:01.978325 INFO: lfq-object 4900
1 day, 11:46:02.089472 INFO: lfq-object 5000
1 day, 11:46:02.181157 INFO: lfq-object 5200
1 day, 11:46:02.198733 INFO: lfq-object 5100
1 day, 11:46:02.317254 INFO: lfq-object 5300
1 day, 11:46:02.331127 INFO: lfq-object 5500
1 day, 11:46:02.376148 INFO: lfq-object 6000
1 day, 11:46:02.411166 INFO: lfq-object 5800
1 day, 11:46:02.434303 INFO: lfq-object 5400
1 day, 11:46:02.439352 INFO: lfq-object 5600
1 day, 11:46:02.477178 INFO: lfq-object 6300
1 day, 11:46:02.486544 INFO: lfq-object 6100
1 day, 11:46:02.519464 INFO: lfq-object 5900
1 day, 11:46:02.548526 INFO: lfq-object 5700
1 day, 11:46:02.586429 INFO: lfq-object 6400
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1 day, 11:46:48.584039 INFO: lfq-object 78000
1 day, 11:46:48.680772 INFO: lfq-object 78200
1 day, 11:46:48.787679 INFO: lfq-object 78300
1 day, 11:46:48.787970 INFO: lfq-object 78400
1 day, 11:46:48.897221 INFO: lfq-object 78500
1 day, 11:46:49.005871 INFO: lfq-object 78600
1 day, 11:46:49.019417 INFO: lfq-object 78700
1 day, 11:46:49.127079 INFO: lfq-object 78800
1 day, 11:46:49.181128 INFO: lfq-object 78900
1 day, 11:46:49.270448 INFO: lfq-object 79200
1 day, 11:46:49.289686 INFO: lfq-object 79000
1 day, 11:46:49.367753 INFO: lfq-object 79700
1 day, 11:46:49.372948 INFO: lfq-object 79500
1 day, 11:46:49.380544 INFO: lfq-object 79300
1 day, 11:46:49.400967 INFO: lfq-object 79100
1 day, 11:46:49.472999 INFO: lfq-object 79800
1 day, 11:46:49.483480 INFO: lfq-object 79600
1 day, 11:46:49.490590 INFO: lfq-object 79400
1 day, 11:46:49.507423 INFO: lfq-object 80000
1 day, 11:46:49.580315 INFO: lfq-object 79900
1 day, 11:46:49.604604 INFO: lfq-object 80300
1 day, 11:46:49.609785 INFO: lfq-object 80100
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1 day, 11:46:49.718925 INFO: lfq-object 80200
1 day, 11:46:49.727233 INFO: lfq-object 80600
1 day, 11:46:49.817031 INFO: lfq-object 80500
1 day, 11:46:49.821457 INFO: lfq-object 80800
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1 day, 11:46:50.155143 INFO: lfq-object 81200
1 day, 11:46:50.199754 INFO: lfq-object 81600
1 day, 11:46:50.205104 INFO: lfq-object 81400
1 day, 11:46:50.266877 INFO: lfq-object 81300
1 day, 11:46:50.310724 INFO: lfq-object 81700
1 day, 11:46:50.320178 INFO: lfq-object 81500
1 day, 11:46:50.340464 INFO: lfq-object 81900
1 day, 11:46:50.419814 INFO: lfq-object 82200
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1 day, 11:46:50.517732 INFO: lfq-object 82500
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1 day, 11:46:50.633425 INFO: lfq-object 82400
1 day, 11:46:50.640655 INFO: lfq-object 82800
1 day, 11:46:50.725337 INFO: lfq-object 83000
1 day, 11:46:50.748185 INFO: lfq-object 82900
1 day, 11:46:50.833706 INFO: lfq-object 83100
1 day, 11:46:50.918053 INFO: lfq-object 83300
1 day, 11:46:50.944611 INFO: lfq-object 83200
1 day, 11:46:51.024397 INFO: lfq-object 83400
1 day, 11:46:51.132461 INFO: lfq-object 83500
1 day, 11:46:51.217279 INFO: lfq-object 83600
1 day, 11:46:51.325986 INFO: lfq-object 83800
1 day, 11:46:51.328488 INFO: lfq-object 83700
1 day, 11:46:51.433570 INFO: lfq-object 83900
1 day, 11:46:51.487521 INFO: lfq-object 84100
1 day, 11:46:51.541166 INFO: lfq-object 84000
1 day, 11:46:51.580581 INFO: lfq-object 84600
1 day, 11:46:51.583696 INFO: lfq-object 84400
1 day, 11:46:51.590959 INFO: lfq-object 84200
1 day, 11:46:51.689276 INFO: lfq-object 84700
1 day, 11:46:51.693000 INFO: lfq-object 84500
1 day, 11:46:51.701732 INFO: lfq-object 84300
1 day, 11:46:51.722596 INFO: lfq-object 84900
1 day, 11:46:51.795535 INFO: lfq-object 84800
1 day, 11:46:51.832557 INFO: lfq-object 85000
1 day, 11:46:51.846991 INFO: lfq-object 85200
1 day, 11:46:51.940582 INFO: lfq-object 85100
1 day, 11:46:51.955714 INFO: lfq-object 85300
1 day, 11:46:51.976602 INFO: lfq-object 85700
1 day, 11:46:52.018075 INFO: lfq-object 85500
1 day, 11:46:52.067023 INFO: lfq-object 85400
1 day, 11:46:52.081288 INFO: lfq-object 85800
1 day, 11:46:52.123811 INFO: lfq-object 85600
1 day, 11:46:52.137253 INFO: lfq-object 86000
1 day, 11:46:52.185805 INFO: lfq-object 85900
1 day, 11:46:52.242002 INFO: lfq-object 86100
1 day, 11:46:52.265123 INFO: lfq-object 86300
1 day, 11:46:52.289663 INFO: lfq-object 86500
1 day, 11:46:52.352396 INFO: lfq-object 86200
1 day, 11:46:52.376777 INFO: lfq-object 86400
1 day, 11:46:52.413719 INFO: lfq-object 86600
1 day, 11:46:52.435313 INFO: lfq-object 86800
1 day, 11:46:52.523673 INFO: lfq-object 86700
1 day, 11:46:52.546567 INFO: lfq-object 86900
1 day, 11:47:01.271084 INFO: Writing precursor output to disk
1 day, 11:47:01.271245 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark/precursor.matrix.tsv to disk
1 day, 11:47:01.664548 PROGRESS: Performing label free quantification on the pg level
1 day, 11:47:01.664673 INFO: Filtering fragments by quality
1 day, 11:47:01.929368 INFO: Performing label-free quantification using directLFQ
1 day, 11:47:02.281496 INFO: 8672 lfq-groups total
1 day, 11:48:21.222715 INFO: using 80 processes
1 day, 11:48:21.286694 INFO: lfq-object 0
1 day, 11:48:21.372523 INFO: lfq-object 200
1 day, 11:48:21.444781 INFO: lfq-object 400
1 day, 11:48:21.523177 INFO: lfq-object 100
1 day, 11:48:21.528865 INFO: lfq-object 700
1 day, 11:48:21.724489 INFO: lfq-object 300
1 day, 11:48:21.738938 INFO: lfq-object 1100
1 day, 11:48:21.883945 INFO: lfq-object 800
1 day, 11:48:21.888949 INFO: lfq-object 600
1 day, 11:48:21.896708 INFO: lfq-object 1400
1 day, 11:48:21.897773 INFO: lfq-object 1000
1 day, 11:48:21.918484 INFO: lfq-object 900
1 day, 11:48:21.984497 INFO: lfq-object 1600
1 day, 11:48:21.989534 INFO: lfq-object 500
1 day, 11:48:22.067216 INFO: lfq-object 1800
1 day, 11:48:22.107815 INFO: lfq-object 1500
1 day, 11:48:22.133662 INFO: lfq-object 1900
1 day, 11:48:22.162993 INFO: lfq-object 1300
1 day, 11:48:22.175107 INFO: lfq-object 1700
1 day, 11:48:22.190815 INFO: lfq-object 2100
1 day, 11:48:22.234312 INFO: lfq-object 1200
1 day, 11:48:22.280654 INFO: lfq-object 2300
1 day, 11:48:22.397058 INFO: lfq-object 2000
1 day, 11:48:22.429799 INFO: lfq-object 2400
1 day, 11:48:22.440050 INFO: lfq-object 2500
1 day, 11:48:22.492941 INFO: lfq-object 2800
1 day, 11:48:22.503103 INFO: lfq-object 2200
1 day, 11:48:22.505194 INFO: lfq-object 2600
1 day, 11:48:22.596643 INFO: lfq-object 2700
1 day, 11:48:22.673517 INFO: lfq-object 2900
1 day, 11:48:22.682370 INFO: lfq-object 3000
1 day, 11:48:22.727906 INFO: lfq-object 3100
1 day, 11:48:22.747199 INFO: lfq-object 3200
1 day, 11:48:22.876280 INFO: lfq-object 3500
1 day, 11:48:22.912609 INFO: lfq-object 3400
1 day, 11:48:22.919521 INFO: lfq-object 3300
1 day, 11:48:22.938723 INFO: lfq-object 3600
1 day, 11:48:22.985122 INFO: lfq-object 3700
1 day, 11:48:23.105274 INFO: lfq-object 3900
1 day, 11:48:23.177022 INFO: lfq-object 3800
1 day, 11:48:23.280066 INFO: lfq-object 4100
1 day, 11:48:23.294251 INFO: lfq-object 4200
1 day, 11:48:23.329865 INFO: lfq-object 4400
1 day, 11:48:23.342737 INFO: lfq-object 4000
1 day, 11:48:23.416883 INFO: lfq-object 4300
1 day, 11:48:23.428065 INFO: lfq-object 4600
1 day, 11:48:23.546620 INFO: lfq-object 4900
1 day, 11:48:23.557107 INFO: lfq-object 4700
1 day, 11:48:23.560898 INFO: lfq-object 4800
1 day, 11:48:23.561241 INFO: lfq-object 4500
1 day, 11:48:23.620785 INFO: lfq-object 5000
1 day, 11:48:23.628617 INFO: lfq-object 5100
1 day, 11:48:23.745341 INFO: lfq-object 5200
1 day, 11:48:23.763779 INFO: lfq-object 5300
1 day, 11:48:23.954338 INFO: lfq-object 5600
1 day, 11:48:23.988259 INFO: lfq-object 5400
1 day, 11:48:24.076447 INFO: lfq-object 5800
1 day, 11:48:24.131635 INFO: lfq-object 5700
1 day, 11:48:24.162325 INFO: lfq-object 5500
1 day, 11:48:24.222596 INFO: lfq-object 5900
1 day, 11:48:24.231969 INFO: lfq-object 6000
1 day, 11:48:24.272657 INFO: lfq-object 6100
1 day, 11:48:24.306322 INFO: lfq-object 6200
1 day, 11:48:24.307545 INFO: lfq-object 6300
1 day, 11:48:24.405574 INFO: lfq-object 6500
1 day, 11:48:24.409840 INFO: lfq-object 6400
1 day, 11:48:24.545504 INFO: lfq-object 6700
1 day, 11:48:24.565953 INFO: lfq-object 6600
1 day, 11:48:24.642617 INFO: lfq-object 7000
1 day, 11:48:24.695786 INFO: lfq-object 6900
1 day, 11:48:24.757496 INFO: lfq-object 6800
1 day, 11:48:24.776031 INFO: lfq-object 7200
1 day, 11:48:24.809708 INFO: lfq-object 7100
1 day, 11:48:24.840446 INFO: lfq-object 7300
1 day, 11:48:24.862292 INFO: lfq-object 7400
1 day, 11:48:24.909811 INFO: lfq-object 7500
1 day, 11:48:24.960378 INFO: lfq-object 7600
1 day, 11:48:24.968377 INFO: lfq-object 7700
1 day, 11:48:25.018003 INFO: lfq-object 7800
1 day, 11:48:25.129627 INFO: lfq-object 8100
1 day, 11:48:25.160161 INFO: lfq-object 8000
1 day, 11:48:25.224099 INFO: lfq-object 7900
1 day, 11:48:25.274184 INFO: lfq-object 8400
1 day, 11:48:25.291113 INFO: lfq-object 8300
1 day, 11:48:25.321960 INFO: lfq-object 8200
1 day, 11:48:25.434065 INFO: lfq-object 8600
1 day, 11:48:25.450531 INFO: lfq-object 8500
1 day, 11:48:29.743160 INFO: Writing pg output to disk
1 day, 11:48:29.743388 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark/pg.matrix.tsv to disk
1 day, 11:48:29.952876 INFO: Writing psm output to disk
1 day, 11:48:29.953032 INFO: Saving run_output/alphadia_1.12.1_rs_benchmark/precursors.tsv to disk
1 day, 11:48:50.072636 PROGRESS: Building MBR spectral library
1 day, 11:48:50.166169 INFO: Running MbrLibraryBuilder
1 day, 11:48:52.492506 INFO: MBR spectral library contains 86,992 precursors, 8,672 proteins
1 day, 11:48:52.492648 INFO: Writing MBR spectral library to disk
1 day, 11:48:53.257872 PROGRESS: =================== Search Finished ===================
