0:00:00.000100 INFO: Output directory: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest, cwd: /app.
0:00:00.000586 INFO: User provided config file: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/alphadia_config.yaml.
0:00:00.024716 PROGRESS:           _      _         ___ ___   _   
0:00:00.025009 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.025035 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.025057 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.025076 PROGRESS:            |_|                           
0:00:00.025095 PROGRESS: 
0:00:00.025132 PROGRESS: version: 2.1.2
0:00:00.025155 PROGRESS: Please cite: Wallmann, et al., Nature Biotechnology (2025), https://doi.org/10.1038/s41587-025-02791-w
0:00:00.025223 INFO: hostname: 2eb1a55fd1be
0:00:00.025295 PROGRESS: os: Linux 6.12.85+deb13-amd64 (x86_64)
0:00:00.025350 PROGRESS: python: 3.10.10 (CPython)
0:00:00.025549 INFO: date: 2026-07-18 21:10:50
0:00:00.025596 INFO: ================ AlphaX Environment ===============
0:00:00.025642 INFO: alphabase       : 1.9.0
0:00:00.025679 INFO: alpharaw        : 0.6.0
0:00:00.025715 INFO: alphapeptdeep   : 1.4.2
0:00:00.025763 INFO: directlfq       : 0.3.1
0:00:00.025794 INFO: ===================================================
0:00:00.025819 INFO: ================= Pip Environment =================
0:00:00.117568 INFO: click==8.1.8 peptdeep==1.4.2 et_xmlfile==2.0.0 nvidia-nvjitlink-cu12==12.4.127 huggingface-hub==0.30.2 pyarrow==20.0.0 rdkit==2024.9.6 tqdm==4.67.1 psutil==7.0.0 alpharaw==0.6.0 torchmetrics==1.7.1 numpy==1.26.4 directlfq==0.3.1 contextlib2==21.6.0 argparse==1.4.0 nvidia-cuda-cupti-cu12==12.4.127 packaging==24.2 narwhals==2.22.0 joblib==1.4.2 transformers==4.51.2 cffi==1.17.1 nvidia-cuda-nvrtc-cu12==12.4.127 numba==0.61.2 pyteomics==4.7.5 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 fsspec==2025.3.2 xxhash==3.5.0 threadpoolctl==3.6.0 alphabase==1.9.0 pythonnet==3.0.5 requests==2.32.3 triton==3.2.0 h5py==3.13.0 pyahocorasick==2.1.0 pycparser==2.22 pytz==2026.2 regex==2024.11.6 certifi==2025.1.31 python-dateutil==2.9.0.post0 torch==2.6.0 plotly==6.7.0 openpyxl==3.1.5 setuptools==78.1.0 nvidia-cusparse-cu12==12.3.1.170 rocket-fft==0.2.5 alphadia==2.1.2 clr_loader==0.2.7.post0 quantselect==0.1.3 pandas==2.2.3 dill==0.3.9 pyparsing==3.2.3 typing_extensions==4.13.2 networkx==3.4.2 biopython==1.85 urllib3==2.4.0 seaborn==0.13.2 alphadia-search-rs==1.1.1 llvmlite==0.44.0 fonttools==4.57.0 scipy==1.12.0 tzdata==2025.2 filelock==3.18.0 matplotlib==3.10.1 contourpy==1.3.1 lxml==5.3.2 Jinja2==3.1.6 nvidia-nvtx-cu12==12.4.127 nvidia-cusolver-cu12==11.6.1.9 safetensors==0.5.3 idna==3.10 nvidia-cufft-cu12==11.2.1.3 sympy==1.13.1 pillow==11.1.0 nvidia-cublas-cu12==12.4.5.8 nvidia-cudnn-cu12==9.1.0.70 tokenizers==0.21.1 nvidia-curand-cu12==10.3.5.147 kiwisolver==1.4.8 nvidia-cuda-runtime-cu12==12.4.127 scikit-learn==1.6.1 nvidia-nccl-cu12==2.21.5 nvidia-cusparselt-cu12==0.6.2 PyYAML==6.0.2 pip==22.3.1 wheel==0.38.4 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
0:00:00.118055 INFO: ===================================================
0:00:00.118139 INFO: =================== Running step 'library' ===================
0:00:00.118516 INFO: loading default config from /usr/local/lib/python3.10/site-packages/alphadia/constants/default.yaml
0:00:00.138100 INFO: loading additional config provided via CLI
0:00:00.138495 INFO: loading additional config provided via CLI parameters
0:00:00.139316 INFO: Updating config with 'user defined'
0:00:00.139500 INFO: Updating config with 'user defined (cli)'
0:00:00.139601 INFO: loading default config from /usr/local/lib/python3.10/site-packages/alphadia/constants/default_python.yaml
0:00:00.141651 INFO: updating config with user defined values: [{'calibration': {'batch_size': 8000, 'optimization_lock_target': 200, 'min_steps': 2}, 'optimization': {'rt_error': {'automatic_update_percentile_range': 0.99, 'automatic_update_factor': 1.1, 'maximal_decrease': 0.2, 'favour_narrower_optimum': True, 'maximum_decrease_from_maximum': 0.1}}}, {'raw_paths': ['/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d'], 'fasta_paths': ['/public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta'], 'output_directory': '/home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest', 'general': {'thread_count': 100, 'mbr_step_enabled': True, 'transfer_step_enabled': False}, 'library_prediction': {'enabled': True, 'enzyme': 'trypsin/p', 'missed_cleavages': 1, 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M', 'max_var_mod_num': 1, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [400.0, 1000.0], 'fragment_mz': [100.0, 1700.0]}, 'search': {'target_ms1_tolerance': 15, 'target_ms2_tolerance': 15, 'extraction_backend': 'python'}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins'}, 'search_output': {'normalize_directlfq': True}}, {'raw_paths': ['/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d']}, {'quant_directory': None, 'general': {'save_mbr_library': True, 'save_library': False}, 'transfer_library': {'enabled': False}, 'transfer_learning': {'enabled': False}, 'output_directory': '/home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library'}]
0:00:00.142205 INFO: Updating config with 'default_python'
0:00:00.142323 INFO: Updating config with 'user defined'
0:00:00.142416 INFO: Updating config with 'user defined (cli)'
0:00:00.142457 INFO: Updating config with 'multistep search'
0:00:00.142559 INFO: ├──version: None
0:00:00.142601 INFO: ├──workflow_name: None
0:00:00.142634 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library [multistep search, default: None][0m
0:00:00.142673 INFO: ├──library_path: None
0:00:00.142702 INFO: ├──raw_paths:
0:00:00.142740 INFO: │   [32;20m- /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d [user defined (cli), default: None][0m
0:00:00.142765 INFO: │   [32;20m- /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d [user defined (cli), default: None][0m
0:00:00.142785 INFO: │   [32;20m- /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d [user defined (cli), default: None][0m
0:00:00.142809 INFO: │   [32;20m- /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d [user defined (cli), default: None][0m
0:00:00.142834 INFO: │   [32;20m- /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d [user defined (cli), default: None][0m
0:00:00.142857 INFO: │   [32;20m- /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d [user defined (cli), default: None][0m
0:00:00.142892 INFO: ├──fasta_paths:
0:00:00.142913 INFO: │   [32;20m- /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta [user defined, default: None][0m
0:00:00.142933 INFO: ├──quant_directory: None
0:00:00.142953 INFO: ├──general
0:00:00.142980 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
0:00:00.143008 INFO: │   ├──transfer_step_enabled: False
0:00:00.143038 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
0:00:00.143067 INFO: │   ├──reuse_calibration: False
0:00:00.143087 INFO: │   ├──reuse_quant: False
0:00:00.143108 INFO: │   ├──log_level: INFO
0:00:00.143130 INFO: │   ├──use_gpu: True
0:00:00.143150 INFO: │   ├──save_figures: True
0:00:00.143171 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.143191 INFO: │   ├──save_flat_library: False
0:00:00.143214 INFO: │   ├──input_library_type: base
0:00:00.143245 INFO: │   ├──save_mbr_library: True
0:00:00.143267 INFO: │   ├──random_state: None
0:00:00.143288 INFO: │   └──fail_fast: False
0:00:00.143309 INFO: ├──library_loading
0:00:00.143330 INFO: │   └──drop_decoys: False
0:00:00.143349 INFO: ├──library_prediction
0:00:00.143372 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.143396 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.143417 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.143439 INFO: │   [32;20m├──variable_modifications: Oxidation@M [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
0:00:00.143463 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.143485 INFO: │   ├──missed_cleavages: 1
0:00:00.143506 INFO: │   ├──precursor_len:
0:00:00.143528 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.143550 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.143571 INFO: │   ├──precursor_charge:
0:00:00.143592 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.143611 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.143630 INFO: │   ├──precursor_mz:
0:00:00.143654 INFO: │   │   - 400.0
0:00:00.143675 INFO: │   │   [32;20m- 1000.0 [user defined, default: 1200][0m
0:00:00.143698 INFO: │   ├──fragment_mz:
0:00:00.143718 INFO: │   │   [32;20m- 100.0 [user defined, default: 200][0m
0:00:00.143738 INFO: │   │   [32;20m- 1700.0 [user defined, default: 2000][0m
0:00:00.143760 INFO: │   ├──nce: 25.0
0:00:00.143781 INFO: │   ├──fragment_types:
0:00:00.143800 INFO: │   │   - b
0:00:00.143820 INFO: │   │   - y
0:00:00.143840 INFO: │   ├──max_fragment_charge: 2
0:00:00.143859 INFO: │   ├──instrument: Lumos
0:00:00.143878 INFO: │   ├──peptdeep_model_path: None
0:00:00.143901 INFO: │   ├──peptdeep_model_type: generic
0:00:00.143923 INFO: │   ├──predict_charge: False
0:00:00.143942 INFO: │   └──min_charge_probability: 0.1
0:00:00.143962 INFO: ├──custom_modifications:
0:00:00.143984 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.144003 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.144024 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.144044 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.144063 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.144081 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.144101 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.144123 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.144145 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.144166 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.144201 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.144223 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.144244 INFO: │   ├──name: Label:13C(12)@K
0:00:00.144265 INFO: │   └──composition: C(12)
0:00:00.144284 INFO: ├──search
0:00:00.144306 INFO: │   [32;20m├──extraction_backend: python [user defined, default: rust][0m
0:00:00.144329 INFO: │   [32;20m├──target_ms1_tolerance: 15 [user defined, default: 5][0m
0:00:00.144348 INFO: │   [32;20m├──target_ms2_tolerance: 15 [user defined, default: 10][0m
0:00:00.144370 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.144392 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.144412 INFO: │   ├──quant_window: 3
0:00:00.144432 INFO: │   ├──target_num_candidates: 3
0:00:00.144451 INFO: │   ├──channel_filter: 
0:00:00.144471 INFO: │   ├──compete_for_fragments: True
0:00:00.144492 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.144514 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.144534 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.144556 INFO: │   ├──optimized_peak_group_score: False
0:00:00.144578 INFO: │   ├──exclude_shared_ions: True
0:00:00.144597 INFO: │   ├──quant_all: True
0:00:00.144619 INFO: │   └──experimental_xic: True
0:00:00.144639 INFO: ├──calibration
0:00:00.144660 INFO: │   [32;20m├──batch_size: 8000 [default_python, default: 1000][0m
0:00:00.144679 INFO: │   [32;20m├──optimization_lock_target: 200 [default_python, default: 1000][0m
0:00:00.144703 INFO: │   ├──max_steps: 20
0:00:00.144722 INFO: │   [32;20m├──min_steps: 2 [default_python, default: 5][0m
0:00:00.144743 INFO: │   ├──max_skips: 1
0:00:00.144762 INFO: │   ├──max_fragments: 5000
0:00:00.144782 INFO: │   └──min_correlation: 0.7
0:00:00.144802 INFO: ├──search_initial
0:00:00.144822 INFO: │   ├──num_candidates: 1
0:00:00.144842 INFO: │   ├──ms1_tolerance: 30
0:00:00.144861 INFO: │   ├──ms2_tolerance: 30
0:00:00.144881 INFO: │   ├──mobility_tolerance: 0.1
0:00:00.144901 INFO: │   └──rt_tolerance: 0.5
0:00:00.144921 INFO: ├──library_multiplexing
0:00:00.144942 INFO: │   ├──enabled: False
0:00:00.144964 INFO: │   ├──input_channel: 0
0:00:00.144986 INFO: │   └──multiplex_mapping:
0:00:00.145004 INFO: ├──multiplexing
0:00:00.145024 INFO: │   ├──enabled: False
0:00:00.145045 INFO: │   ├──target_channels: 4,8
0:00:00.145066 INFO: │   ├──decoy_channel: 12
0:00:00.145084 INFO: │   ├──reference_channel: 0
0:00:00.145103 INFO: │   └──competitive_scoring: True
0:00:00.145122 INFO: ├──fdr
0:00:00.145144 INFO: │   ├──fdr: 0.01
0:00:00.145163 INFO: │   ├──group_level: proteins
0:00:00.145182 INFO: │   ├──inference_strategy: heuristic
0:00:00.145202 INFO: │   ├──competitive_scoring: True
0:00:00.145221 INFO: │   ├──keep_decoys: False
0:00:00.145241 INFO: │   ├──keep_decoys_in_mbr_library: False
0:00:00.145265 INFO: │   ├──channel_wise_fdr: False
0:00:00.145286 INFO: │   └──enable_nn_hyperparameter_tuning: True
0:00:00.145306 INFO: ├──search_output
0:00:00.145329 INFO: │   ├──file_format: parquet
0:00:00.145348 INFO: │   ├──precursor_level_lfq: True
0:00:00.145367 INFO: │   ├──peptide_level_lfq: True
0:00:00.145388 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.145407 INFO: │   ├──min_k_fragments: 12
0:00:00.145429 INFO: │   ├──min_correlation: 0.9
0:00:00.145456 INFO: │   ├──num_samples_quadratic: 50
0:00:00.145475 INFO: │   ├──min_nonnan: 3
0:00:00.145494 INFO: │   ├──normalization_method: directlfq
0:00:00.145514 INFO: │   └──normalize_directlfq: True
0:00:00.145534 INFO: ├──optimization
0:00:00.145565 INFO: │   ├──order_of_optimization: None
0:00:00.145591 INFO: │   ├──ms2_error
0:00:00.145615 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.145638 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.145658 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.145678 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.145699 INFO: │   │   ├──try_narrower_values: True
0:00:00.145722 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.145832 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.145887 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.145916 INFO: │   ├──ms1_error
0:00:00.145947 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.145976 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.146004 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.146066 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.146096 INFO: │   │   ├──try_narrower_values: False
0:00:00.146126 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.146156 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.146186 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.146215 INFO: │   ├──mobility_error
0:00:00.146247 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.146276 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.146309 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.146339 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.146372 INFO: │   │   ├──try_narrower_values: False
0:00:00.146424 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.146455 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.146483 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.146514 INFO: │   └──rt_error
0:00:00.146547 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.146578 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.146615 INFO: │       [32;20m├──automatic_update_percentile_range: 0.99 [default_python, default: 0.999][0m
0:00:00.146647 INFO: │       [32;20m├──automatic_update_factor: 1.1 [default_python, default: 1.5][0m
0:00:00.146680 INFO: │       ├──try_narrower_values: True
0:00:00.146713 INFO: │       [32;20m├──maximal_decrease: 0.2 [default_python, default: 0.1][0m
0:00:00.146748 INFO: │       [32;20m├──favour_narrower_optimum: True [default_python, default: False][0m
0:00:00.146779 INFO: │       [32;20m└──maximum_decrease_from_maximum: 0.1 [default_python, default: 0.5][0m
0:00:00.146811 INFO: ├──optimization_manager
0:00:00.146846 INFO: │   ├──fwhm_rt: 5
0:00:00.146882 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.146912 INFO: │   └──score_cutoff: 0
0:00:00.146960 INFO: ├──transfer_library
0:00:00.146990 INFO: │   ├──enabled: False
0:00:00.147022 INFO: │   ├──fragment_types:
0:00:00.147050 INFO: │   │   - b
0:00:00.147080 INFO: │   │   - y
0:00:00.147114 INFO: │   ├──max_charge: 2
0:00:00.147146 INFO: │   ├──top_k_samples: 3
0:00:00.147197 INFO: │   ├──norm_delta_max: True
0:00:00.147223 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.147253 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.147284 INFO: └──transfer_learning
0:00:00.147320 INFO:     ├──enabled: False
0:00:00.147349 INFO:     ├──batch_size: 2000
0:00:00.147381 INFO:     ├──max_lr: 0.0001
0:00:00.147409 INFO:     ├──train_fraction: 0.7
0:00:00.147440 INFO:     ├──validation_fraction: 0.2
0:00:00.147471 INFO:     ├──test_fraction: 0.1
0:00:00.147507 INFO:     ├──test_interval: 1
0:00:00.147536 INFO:     ├──lr_patience: 3
0:00:00.147570 INFO:     ├──epochs: 51
0:00:00.147599 INFO:     ├──warmup_epochs: 5
0:00:00.147629 INFO:     ├──nce: 25
0:00:00.147659 INFO:     └──instrument: Lumos
0:00:00.157029 INFO: Registering 7 custom modifications
0:00:00.213987 INFO: Searching 6 files:
0:00:00.214389 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:00:00.214429 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
0:00:00.214456 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
0:00:00.214480 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
0:00:00.214502 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
0:00:00.214521 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
0:00:00.214546 INFO: Using 1 fasta files:
0:00:00.214571 INFO:   /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
0:00:00.214596 INFO: Using library: None
0:00:00.214621 INFO: Saving output to: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library
0:00:00.214699 PROGRESS: Loading spectral library
0:00:00.214795 PROGRESS: No library provided. Building library from fasta files.
0:00:00.214938 INFO: Running FastaDigest
0:00:00.220337 INFO: Digesting fasta file
0:00:21.253431 INFO: Adding modifications
0:03:45.114949 INFO: Removing non-canonical amino acids
0:04:00.167384 INFO: Fasta library contains 5,845,771 precursors
0:04:00.168104 PROGRESS: Predicting library properties.
0:04:00.168244 INFO: Running PeptDeepPrediction
0:04:00.171406 INFO: Device set to cpu
0:04:00.172361 INFO: Downloading pretrained models from https://github.com/MannLabs/alphapeptdeep/releases/download/pre-trained-models/pretrained_models_v3.zip to /tmp/peptdeep/pretrained_models/pretrained_models_v3.zip ...
0:04:01.253267 INFO: Successfully downloaded pretrained models.
0:04:05.450561 INFO: Loading PeptDeep models of type generic
0:04:08.210628 INFO: Predicting RT, MS2 and mobility
0:04:08.211246 INFO: Using multiprocessing with 100 processes ...
0:04:10.193858 INFO: Predicting rt,ms2,mobility ...
0:22:40.257533 INFO: Adding fragment mz information
0:22:40.552843 INFO: Adding fragment intensity information
0:22:40.846390 INFO: Adding precursor information
0:22:41.174237 INFO: Running PrecursorInitializer
0:22:41.218386 INFO: Running AnnotateFasta
0:23:10.227005 INFO: Running IsotopeGenerator
0:23:10.228542 WARNING: Multiprocessing not compatible with custom modifications yet, falling back to single process.
0:27:17.840560 INFO: Running RTNormalization
0:27:17.840918 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:27:17.841021 INFO: Saving library to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/speclib.hdf
0:27:52.387681 INFO: Running DecoyGenerator
0:31:39.873525 INFO: Running FlattenLibrary
0:33:15.655159 INFO: Running InitFlatColumns
0:33:16.787988 INFO: Running LogFlatLibraryStats
0:33:16.788745 INFO: ============ Library Stats ============
0:33:16.788821 INFO: Number of precursors: 11,663,200
0:33:22.386095 INFO: 	thereof targets:5,845,771
0:33:22.386718 INFO: 	thereof decoys: 5,817,429
0:33:22.512936 INFO: Number of elution groups: 5,845,771
0:33:22.513416 INFO: 	average size: 2.00
0:33:23.743061 INFO: Number of proteins: 117,993
0:33:23.774531 INFO: Number of channels: 1 ([0])
0:33:23.775138 INFO: Isotopes Distribution for 4 isotopes
0:33:23.775187 INFO: =======================================
0:33:23.809569 PROGRESS: =================== Starting Search Workflows for step library ===================
0:33:23.810205 PROGRESS: Loading raw file 1/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494 
0:33:23.810324 INFO: Quantification results path: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant
0:33:23.810508 INFO: Creating folder /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/figures
0:33:23.810926 INFO: Initializing TimingManager
0:33:23.811665 INFO: Initializing RawFileManager
0:33:23.811855 INFO: Importing data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:33:23.811941 INFO: Using .d import for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:33:23.812012 INFO: Reading frame metadata for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:33:24.927509 INFO: Reading 39,128 frames with 2,835,410,867 detector events for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:34:25.972000 INFO: Indexing /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d...
0:34:25.990369 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:34:26.009327 INFO: Fetching mobility values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:34:26.011203 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:34:26.012721 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:34:26.018746 INFO: Fetching mz values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:34:26.066711 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:34:26.067752 INFO: Indexing quadrupole dimension
0:34:28.192354 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:34:28.192875 INFO: Transposing detector events
0:34:58.295218 INFO: Finished transposing data
0:34:58.483159 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
0:34:58.487241 INFO: RT (min)            : 0.0 - 70.0
0:34:58.487709 INFO: RT duration (sec)   : 4199.9
0:34:58.487950 INFO: RT duration (min)   : 70.0
0:34:58.488179 INFO: Cycle len (scans)   : 9
0:34:58.488393 INFO: Cycle len (sec)     : 0.97
0:34:58.488490 INFO: Number of cycles    : 4347
0:34:58.488575 INFO: MS2 range (m/z)     : 400.0 - 1000.0
0:34:58.488746 INFO: Creating DIA data object took: 94.67691040039062
0:35:05.286322 INFO: Initializing CalibrationManager
0:35:05.287808 INFO: Setting up calibration estimators ..
0:35:05.287972 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:35:05.288147 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
0:35:05.288416 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:35:05.288539 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'}' ..
0:35:05.288674 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
0:35:05.288835 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}}' ..
0:35:05.288952 INFO: Done setting up calibration estimators.
0:35:05.289609 INFO: Initializing OptimizationManager
0:35:05.289917 INFO: initial parameter: ms1_error = 30
0:35:05.290021 INFO: initial parameter: ms2_error = 30
0:35:05.290168 INFO: initial parameter: rt_error = 2099.928159
0:35:05.290274 INFO: initial parameter: mobility_error = 0.1
0:35:05.290371 INFO: initial parameter: num_candidates = 1
0:35:05.290481 INFO: initial parameter: fwhm_rt = 5
0:35:05.290572 INFO: initial parameter: fwhm_mobility = 0.01
0:35:05.290690 INFO: initial parameter: score_cutoff = 0
0:35:05.290814 INFO: initial parameter: classifier_version = -1
0:35:05.291019 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
0:35:05.292061 INFO: FDRManager: loading saved state not requested, will be initialized.
0:35:05.292166 INFO: Initializing FDRManager
0:35:05.292347 INFO: Loading classifier store from /usr/local/lib/python3.10/site-packages/alphadia/constants/classifier
0:35:11.585631 PROGRESS: Initializing spectral library: 5,845,771 target precursors potentially observable (0 removed)
0:35:17.333353 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
0:35:17.335001 INFO: Updating optimization_manager: rt_error            : 2099.928159 -> 2099.928159
0:35:17.335170 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
0:35:17.335515 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
0:35:17.335728 PROGRESS: Starting initial search for precursors.
0:35:17.335955 INFO: Starting optimization step 0.
0:35:17.336069 PROGRESS: === Extracting elution groups 0 to 8000 ===
0:35:17.336227 INFO: Using python extraction backend
0:35:17.336514 PROGRESS: Extracting batch of 15766 precursors
0:35:17.336624 INFO: === Search parameters used ===
0:35:17.336698 INFO: rt_error       : 2099.928159
0:35:17.336767 INFO: mobility_error : 0.1
0:35:17.336834 INFO: num_candidates : 1
0:35:17.336900 INFO: ms1_error      : 30
0:35:17.336962 INFO: ms2_error      : 30
0:35:17.337025 INFO: fwhm_rt        : 5
0:35:17.337088 INFO: quant_window   : 3
0:35:17.337148 INFO: ==============================================
0:35:22.161637 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:35:22.162077 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:35:22.162195 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:35:22.162232 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:35:26.862835 INFO: Starting candidate selection
0:43:10.586893 INFO: Starting candidate scoring
0:52:06.155861 INFO: Finished candidate processing
0:52:06.156888 INFO: Collecting candidate features
0:52:06.647157 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 15080)
0:52:06.651691 INFO: Collecting fragment features
0:52:07.947164 INFO: Finished candidate scoring
0:52:07.961483 INFO: performing precursor FDR with 47 features
0:52:07.961603 INFO: Decoy channel: -1
0:52:07.961632 INFO: competitive: True
0:52:07.966652 INFO: Setting torch num_threads to 2 for FDR classification task
0:52:07.969814 WARNING: dropped 1 target PSMs due to missing features
0:52:07.973043 INFO: Estimating optimal hyperparameters - samples: 12,063, batch_size: 128, learning_rate: 1.77e-04
0:52:07.974329 INFO: Using random state 299506 for train-test-split
0:52:09.273702 INFO: Test AUC: 0.551
0:52:09.273855 INFO: Train AUC: 0.594
0:52:09.273897 INFO: AUC difference: 7.25%
0:52:09.273928 WARNING: AUC difference > 5%. This may indicate overfitting.
0:52:09.581148 INFO: Resetting torch num_threads to 128
0:52:09.582331 PROGRESS: === Extracted 15080 precursors and 163208 fragments ===
0:52:09.582927 INFO: === FDR correction performed with classifier version -1 ===
0:52:09.584453 PROGRESS: ============================= Precursor FDR =============================
0:52:09.584568 PROGRESS: Total precursors accumulated: 7,722
0:52:09.584641 PROGRESS: Target precursors: 4,773 (61.81%)
0:52:09.584705 PROGRESS: Decoy precursors: 2,949 (38.19%)
0:52:09.584762 PROGRESS: 
0:52:09.584815 PROGRESS: Precursor Summary:
0:52:09.585916 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:52:09.586022 PROGRESS: 
0:52:09.586097 PROGRESS: Protein Summary:
0:52:09.587244 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:52:09.587344 PROGRESS: =========================================================================
0:52:09.587859 INFO: Target number of precursors not reached yet.
0:52:09.804190 INFO: Starting optimization step 1.
0:52:09.804504 PROGRESS: === Extracting elution groups 8000 to 24000 ===
0:52:09.804653 INFO: Using python extraction backend
0:52:09.804933 PROGRESS: Extracting batch of 31523 precursors
0:52:09.805032 INFO: === Search parameters used ===
0:52:09.805094 INFO: rt_error       : 2099.928159
0:52:09.805148 INFO: mobility_error : 0.1
0:52:09.805204 INFO: num_candidates : 1
0:52:09.805256 INFO: ms1_error      : 30
0:52:09.805304 INFO: ms2_error      : 30
0:52:09.805351 INFO: fwhm_rt        : 5
0:52:09.805398 INFO: quant_window   : 3
0:52:09.805445 INFO: ==============================================
0:52:09.812237 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:52:09.812320 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:52:09.812385 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:52:09.812412 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:52:09.813348 INFO: Starting candidate selection
0:55:38.085476 INFO: Starting candidate scoring
0:55:40.138118 INFO: Finished candidate processing
0:55:40.138390 INFO: Collecting candidate features
0:55:40.228828 WARNING: intensity_correlation has 9 NaNs ( 0.03 % out of 30048)
0:55:40.229118 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 30048)
0:55:40.233553 INFO: Collecting fragment features
0:55:40.254453 INFO: Finished candidate scoring
0:55:40.278251 INFO: performing precursor FDR with 47 features
0:55:40.278406 INFO: Decoy channel: -1
0:55:40.278435 INFO: competitive: True
0:55:40.294381 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:40.303551 WARNING: dropped 4 target PSMs due to missing features
0:55:40.303690 WARNING: dropped 6 decoy PSMs due to missing features
0:55:40.310372 INFO: Estimating optimal hyperparameters - samples: 36,094, batch_size: 147, learning_rate: 1.89e-04
0:55:40.310593 INFO: Using random state 982259 for train-test-split
0:55:44.267935 INFO: Test AUC: 0.552
0:55:44.268122 INFO: Train AUC: 0.599
0:55:44.268158 INFO: AUC difference: 7.77%
0:55:44.268183 WARNING: AUC difference > 5%. This may indicate overfitting.
0:55:44.550735 INFO: Resetting torch num_threads to 128
0:55:44.557885 PROGRESS: === Extracted 45128 precursors and 487343 fragments ===
0:55:44.558728 INFO: === FDR correction performed with classifier version -1 ===
0:55:44.562645 PROGRESS: ============================= Precursor FDR =============================
0:55:44.562781 PROGRESS: Total precursors accumulated: 23,116
0:55:44.562867 PROGRESS: Target precursors: 14,219 (61.51%)
0:55:44.562947 PROGRESS: Decoy precursors: 8,897 (38.49%)
0:55:44.563033 PROGRESS: 
0:55:44.563114 PROGRESS: Precursor Summary:
0:55:44.564423 PROGRESS: Channel   0:	 0.050 FDR:    84; 0.010 FDR:    39; 0.001 FDR:    39
0:55:44.564529 PROGRESS: 
0:55:44.564596 PROGRESS: Protein Summary:
0:55:44.566004 PROGRESS: Channel   0:	 0.050 FDR:    84; 0.010 FDR:    39; 0.001 FDR:    39
0:55:44.566123 PROGRESS: =========================================================================
0:55:44.566552 INFO: Target number of precursors not reached yet.
0:55:44.793268 INFO: Starting optimization step 2.
0:55:44.793578 PROGRESS: === Extracting elution groups 24000 to 56000 ===
0:55:44.793769 INFO: Using python extraction backend
0:55:44.793995 PROGRESS: Extracting batch of 63149 precursors
0:55:44.794106 INFO: === Search parameters used ===
0:55:44.794188 INFO: rt_error       : 2099.928159
0:55:44.794266 INFO: mobility_error : 0.1
0:55:44.794341 INFO: num_candidates : 1
0:55:44.794413 INFO: ms1_error      : 30
0:55:44.794487 INFO: ms2_error      : 30
0:55:44.794559 INFO: fwhm_rt        : 5
0:55:44.794631 INFO: quant_window   : 3
0:55:44.794698 INFO: ==============================================
0:55:44.811173 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
0:55:44.811327 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
0:55:44.811368 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
0:55:44.811402 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
0:55:44.812220 INFO: Starting candidate selection
1:02:01.795542 INFO: Starting candidate scoring
1:02:05.832458 INFO: Finished candidate processing
1:02:05.832715 INFO: Collecting candidate features
1:02:05.972395 WARNING: intensity_correlation has 12 NaNs ( 0.02 % out of 60221)
1:02:05.972712 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 60221)
1:02:05.978141 INFO: Collecting fragment features
1:02:06.019533 INFO: Finished candidate scoring
1:02:06.081870 INFO: performing precursor FDR with 47 features
1:02:06.082021 INFO: Decoy channel: -1
1:02:06.082057 INFO: competitive: True
1:02:06.119998 INFO: Setting torch num_threads to 2 for FDR classification task
1:02:06.141343 WARNING: dropped 10 target PSMs due to missing features
1:02:06.141484 WARNING: dropped 14 decoy PSMs due to missing features
1:02:06.157688 INFO: Estimating optimal hyperparameters - samples: 84,260, batch_size: 345, learning_rate: 2.90e-04
1:02:06.158092 INFO: Using random state 391580 for train-test-split
1:02:10.796416 INFO: Test AUC: 0.550
1:02:10.796555 INFO: Train AUC: 0.595
1:02:10.796587 INFO: AUC difference: 7.44%
1:02:10.796612 WARNING: AUC difference > 5%. This may indicate overfitting.
1:02:11.090411 INFO: Resetting torch num_threads to 128
1:02:11.107225 PROGRESS: === Extracted 105349 precursors and 1138136 fragments ===
1:02:11.108029 INFO: === FDR correction performed with classifier version -1 ===
1:02:11.116489 PROGRESS: ============================= Precursor FDR =============================
1:02:11.116661 PROGRESS: Total precursors accumulated: 53,947
1:02:11.116749 PROGRESS: Target precursors: 32,586 (60.40%)
1:02:11.116853 PROGRESS: Decoy precursors: 21,361 (39.60%)
1:02:11.116935 PROGRESS: 
1:02:11.117000 PROGRESS: Precursor Summary:
1:02:11.118598 PROGRESS: Channel   0:	 0.050 FDR:   283; 0.010 FDR:   153; 0.001 FDR:   141
1:02:11.118718 PROGRESS: 
1:02:11.118792 PROGRESS: Protein Summary:
1:02:11.120355 PROGRESS: Channel   0:	 0.050 FDR:   273; 0.010 FDR:   150; 0.001 FDR:   138
1:02:11.120465 PROGRESS: =========================================================================
1:02:11.121163 INFO: Target number of precursors not reached yet.
1:02:11.406692 INFO: Starting optimization step 3.
1:02:11.406984 PROGRESS: === Extracting elution groups 56000 to 120000 ===
1:02:11.407089 INFO: Using python extraction backend
1:02:11.407264 PROGRESS: Extracting batch of 126145 precursors
1:02:11.407353 INFO: === Search parameters used ===
1:02:11.407417 INFO: rt_error       : 2099.928159
1:02:11.407486 INFO: mobility_error : 0.1
1:02:11.407541 INFO: num_candidates : 1
1:02:11.407594 INFO: ms1_error      : 30
1:02:11.407646 INFO: ms2_error      : 30
1:02:11.407698 INFO: fwhm_rt        : 5
1:02:11.407756 INFO: quant_window   : 3
1:02:11.407810 INFO: ==============================================
1:02:11.434685 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:02:11.434825 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:02:11.434861 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1:02:11.434886 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1:02:11.435698 INFO: Starting candidate selection
1:33:21.662261 INFO: Starting candidate scoring
1:33:36.642456 INFO: Finished candidate processing
1:33:36.642925 INFO: Collecting candidate features
1:33:37.552361 WARNING: intensity_correlation has 14 NaNs ( 0.01 % out of 120364)
1:33:37.553262 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 120364)
1:33:37.567499 INFO: Collecting fragment features
1:33:37.922727 INFO: Finished candidate scoring
1:33:38.742375 INFO: performing precursor FDR with 47 features
1:33:38.742838 INFO: Decoy channel: -1
1:33:38.742934 INFO: competitive: True
1:33:39.247600 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:39.454242 WARNING: dropped 19 target PSMs due to missing features
1:33:39.454882 WARNING: dropped 20 decoy PSMs due to missing features
1:33:39.761484 INFO: Estimating optimal hyperparameters - samples: 180,539, batch_size: 739, learning_rate: 4.25e-04
1:33:39.763916 INFO: Using random state 622005 for train-test-split
1:33:54.973446 INFO: Test AUC: 0.555
1:33:54.975381 INFO: Train AUC: 0.588
1:33:54.975500 INFO: AUC difference: 5.64%
1:33:54.975543 WARNING: AUC difference > 5%. This may indicate overfitting.
1:33:55.851785 INFO: Resetting torch num_threads to 128
1:33:56.678801 PROGRESS: === Extracted 225713 precursors and 2438527 fragments ===
1:33:56.682673 INFO: === FDR correction performed with classifier version -1 ===
1:33:56.784013 PROGRESS: ============================= Precursor FDR =============================
1:33:56.786000 PROGRESS: Total precursors accumulated: 115,601
1:33:56.786159 PROGRESS: Target precursors: 69,476 (60.10%)
1:33:56.786268 PROGRESS: Decoy precursors: 46,125 (39.90%)
1:33:56.786362 PROGRESS: 
1:33:56.786454 PROGRESS: Precursor Summary:
1:33:56.794715 PROGRESS: Channel   0:	 0.050 FDR:   892; 0.010 FDR:   641; 0.001 FDR:   404
1:33:56.795623 PROGRESS: 
1:33:56.795719 PROGRESS: Protein Summary:
1:33:56.799347 PROGRESS: Channel   0:	 0.050 FDR:   787; 0.010 FDR:   577; 0.001 FDR:   374
1:33:56.799883 PROGRESS: =========================================================================
1:33:56.811705 INFO: Target number of precursors reached.
1:33:57.168137 INFO: fragments_df: keeping 5000 of 2438527 [sum(precursor_idx_mask)=7383 sum(mass_error_mask)=2438525 stop_rank=5000
1:33:58.635945 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:33:59.039343 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:33:59.427214 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:33:59.802176 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:34:04.330184 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:34:04.331797 INFO: Using score_cutoff 53.08445908355713 (fac=0.99, q=1)
1:34:04.332594 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.1359496116638184
1:34:04.332718 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010840683244168758
1:34:04.332808 INFO: Updating optimization_manager: score_cutoff        : 0 -> 53.08445908355713
1:34:04.332954 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:34:04.359043 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:04.473719 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:34:04.495517 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:04.821189 INFO: Updating optimization_manager: classifier_version  : -1 -> 3
1:34:04.821939 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:34:04.822215 INFO: Starting optimization step 4.
1:34:04.822384 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:34:04.822559 INFO: Using python extraction backend
1:34:04.822982 PROGRESS: Extracting batch of 110438 precursors
1:34:04.823144 INFO: === Search parameters used ===
1:34:04.823239 INFO: rt_error       : 2099.928159
1:34:04.823376 INFO: mobility_error : 0.1
1:34:04.823456 INFO: num_candidates : 3
1:34:04.823531 INFO: ms1_error      : 30
1:34:04.823596 INFO: ms2_error      : 30
1:34:04.823662 INFO: fwhm_rt        : 3.1359496116638184
1:34:04.823725 INFO: quant_window   : 3
1:34:04.823793 INFO: ==============================================
1:34:05.242880 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:34:05.243292 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:34:05.243394 INFO: FWHM in RT is 3.14 seconds, sigma is 0.69
1:34:05.243429 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.03
1:34:05.250113 INFO: Starting candidate selection
1:50:15.397201 INFO: Starting candidate scoring
1:50:34.251932 INFO: Finished candidate processing
1:50:34.252145 INFO: Collecting candidate features
1:50:34.805408 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 306343)
1:50:34.819077 INFO: Collecting fragment features
1:50:35.012528 INFO: Finished candidate scoring
1:50:35.183865 INFO: performing precursor FDR with 47 features
1:50:35.183998 INFO: Decoy channel: -1
1:50:35.184035 INFO: competitive: True
1:50:35.261718 INFO: Setting torch num_threads to 2 for FDR classification task
1:50:35.306272 WARNING: dropped 1 decoy PSMs due to missing features
1:50:35.403037 INFO: Estimating optimal hyperparameters - samples: 245,073, batch_size: 1,003, learning_rate: 4.95e-04
1:50:35.403710 INFO: Using random state 516399 for train-test-split
1:50:43.249378 INFO: Test AUC: 0.559
1:50:43.249596 INFO: Train AUC: 0.601
1:50:43.249632 INFO: AUC difference: 6.97%
1:50:43.249663 WARNING: AUC difference > 5%. This may indicate overfitting.
1:50:43.616197 INFO: Resetting torch num_threads to 128
1:50:43.622334 PROGRESS: === Extracted 306343 precursors and 3350642 fragments ===
1:50:43.623143 INFO: === FDR correction performed with classifier version 3 ===
1:50:43.631865 PROGRESS: ============================= Precursor FDR =============================
1:50:43.632098 PROGRESS: Total precursors accumulated: 54,912
1:50:43.632175 PROGRESS: Target precursors: 35,162 (64.03%)
1:50:43.632238 PROGRESS: Decoy precursors: 19,750 (35.97%)
1:50:43.632295 PROGRESS: 
1:50:43.632352 PROGRESS: Precursor Summary:
1:50:43.634111 PROGRESS: Channel   0:	 0.050 FDR:   487; 0.010 FDR:   265; 0.001 FDR:   161
1:50:43.634234 PROGRESS: 
1:50:43.634328 PROGRESS: Protein Summary:
1:50:43.636010 PROGRESS: Channel   0:	 0.050 FDR:   463; 0.010 FDR:   259; 0.001 FDR:   158
1:50:43.636137 PROGRESS: =========================================================================
1:50:43.734885 INFO: Target number of precursors reached.
1:50:43.986759 INFO: fragments_df: keeping 4116 of 3350642 [sum(precursor_idx_mask)=8733 sum(mass_error_mask)=3350642 stop_rank=4116
1:50:44.207828 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1:50:44.349973 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:50:44.487003 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1:50:44.620551 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:50:45.161418 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:50:45.161949 INFO: Using score_cutoff 58.115186471557614 (fac=0.99, q=1)
1:50:45.162401 INFO: Updating optimization_manager: fwhm_rt             : 3.1359496116638184 -> 3.049532413482666
1:50:45.162503 INFO: Updating optimization_manager: fwhm_mobility       : 0.010840683244168758 -> 0.010639275424182415
1:50:45.162580 INFO: Updating optimization_manager: score_cutoff        : 53.08445908355713 -> 58.115186471557614
1:50:45.162670 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1:50:45.177979 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:50:45.244159 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1:50:45.262464 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:50:45.406285 INFO: === checking if optimization conditions were reached ===
1:50:45.409009 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1:50:45.409144 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
1:50:45.409244 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1:50:45.410395 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1:50:45.410511 INFO: Updating optimization_manager: classifier_version  : 4 -> 4
1:50:45.410587 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1:50:45.410666 INFO: ==============================================
1:50:45.410770 INFO: Starting optimization step 5.
1:50:45.410851 PROGRESS: === Extracting elution groups 0 to 56000 ===
1:50:45.410989 INFO: Using python extraction backend
1:50:45.411300 PROGRESS: Extracting batch of 110438 precursors
1:50:45.411409 INFO: === Search parameters used ===
1:50:45.411475 INFO: rt_error       : 2099.928159
1:50:45.411532 INFO: mobility_error : 0.1
1:50:45.411584 INFO: num_candidates : 3
1:50:45.411637 INFO: ms1_error      : 15.0
1:50:45.411690 INFO: ms2_error      : 15.0
1:50:45.411741 INFO: fwhm_rt        : 3.049532413482666
1:50:45.411792 INFO: quant_window   : 3
1:50:45.411843 INFO: ==============================================
1:50:45.447710 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1:50:45.447915 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1:50:45.448039 INFO: FWHM in RT is 3.05 seconds, sigma is 0.67
1:50:45.448070 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.93
1:50:45.449164 INFO: Starting candidate selection
2:14:21.319149 INFO: Starting candidate scoring
2:14:41.866292 INFO: Finished candidate processing
2:14:41.867744 INFO: Collecting candidate features
2:14:44.609981 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 306835)
2:14:44.631255 INFO: Collecting fragment features
2:14:45.092983 INFO: Finished candidate scoring
2:14:46.739424 INFO: performing precursor FDR with 47 features
2:14:46.739964 INFO: Decoy channel: -1
2:14:46.740043 INFO: competitive: True
2:14:47.194752 INFO: Setting torch num_threads to 2 for FDR classification task
2:14:47.476506 WARNING: dropped 4 target PSMs due to missing features
2:14:47.477168 WARNING: dropped 2 decoy PSMs due to missing features
2:14:48.390292 INFO: Estimating optimal hyperparameters - samples: 245,463, batch_size: 1,005, learning_rate: 4.95e-04
2:14:48.394013 INFO: Using random state 291807 for train-test-split
2:15:19.845597 INFO: Test AUC: 0.557
2:15:19.847371 INFO: Train AUC: 0.598
2:15:19.847642 INFO: AUC difference: 6.87%
2:15:19.847720 WARNING: AUC difference > 5%. This may indicate overfitting.
2:15:20.955351 INFO: Resetting torch num_threads to 128
2:15:21.033473 PROGRESS: === Extracted 306835 precursors and 3196376 fragments ===
2:15:21.038370 INFO: === FDR correction performed with classifier version 4 ===
2:15:21.102176 PROGRESS: ============================= Precursor FDR =============================
2:15:21.103636 PROGRESS: Total precursors accumulated: 54,892
2:15:21.103779 PROGRESS: Target precursors: 34,498 (62.85%)
2:15:21.103873 PROGRESS: Decoy precursors: 20,394 (37.15%)
2:15:21.103989 PROGRESS: 
2:15:21.104066 PROGRESS: Precursor Summary:
2:15:21.111576 PROGRESS: Channel   0:	 0.050 FDR:   698; 0.010 FDR:   365; 0.001 FDR:   270
2:15:21.112701 PROGRESS: 
2:15:21.112848 PROGRESS: Protein Summary:
2:15:21.116255 PROGRESS: Channel   0:	 0.050 FDR:   652; 0.010 FDR:   344; 0.001 FDR:   261
2:15:21.116737 PROGRESS: =========================================================================
2:15:21.131297 INFO: Target number of precursors reached.
2:15:21.453933 INFO: fragments_df: keeping 5000 of 3196376 [sum(precursor_idx_mask)=11833 sum(mass_error_mask)=3196376 stop_rank=5000
2:15:23.639196 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:15:24.081676 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:15:24.538113 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:15:24.988565 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:15:26.047498 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:15:26.050149 INFO: Using score_cutoff 48.922882237243655 (fac=0.99, q=1)
2:15:26.052711 INFO: Updating optimization_manager: fwhm_rt             : 3.049532413482666 -> 2.8507189750671387
2:15:26.053358 INFO: Updating optimization_manager: fwhm_mobility       : 0.010639275424182415 -> 0.00899248756468296
2:15:26.053630 INFO: Updating optimization_manager: score_cutoff        : 58.115186471557614 -> 48.922882237243655
2:15:26.054094 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:15:26.086653 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:15:26.207495 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:15:26.236250 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:15:26.703118 INFO: === checking if optimization conditions were reached ===
2:15:26.721305 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
2:15:26.723120 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:15:26.723785 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
2:15:26.738229 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
2:15:26.740525 INFO: Updating optimization_manager: classifier_version  : 5 -> 5
2:15:26.741329 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
2:15:26.742181 INFO: ==============================================
2:15:26.743198 PROGRESS: Optimization finished for ms2_error, ms1_error.
2:15:28.220121 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:15:28.252181 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:15:28.377858 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:15:28.407500 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:15:28.918909 INFO: Starting optimization step 0.
2:15:28.920329 PROGRESS: === Extracting elution groups 0 to 56000 ===
2:15:28.920659 INFO: Using python extraction backend
2:15:28.921473 PROGRESS: Extracting batch of 110438 precursors
2:15:28.921758 INFO: === Search parameters used ===
2:15:28.921875 INFO: rt_error       : 2099.928159
2:15:28.921949 INFO: mobility_error : 0.1
2:15:28.922029 INFO: num_candidates : 3
2:15:28.922091 INFO: ms1_error      : 15.0
2:15:28.922148 INFO: ms2_error      : 15.0
2:15:28.922201 INFO: fwhm_rt        : 2.8507189750671387
2:15:28.922329 INFO: quant_window   : 3
2:15:28.922412 INFO: ==============================================
2:15:29.108174 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:15:29.108889 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:15:29.109056 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
2:15:29.109094 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.17
2:15:29.114748 INFO: Starting candidate selection
2:33:56.497483 INFO: Starting candidate scoring
2:34:08.648004 INFO: Finished candidate processing
2:34:08.648189 INFO: Collecting candidate features
2:34:09.261729 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 305775)
2:34:09.277337 INFO: Collecting fragment features
2:34:09.503780 INFO: Finished candidate scoring
2:34:09.682508 INFO: performing precursor FDR with 47 features
2:34:09.682748 INFO: Decoy channel: -1
2:34:09.682812 INFO: competitive: True
2:34:09.788558 INFO: Setting torch num_threads to 2 for FDR classification task
2:34:09.858958 WARNING: dropped 5 target PSMs due to missing features
2:34:09.859212 WARNING: dropped 4 decoy PSMs due to missing features
2:34:09.999534 INFO: Estimating optimal hyperparameters - samples: 244,612, batch_size: 1,001, learning_rate: 4.94e-04
2:34:10.000360 INFO: Using random state 189493 for train-test-split
2:34:20.859075 INFO: Test AUC: 0.572
2:34:20.859424 INFO: Train AUC: 0.613
2:34:20.859485 INFO: AUC difference: 6.64%
2:34:20.859530 WARNING: AUC difference > 5%. This may indicate overfitting.
2:34:21.311158 INFO: Resetting torch num_threads to 128
2:34:21.374550 PROGRESS: === Extracted 305775 precursors and 3175188 fragments ===
2:34:21.375583 INFO: === FDR correction performed with classifier version 5 ===
2:34:21.388062 PROGRESS: ============================= Precursor FDR =============================
2:34:21.388450 PROGRESS: Total precursors accumulated: 54,796
2:34:21.388561 PROGRESS: Target precursors: 35,427 (64.65%)
2:34:21.388655 PROGRESS: Decoy precursors: 19,369 (35.35%)
2:34:21.388742 PROGRESS: 
2:34:21.388825 PROGRESS: Precursor Summary:
2:34:21.390839 PROGRESS: Channel   0:	 0.050 FDR:   729; 0.010 FDR:   545; 0.001 FDR:   398
2:34:21.391009 PROGRESS: 
2:34:21.391108 PROGRESS: Protein Summary:
2:34:21.393187 PROGRESS: Channel   0:	 0.050 FDR:   681; 0.010 FDR:   507; 0.001 FDR:   376
2:34:21.393332 PROGRESS: =========================================================================
2:34:21.396019 INFO: Target number of precursors reached.
2:34:21.757868 INFO: fragments_df: keeping 5000 of 3175188 [sum(precursor_idx_mask)=17228 sum(mass_error_mask)=3175188 stop_rank=5000
2:34:22.079061 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:34:22.250197 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:34:22.416828 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:34:22.594689 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:34:23.448458 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:34:23.449293 INFO: Using score_cutoff 45.26946364746094 (fac=0.99, q=1)
2:34:23.449909 INFO: Updating optimization_manager: fwhm_rt             : 2.8507189750671387 -> 2.893890142440796
2:34:23.450041 INFO: Updating optimization_manager: fwhm_mobility       : 0.00899248756468296 -> 0.008746477775275707
2:34:23.450135 INFO: Updating optimization_manager: score_cutoff        : 48.922882237243655 -> 45.26946364746094
2:34:23.450247 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:34:23.457558 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:34:23.488190 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:34:23.494738 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:34:23.562229 INFO: === checking if optimization conditions were reached ===
2:34:23.562709 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
2:34:23.566303 INFO: Updating optimization_manager: rt_error            : 2099.928159 -> 577.1797880819178
2:34:23.566476 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 577.1798.
2:34:23.566608 INFO: ==============================================
2:34:23.566747 INFO: Starting optimization step 1.
2:34:23.566872 PROGRESS: === Extracting elution groups 0 to 24000 ===
2:34:23.567041 INFO: Using python extraction backend
2:34:23.567369 PROGRESS: Extracting batch of 47289 precursors
2:34:23.567501 INFO: === Search parameters used ===
2:34:23.567595 INFO: rt_error       : 577.1797880819178
2:34:23.567682 INFO: mobility_error : 0.1
2:34:23.567766 INFO: num_candidates : 3
2:34:23.567849 INFO: ms1_error      : 15.0
2:34:23.567930 INFO: ms2_error      : 15.0
2:34:23.568013 INFO: fwhm_rt        : 2.893890142440796
2:34:23.568092 INFO: quant_window   : 3
2:34:23.568173 INFO: ==============================================
2:34:23.589957 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:34:23.590207 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:34:23.590306 INFO: FWHM in RT is 2.89 seconds, sigma is 0.64
2:34:23.590358 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.06
2:34:23.594041 INFO: Starting candidate selection
2:35:43.713139 INFO: Starting candidate scoring
2:35:48.924956 INFO: Finished candidate processing
2:35:48.925170 INFO: Collecting candidate features
2:35:49.274581 WARNING: intensity_correlation has 27 NaNs ( 0.02 % out of 127444)
2:35:49.275123 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 127444)
2:35:49.284562 INFO: Collecting fragment features
2:35:49.394194 INFO: Finished candidate scoring
2:35:49.507514 INFO: performing precursor FDR with 47 features
2:35:49.507715 INFO: Decoy channel: -1
2:35:49.507752 INFO: competitive: True
2:35:49.569268 INFO: Setting torch num_threads to 2 for FDR classification task
2:35:49.603304 WARNING: dropped 19 target PSMs due to missing features
2:35:49.603530 WARNING: dropped 11 decoy PSMs due to missing features
2:35:49.656598 INFO: Estimating optimal hyperparameters - samples: 101,931, batch_size: 417, learning_rate: 3.19e-04
2:35:49.657167 INFO: Using random state 189493 for train-test-split
2:35:55.520468 INFO: Test AUC: 0.543
2:35:55.520804 INFO: Train AUC: 0.600
2:35:55.520845 INFO: AUC difference: 9.49%
2:35:55.520873 WARNING: AUC difference > 5%. This may indicate overfitting.
2:35:55.838582 INFO: Resetting torch num_threads to 128
2:35:55.842201 PROGRESS: === Extracted 127444 precursors and 1298365 fragments ===
2:35:55.842936 INFO: === FDR correction performed with classifier version 5 ===
2:35:55.846694 PROGRESS: ============================= Precursor FDR =============================
2:35:55.846829 PROGRESS: Total precursors accumulated: 23,160
2:35:55.846905 PROGRESS: Target precursors: 14,426 (62.29%)
2:35:55.846981 PROGRESS: Decoy precursors: 8,734 (37.71%)
2:35:55.847059 PROGRESS: 
2:35:55.847145 PROGRESS: Precursor Summary:
2:35:55.848499 PROGRESS: Channel   0:	 0.050 FDR:   301; 0.010 FDR:   221; 0.001 FDR:   166
2:35:55.848614 PROGRESS: 
2:35:55.848699 PROGRESS: Protein Summary:
2:35:55.850154 PROGRESS: Channel   0:	 0.050 FDR:   295; 0.010 FDR:   216; 0.001 FDR:   165
2:35:55.850270 PROGRESS: =========================================================================
2:35:55.876687 INFO: Target number of precursors reached.
2:35:55.976751 INFO: fragments_df: keeping 2990 of 1298365 [sum(precursor_idx_mask)=6986 sum(mass_error_mask)=1298362 stop_rank=2990
2:35:56.195906 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:35:56.325339 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:35:56.456872 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:35:56.592263 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:35:57.018047 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:35:57.018586 INFO: Using score_cutoff 40.45861532592774 (fac=0.99, q=1)
2:35:57.019035 INFO: Updating optimization_manager: fwhm_rt             : 2.893890142440796 -> 2.8225247859954834
2:35:57.019130 INFO: Updating optimization_manager: fwhm_mobility       : 0.008746477775275707 -> 0.008418763987720013
2:35:57.019193 INFO: Updating optimization_manager: score_cutoff        : 45.26946364746094 -> 40.45861532592774
2:35:57.019271 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:35:57.026727 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:35:57.058918 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:35:57.065757 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:35:57.132234 INFO: === checking if optimization conditions were reached ===
2:35:57.132625 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
2:35:57.135361 INFO: Updating optimization_manager: rt_error            : 577.1797880819178 -> 247.36522548292558
2:35:57.135532 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 247.3652.
2:35:57.135621 INFO: ==============================================
2:35:57.135727 INFO: Starting optimization step 2.
2:35:57.135825 PROGRESS: === Extracting elution groups 0 to 24000 ===
2:35:57.135988 INFO: Using python extraction backend
2:35:57.136299 PROGRESS: Extracting batch of 47289 precursors
2:35:57.136416 INFO: === Search parameters used ===
2:35:57.136500 INFO: rt_error       : 247.36522548292558
2:35:57.136584 INFO: mobility_error : 0.1
2:35:57.136661 INFO: num_candidates : 3
2:35:57.136735 INFO: ms1_error      : 15.0
2:35:57.136817 INFO: ms2_error      : 15.0
2:35:57.136894 INFO: fwhm_rt        : 2.8225247859954834
2:35:57.136964 INFO: quant_window   : 3
2:35:57.137023 INFO: ==============================================
2:35:57.167564 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:35:57.167695 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:35:57.167760 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
2:35:57.167804 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.90
2:35:57.168705 INFO: Starting candidate selection
2:36:30.906372 INFO: Starting candidate scoring
2:36:35.802173 INFO: Finished candidate processing
2:36:35.802707 INFO: Collecting candidate features
2:36:36.026308 WARNING: intensity_correlation has 54 NaNs ( 0.04 % out of 126066)
2:36:36.026761 WARNING: height_correlation has 5 NaNs ( 0.00 % out of 126066)
2:36:36.035551 INFO: Collecting fragment features
2:36:36.111109 INFO: Finished candidate scoring
2:36:36.185342 INFO: performing precursor FDR with 47 features
2:36:36.185502 INFO: Decoy channel: -1
2:36:36.185543 INFO: competitive: True
2:36:36.232453 INFO: Setting torch num_threads to 2 for FDR classification task
2:36:36.262355 WARNING: dropped 28 target PSMs due to missing features
2:36:36.262528 WARNING: dropped 29 decoy PSMs due to missing features
2:36:36.289088 INFO: Estimating optimal hyperparameters - samples: 100,807, batch_size: 412, learning_rate: 3.17e-04
2:36:36.289514 INFO: Using random state 189493 for train-test-split
2:36:42.489558 INFO: Test AUC: 0.555
2:36:42.489741 INFO: Train AUC: 0.603
2:36:42.489784 INFO: AUC difference: 7.97%
2:36:42.489808 WARNING: AUC difference > 5%. This may indicate overfitting.
2:36:42.805200 INFO: Resetting torch num_threads to 128
2:36:42.809314 PROGRESS: === Extracted 126066 precursors and 1256614 fragments ===
2:36:42.810084 INFO: === FDR correction performed with classifier version 5 ===
2:36:42.814119 PROGRESS: ============================= Precursor FDR =============================
2:36:42.814245 PROGRESS: Total precursors accumulated: 23,032
2:36:42.814322 PROGRESS: Target precursors: 14,437 (62.68%)
2:36:42.814385 PROGRESS: Decoy precursors: 8,595 (37.32%)
2:36:42.814439 PROGRESS: 
2:36:42.814491 PROGRESS: Precursor Summary:
2:36:42.815830 PROGRESS: Channel   0:	 0.050 FDR:   369; 0.010 FDR:   253; 0.001 FDR:   128
2:36:42.815937 PROGRESS: 
2:36:42.816003 PROGRESS: Protein Summary:
2:36:42.817404 PROGRESS: Channel   0:	 0.050 FDR:   360; 0.010 FDR:   246; 0.001 FDR:   126
2:36:42.817507 PROGRESS: =========================================================================
2:36:42.818357 INFO: Target number of precursors reached.
2:36:42.914668 INFO: fragments_df: keeping 3244 of 1256614 [sum(precursor_idx_mask)=7865 sum(mass_error_mask)=1256611 stop_rank=3244
2:36:43.103120 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:36:43.224217 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:36:43.351034 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:36:43.470638 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:36:43.861647 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:36:43.862229 INFO: Using score_cutoff 41.99551101837159 (fac=0.99, q=1)
2:36:43.862650 INFO: Updating optimization_manager: fwhm_rt             : 2.8225247859954834 -> 2.848642349243164
2:36:43.862752 INFO: Updating optimization_manager: fwhm_mobility       : 0.008418763987720013 -> 0.008267070166766644
2:36:43.862838 INFO: Updating optimization_manager: score_cutoff        : 40.45861532592774 -> 41.99551101837159
2:36:43.862934 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:36:43.869830 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:36:43.898944 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:36:43.905190 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:36:43.981286 INFO: === checking if optimization conditions were reached ===
2:36:43.981688 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
2:36:43.984197 INFO: Updating optimization_manager: rt_error            : 247.36522548292558 -> 162.73142633570424
2:36:43.984324 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 162.7314.
2:36:43.984415 INFO: ==============================================
2:36:43.984513 INFO: Starting optimization step 3.
2:36:43.984599 PROGRESS: === Extracting elution groups 0 to 24000 ===
2:36:43.984708 INFO: Using python extraction backend
2:36:43.984877 PROGRESS: Extracting batch of 47289 precursors
2:36:43.984971 INFO: === Search parameters used ===
2:36:43.985057 INFO: rt_error       : 162.73142633570424
2:36:43.985129 INFO: mobility_error : 0.1
2:36:43.985198 INFO: num_candidates : 3
2:36:43.985274 INFO: ms1_error      : 15.0
2:36:43.985340 INFO: ms2_error      : 15.0
2:36:43.985415 INFO: fwhm_rt        : 2.848642349243164
2:36:43.985483 INFO: quant_window   : 3
2:36:43.985560 INFO: ==============================================
2:36:43.998465 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:36:43.998603 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:36:43.998664 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
2:36:43.998698 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.83
2:36:43.999564 INFO: Starting candidate selection
2:37:06.118611 INFO: Starting candidate scoring
2:37:11.166117 INFO: Finished candidate processing
2:37:11.166298 INFO: Collecting candidate features
2:37:11.345808 WARNING: intensity_correlation has 53 NaNs ( 0.04 % out of 125622)
2:37:11.346240 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 125622)
2:37:11.354490 INFO: Collecting fragment features
2:37:11.430635 INFO: Finished candidate scoring
2:37:11.508206 INFO: performing precursor FDR with 47 features
2:37:11.508369 INFO: Decoy channel: -1
2:37:11.508397 INFO: competitive: True
2:37:11.548397 INFO: Setting torch num_threads to 2 for FDR classification task
2:37:11.572872 WARNING: dropped 22 target PSMs due to missing features
2:37:11.573051 WARNING: dropped 33 decoy PSMs due to missing features
2:37:11.601320 INFO: Estimating optimal hyperparameters - samples: 100,453, batch_size: 411, learning_rate: 3.17e-04
2:37:11.601733 INFO: Using random state 189493 for train-test-split
2:37:17.521384 INFO: Test AUC: 0.547
2:37:17.521610 INFO: Train AUC: 0.611
2:37:17.521646 INFO: AUC difference: 10.36%
2:37:17.521671 WARNING: AUC difference > 5%. This may indicate overfitting.
2:37:17.842363 INFO: Resetting torch num_threads to 128
2:37:17.845768 PROGRESS: === Extracted 125622 precursors and 1240575 fragments ===
2:37:17.846455 INFO: === FDR correction performed with classifier version 5 ===
2:37:17.850349 PROGRESS: ============================= Precursor FDR =============================
2:37:17.850485 PROGRESS: Total precursors accumulated: 22,989
2:37:17.850560 PROGRESS: Target precursors: 14,538 (63.24%)
2:37:17.850624 PROGRESS: Decoy precursors: 8,451 (36.76%)
2:37:17.850684 PROGRESS: 
2:37:17.850739 PROGRESS: Precursor Summary:
2:37:17.852095 PROGRESS: Channel   0:	 0.050 FDR:   351; 0.010 FDR:   290; 0.001 FDR:   255
2:37:17.852202 PROGRESS: 
2:37:17.852283 PROGRESS: Protein Summary:
2:37:17.853771 PROGRESS: Channel   0:	 0.050 FDR:   341; 0.010 FDR:   281; 0.001 FDR:   248
2:37:17.853878 PROGRESS: =========================================================================
2:37:17.854587 INFO: Target number of precursors reached.
2:37:17.952070 INFO: fragments_df: keeping 3528 of 1240575 [sum(precursor_idx_mask)=9008 sum(mass_error_mask)=1240572 stop_rank=3528
2:37:18.153088 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:37:18.294537 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:37:18.437637 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:37:18.574929 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:37:19.919072 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:37:19.919634 INFO: Using score_cutoff 42.35165534591675 (fac=0.99, q=1)
2:37:19.919996 INFO: Updating optimization_manager: fwhm_rt             : 2.848642349243164 -> 2.8559350967407227
2:37:19.920087 INFO: Updating optimization_manager: fwhm_mobility       : 0.008267070166766644 -> 0.008290013298392296
2:37:19.920155 INFO: Updating optimization_manager: score_cutoff        : 41.99551101837159 -> 42.35165534591675
2:37:19.920255 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:37:19.927088 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:37:19.956238 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:37:19.962621 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:37:20.024126 INFO: === checking if optimization conditions were reached ===
2:37:20.024474 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
2:37:20.026994 INFO: Updating optimization_manager: rt_error            : 162.73142633570424 -> 153.67216234393808
2:37:20.027135 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 153.6722.
2:37:20.027234 INFO: ==============================================
2:37:20.027343 INFO: Starting optimization step 4.
2:37:20.027436 PROGRESS: === Extracting elution groups 0 to 24000 ===
2:37:20.027531 INFO: Using python extraction backend
2:37:20.027694 PROGRESS: Extracting batch of 47289 precursors
2:37:20.027789 INFO: === Search parameters used ===
2:37:20.027863 INFO: rt_error       : 153.67216234393808
2:37:20.027945 INFO: mobility_error : 0.1
2:37:20.028016 INFO: num_candidates : 3
2:37:20.028090 INFO: ms1_error      : 15.0
2:37:20.028159 INFO: ms2_error      : 15.0
2:37:20.028227 INFO: fwhm_rt        : 2.8559350967407227
2:37:20.028301 INFO: quant_window   : 3
2:37:20.028370 INFO: ==============================================
2:37:20.040638 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:37:20.040753 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:37:20.040816 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
2:37:20.040852 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.85
2:37:20.041706 INFO: Starting candidate selection
2:37:40.094953 INFO: Starting candidate scoring
2:37:44.818399 INFO: Finished candidate processing
2:37:44.818600 INFO: Collecting candidate features
2:37:45.024738 WARNING: intensity_correlation has 57 NaNs ( 0.05 % out of 125355)
2:37:45.025147 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 125355)
2:37:45.032949 INFO: Collecting fragment features
2:37:45.111303 INFO: Finished candidate scoring
2:37:45.183231 INFO: performing precursor FDR with 47 features
2:37:45.183375 INFO: Decoy channel: -1
2:37:45.183404 INFO: competitive: True
2:37:45.223743 INFO: Setting torch num_threads to 2 for FDR classification task
2:37:45.248442 WARNING: dropped 25 target PSMs due to missing features
2:37:45.248592 WARNING: dropped 33 decoy PSMs due to missing features
2:37:45.275989 INFO: Estimating optimal hyperparameters - samples: 100,237, batch_size: 410, learning_rate: 3.16e-04
2:37:45.276460 INFO: Using random state 189493 for train-test-split
2:37:50.988656 INFO: Test AUC: 0.542
2:37:50.988821 INFO: Train AUC: 0.595
2:37:50.988857 INFO: AUC difference: 8.82%
2:37:50.988881 WARNING: AUC difference > 5%. This may indicate overfitting.
2:37:51.300413 INFO: Resetting torch num_threads to 128
2:37:51.304108 PROGRESS: === Extracted 125355 precursors and 1235482 fragments ===
2:37:51.304721 INFO: === FDR correction performed with classifier version 5 ===
2:37:51.308924 PROGRESS: ============================= Precursor FDR =============================
2:37:51.309064 PROGRESS: Total precursors accumulated: 22,955
2:37:51.309150 PROGRESS: Target precursors: 14,142 (61.61%)
2:37:51.309224 PROGRESS: Decoy precursors: 8,813 (38.39%)
2:37:51.309291 PROGRESS: 
2:37:51.309354 PROGRESS: Precursor Summary:
2:37:51.310757 PROGRESS: Channel   0:	 0.050 FDR:   367; 0.010 FDR:   281; 0.001 FDR:   213
2:37:51.310878 PROGRESS: 
2:37:51.310959 PROGRESS: Protein Summary:
2:37:51.312452 PROGRESS: Channel   0:	 0.050 FDR:   356; 0.010 FDR:   273; 0.001 FDR:   207
2:37:51.312569 PROGRESS: =========================================================================
2:37:51.313300 INFO: Target number of precursors reached.
2:37:51.408124 INFO: fragments_df: keeping 3508 of 1235482 [sum(precursor_idx_mask)=8740 sum(mass_error_mask)=1235479 stop_rank=3508
2:37:51.610048 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:37:51.753785 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:37:51.896960 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:37:52.034972 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:37:52.524779 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:37:52.525329 INFO: Using score_cutoff 40.03893560028076 (fac=0.99, q=1)
2:37:52.525696 INFO: Updating optimization_manager: fwhm_rt             : 2.8559350967407227 -> 2.8495731353759766
2:37:52.525823 INFO: Updating optimization_manager: fwhm_mobility       : 0.008290013298392296 -> 0.008175810799002647
2:37:52.525899 INFO: Updating optimization_manager: score_cutoff        : 42.35165534591675 -> 40.03893560028076
2:37:52.525990 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:37:52.532779 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:37:52.562213 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:37:52.568616 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:37:52.630750 INFO: === checking if optimization conditions were reached ===
2:37:52.631135 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
2:37:52.633647 INFO: Updating optimization_manager: rt_error            : 153.67216234393808 -> 132.6354785602929
2:37:52.633806 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 132.6355.
2:37:52.633911 INFO: ==============================================
2:37:52.634019 INFO: Starting optimization step 5.
2:37:52.634111 PROGRESS: === Extracting elution groups 0 to 24000 ===
2:37:52.634219 INFO: Using python extraction backend
2:37:52.634395 PROGRESS: Extracting batch of 47289 precursors
2:37:52.634489 INFO: === Search parameters used ===
2:37:52.634567 INFO: rt_error       : 132.6354785602929
2:37:52.634639 INFO: mobility_error : 0.1
2:37:52.634708 INFO: num_candidates : 3
2:37:52.634773 INFO: ms1_error      : 15.0
2:37:52.634839 INFO: ms2_error      : 15.0
2:37:52.634915 INFO: fwhm_rt        : 2.8495731353759766
2:37:52.634980 INFO: quant_window   : 3
2:37:52.635043 INFO: ==============================================
2:37:52.647554 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:37:52.647673 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:37:52.647724 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
2:37:52.647757 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
2:37:52.648646 INFO: Starting candidate selection
2:38:10.783778 INFO: Starting candidate scoring
2:38:15.697839 INFO: Finished candidate processing
2:38:15.698052 INFO: Collecting candidate features
2:38:15.924823 WARNING: intensity_correlation has 59 NaNs ( 0.05 % out of 124915)
2:38:15.925250 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 124915)
2:38:15.934874 INFO: Collecting fragment features
2:38:16.011645 INFO: Finished candidate scoring
2:38:16.083522 INFO: performing precursor FDR with 47 features
2:38:16.083683 INFO: Decoy channel: -1
2:38:16.083712 INFO: competitive: True
2:38:16.124146 INFO: Setting torch num_threads to 2 for FDR classification task
2:38:16.148656 WARNING: dropped 32 target PSMs due to missing features
2:38:16.149055 WARNING: dropped 29 decoy PSMs due to missing features
2:38:16.173279 INFO: Estimating optimal hyperparameters - samples: 99,883, batch_size: 409, learning_rate: 3.16e-04
2:38:16.173786 INFO: Using random state 189493 for train-test-split
2:38:21.669558 INFO: Test AUC: 0.548
2:38:21.669721 INFO: Train AUC: 0.609
2:38:21.669766 INFO: AUC difference: 9.99%
2:38:21.669793 WARNING: AUC difference > 5%. This may indicate overfitting.
2:38:21.969348 INFO: Resetting torch num_threads to 128
2:38:21.972830 PROGRESS: === Extracted 124915 precursors and 1228588 fragments ===
2:38:21.973417 INFO: === FDR correction performed with classifier version 5 ===
2:38:21.977403 PROGRESS: ============================= Precursor FDR =============================
2:38:21.977544 PROGRESS: Total precursors accumulated: 22,895
2:38:21.977629 PROGRESS: Target precursors: 14,436 (63.05%)
2:38:21.977694 PROGRESS: Decoy precursors: 8,459 (36.95%)
2:38:21.977765 PROGRESS: 
2:38:21.977825 PROGRESS: Precursor Summary:
2:38:21.979197 PROGRESS: Channel   0:	 0.050 FDR:   393; 0.010 FDR:   253; 0.001 FDR:   228
2:38:21.979303 PROGRESS: 
2:38:21.979380 PROGRESS: Protein Summary:
2:38:21.980841 PROGRESS: Channel   0:	 0.050 FDR:   381; 0.010 FDR:   245; 0.001 FDR:   221
2:38:21.980965 PROGRESS: =========================================================================
2:38:21.981637 INFO: Target number of precursors reached.
2:38:22.078615 INFO: fragments_df: keeping 3231 of 1228588 [sum(precursor_idx_mask)=7828 sum(mass_error_mask)=1228585 stop_rank=3231
2:38:22.278918 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:38:22.399807 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:38:22.515716 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:38:22.631874 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:38:23.018584 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:38:23.019180 INFO: Using score_cutoff 41.19697819061279 (fac=0.99, q=1)
2:38:23.019569 INFO: Updating optimization_manager: fwhm_rt             : 2.8495731353759766 -> 2.8722598552703857
2:38:23.019660 INFO: Updating optimization_manager: fwhm_mobility       : 0.008175810799002647 -> 0.008219392970204353
2:38:23.019740 INFO: Updating optimization_manager: score_cutoff        : 40.03893560028076 -> 41.19697819061279
2:38:23.019817 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:38:23.027141 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:38:23.056706 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:38:23.063453 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:38:23.123404 INFO: === checking if optimization conditions were reached ===
2:38:23.123740 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
2:38:23.126201 INFO: Updating optimization_manager: rt_error            : 132.6354785602929 -> 129.66282998902386
2:38:23.126328 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 129.6628.
2:38:23.126421 INFO: ==============================================
2:38:23.126518 INFO: Starting optimization step 6.
2:38:23.126603 PROGRESS: === Extracting elution groups 0 to 24000 ===
2:38:23.126688 INFO: Using python extraction backend
2:38:23.126854 PROGRESS: Extracting batch of 47289 precursors
2:38:23.126942 INFO: === Search parameters used ===
2:38:23.127016 INFO: rt_error       : 129.66282998902386
2:38:23.127080 INFO: mobility_error : 0.1
2:38:23.127146 INFO: num_candidates : 3
2:38:23.127213 INFO: ms1_error      : 15.0
2:38:23.127275 INFO: ms2_error      : 15.0
2:38:23.127337 INFO: fwhm_rt        : 2.8722598552703857
2:38:23.127400 INFO: quant_window   : 3
2:38:23.127462 INFO: ==============================================
2:38:23.139771 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:38:23.139875 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:38:23.139915 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
2:38:23.139938 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.81
2:38:23.140738 INFO: Starting candidate selection
2:38:40.816997 INFO: Starting candidate scoring
2:38:45.722350 INFO: Finished candidate processing
2:38:45.722548 INFO: Collecting candidate features
2:38:45.933784 WARNING: intensity_correlation has 59 NaNs ( 0.05 % out of 124849)
2:38:45.934174 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 124849)
2:38:45.942606 INFO: Collecting fragment features
2:38:46.011561 INFO: Finished candidate scoring
2:38:46.069164 INFO: performing precursor FDR with 47 features
2:38:46.069330 INFO: Decoy channel: -1
2:38:46.069358 INFO: competitive: True
2:38:46.111267 INFO: Setting torch num_threads to 2 for FDR classification task
2:38:46.138562 WARNING: dropped 33 target PSMs due to missing features
2:38:46.138738 WARNING: dropped 29 decoy PSMs due to missing features
2:38:46.169524 INFO: Estimating optimal hyperparameters - samples: 99,829, batch_size: 408, learning_rate: 3.16e-04
2:38:46.170068 INFO: Using random state 189493 for train-test-split
2:38:52.193568 INFO: Test AUC: 0.537
2:38:52.193738 INFO: Train AUC: 0.597
2:38:52.193784 INFO: AUC difference: 10.14%
2:38:52.193809 WARNING: AUC difference > 5%. This may indicate overfitting.
2:38:52.509995 INFO: Resetting torch num_threads to 128
2:38:52.513998 PROGRESS: === Extracted 124849 precursors and 1228626 fragments ===
2:38:52.514665 INFO: === FDR correction performed with classifier version 5 ===
2:38:52.519083 PROGRESS: ============================= Precursor FDR =============================
2:38:52.519228 PROGRESS: Total precursors accumulated: 22,890
2:38:52.519339 PROGRESS: Target precursors: 14,120 (61.69%)
2:38:52.519418 PROGRESS: Decoy precursors: 8,770 (38.31%)
2:38:52.519489 PROGRESS: 
2:38:52.519564 PROGRESS: Precursor Summary:
2:38:52.520921 PROGRESS: Channel   0:	 0.050 FDR:   381; 0.010 FDR:   311; 0.001 FDR:   217
2:38:52.521045 PROGRESS: 
2:38:52.521125 PROGRESS: Protein Summary:
2:38:52.522641 PROGRESS: Channel   0:	 0.050 FDR:   370; 0.010 FDR:   302; 0.001 FDR:   209
2:38:52.522757 PROGRESS: =========================================================================
2:38:52.523493 INFO: Target number of precursors reached.
2:38:52.620387 INFO: fragments_df: keeping 3767 of 1228626 [sum(precursor_idx_mask)=9679 sum(mass_error_mask)=1228623 stop_rank=3767
2:38:52.811552 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:38:52.963408 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:38:53.099103 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:38:53.221214 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:38:53.687632 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:38:53.688224 INFO: Using score_cutoff 35.47437598800659 (fac=0.99, q=1)
2:38:53.688599 INFO: Updating optimization_manager: fwhm_rt             : 2.8722598552703857 -> 2.836228370666504
2:38:53.688689 INFO: Updating optimization_manager: fwhm_mobility       : 0.008219392970204353 -> 0.008086094632744789
2:38:53.688754 INFO: Updating optimization_manager: score_cutoff        : 41.19697819061279 -> 35.47437598800659
2:38:53.688822 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:38:53.695801 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:38:53.724878 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:38:53.731401 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:38:53.791826 INFO: === checking if optimization conditions were reached ===
2:38:53.792212 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
2:38:53.794159 INFO: Updating optimization_manager: rt_error            : 129.66282998902386 -> 129.66282998902386
2:38:53.794343 INFO: Updating optimization_manager: classifier_version  : 5 -> 12
2:38:53.794476 INFO: Updating optimization_manager: score_cutoff        : 35.47437598800659 -> 35.47437598800659
2:38:53.794600 INFO: Updating optimization_manager: fwhm_rt             : 2.836228370666504 -> 2.836228370666504
2:38:53.794721 INFO: Updating optimization_manager: fwhm_mobility       : 0.008086094632744789 -> 0.008086094632744789
2:38:53.794848 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 129.6628 found after 7 searches.
2:38:53.794973 INFO: ==============================================
2:38:53.795091 PROGRESS: Optimization finished for rt_error.
2:38:53.991330 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:38:53.998767 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:38:54.027618 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:38:54.034164 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:38:54.094974 INFO: Starting optimization step 0.
2:38:54.095394 PROGRESS: === Extracting elution groups 0 to 24000 ===
2:38:54.095531 INFO: Using python extraction backend
2:38:54.095745 PROGRESS: Extracting batch of 47289 precursors
2:38:54.095874 INFO: === Search parameters used ===
2:38:54.095974 INFO: rt_error       : 129.66282998902386
2:38:54.096062 INFO: mobility_error : 0.1
2:38:54.096144 INFO: num_candidates : 3
2:38:54.096238 INFO: ms1_error      : 15.0
2:38:54.096322 INFO: ms2_error      : 15.0
2:38:54.096403 INFO: fwhm_rt        : 2.836228370666504
2:38:54.096482 INFO: quant_window   : 3
2:38:54.096562 INFO: ==============================================
2:38:54.117036 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:38:54.117276 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:38:54.117353 INFO: FWHM in RT is 2.84 seconds, sigma is 0.62
2:38:54.117397 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.75
2:38:54.118385 INFO: Starting candidate selection
2:39:12.578350 INFO: Starting candidate scoring
2:39:17.221480 INFO: Finished candidate processing
2:39:17.221694 INFO: Collecting candidate features
2:39:17.441509 WARNING: intensity_correlation has 58 NaNs ( 0.05 % out of 125110)
2:39:17.441905 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 125110)
2:39:17.450140 INFO: Collecting fragment features
2:39:17.519397 INFO: Finished candidate scoring
2:39:17.587822 INFO: performing precursor FDR with 47 features
2:39:17.587980 INFO: Decoy channel: -1
2:39:17.588006 INFO: competitive: True
2:39:17.629950 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:17.657306 WARNING: dropped 30 target PSMs due to missing features
2:39:17.657475 WARNING: dropped 30 decoy PSMs due to missing features
2:39:17.687499 INFO: Estimating optimal hyperparameters - samples: 100,040, batch_size: 409, learning_rate: 3.16e-04
2:39:17.687910 INFO: Using random state 384192 for train-test-split
2:39:23.977177 INFO: Test AUC: 0.558
2:39:23.977341 INFO: Train AUC: 0.601
2:39:23.977374 INFO: AUC difference: 7.08%
2:39:23.977398 WARNING: AUC difference > 5%. This may indicate overfitting.
2:39:24.281428 INFO: Resetting torch num_threads to 128
2:39:24.285430 PROGRESS: === Extracted 125110 precursors and 1228712 fragments ===
2:39:24.286134 INFO: === FDR correction performed with classifier version 12 ===
2:39:24.290300 PROGRESS: ============================= Precursor FDR =============================
2:39:24.290442 PROGRESS: Total precursors accumulated: 22,936
2:39:24.290521 PROGRESS: Target precursors: 14,300 (62.35%)
2:39:24.290586 PROGRESS: Decoy precursors: 8,636 (37.65%)
2:39:24.290643 PROGRESS: 
2:39:24.290700 PROGRESS: Precursor Summary:
2:39:24.292069 PROGRESS: Channel   0:	 0.050 FDR:   451; 0.010 FDR:   321; 0.001 FDR:   247
2:39:24.292177 PROGRESS: 
2:39:24.292248 PROGRESS: Protein Summary:
2:39:24.293700 PROGRESS: Channel   0:	 0.050 FDR:   440; 0.010 FDR:   312; 0.001 FDR:   240
2:39:24.293816 PROGRESS: =========================================================================
2:39:24.294577 INFO: Target number of precursors reached.
2:39:24.391028 INFO: fragments_df: keeping 3942 of 1228712 [sum(precursor_idx_mask)=9881 sum(mass_error_mask)=1228709 stop_rank=3942
2:39:24.583123 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:39:24.732085 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:39:24.878670 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:39:25.011731 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:39:25.563165 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:39:25.563696 INFO: Using score_cutoff 32.54279294586181 (fac=0.99, q=1)
2:39:25.564069 INFO: Updating optimization_manager: fwhm_rt             : 2.836228370666504 -> 2.783757209777832
2:39:25.564161 INFO: Updating optimization_manager: fwhm_mobility       : 0.008086094632744789 -> 0.007883971557021141
2:39:25.564234 INFO: Updating optimization_manager: score_cutoff        : 35.47437598800659 -> 32.54279294586181
2:39:25.564309 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:39:25.571299 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:39:25.600890 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:39:25.607330 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:39:25.668110 INFO: === checking if optimization conditions were reached ===
2:39:25.668436 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
2:39:25.670538 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.0863308748677907
2:39:25.670663 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0863.
2:39:25.670742 INFO: ==============================================
2:39:25.670825 INFO: Starting optimization step 1.
2:39:25.670917 PROGRESS: === Extracting elution groups 0 to 24000 ===
2:39:25.670996 INFO: Using python extraction backend
2:39:25.671134 PROGRESS: Extracting batch of 47289 precursors
2:39:25.671215 INFO: === Search parameters used ===
2:39:25.671283 INFO: rt_error       : 129.66282998902386
2:39:25.671338 INFO: mobility_error : 0.0863308748677907
2:39:25.671387 INFO: num_candidates : 3
2:39:25.671439 INFO: ms1_error      : 15.0
2:39:25.671487 INFO: ms2_error      : 15.0
2:39:25.671535 INFO: fwhm_rt        : 2.783757209777832
2:39:25.671583 INFO: quant_window   : 3
2:39:25.671640 INFO: ==============================================
2:39:25.684652 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:39:25.684801 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:39:25.684847 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
2:39:25.684878 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
2:39:25.685675 INFO: Starting candidate selection
2:39:47.429258 INFO: Starting candidate scoring
2:39:57.188533 INFO: Finished candidate processing
2:39:57.188718 INFO: Collecting candidate features
2:39:57.475879 WARNING: intensity_correlation has 57 NaNs ( 0.05 % out of 123754)
2:39:57.476493 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 123754)
2:39:57.488178 INFO: Collecting fragment features
2:39:57.585871 INFO: Finished candidate scoring
2:39:57.684377 INFO: performing precursor FDR with 47 features
2:39:57.684648 INFO: Decoy channel: -1
2:39:57.684698 INFO: competitive: True
2:39:57.741594 INFO: Setting torch num_threads to 2 for FDR classification task
2:39:57.777524 WARNING: dropped 33 target PSMs due to missing features
2:39:57.777837 WARNING: dropped 25 decoy PSMs due to missing features
2:39:57.814913 INFO: Estimating optimal hyperparameters - samples: 98,956, batch_size: 405, learning_rate: 3.14e-04
2:39:57.815536 INFO: Using random state 384192 for train-test-split
2:40:04.645823 INFO: Test AUC: 0.561
2:40:04.646069 INFO: Train AUC: 0.601
2:40:04.646113 INFO: AUC difference: 6.69%
2:40:04.646141 WARNING: AUC difference > 5%. This may indicate overfitting.
2:40:04.945093 INFO: Resetting torch num_threads to 128
2:40:04.949837 PROGRESS: === Extracted 123754 precursors and 1214281 fragments ===
2:40:04.950609 INFO: === FDR correction performed with classifier version 12 ===
2:40:04.955961 PROGRESS: ============================= Precursor FDR =============================
2:40:04.956147 PROGRESS: Total precursors accumulated: 22,752
2:40:04.956234 PROGRESS: Target precursors: 14,173 (62.29%)
2:40:04.956315 PROGRESS: Decoy precursors: 8,579 (37.71%)
2:40:04.956393 PROGRESS: 
2:40:04.956469 PROGRESS: Precursor Summary:
2:40:04.957896 PROGRESS: Channel   0:	 0.050 FDR:   425; 0.010 FDR:   286; 0.001 FDR:   244
2:40:04.958027 PROGRESS: 
2:40:04.958105 PROGRESS: Protein Summary:
2:40:04.959580 PROGRESS: Channel   0:	 0.050 FDR:   414; 0.010 FDR:   277; 0.001 FDR:   236
2:40:04.959697 PROGRESS: =========================================================================
2:40:04.960570 INFO: Target number of precursors reached.
2:40:05.055740 INFO: fragments_df: keeping 3566 of 1214281 [sum(precursor_idx_mask)=8808 sum(mass_error_mask)=1214276 stop_rank=3566
2:40:05.414204 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:40:05.632489 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:05.865306 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:40:06.102433 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:06.705137 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:06.706060 INFO: Using score_cutoff 39.48065647888184 (fac=0.99, q=1)
2:40:06.706634 INFO: Updating optimization_manager: fwhm_rt             : 2.783757209777832 -> 2.8654398918151855
2:40:06.706742 INFO: Updating optimization_manager: fwhm_mobility       : 0.007883971557021141 -> 0.008320012129843235
2:40:06.706825 INFO: Updating optimization_manager: score_cutoff        : 32.54279294586181 -> 39.48065647888184
2:40:06.706945 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:40:06.717093 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:06.752047 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:40:06.762029 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:06.844792 INFO: === checking if optimization conditions were reached ===
2:40:06.845469 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
2:40:06.849169 INFO: Updating optimization_manager: mobility_error      : 0.0863308748677907 -> 0.07289939293308839
2:40:06.849553 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0729.
2:40:06.849679 INFO: ==============================================
2:40:06.849830 INFO: Starting optimization step 2.
2:40:06.849949 PROGRESS: === Extracting elution groups 0 to 24000 ===
2:40:06.850060 INFO: Using python extraction backend
2:40:06.850280 PROGRESS: Extracting batch of 47289 precursors
2:40:06.850392 INFO: === Search parameters used ===
2:40:06.850475 INFO: rt_error       : 129.66282998902386
2:40:06.850554 INFO: mobility_error : 0.07289939293308839
2:40:06.850630 INFO: num_candidates : 3
2:40:06.850709 INFO: ms1_error      : 15.0
2:40:06.850786 INFO: ms2_error      : 15.0
2:40:06.850863 INFO: fwhm_rt        : 2.8654398918151855
2:40:06.850941 INFO: quant_window   : 3
2:40:06.851020 INFO: ==============================================
2:40:06.885933 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:40:06.886341 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:40:06.886425 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
2:40:06.886461 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.86
2:40:06.898144 INFO: Starting candidate selection
2:40:39.124120 INFO: Starting candidate scoring
2:40:48.867246 INFO: Finished candidate processing
2:40:48.867589 INFO: Collecting candidate features
2:40:49.778860 WARNING: intensity_correlation has 63 NaNs ( 0.05 % out of 122413)
2:40:49.779780 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 122413)
2:40:49.793962 INFO: Collecting fragment features
2:40:50.019897 INFO: Finished candidate scoring
2:40:50.694551 INFO: performing precursor FDR with 47 features
2:40:50.694912 INFO: Decoy channel: -1
2:40:50.694954 INFO: competitive: True
2:40:50.909924 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:51.054189 WARNING: dropped 38 target PSMs due to missing features
2:40:51.054723 WARNING: dropped 28 decoy PSMs due to missing features
2:40:51.222604 INFO: Estimating optimal hyperparameters - samples: 97,877, batch_size: 400, learning_rate: 3.13e-04
2:40:51.224649 INFO: Using random state 384192 for train-test-split
2:41:02.561520 INFO: Test AUC: 0.562
2:41:02.562269 INFO: Train AUC: 0.610
2:41:02.562368 INFO: AUC difference: 7.94%
2:41:02.562416 WARNING: AUC difference > 5%. This may indicate overfitting.
2:41:03.179403 INFO: Resetting torch num_threads to 128
2:41:03.196243 PROGRESS: === Extracted 122413 precursors and 1192413 fragments ===
2:41:03.199906 INFO: === FDR correction performed with classifier version 12 ===
2:41:03.231566 PROGRESS: ============================= Precursor FDR =============================
2:41:03.233311 PROGRESS: Total precursors accumulated: 22,523
2:41:03.233458 PROGRESS: Target precursors: 14,388 (63.88%)
2:41:03.233633 PROGRESS: Decoy precursors: 8,135 (36.12%)
2:41:03.233731 PROGRESS: 
2:41:03.233847 PROGRESS: Precursor Summary:
2:41:03.238981 PROGRESS: Channel   0:	 0.050 FDR:   402; 0.010 FDR:   273; 0.001 FDR:     1
2:41:03.239485 PROGRESS: 
2:41:03.239590 PROGRESS: Protein Summary:
2:41:03.242321 PROGRESS: Channel   0:	 0.050 FDR:   391; 0.010 FDR:   265; 0.001 FDR:     1
2:41:03.242617 PROGRESS: =========================================================================
2:41:03.248886 INFO: Target number of precursors reached.
2:41:03.371672 INFO: fragments_df: keeping 3295 of 1192413 [sum(precursor_idx_mask)=8343 sum(mass_error_mask)=1192409 stop_rank=3295
2:41:04.030522 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
2:41:04.305161 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:04.588562 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
2:41:04.911405 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:05.589338 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:41:05.592103 INFO: Using score_cutoff 34.94822042999267 (fac=0.99, q=1)
2:41:05.594718 INFO: Updating optimization_manager: fwhm_rt             : 2.8654398918151855 -> 2.885714292526245
2:41:05.595320 INFO: Updating optimization_manager: fwhm_mobility       : 0.008320012129843235 -> 0.008219392970204353
2:41:05.595526 INFO: Updating optimization_manager: score_cutoff        : 39.48065647888184 -> 34.94822042999267
2:41:05.595751 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:41:05.613082 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:05.663353 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:41:05.680611 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:05.840390 INFO: === checking if optimization conditions were reached ===
2:41:05.841757 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
2:41:05.844902 INFO: Updating optimization_manager: mobility_error      : 0.07289939293308839 -> 0.1
2:41:05.845399 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
2:41:05.845559 INFO: Updating optimization_manager: score_cutoff        : 34.94822042999267 -> 32.54279294586181
2:41:05.845696 INFO: Updating optimization_manager: fwhm_rt             : 2.885714292526245 -> 2.783757209777832
2:41:05.845881 INFO: Updating optimization_manager: fwhm_mobility       : 0.008219392970204353 -> 0.007883971557021141
2:41:05.846040 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
2:41:05.846164 INFO: ==============================================
2:41:05.846310 PROGRESS: Optimization finished for mobility_error.
2:41:06.530739 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:41:06.549485 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:06.597911 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:41:06.616887 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:06.782265 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:41:06.783681 PROGRESS: ==============================================
2:41:06.783947 PROGRESS: ms2_error      : 15.0000
2:41:06.784086 PROGRESS: ms1_error      : 15.0000
2:41:06.784224 PROGRESS: rt_error       : 129.6628
2:41:06.784315 PROGRESS: mobility_error : 0.1000
2:41:06.784385 PROGRESS: ==============================================
2:41:06.801311 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
2:41:09.903867 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:21.113906 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
2:41:24.777712 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:53.663642 INFO: Using python extraction backend
2:41:53.665718 PROGRESS: Extracting batch of 11524154 precursors
2:41:53.677295 INFO: === Search parameters used ===
2:41:53.677471 INFO: rt_error       : 129.66282998902386
2:41:53.677559 INFO: mobility_error : 0.1
2:41:53.677665 INFO: num_candidates : 3
2:41:53.677774 INFO: ms1_error      : 15.0
2:41:53.677879 INFO: ms2_error      : 15.0
2:41:53.678003 INFO: fwhm_rt        : 2.783757209777832
2:41:53.678104 INFO: quant_window   : 3
2:41:53.678177 INFO: ==============================================
2:42:02.719010 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
2:42:02.720146 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
2:42:02.720264 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
2:42:02.720291 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.66
2:42:02.734719 INFO: Starting candidate selection
4:34:51.902765 INFO: Removed 8715766 precursors with score below cutoff 32.54279294586181
4:34:59.419188 INFO: Starting candidate scoring
4:54:26.063803 INFO: Finished candidate processing
4:54:26.065821 INFO: Collecting candidate features
4:55:55.100715 WARNING: intensity_correlation has 24 NaNs ( 0.00 % out of 23309062)
4:55:57.416836 INFO: Collecting fragment features
4:56:39.215993 INFO: Finished candidate scoring
4:58:32.210172 INFO: === Performing FDR correction with classifier version 13 ===
4:58:32.212820 INFO: performing precursor FDR with 47 features
4:58:32.212897 INFO: Decoy channel: -1
4:58:32.212965 INFO: competitive: True
4:58:54.318614 INFO: Setting torch num_threads to 2 for FDR classification task
4:59:17.671540 WARNING: dropped 10 target PSMs due to missing features
4:59:17.672710 WARNING: dropped 14 decoy PSMs due to missing features
5:02:15.038162 INFO: Estimating optimal hyperparameters - samples: 18,647,230, batch_size: 4,096, learning_rate: 1.00e-03
5:02:15.238447 INFO: Using random state 981204 for train-test-split
5:18:22.804837 INFO: Test AUC: 0.559
5:18:22.805267 INFO: Train AUC: 0.559
5:18:22.805310 INFO: AUC difference: 0.14%
5:18:27.956140 INFO: Resetting torch num_threads to 128
5:18:28.773350 INFO: Removing fragments below FDR threshold
5:18:31.518518 PROGRESS: ============================= Precursor FDR =============================
5:18:31.518850 PROGRESS: Total precursors accumulated: 68,941
5:18:31.518929 PROGRESS: Target precursors: 68,259 (99.01%)
5:18:31.518999 PROGRESS: Decoy precursors: 682 (0.99%)
5:18:31.519060 PROGRESS: 
5:18:31.519134 PROGRESS: Precursor Summary:
5:18:31.543343 PROGRESS: Channel   0:	 0.050 FDR: 68,259; 0.010 FDR: 68,259; 0.001 FDR: 43,836
5:18:31.543658 PROGRESS: 
5:18:31.543756 PROGRESS: Protein Summary:
5:18:31.575499 PROGRESS: Channel   0:	 0.050 FDR: 11,031; 0.010 FDR: 11,031; 0.001 FDR: 8,219
5:18:31.575799 PROGRESS: =========================================================================
5:18:31.879503 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/psm.parquet
5:18:32.175275 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/frag.parquet
5:18:32.444645 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
5:18:33.148011 PROGRESS: Loading raw file 2/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500 
5:18:33.148224 INFO: Quantification results path: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant
5:18:33.148330 INFO: Creating folder /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/figures
5:18:33.148549 INFO: Initializing TimingManager
5:18:33.149125 INFO: Initializing RawFileManager
5:18:33.149274 INFO: Importing data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
5:18:33.149333 INFO: Using .d import for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
5:18:33.149371 INFO: Reading frame metadata for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
5:18:34.652663 INFO: Reading 39,128 frames with 2,860,596,893 detector events for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
5:19:59.887393 INFO: Indexing /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d...
5:19:59.890454 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
5:19:59.892773 INFO: Fetching mobility values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
5:19:59.893014 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
5:19:59.893421 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
5:19:59.895171 INFO: Fetching mz values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
5:19:59.946942 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
5:19:59.947481 INFO: Indexing quadrupole dimension
5:20:00.868786 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
5:20:00.869047 INFO: Transposing detector events
5:20:13.193464 INFO: Finished transposing data
5:20:13.193699 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
5:20:13.194776 INFO: RT (min)            : 0.0 - 70.0
5:20:13.194890 INFO: RT duration (sec)   : 4199.8
5:20:13.194956 INFO: RT duration (min)   : 70.0
5:20:13.195011 INFO: Cycle len (scans)   : 9
5:20:13.195087 INFO: Cycle len (sec)     : 0.97
5:20:13.195166 INFO: Number of cycles    : 4347
5:20:13.195231 INFO: MS2 range (m/z)     : 400.0 - 1000.0
5:20:13.195379 INFO: Creating DIA data object took: 100.04610013961792
5:20:15.967850 INFO: Initializing CalibrationManager
5:20:15.968343 INFO: Setting up calibration estimators ..
5:20:15.968434 INFO: Found 1 estimator(s) in calibration group 'fragment'
5:20:15.968554 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'}' ..
5:20:15.968713 INFO: Found 3 estimator(s) in calibration group 'precursor'
5:20:15.968809 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'}' ..
5:20:15.968897 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}}' ..
5:20:15.968988 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}}' ..
5:20:15.969064 INFO: Done setting up calibration estimators.
5:20:15.969250 INFO: Initializing OptimizationManager
5:20:15.969389 INFO: initial parameter: ms1_error = 30
5:20:15.969461 INFO: initial parameter: ms2_error = 30
5:20:15.969534 INFO: initial parameter: rt_error = 2099.894844
5:20:15.969601 INFO: initial parameter: mobility_error = 0.1
5:20:15.969665 INFO: initial parameter: num_candidates = 1
5:20:15.969730 INFO: initial parameter: fwhm_rt = 5
5:20:15.969891 INFO: initial parameter: fwhm_mobility = 0.01
5:20:15.969987 INFO: initial parameter: score_cutoff = 0
5:20:15.970078 INFO: initial parameter: classifier_version = -1
5:20:15.970217 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
5:20:15.970597 INFO: FDRManager: loading saved state not requested, will be initialized.
5:20:15.970668 INFO: Initializing FDRManager
5:20:15.970741 INFO: Loading classifier store from /usr/local/lib/python3.10/site-packages/alphadia/constants/classifier
5:20:17.712311 PROGRESS: Initializing spectral library: 5,845,771 target precursors potentially observable (0 removed)
5:20:18.645715 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
5:20:18.646582 INFO: Updating optimization_manager: rt_error            : 2099.894844 -> 2099.894844
5:20:18.646771 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
5:20:18.647043 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
5:20:18.647197 PROGRESS: Starting initial search for precursors.
5:20:18.647354 INFO: Starting optimization step 0.
5:20:18.647486 PROGRESS: === Extracting elution groups 0 to 8000 ===
5:20:18.647611 INFO: Using python extraction backend
5:20:18.647926 PROGRESS: Extracting batch of 15766 precursors
5:20:18.648053 INFO: === Search parameters used ===
5:20:18.648153 INFO: rt_error       : 2099.894844
5:20:18.648239 INFO: mobility_error : 0.1
5:20:18.648317 INFO: num_candidates : 1
5:20:18.648397 INFO: ms1_error      : 30
5:20:18.648479 INFO: ms2_error      : 30
5:20:18.648555 INFO: fwhm_rt        : 5
5:20:18.648633 INFO: quant_window   : 3
5:20:18.648708 INFO: ==============================================
5:20:18.653817 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:20:18.653986 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:20:18.654050 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
5:20:18.654092 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
5:20:18.662027 INFO: Starting candidate selection
5:24:17.136214 INFO: Starting candidate scoring
5:24:19.400879 INFO: Finished candidate processing
5:24:19.401292 INFO: Collecting candidate features
5:24:19.537606 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 15087)
5:24:19.538283 WARNING: height_correlation has 1 NaNs ( 0.01 % out of 15087)
5:24:19.544136 INFO: Collecting fragment features
5:24:19.579124 INFO: Finished candidate scoring
5:24:19.638668 INFO: performing precursor FDR with 47 features
5:24:19.638995 INFO: Decoy channel: -1
5:24:19.639035 INFO: competitive: True
5:24:19.663845 INFO: Setting torch num_threads to 2 for FDR classification task
5:24:19.679290 WARNING: dropped 2 target PSMs due to missing features
5:24:19.690613 INFO: Estimating optimal hyperparameters - samples: 12,068, batch_size: 128, learning_rate: 1.77e-04
5:24:19.692863 INFO: Using random state 841570 for train-test-split
5:24:22.086701 INFO: Test AUC: 0.545
5:24:22.087769 INFO: Train AUC: 0.571
5:24:22.087932 INFO: AUC difference: 4.43%
5:24:22.690435 INFO: Resetting torch num_threads to 128
5:24:22.700639 PROGRESS: === Extracted 15087 precursors and 163504 fragments ===
5:24:22.704321 INFO: === FDR correction performed with classifier version -1 ===
5:24:22.715398 PROGRESS: ============================= Precursor FDR =============================
5:24:22.716720 PROGRESS: Total precursors accumulated: 7,726
5:24:22.716858 PROGRESS: Target precursors: 4,588 (59.38%)
5:24:22.716957 PROGRESS: Decoy precursors: 3,138 (40.62%)
5:24:22.717069 PROGRESS: 
5:24:22.717158 PROGRESS: Precursor Summary:
5:24:22.719461 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
5:24:22.719689 PROGRESS: 
5:24:22.719853 PROGRESS: Protein Summary:
5:24:22.721762 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
5:24:22.722001 PROGRESS: =========================================================================
5:24:22.722365 INFO: Target number of precursors not reached yet.
5:24:23.005536 INFO: Starting optimization step 1.
5:24:23.007155 PROGRESS: === Extracting elution groups 8000 to 24000 ===
5:24:23.007393 INFO: Using python extraction backend
5:24:23.007860 PROGRESS: Extracting batch of 31523 precursors
5:24:23.008045 INFO: === Search parameters used ===
5:24:23.008128 INFO: rt_error       : 2099.894844
5:24:23.008190 INFO: mobility_error : 0.1
5:24:23.008250 INFO: num_candidates : 1
5:24:23.008301 INFO: ms1_error      : 30
5:24:23.008355 INFO: ms2_error      : 30
5:24:23.008414 INFO: fwhm_rt        : 5
5:24:23.008464 INFO: quant_window   : 3
5:24:23.008556 INFO: ==============================================
5:24:23.046094 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:24:23.046752 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:24:23.046855 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
5:24:23.046894 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
5:24:23.054573 INFO: Starting candidate selection
5:31:51.734392 INFO: Starting candidate scoring
5:31:56.185483 INFO: Finished candidate processing
5:31:56.186114 INFO: Collecting candidate features
5:31:56.446283 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 30047)
5:31:56.454733 INFO: Collecting fragment features
5:31:56.516898 INFO: Finished candidate scoring
5:31:56.696794 INFO: performing precursor FDR with 47 features
5:31:56.697280 INFO: Decoy channel: -1
5:31:56.697331 INFO: competitive: True
5:31:56.811652 INFO: Setting torch num_threads to 2 for FDR classification task
5:31:56.864152 WARNING: dropped 4 target PSMs due to missing features
5:31:56.864712 WARNING: dropped 1 decoy PSMs due to missing features
5:31:56.909322 INFO: Estimating optimal hyperparameters - samples: 36,103, batch_size: 147, learning_rate: 1.89e-04
5:31:56.910092 INFO: Using random state 536535 for train-test-split
5:32:03.460406 INFO: Test AUC: 0.558
5:32:03.461196 INFO: Train AUC: 0.587
5:32:03.461256 INFO: AUC difference: 4.98%
5:32:04.233594 INFO: Resetting torch num_threads to 128
5:32:04.297448 PROGRESS: === Extracted 45134 precursors and 488191 fragments ===
5:32:04.300345 INFO: === FDR correction performed with classifier version -1 ===
5:32:04.332755 PROGRESS: ============================= Precursor FDR =============================
5:32:04.334029 PROGRESS: Total precursors accumulated: 23,118
5:32:04.334411 PROGRESS: Target precursors: 14,004 (60.58%)
5:32:04.334660 PROGRESS: Decoy precursors: 9,114 (39.42%)
5:32:04.334801 PROGRESS: 
5:32:04.334908 PROGRESS: Precursor Summary:
5:32:04.341805 PROGRESS: Channel   0:	 0.050 FDR:    76; 0.010 FDR:    42; 0.001 FDR:    42
5:32:04.342771 PROGRESS: 
5:32:04.343000 PROGRESS: Protein Summary:
5:32:04.347704 PROGRESS: Channel   0:	 0.050 FDR:    76; 0.010 FDR:    42; 0.001 FDR:    42
5:32:04.348521 PROGRESS: =========================================================================
5:32:04.352006 INFO: Target number of precursors not reached yet.
5:32:04.862942 INFO: Starting optimization step 2.
5:32:04.864442 PROGRESS: === Extracting elution groups 24000 to 56000 ===
5:32:04.865005 INFO: Using python extraction backend
5:32:04.865482 PROGRESS: Extracting batch of 63149 precursors
5:32:04.865739 INFO: === Search parameters used ===
5:32:04.865878 INFO: rt_error       : 2099.894844
5:32:04.865969 INFO: mobility_error : 0.1
5:32:04.866050 INFO: num_candidates : 1
5:32:04.866126 INFO: ms1_error      : 30
5:32:04.866214 INFO: ms2_error      : 30
5:32:04.866296 INFO: fwhm_rt        : 5
5:32:04.866369 INFO: quant_window   : 3
5:32:04.866472 INFO: ==============================================
5:32:04.917613 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:32:04.918091 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:32:04.918160 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
5:32:04.918192 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
5:32:04.922472 INFO: Starting candidate selection
5:44:47.159621 INFO: Starting candidate scoring
5:44:53.788780 INFO: Finished candidate processing
5:44:53.789007 INFO: Collecting candidate features
5:44:53.928934 WARNING: intensity_correlation has 14 NaNs ( 0.02 % out of 60202)
5:44:53.929340 WARNING: height_correlation has 4 NaNs ( 0.01 % out of 60202)
5:44:53.936787 INFO: Collecting fragment features
5:44:53.994564 INFO: Finished candidate scoring
5:44:54.092214 INFO: performing precursor FDR with 47 features
5:44:54.092466 INFO: Decoy channel: -1
5:44:54.092503 INFO: competitive: True
5:44:54.149421 INFO: Setting torch num_threads to 2 for FDR classification task
5:44:54.181217 WARNING: dropped 13 target PSMs due to missing features
5:44:54.181437 WARNING: dropped 9 decoy PSMs due to missing features
5:44:54.215258 INFO: Estimating optimal hyperparameters - samples: 84,251, batch_size: 345, learning_rate: 2.90e-04
5:44:54.215810 INFO: Using random state 679158 for train-test-split
5:45:00.307950 INFO: Test AUC: 0.556
5:45:00.308361 INFO: Train AUC: 0.597
5:45:00.308412 INFO: AUC difference: 6.75%
5:45:00.308443 WARNING: AUC difference > 5%. This may indicate overfitting.
5:45:00.690985 INFO: Resetting torch num_threads to 128
5:45:00.730840 PROGRESS: === Extracted 105336 precursors and 1140108 fragments ===
5:45:00.732496 INFO: === FDR correction performed with classifier version -1 ===
5:45:00.757875 PROGRESS: ============================= Precursor FDR =============================
5:45:00.758445 PROGRESS: Total precursors accumulated: 53,921
5:45:00.758540 PROGRESS: Target precursors: 32,954 (61.12%)
5:45:00.758619 PROGRESS: Decoy precursors: 20,967 (38.88%)
5:45:00.758689 PROGRESS: 
5:45:00.758749 PROGRESS: Precursor Summary:
5:45:00.760730 PROGRESS: Channel   0:	 0.050 FDR:   345; 0.010 FDR:   247; 0.001 FDR:   119
5:45:00.760881 PROGRESS: 
5:45:00.760964 PROGRESS: Protein Summary:
5:45:00.762689 PROGRESS: Channel   0:	 0.050 FDR:   326; 0.010 FDR:   237; 0.001 FDR:   117
5:45:00.762811 PROGRESS: =========================================================================
5:45:00.764107 INFO: Target number of precursors reached.
5:45:00.867173 INFO: fragments_df: keeping 2344 of 1140108 [sum(precursor_idx_mask)=2816 sum(mass_error_mask)=1140108 stop_rank=2344
5:45:01.152074 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
5:45:01.279638 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:45:01.429813 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
5:45:01.560189 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:45:01.883236 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
5:45:01.884042 INFO: Using score_cutoff 55.44483164291382 (fac=0.99, q=1)
5:45:01.884495 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.258119583129883
5:45:01.884600 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010784967802464962
5:45:01.884677 INFO: Updating optimization_manager: score_cutoff        : 0 -> 55.44483164291382
5:45:01.884765 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
5:45:01.900134 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:45:01.973151 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
5:45:01.991385 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:45:02.156227 INFO: Updating optimization_manager: classifier_version  : -1 -> 2
5:45:02.156718 PROGRESS: Required number of precursors found. Starting search parameter optimization.
5:45:02.156875 INFO: Starting optimization step 3.
5:45:02.156986 PROGRESS: === Extracting elution groups 0 to 56000 ===
5:45:02.157108 INFO: Using python extraction backend
5:45:02.157355 PROGRESS: Extracting batch of 110438 precursors
5:45:02.157473 INFO: === Search parameters used ===
5:45:02.157554 INFO: rt_error       : 2099.894844
5:45:02.157625 INFO: mobility_error : 0.1
5:45:02.157679 INFO: num_candidates : 3
5:45:02.157740 INFO: ms1_error      : 30
5:45:02.157819 INFO: ms2_error      : 30
5:45:02.157907 INFO: fwhm_rt        : 3.258119583129883
5:45:02.157969 INFO: quant_window   : 3
5:45:02.158031 INFO: ==============================================
5:45:02.267740 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
5:45:02.268025 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
5:45:02.268100 INFO: FWHM in RT is 3.26 seconds, sigma is 0.72
5:45:02.268133 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.00
5:45:02.277961 INFO: Starting candidate selection
6:00:20.635692 INFO: Starting candidate scoring
6:00:40.929626 INFO: Finished candidate processing
6:00:40.929924 INFO: Collecting candidate features
6:00:41.514049 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 306297)
6:00:41.528203 INFO: Collecting fragment features
6:00:41.712803 INFO: Finished candidate scoring
6:00:41.878019 INFO: performing precursor FDR with 47 features
6:00:41.878168 INFO: Decoy channel: -1
6:00:41.878202 INFO: competitive: True
6:00:41.968300 INFO: Setting torch num_threads to 2 for FDR classification task
6:00:42.027933 WARNING: dropped 3 target PSMs due to missing features
6:00:42.028105 WARNING: dropped 1 decoy PSMs due to missing features
6:00:42.137085 INFO: Estimating optimal hyperparameters - samples: 245,034, batch_size: 1,003, learning_rate: 4.95e-04
6:00:42.137695 INFO: Using random state 679403 for train-test-split
6:00:50.706000 INFO: Test AUC: 0.564
6:00:50.706391 INFO: Train AUC: 0.589
6:00:50.706458 INFO: AUC difference: 4.19%
6:00:51.070019 INFO: Resetting torch num_threads to 128
6:00:51.076926 PROGRESS: === Extracted 306297 precursors and 3346361 fragments ===
6:00:51.077691 INFO: === FDR correction performed with classifier version 2 ===
6:00:51.087336 PROGRESS: ============================= Precursor FDR =============================
6:00:51.087657 PROGRESS: Total precursors accumulated: 54,911
6:00:51.087736 PROGRESS: Target precursors: 34,761 (63.30%)
6:00:51.087803 PROGRESS: Decoy precursors: 20,150 (36.70%)
6:00:51.087866 PROGRESS: 
6:00:51.087926 PROGRESS: Precursor Summary:
6:00:51.089438 PROGRESS: Channel   0:	 0.050 FDR:   313; 0.010 FDR:     1; 0.001 FDR:     1
6:00:51.089551 PROGRESS: 
6:00:51.089627 PROGRESS: Protein Summary:
6:00:51.095191 PROGRESS: Channel   0:	 0.050 FDR:   300; 0.010 FDR:     1; 0.001 FDR:     1
6:00:51.095342 PROGRESS: =========================================================================
6:00:51.110597 INFO: Target number of precursors not reached yet.
6:00:51.456302 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:00:51.473686 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:00:51.550543 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
6:00:51.571898 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:00:51.751524 INFO: === skipping optimization until target number of precursors are found ===
6:00:51.751932 INFO: Starting optimization step 4.
6:00:51.752050 PROGRESS: === Extracting elution groups 56000 to 120000 ===
6:00:51.752236 INFO: Using python extraction backend
6:00:51.752508 PROGRESS: Extracting batch of 126145 precursors
6:00:51.752642 INFO: === Search parameters used ===
6:00:51.752724 INFO: rt_error       : 2099.894844
6:00:51.752795 INFO: mobility_error : 0.1
6:00:51.752860 INFO: num_candidates : 3
6:00:51.752934 INFO: ms1_error      : 30
6:00:51.753005 INFO: ms2_error      : 30
6:00:51.753075 INFO: fwhm_rt        : 3.258119583129883
6:00:51.753131 INFO: quant_window   : 3
6:00:51.753195 INFO: ==============================================
6:00:51.796995 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
6:00:51.797166 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
6:00:51.797222 INFO: FWHM in RT is 3.26 seconds, sigma is 0.72
6:00:51.797246 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.00
6:00:51.798673 INFO: Starting candidate selection
6:26:21.834562 INFO: Starting candidate scoring
6:27:07.431237 INFO: Finished candidate processing
6:27:07.432490 INFO: Collecting candidate features
6:27:09.427319 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 349881)
6:27:09.464210 INFO: Collecting fragment features
6:27:10.164039 INFO: Finished candidate scoring
6:27:12.696467 INFO: performing precursor FDR with 47 features
6:27:12.697320 INFO: Decoy channel: -1
6:27:12.697380 INFO: competitive: True
6:27:13.823689 INFO: Setting torch num_threads to 2 for FDR classification task
6:27:14.306751 WARNING: dropped 5 target PSMs due to missing features
6:27:14.307849 WARNING: dropped 3 decoy PSMs due to missing features
6:27:15.366474 INFO: Estimating optimal hyperparameters - samples: 524,936, batch_size: 2,150, learning_rate: 7.25e-04
6:27:15.385826 INFO: Using random state 679403 for train-test-split
6:27:40.664462 INFO: Test AUC: 0.568
6:27:40.665860 INFO: Train AUC: 0.582
6:27:40.665943 INFO: AUC difference: 2.43%
6:27:41.526426 INFO: Resetting torch num_threads to 128
6:27:42.146650 PROGRESS: === Extracted 656178 precursors and 7167447 fragments ===
6:27:42.150011 INFO: === FDR correction performed with classifier version 2 ===
6:27:42.236311 PROGRESS: ============================= Precursor FDR =============================
6:27:42.237725 PROGRESS: Total precursors accumulated: 117,709
6:27:42.237872 PROGRESS: Target precursors: 74,049 (62.91%)
6:27:42.237991 PROGRESS: Decoy precursors: 43,660 (37.09%)
6:27:42.238158 PROGRESS: 
6:27:42.238277 PROGRESS: Precursor Summary:
6:27:42.245133 PROGRESS: Channel   0:	 0.050 FDR: 1,029; 0.010 FDR:   677; 0.001 FDR:   386
6:27:42.246168 PROGRESS: 
6:27:42.246292 PROGRESS: Protein Summary:
6:27:42.250525 PROGRESS: Channel   0:	 0.050 FDR:   911; 0.010 FDR:   606; 0.001 FDR:   361
6:27:42.251310 PROGRESS: =========================================================================
6:27:42.261932 INFO: Target number of precursors reached.
6:27:43.112995 INFO: fragments_df: keeping 5000 of 7167447 [sum(precursor_idx_mask)=22136 sum(mass_error_mask)=7167447 stop_rank=5000
6:27:44.100201 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
6:27:44.381961 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:27:44.667597 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
6:27:44.994362 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:27:45.984903 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:27:45.988497 INFO: Using score_cutoff 57.898928814697264 (fac=0.99, q=1)
6:27:45.991033 INFO: Updating optimization_manager: fwhm_rt             : 3.258119583129883 -> 3.070995330810547
6:27:45.991556 INFO: Updating optimization_manager: fwhm_mobility       : 0.010784967802464962 -> 0.010723287239670753
6:27:45.991742 INFO: Updating optimization_manager: score_cutoff        : 55.44483164291382 -> 57.898928814697264
6:27:45.991938 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:27:46.018635 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:27:46.111308 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
6:27:46.136713 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:27:46.387129 INFO: === checking if optimization conditions were reached ===
6:27:46.395657 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
6:27:46.396945 INFO: Updating optimization_manager: classifier_version  : 2 -> 4
6:27:46.397123 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
6:27:46.401868 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
6:27:46.402347 INFO: Updating optimization_manager: classifier_version  : 4 -> 4
6:27:46.402510 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
6:27:46.402652 INFO: ==============================================
6:27:46.402843 INFO: Starting optimization step 5.
6:27:46.403025 PROGRESS: === Extracting elution groups 0 to 56000 ===
6:27:46.403333 INFO: Using python extraction backend
6:27:46.404109 PROGRESS: Extracting batch of 110438 precursors
6:27:46.404303 INFO: === Search parameters used ===
6:27:46.404425 INFO: rt_error       : 2099.894844
6:27:46.404528 INFO: mobility_error : 0.1
6:27:46.404660 INFO: num_candidates : 3
6:27:46.404780 INFO: ms1_error      : 15.0
6:27:46.404879 INFO: ms2_error      : 15.0
6:27:46.405056 INFO: fwhm_rt        : 3.070995330810547
6:27:46.405143 INFO: quant_window   : 3
6:27:46.405210 INFO: ==============================================
6:27:46.519774 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
6:27:46.520432 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
6:27:46.520574 INFO: FWHM in RT is 3.07 seconds, sigma is 0.68
6:27:46.520613 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.97
6:27:46.527411 INFO: Starting candidate selection
6:43:36.882059 INFO: Starting candidate scoring
6:43:47.877729 INFO: Finished candidate processing
6:43:47.878241 INFO: Collecting candidate features
6:43:48.528706 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 306104)
6:43:48.542403 INFO: Collecting fragment features
6:43:48.758440 INFO: Finished candidate scoring
6:43:48.914150 INFO: performing precursor FDR with 47 features
6:43:48.914303 INFO: Decoy channel: -1
6:43:48.914343 INFO: competitive: True
6:43:48.998427 INFO: Setting torch num_threads to 2 for FDR classification task
6:43:49.055356 WARNING: dropped 4 target PSMs due to missing features
6:43:49.055531 WARNING: dropped 2 decoy PSMs due to missing features
6:43:49.143980 INFO: Estimating optimal hyperparameters - samples: 244,878, batch_size: 1,003, learning_rate: 4.95e-04
6:43:49.144630 INFO: Using random state 380179 for train-test-split
6:43:57.065584 INFO: Test AUC: 0.564
6:43:57.065936 INFO: Train AUC: 0.589
6:43:57.065974 INFO: AUC difference: 4.24%
6:43:57.437119 INFO: Resetting torch num_threads to 128
6:43:57.445062 PROGRESS: === Extracted 306104 precursors and 3191446 fragments ===
6:43:57.445844 INFO: === FDR correction performed with classifier version 4 ===
6:43:57.455311 PROGRESS: ============================= Precursor FDR =============================
6:43:57.455620 PROGRESS: Total precursors accumulated: 54,832
6:43:57.455709 PROGRESS: Target precursors: 34,500 (62.92%)
6:43:57.455783 PROGRESS: Decoy precursors: 20,332 (37.08%)
6:43:57.455850 PROGRESS: 
6:43:57.455918 PROGRESS: Precursor Summary:
6:43:57.457598 PROGRESS: Channel   0:	 0.050 FDR:   669; 0.010 FDR:   529; 0.001 FDR:   348
6:43:57.457719 PROGRESS: 
6:43:57.457813 PROGRESS: Protein Summary:
6:43:57.459579 PROGRESS: Channel   0:	 0.050 FDR:   616; 0.010 FDR:   488; 0.001 FDR:   325
6:43:57.459690 PROGRESS: =========================================================================
6:43:57.487820 INFO: Target number of precursors reached.
6:43:57.730814 INFO: fragments_df: keeping 5000 of 3191446 [sum(precursor_idx_mask)=16975 sum(mass_error_mask)=3191446 stop_rank=5000
6:43:58.354064 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
6:43:58.507766 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:43:58.660122 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
6:43:58.813401 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:43:59.503831 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:43:59.504398 INFO: Using score_cutoff 41.92648564910888 (fac=0.99, q=1)
6:43:59.504821 INFO: Updating optimization_manager: fwhm_rt             : 3.070995330810547 -> 2.7998087406158447
6:43:59.504922 INFO: Updating optimization_manager: fwhm_mobility       : 0.010723287239670753 -> 0.008552542887628078
6:43:59.505003 INFO: Updating optimization_manager: score_cutoff        : 57.898928814697264 -> 41.92648564910888
6:43:59.505092 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:43:59.511917 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:43:59.540597 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
6:43:59.547242 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:43:59.609619 INFO: === checking if optimization conditions were reached ===
6:43:59.612115 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
6:43:59.612257 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
6:43:59.612366 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
6:43:59.613583 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
6:43:59.613709 INFO: Updating optimization_manager: classifier_version  : 5 -> 5
6:43:59.613820 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
6:43:59.613925 INFO: ==============================================
6:43:59.614056 PROGRESS: Optimization finished for ms2_error, ms1_error.
6:43:59.893448 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:43:59.900686 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:43:59.928977 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
6:43:59.935632 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:43:59.995825 INFO: Starting optimization step 0.
6:43:59.996181 PROGRESS: === Extracting elution groups 0 to 24000 ===
6:43:59.996319 INFO: Using python extraction backend
6:43:59.996598 PROGRESS: Extracting batch of 47289 precursors
6:43:59.996721 INFO: === Search parameters used ===
6:43:59.996807 INFO: rt_error       : 2099.894844
6:43:59.996885 INFO: mobility_error : 0.1
6:43:59.996964 INFO: num_candidates : 3
6:43:59.997038 INFO: ms1_error      : 15.0
6:43:59.997114 INFO: ms2_error      : 15.0
6:43:59.997190 INFO: fwhm_rt        : 2.7998087406158447
6:43:59.997283 INFO: quant_window   : 3
6:43:59.997355 INFO: ==============================================
6:44:00.010288 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
6:44:00.010430 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
6:44:00.010500 INFO: FWHM in RT is 2.80 seconds, sigma is 0.62
6:44:00.010541 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.97
6:44:00.070079 INFO: Starting candidate selection
6:53:44.990668 INFO: Starting candidate scoring
6:53:55.562497 INFO: Finished candidate processing
6:53:55.563203 INFO: Collecting candidate features
6:53:56.385845 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 130894)
6:53:56.400560 INFO: Collecting fragment features
6:53:56.625010 INFO: Finished candidate scoring
6:53:57.273615 INFO: performing precursor FDR with 47 features
6:53:57.274215 INFO: Decoy channel: -1
6:53:57.274275 INFO: competitive: True
6:53:57.454647 INFO: Setting torch num_threads to 2 for FDR classification task
6:53:57.575381 WARNING: dropped 1 target PSMs due to missing features
6:53:57.576226 WARNING: dropped 1 decoy PSMs due to missing features
6:53:57.707095 INFO: Estimating optimal hyperparameters - samples: 104,713, batch_size: 428, learning_rate: 3.23e-04
6:53:57.708963 INFO: Using random state 656545 for train-test-split
6:54:07.293165 INFO: Test AUC: 0.572
6:54:07.294118 INFO: Train AUC: 0.616
6:54:07.294176 INFO: AUC difference: 7.17%
6:54:07.294222 WARNING: AUC difference > 5%. This may indicate overfitting.
6:54:08.002970 INFO: Resetting torch num_threads to 128
6:54:08.046387 PROGRESS: === Extracted 130894 precursors and 1362205 fragments ===
6:54:08.050945 INFO: === FDR correction performed with classifier version 5 ===
6:54:08.095496 PROGRESS: ============================= Precursor FDR =============================
6:54:08.098128 PROGRESS: Total precursors accumulated: 23,513
6:54:08.098293 PROGRESS: Target precursors: 15,292 (65.04%)
6:54:08.098392 PROGRESS: Decoy precursors: 8,221 (34.96%)
6:54:08.098477 PROGRESS: 
6:54:08.098560 PROGRESS: Precursor Summary:
6:54:08.105966 PROGRESS: Channel   0:	 0.050 FDR:   355; 0.010 FDR:   225; 0.001 FDR:   178
6:54:08.106996 PROGRESS: 
6:54:08.107123 PROGRESS: Protein Summary:
6:54:08.110936 PROGRESS: Channel   0:	 0.050 FDR:   346; 0.010 FDR:   218; 0.001 FDR:   175
6:54:08.111379 PROGRESS: =========================================================================
6:54:08.235691 INFO: Target number of precursors reached.
6:54:08.363150 INFO: fragments_df: keeping 3021 of 1362205 [sum(precursor_idx_mask)=7038 sum(mass_error_mask)=1362205 stop_rank=3021
6:54:09.532878 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
6:54:09.742644 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:54:09.981791 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
6:54:10.248293 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:54:10.833249 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:54:10.835173 INFO: Using score_cutoff 40.73839561614991 (fac=0.99, q=1)
6:54:10.836936 INFO: Updating optimization_manager: fwhm_rt             : 2.7998087406158447 -> 2.6956613063812256
6:54:10.837450 INFO: Updating optimization_manager: fwhm_mobility       : 0.008552542887628078 -> 0.008400889113545418
6:54:10.837711 INFO: Updating optimization_manager: score_cutoff        : 41.92648564910888 -> 40.73839561614991
6:54:10.838022 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:54:10.851111 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:54:10.889261 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
6:54:10.902084 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:54:10.999698 INFO: === checking if optimization conditions were reached ===
6:54:11.001002 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
6:54:11.007782 INFO: Updating optimization_manager: rt_error            : 2099.894844 -> 880.4263998374789
6:54:11.008484 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 880.4264.
6:54:11.008847 INFO: ==============================================
6:54:11.009200 INFO: Starting optimization step 1.
6:54:11.009479 PROGRESS: === Extracting elution groups 0 to 24000 ===
6:54:11.009772 INFO: Using python extraction backend
6:54:11.010343 PROGRESS: Extracting batch of 47289 precursors
6:54:11.010550 INFO: === Search parameters used ===
6:54:11.010673 INFO: rt_error       : 880.4263998374789
6:54:11.010765 INFO: mobility_error : 0.1
6:54:11.010905 INFO: num_candidates : 3
6:54:11.011039 INFO: ms1_error      : 15.0
6:54:11.011139 INFO: ms2_error      : 15.0
6:54:11.011255 INFO: fwhm_rt        : 2.6956613063812256
6:54:11.011353 INFO: quant_window   : 3
6:54:11.011484 INFO: ==============================================
6:54:11.057445 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
6:54:11.058059 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
6:54:11.058299 INFO: FWHM in RT is 2.70 seconds, sigma is 0.59
6:54:11.058424 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.90
6:54:11.062892 INFO: Starting candidate selection
6:58:57.779878 INFO: Starting candidate scoring
6:59:08.667769 INFO: Finished candidate processing
6:59:08.668104 INFO: Collecting candidate features
6:59:09.316008 WARNING: intensity_correlation has 9 NaNs ( 0.01 % out of 129730)
6:59:09.326763 INFO: Collecting fragment features
6:59:09.444297 INFO: Finished candidate scoring
6:59:09.803419 INFO: performing precursor FDR with 47 features
6:59:09.804011 INFO: Decoy channel: -1
6:59:09.804081 INFO: competitive: True
6:59:09.918381 INFO: Setting torch num_threads to 2 for FDR classification task
6:59:10.026304 WARNING: dropped 5 target PSMs due to missing features
6:59:10.026938 WARNING: dropped 4 decoy PSMs due to missing features
6:59:10.196585 INFO: Estimating optimal hyperparameters - samples: 103,776, batch_size: 425, learning_rate: 3.22e-04
6:59:10.197897 INFO: Using random state 656545 for train-test-split
6:59:20.364048 INFO: Test AUC: 0.563
6:59:20.365024 INFO: Train AUC: 0.610
6:59:20.365080 INFO: AUC difference: 7.75%
6:59:20.365127 WARNING: AUC difference > 5%. This may indicate overfitting.
6:59:20.980067 INFO: Resetting torch num_threads to 128
6:59:20.999304 PROGRESS: === Extracted 129730 precursors and 1336657 fragments ===
6:59:21.002246 INFO: === FDR correction performed with classifier version 5 ===
6:59:21.032906 PROGRESS: ============================= Precursor FDR =============================
6:59:21.034560 PROGRESS: Total precursors accumulated: 23,418
6:59:21.034881 PROGRESS: Target precursors: 15,121 (64.57%)
6:59:21.035061 PROGRESS: Decoy precursors: 8,297 (35.43%)
6:59:21.035197 PROGRESS: 
6:59:21.035283 PROGRESS: Precursor Summary:
6:59:21.042885 PROGRESS: Channel   0:	 0.050 FDR:   372; 0.010 FDR:   240; 0.001 FDR:   137
6:59:21.043605 PROGRESS: 
6:59:21.043777 PROGRESS: Protein Summary:
6:59:21.049774 PROGRESS: Channel   0:	 0.050 FDR:   361; 0.010 FDR:   234; 0.001 FDR:   135
6:59:21.050199 PROGRESS: =========================================================================
6:59:21.058943 INFO: Target number of precursors reached.
6:59:21.186593 INFO: fragments_df: keeping 3281 of 1336657 [sum(precursor_idx_mask)=7554 sum(mass_error_mask)=1336657 stop_rank=3281
6:59:22.057360 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
6:59:22.348813 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:59:22.632327 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
6:59:22.954186 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:59:27.756052 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:59:27.758200 INFO: Using score_cutoff 39.88516617965698 (fac=0.99, q=1)
6:59:27.759789 INFO: Updating optimization_manager: fwhm_rt             : 2.6956613063812256 -> 2.6866464614868164
6:59:27.760190 INFO: Updating optimization_manager: fwhm_mobility       : 0.008400889113545418 -> 0.0083256084471941
6:59:27.760465 INFO: Updating optimization_manager: score_cutoff        : 40.73839561614991 -> 39.88516617965698
6:59:27.760642 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
6:59:27.773702 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:59:27.810625 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
6:59:27.822367 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:59:27.918281 INFO: === checking if optimization conditions were reached ===
6:59:27.919787 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
6:59:27.932735 INFO: Updating optimization_manager: rt_error            : 880.4263998374789 -> 740.7541736857925
6:59:27.935483 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 740.7542.
6:59:27.936070 INFO: ==============================================
6:59:27.936585 INFO: Starting optimization step 2.
6:59:27.936982 PROGRESS: === Extracting elution groups 0 to 24000 ===
6:59:27.937201 INFO: Using python extraction backend
6:59:27.937739 PROGRESS: Extracting batch of 47289 precursors
6:59:27.938035 INFO: === Search parameters used ===
6:59:27.938185 INFO: rt_error       : 740.7541736857925
6:59:27.938341 INFO: mobility_error : 0.1
6:59:27.938463 INFO: num_candidates : 3
6:59:27.938611 INFO: ms1_error      : 15.0
6:59:27.938713 INFO: ms2_error      : 15.0
6:59:27.938779 INFO: fwhm_rt        : 2.6866464614868164
6:59:27.938850 INFO: quant_window   : 3
6:59:27.938907 INFO: ==============================================
6:59:28.006441 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
6:59:28.007075 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
6:59:28.007165 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
6:59:28.007194 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.86
6:59:28.010684 INFO: Starting candidate selection
7:03:02.910615 INFO: Starting candidate scoring
7:03:13.066016 INFO: Finished candidate processing
7:03:13.066263 INFO: Collecting candidate features
7:03:13.392776 WARNING: intensity_correlation has 10 NaNs ( 0.01 % out of 129737)
7:03:13.402671 INFO: Collecting fragment features
7:03:13.498728 INFO: Finished candidate scoring
7:03:13.757242 INFO: performing precursor FDR with 47 features
7:03:13.757732 INFO: Decoy channel: -1
7:03:13.757792 INFO: competitive: True
7:03:13.856634 INFO: Setting torch num_threads to 2 for FDR classification task
7:03:13.916559 WARNING: dropped 6 target PSMs due to missing features
7:03:13.917123 WARNING: dropped 4 decoy PSMs due to missing features
7:03:13.982520 INFO: Estimating optimal hyperparameters - samples: 103,781, batch_size: 425, learning_rate: 3.22e-04
7:03:13.983836 INFO: Using random state 656545 for train-test-split
7:03:23.491719 INFO: Test AUC: 0.557
7:03:23.492876 INFO: Train AUC: 0.606
7:03:23.492929 INFO: AUC difference: 8.11%
7:03:23.492959 WARNING: AUC difference > 5%. This may indicate overfitting.
7:03:24.177386 INFO: Resetting torch num_threads to 128
7:03:24.196002 PROGRESS: === Extracted 129737 precursors and 1331961 fragments ===
7:03:24.199087 INFO: === FDR correction performed with classifier version 5 ===
7:03:24.228157 PROGRESS: ============================= Precursor FDR =============================
7:03:24.229485 PROGRESS: Total precursors accumulated: 23,402
7:03:24.229881 PROGRESS: Target precursors: 14,961 (63.93%)
7:03:24.230149 PROGRESS: Decoy precursors: 8,441 (36.07%)
7:03:24.230363 PROGRESS: 
7:03:24.230501 PROGRESS: Precursor Summary:
7:03:24.237007 PROGRESS: Channel   0:	 0.050 FDR:   326; 0.010 FDR:   248; 0.001 FDR:   197
7:03:24.238081 PROGRESS: 
7:03:24.238445 PROGRESS: Protein Summary:
7:03:24.245033 PROGRESS: Channel   0:	 0.050 FDR:   319; 0.010 FDR:   243; 0.001 FDR:   192
7:03:24.246197 PROGRESS: =========================================================================
7:03:24.252994 INFO: Target number of precursors reached.
7:03:24.374260 INFO: fragments_df: keeping 3342 of 1331961 [sum(precursor_idx_mask)=7777 sum(mass_error_mask)=1331961 stop_rank=3342
7:03:25.334780 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:03:25.569489 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:03:25.842705 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
7:03:26.100484 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:03:26.789082 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:03:26.791034 INFO: Using score_cutoff 40.81344503631592 (fac=0.99, q=1)
7:03:26.792756 INFO: Updating optimization_manager: fwhm_rt             : 2.6866464614868164 -> 2.889373302459717
7:03:26.793213 INFO: Updating optimization_manager: fwhm_mobility       : 0.0083256084471941 -> 0.008530602790415287
7:03:26.793406 INFO: Updating optimization_manager: score_cutoff        : 39.88516617965698 -> 40.81344503631592
7:03:26.793597 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:03:26.806638 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:03:26.844261 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
7:03:26.857927 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:03:26.946211 INFO: === checking if optimization conditions were reached ===
7:03:26.947644 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
7:03:26.955518 INFO: Updating optimization_manager: rt_error            : 740.7541736857925 -> 586.1357514569846
7:03:26.956655 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 586.1358.
7:03:26.957064 INFO: ==============================================
7:03:26.957464 INFO: Starting optimization step 3.
7:03:26.957757 PROGRESS: === Extracting elution groups 0 to 24000 ===
7:03:26.958025 INFO: Using python extraction backend
7:03:26.958472 PROGRESS: Extracting batch of 47289 precursors
7:03:26.958685 INFO: === Search parameters used ===
7:03:26.958842 INFO: rt_error       : 586.1357514569846
7:03:26.958947 INFO: mobility_error : 0.1
7:03:26.959050 INFO: num_candidates : 3
7:03:26.959137 INFO: ms1_error      : 15.0
7:03:26.959222 INFO: ms2_error      : 15.0
7:03:26.959323 INFO: fwhm_rt        : 2.889373302459717
7:03:26.959423 INFO: quant_window   : 3
7:03:26.959519 INFO: ==============================================
7:03:27.002176 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
7:03:27.002864 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
7:03:27.003067 INFO: FWHM in RT is 2.89 seconds, sigma is 0.64
7:03:27.003143 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.96
7:03:27.014508 INFO: Starting candidate selection
7:06:13.805265 INFO: Starting candidate scoring
7:06:23.786477 INFO: Finished candidate processing
7:06:23.786721 INFO: Collecting candidate features
7:06:24.240296 WARNING: intensity_correlation has 14 NaNs ( 0.01 % out of 129126)
7:06:24.241109 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 129126)
7:06:24.251720 INFO: Collecting fragment features
7:06:24.374871 INFO: Finished candidate scoring
7:06:24.656414 INFO: performing precursor FDR with 47 features
7:06:24.657127 INFO: Decoy channel: -1
7:06:24.657180 INFO: competitive: True
7:06:24.768775 INFO: Setting torch num_threads to 2 for FDR classification task
7:06:24.837024 WARNING: dropped 8 target PSMs due to missing features
7:06:24.837593 WARNING: dropped 7 decoy PSMs due to missing features
7:06:24.924511 INFO: Estimating optimal hyperparameters - samples: 103,288, batch_size: 423, learning_rate: 3.21e-04
7:06:24.925888 INFO: Using random state 656545 for train-test-split
7:06:30.983214 INFO: Test AUC: 0.556
7:06:30.983742 INFO: Train AUC: 0.608
7:06:30.983793 INFO: AUC difference: 8.43%
7:06:30.983824 WARNING: AUC difference > 5%. This may indicate overfitting.
7:06:31.417235 INFO: Resetting torch num_threads to 128
7:06:31.426315 PROGRESS: === Extracted 129126 precursors and 1320738 fragments ===
7:06:31.427703 INFO: === FDR correction performed with classifier version 5 ===
7:06:31.439908 PROGRESS: ============================= Precursor FDR =============================
7:06:31.440674 PROGRESS: Total precursors accumulated: 23,358
7:06:31.440837 PROGRESS: Target precursors: 14,873 (63.67%)
7:06:31.440958 PROGRESS: Decoy precursors: 8,485 (36.33%)
7:06:31.441043 PROGRESS: 
7:06:31.441116 PROGRESS: Precursor Summary:
7:06:31.443598 PROGRESS: Channel   0:	 0.050 FDR:   284; 0.010 FDR:   213; 0.001 FDR:   162
7:06:31.443842 PROGRESS: 
7:06:31.443932 PROGRESS: Protein Summary:
7:06:31.446047 PROGRESS: Channel   0:	 0.050 FDR:   276; 0.010 FDR:   208; 0.001 FDR:   159
7:06:31.446258 PROGRESS: =========================================================================
7:06:31.449353 INFO: Target number of precursors reached.
7:06:31.551923 INFO: fragments_df: keeping 2962 of 1320738 [sum(precursor_idx_mask)=6753 sum(mass_error_mask)=1320738 stop_rank=2962
7:06:31.776894 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:06:31.953412 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:06:32.259129 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
7:06:32.628201 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:06:33.436617 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:06:33.440235 INFO: Using score_cutoff 43.04147496185303 (fac=0.99, q=1)
7:06:33.442031 INFO: Updating optimization_manager: fwhm_rt             : 2.889373302459717 -> 2.849752187728882
7:06:33.443318 INFO: Updating optimization_manager: fwhm_mobility       : 0.008530602790415287 -> 0.008501575328409672
7:06:33.443860 INFO: Updating optimization_manager: score_cutoff        : 40.81344503631592 -> 43.04147496185303
7:06:33.444359 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:06:33.463630 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:06:33.507707 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
7:06:33.523582 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:06:33.613500 INFO: === checking if optimization conditions were reached ===
7:06:33.614882 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
7:06:33.628746 INFO: Updating optimization_manager: rt_error            : 586.1357514569846 -> 181.52751770405226
7:06:33.630693 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 181.5275.
7:06:33.631400 INFO: ==============================================
7:06:33.631828 INFO: Starting optimization step 4.
7:06:33.632083 PROGRESS: === Extracting elution groups 0 to 24000 ===
7:06:33.632283 INFO: Using python extraction backend
7:06:33.632582 PROGRESS: Extracting batch of 47289 precursors
7:06:33.632710 INFO: === Search parameters used ===
7:06:33.632790 INFO: rt_error       : 181.52751770405226
7:06:33.632926 INFO: mobility_error : 0.1
7:06:33.633005 INFO: num_candidates : 3
7:06:33.633110 INFO: ms1_error      : 15.0
7:06:33.633215 INFO: ms2_error      : 15.0
7:06:33.633312 INFO: fwhm_rt        : 2.849752187728882
7:06:33.633423 INFO: quant_window   : 3
7:06:33.633519 INFO: ==============================================
7:06:33.686130 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
7:06:33.686608 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
7:06:33.686702 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
7:06:33.686738 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.94
7:06:33.690499 INFO: Starting candidate selection
7:07:23.442677 INFO: Starting candidate scoring
7:07:32.610478 INFO: Finished candidate processing
7:07:32.610751 INFO: Collecting candidate features
7:07:32.964792 WARNING: intensity_correlation has 44 NaNs ( 0.03 % out of 126080)
7:07:32.965277 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 126080)
7:07:32.973609 INFO: Collecting fragment features
7:07:33.049062 INFO: Finished candidate scoring
7:07:33.118263 INFO: performing precursor FDR with 47 features
7:07:33.118536 INFO: Decoy channel: -1
7:07:33.118567 INFO: competitive: True
7:07:33.164272 INFO: Setting torch num_threads to 2 for FDR classification task
7:07:33.193231 WARNING: dropped 29 target PSMs due to missing features
7:07:33.193522 WARNING: dropped 20 decoy PSMs due to missing features
7:07:33.218633 INFO: Estimating optimal hyperparameters - samples: 100,824, batch_size: 412, learning_rate: 3.17e-04
7:07:33.219204 INFO: Using random state 656545 for train-test-split
7:07:38.663010 INFO: Test AUC: 0.548
7:07:38.663460 INFO: Train AUC: 0.599
7:07:38.663506 INFO: AUC difference: 8.43%
7:07:38.663544 WARNING: AUC difference > 5%. This may indicate overfitting.
7:07:39.079071 INFO: Resetting torch num_threads to 128
7:07:39.087203 PROGRESS: === Extracted 126080 precursors and 1250486 fragments ===
7:07:39.088554 INFO: === FDR correction performed with classifier version 5 ===
7:07:39.101586 PROGRESS: ============================= Precursor FDR =============================
7:07:39.102288 PROGRESS: Total precursors accumulated: 23,085
7:07:39.102446 PROGRESS: Target precursors: 14,442 (62.56%)
7:07:39.102555 PROGRESS: Decoy precursors: 8,643 (37.44%)
7:07:39.102632 PROGRESS: 
7:07:39.102698 PROGRESS: Precursor Summary:
7:07:39.105851 PROGRESS: Channel   0:	 0.050 FDR:   353; 0.010 FDR:   232; 0.001 FDR:   209
7:07:39.106207 PROGRESS: 
7:07:39.106313 PROGRESS: Protein Summary:
7:07:39.108818 PROGRESS: Channel   0:	 0.050 FDR:   342; 0.010 FDR:   225; 0.001 FDR:   204
7:07:39.109094 PROGRESS: =========================================================================
7:07:39.112054 INFO: Target number of precursors reached.
7:07:39.216158 INFO: fragments_df: keeping 3154 of 1250486 [sum(precursor_idx_mask)=7345 sum(mass_error_mask)=1250483 stop_rank=3154
7:07:39.462511 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:07:39.610068 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:07:39.778757 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
7:07:39.936094 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:07:40.459406 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:07:40.460834 INFO: Using score_cutoff 42.294805952453615 (fac=0.99, q=1)
7:07:40.461976 INFO: Updating optimization_manager: fwhm_rt             : 2.849752187728882 -> 2.8053765296936035
7:07:40.462295 INFO: Updating optimization_manager: fwhm_mobility       : 0.008501575328409672 -> 0.008453242480754852
7:07:40.462407 INFO: Updating optimization_manager: score_cutoff        : 43.04147496185303 -> 42.294805952453615
7:07:40.462544 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:07:40.473184 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:07:40.507025 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
7:07:40.517094 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:07:40.587411 INFO: === checking if optimization conditions were reached ===
7:07:40.588548 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
7:07:40.595433 INFO: Updating optimization_manager: rt_error            : 181.52751770405226 -> 141.32557385660576
7:07:40.596002 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 141.3256.
7:07:40.596196 INFO: ==============================================
7:07:40.596334 INFO: Starting optimization step 5.
7:07:40.596449 PROGRESS: === Extracting elution groups 0 to 24000 ===
7:07:40.596575 INFO: Using python extraction backend
7:07:40.596867 PROGRESS: Extracting batch of 47289 precursors
7:07:40.597078 INFO: === Search parameters used ===
7:07:40.597164 INFO: rt_error       : 141.32557385660576
7:07:40.597244 INFO: mobility_error : 0.1
7:07:40.597313 INFO: num_candidates : 3
7:07:40.597376 INFO: ms1_error      : 15.0
7:07:40.597442 INFO: ms2_error      : 15.0
7:07:40.597500 INFO: fwhm_rt        : 2.8053765296936035
7:07:40.597566 INFO: quant_window   : 3
7:07:40.597624 INFO: ==============================================
7:07:40.641151 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
7:07:40.641905 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
7:07:40.642060 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
7:07:40.642096 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.92
7:07:40.654065 INFO: Starting candidate selection
7:08:23.294351 INFO: Starting candidate scoring
7:08:32.967081 INFO: Finished candidate processing
7:08:32.967409 INFO: Collecting candidate features
7:08:33.339661 WARNING: intensity_correlation has 53 NaNs ( 0.04 % out of 125497)
7:08:33.340305 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 125497)
7:08:33.352369 INFO: Collecting fragment features
7:08:33.464188 INFO: Finished candidate scoring
7:08:33.685655 INFO: performing precursor FDR with 47 features
7:08:33.686024 INFO: Decoy channel: -1
7:08:33.686068 INFO: competitive: True
7:08:33.769283 INFO: Setting torch num_threads to 2 for FDR classification task
7:08:33.822741 WARNING: dropped 27 target PSMs due to missing features
7:08:33.823200 WARNING: dropped 26 decoy PSMs due to missing features
7:08:33.956743 INFO: Estimating optimal hyperparameters - samples: 100,355, batch_size: 411, learning_rate: 3.17e-04
7:08:33.957594 INFO: Using random state 656545 for train-test-split
7:08:39.917066 INFO: Test AUC: 0.549
7:08:39.917522 INFO: Train AUC: 0.590
7:08:39.917575 INFO: AUC difference: 6.95%
7:08:39.917609 WARNING: AUC difference > 5%. This may indicate overfitting.
7:08:40.328711 INFO: Resetting torch num_threads to 128
7:08:40.337861 PROGRESS: === Extracted 125497 precursors and 1236400 fragments ===
7:08:40.339296 INFO: === FDR correction performed with classifier version 5 ===
7:08:40.350177 PROGRESS: ============================= Precursor FDR =============================
7:08:40.350776 PROGRESS: Total precursors accumulated: 23,002
7:08:40.350954 PROGRESS: Target precursors: 14,023 (60.96%)
7:08:40.351069 PROGRESS: Decoy precursors: 8,979 (39.04%)
7:08:40.351160 PROGRESS: 
7:08:40.351244 PROGRESS: Precursor Summary:
7:08:40.353530 PROGRESS: Channel   0:	 0.050 FDR:   314; 0.010 FDR:   211; 0.001 FDR:     1
7:08:40.353765 PROGRESS: 
7:08:40.353871 PROGRESS: Protein Summary:
7:08:40.356061 PROGRESS: Channel   0:	 0.050 FDR:   305; 0.010 FDR:   203; 0.001 FDR:     1
7:08:40.356256 PROGRESS: =========================================================================
7:08:40.359141 INFO: Target number of precursors reached.
7:08:40.458367 INFO: fragments_df: keeping 2872 of 1236400 [sum(precursor_idx_mask)=6667 sum(mass_error_mask)=1236395 stop_rank=2872
7:08:40.679581 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:08:40.819078 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:08:41.024211 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
7:08:41.224667 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:08:41.706815 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:08:41.708486 INFO: Using score_cutoff 42.390127819061284 (fac=0.99, q=1)
7:08:41.709620 INFO: Updating optimization_manager: fwhm_rt             : 2.8053765296936035 -> 2.881129741668701
7:08:41.709939 INFO: Updating optimization_manager: fwhm_mobility       : 0.008453242480754852 -> 0.0086009306833148
7:08:41.710085 INFO: Updating optimization_manager: score_cutoff        : 42.294805952453615 -> 42.390127819061284
7:08:41.710259 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:08:41.721915 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:08:41.757527 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
7:08:41.767808 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:08:41.853487 INFO: === checking if optimization conditions were reached ===
7:08:41.855113 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
7:08:41.863467 INFO: Updating optimization_manager: rt_error            : 141.32557385660576 -> 117.66558700595121
7:08:41.864273 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 117.6656.
7:08:41.864518 INFO: ==============================================
7:08:41.864698 INFO: Starting optimization step 6.
7:08:41.864848 PROGRESS: === Extracting elution groups 0 to 24000 ===
7:08:41.865012 INFO: Using python extraction backend
7:08:41.865414 PROGRESS: Extracting batch of 47289 precursors
7:08:41.865599 INFO: === Search parameters used ===
7:08:41.865715 INFO: rt_error       : 117.66558700595121
7:08:41.865844 INFO: mobility_error : 0.1
7:08:41.865935 INFO: num_candidates : 3
7:08:41.866021 INFO: ms1_error      : 15.0
7:08:41.866276 INFO: ms2_error      : 15.0
7:08:41.866415 INFO: fwhm_rt        : 2.881129741668701
7:08:41.866548 INFO: quant_window   : 3
7:08:41.866660 INFO: ==============================================
7:08:41.916064 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
7:08:41.916662 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
7:08:41.916761 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
7:08:41.916796 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
7:08:41.926290 INFO: Starting candidate selection
7:09:14.318282 INFO: Starting candidate scoring
7:09:22.876151 INFO: Finished candidate processing
7:09:22.876397 INFO: Collecting candidate features
7:09:23.159943 WARNING: intensity_correlation has 54 NaNs ( 0.04 % out of 125299)
7:09:23.160386 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 125299)
7:09:23.168549 INFO: Collecting fragment features
7:09:23.239919 INFO: Finished candidate scoring
7:09:23.308767 INFO: performing precursor FDR with 47 features
7:09:23.308966 INFO: Decoy channel: -1
7:09:23.308996 INFO: competitive: True
7:09:23.348241 INFO: Setting torch num_threads to 2 for FDR classification task
7:09:23.375915 WARNING: dropped 35 target PSMs due to missing features
7:09:23.376143 WARNING: dropped 21 decoy PSMs due to missing features
7:09:23.398269 INFO: Estimating optimal hyperparameters - samples: 100,194, batch_size: 410, learning_rate: 3.16e-04
7:09:23.398782 INFO: Using random state 656545 for train-test-split
7:09:28.875348 INFO: Test AUC: 0.545
7:09:28.875772 INFO: Train AUC: 0.586
7:09:28.875817 INFO: AUC difference: 6.99%
7:09:28.875853 WARNING: AUC difference > 5%. This may indicate overfitting.
7:09:29.304258 INFO: Resetting torch num_threads to 128
7:09:29.319107 PROGRESS: === Extracted 125299 precursors and 1233471 fragments ===
7:09:29.321904 INFO: === FDR correction performed with classifier version 5 ===
7:09:29.343490 PROGRESS: ============================= Precursor FDR =============================
7:09:29.344706 PROGRESS: Total precursors accumulated: 22,957
7:09:29.344859 PROGRESS: Target precursors: 14,007 (61.01%)
7:09:29.344975 PROGRESS: Decoy precursors: 8,950 (38.99%)
7:09:29.345115 PROGRESS: 
7:09:29.345219 PROGRESS: Precursor Summary:
7:09:29.349544 PROGRESS: Channel   0:	 0.050 FDR:   328; 0.010 FDR:   248; 0.001 FDR:   158
7:09:29.349892 PROGRESS: 
7:09:29.350039 PROGRESS: Protein Summary:
7:09:29.352473 PROGRESS: Channel   0:	 0.050 FDR:   316; 0.010 FDR:   239; 0.001 FDR:   153
7:09:29.352699 PROGRESS: =========================================================================
7:09:29.357947 INFO: Target number of precursors reached.
7:09:29.458808 INFO: fragments_df: keeping 3270 of 1233471 [sum(precursor_idx_mask)=7780 sum(mass_error_mask)=1233467 stop_rank=3270
7:09:29.779792 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:09:29.940295 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:09:30.139572 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
7:09:30.327463 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:09:30.876581 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:09:30.878430 INFO: Using score_cutoff 43.548162365341184 (fac=0.99, q=1)
7:09:30.879999 INFO: Updating optimization_manager: fwhm_rt             : 2.881129741668701 -> 2.9178977012634277
7:09:30.880396 INFO: Updating optimization_manager: fwhm_mobility       : 0.0086009306833148 -> 0.008588827215135098
7:09:30.880558 INFO: Updating optimization_manager: score_cutoff        : 42.390127819061284 -> 43.548162365341184
7:09:30.880717 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:09:30.891863 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:09:30.925380 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
7:09:30.934679 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:09:31.012011 INFO: === checking if optimization conditions were reached ===
7:09:31.013159 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
7:09:31.020823 INFO: Updating optimization_manager: rt_error            : 117.66558700595121 -> 114.95886318301656
7:09:31.021508 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 114.9589.
7:09:31.021713 INFO: ==============================================
7:09:31.021878 INFO: Starting optimization step 7.
7:09:31.022024 PROGRESS: === Extracting elution groups 0 to 24000 ===
7:09:31.022156 INFO: Using python extraction backend
7:09:31.022475 PROGRESS: Extracting batch of 47289 precursors
7:09:31.022610 INFO: === Search parameters used ===
7:09:31.022697 INFO: rt_error       : 114.95886318301656
7:09:31.022766 INFO: mobility_error : 0.1
7:09:31.022831 INFO: num_candidates : 3
7:09:31.022897 INFO: ms1_error      : 15.0
7:09:31.023131 INFO: ms2_error      : 15.0
7:09:31.023241 INFO: fwhm_rt        : 2.9178977012634277
7:09:31.023304 INFO: quant_window   : 3
7:09:31.023366 INFO: ==============================================
7:09:31.058337 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
7:09:31.059010 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
7:09:31.059258 INFO: FWHM in RT is 2.92 seconds, sigma is 0.64
7:09:31.059303 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.98
7:09:31.062627 INFO: Starting candidate selection
7:10:02.205422 INFO: Starting candidate scoring
7:10:12.019762 INFO: Finished candidate processing
7:10:12.020080 INFO: Collecting candidate features
7:10:12.453308 WARNING: intensity_correlation has 52 NaNs ( 0.04 % out of 125077)
7:10:12.454287 WARNING: height_correlation has 5 NaNs ( 0.00 % out of 125077)
7:10:12.466904 INFO: Collecting fragment features
7:10:12.576110 INFO: Finished candidate scoring
7:10:12.857609 INFO: performing precursor FDR with 47 features
7:10:12.858054 INFO: Decoy channel: -1
7:10:12.858112 INFO: competitive: True
7:10:12.946730 INFO: Setting torch num_threads to 2 for FDR classification task
7:10:13.001045 WARNING: dropped 30 target PSMs due to missing features
7:10:13.001551 WARNING: dropped 25 decoy PSMs due to missing features
7:10:13.063993 INFO: Estimating optimal hyperparameters - samples: 100,017, batch_size: 409, learning_rate: 3.16e-04
7:10:13.064899 INFO: Using random state 656545 for train-test-split
7:10:18.912047 INFO: Test AUC: 0.547
7:10:18.912655 INFO: Train AUC: 0.596
7:10:18.912736 INFO: AUC difference: 8.20%
7:10:18.912777 WARNING: AUC difference > 5%. This may indicate overfitting.
7:10:19.330965 INFO: Resetting torch num_threads to 128
7:10:19.371789 PROGRESS: === Extracted 125077 precursors and 1229883 fragments ===
7:10:19.373854 INFO: === FDR correction performed with classifier version 5 ===
7:10:19.391189 PROGRESS: ============================= Precursor FDR =============================
7:10:19.392120 PROGRESS: Total precursors accumulated: 22,924
7:10:19.392326 PROGRESS: Target precursors: 14,209 (61.98%)
7:10:19.392441 PROGRESS: Decoy precursors: 8,715 (38.02%)
7:10:19.392523 PROGRESS: 
7:10:19.392604 PROGRESS: Precursor Summary:
7:10:19.395827 PROGRESS: Channel   0:	 0.050 FDR:   341; 0.010 FDR:   277; 0.001 FDR:   237
7:10:19.396163 PROGRESS: 
7:10:19.396257 PROGRESS: Protein Summary:
7:10:19.398157 PROGRESS: Channel   0:	 0.050 FDR:   331; 0.010 FDR:   268; 0.001 FDR:   228
7:10:19.398351 PROGRESS: =========================================================================
7:10:19.402924 INFO: Target number of precursors reached.
7:10:19.504898 INFO: fragments_df: keeping 3531 of 1229883 [sum(precursor_idx_mask)=8628 sum(mass_error_mask)=1229879 stop_rank=3531
7:10:19.809362 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:10:19.975585 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:10:20.154963 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
7:10:20.424959 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:10:21.230997 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:10:21.235182 INFO: Using score_cutoff 39.315083903503414 (fac=0.99, q=1)
7:10:21.237723 INFO: Updating optimization_manager: fwhm_rt             : 2.9178977012634277 -> 2.881129741668701
7:10:21.238364 INFO: Updating optimization_manager: fwhm_mobility       : 0.008588827215135098 -> 0.008440856821835041
7:10:21.238553 INFO: Updating optimization_manager: score_cutoff        : 43.548162365341184 -> 39.315083903503414
7:10:21.238808 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:10:21.258379 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:10:21.302230 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
7:10:21.330061 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:10:21.436489 INFO: === checking if optimization conditions were reached ===
7:10:21.438838 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
7:10:21.448701 INFO: Updating optimization_manager: rt_error            : 114.95886318301656 -> 114.95886318301656
7:10:21.450938 INFO: Updating optimization_manager: classifier_version  : 5 -> 13
7:10:21.451475 INFO: Updating optimization_manager: score_cutoff        : 39.315083903503414 -> 39.315083903503414
7:10:21.451766 INFO: Updating optimization_manager: fwhm_rt             : 2.881129741668701 -> 2.881129741668701
7:10:21.451933 INFO: Updating optimization_manager: fwhm_mobility       : 0.008440856821835041 -> 0.008440856821835041
7:10:21.452156 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 114.9589 found after 8 searches.
7:10:21.452311 INFO: ==============================================
7:10:21.452512 PROGRESS: Optimization finished for rt_error.
7:10:22.042927 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:10:22.063176 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:10:22.105569 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
7:10:22.118842 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:10:22.228151 INFO: Starting optimization step 0.
7:10:22.229481 PROGRESS: === Extracting elution groups 0 to 24000 ===
7:10:22.229735 INFO: Using python extraction backend
7:10:22.230209 PROGRESS: Extracting batch of 47289 precursors
7:10:22.230405 INFO: === Search parameters used ===
7:10:22.230483 INFO: rt_error       : 114.95886318301656
7:10:22.230549 INFO: mobility_error : 0.1
7:10:22.230619 INFO: num_candidates : 3
7:10:22.230701 INFO: ms1_error      : 15.0
7:10:22.230859 INFO: ms2_error      : 15.0
7:10:22.230962 INFO: fwhm_rt        : 2.881129741668701
7:10:22.231040 INFO: quant_window   : 3
7:10:22.231129 INFO: ==============================================
7:10:22.319907 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
7:10:22.320895 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
7:10:22.321021 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
7:10:22.321046 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.92
7:10:22.326262 INFO: Starting candidate selection
7:10:54.409500 INFO: Starting candidate scoring
7:11:04.506725 INFO: Finished candidate processing
7:11:04.506985 INFO: Collecting candidate features
7:11:04.747550 WARNING: intensity_correlation has 56 NaNs ( 0.04 % out of 124918)
7:11:04.748223 WARNING: height_correlation has 5 NaNs ( 0.00 % out of 124918)
7:11:04.757645 INFO: Collecting fragment features
7:11:04.860262 INFO: Finished candidate scoring
7:11:05.073590 INFO: performing precursor FDR with 47 features
7:11:05.074360 INFO: Decoy channel: -1
7:11:05.074419 INFO: competitive: True
7:11:05.157924 INFO: Setting torch num_threads to 2 for FDR classification task
7:11:05.208263 WARNING: dropped 34 target PSMs due to missing features
7:11:05.208591 WARNING: dropped 25 decoy PSMs due to missing features
7:11:05.261245 INFO: Estimating optimal hyperparameters - samples: 99,887, batch_size: 409, learning_rate: 3.16e-04
7:11:05.262011 INFO: Using random state 428026 for train-test-split
7:11:10.643256 INFO: Test AUC: 0.557
7:11:10.643631 INFO: Train AUC: 0.595
7:11:10.643685 INFO: AUC difference: 6.48%
7:11:10.643725 WARNING: AUC difference > 5%. This may indicate overfitting.
7:11:11.056673 INFO: Resetting torch num_threads to 128
7:11:11.071828 PROGRESS: === Extracted 124918 precursors and 1228163 fragments ===
7:11:11.074325 INFO: === FDR correction performed with classifier version 13 ===
7:11:11.092873 PROGRESS: ============================= Precursor FDR =============================
7:11:11.094096 PROGRESS: Total precursors accumulated: 22,901
7:11:11.094321 PROGRESS: Target precursors: 14,200 (62.01%)
7:11:11.094427 PROGRESS: Decoy precursors: 8,701 (37.99%)
7:11:11.094537 PROGRESS: 
7:11:11.094630 PROGRESS: Precursor Summary:
7:11:11.098452 PROGRESS: Channel   0:	 0.050 FDR:   395; 0.010 FDR:   304; 0.001 FDR:   219
7:11:11.098807 PROGRESS: 
7:11:11.098935 PROGRESS: Protein Summary:
7:11:11.101459 PROGRESS: Channel   0:	 0.050 FDR:   383; 0.010 FDR:   294; 0.001 FDR:   211
7:11:11.101703 PROGRESS: =========================================================================
7:11:11.106550 INFO: Target number of precursors reached.
7:11:11.209443 INFO: fragments_df: keeping 3833 of 1228163 [sum(precursor_idx_mask)=9513 sum(mass_error_mask)=1228159 stop_rank=3833
7:11:11.989080 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:11:12.149663 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:11:12.309970 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
7:11:12.472596 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:11:13.052171 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:11:13.053723 INFO: Using score_cutoff 36.06045463600159 (fac=0.99, q=1)
7:11:13.054744 INFO: Updating optimization_manager: fwhm_rt             : 2.881129741668701 -> 2.8172197341918945
7:11:13.054893 INFO: Updating optimization_manager: fwhm_mobility       : 0.008440856821835041 -> 0.00825563259422779
7:11:13.055006 INFO: Updating optimization_manager: score_cutoff        : 39.315083903503414 -> 36.06045463600159
7:11:13.055153 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:11:13.065299 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:11:13.098921 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
7:11:13.108312 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:11:13.188336 INFO: === checking if optimization conditions were reached ===
7:11:13.189488 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
7:11:13.194169 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07922692303938611
7:11:13.194804 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0792.
7:11:13.195066 INFO: ==============================================
7:11:13.195360 INFO: Starting optimization step 1.
7:11:13.195723 PROGRESS: === Extracting elution groups 0 to 24000 ===
7:11:13.195958 INFO: Using python extraction backend
7:11:13.196605 PROGRESS: Extracting batch of 47289 precursors
7:11:13.196842 INFO: === Search parameters used ===
7:11:13.197087 INFO: rt_error       : 114.95886318301656
7:11:13.197214 INFO: mobility_error : 0.07922692303938611
7:11:13.197362 INFO: num_candidates : 3
7:11:13.197499 INFO: ms1_error      : 15.0
7:11:13.197675 INFO: ms2_error      : 15.0
7:11:13.197951 INFO: fwhm_rt        : 2.8172197341918945
7:11:13.198158 INFO: quant_window   : 3
7:11:13.198309 INFO: ==============================================
7:11:13.328003 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
7:11:13.328998 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
7:11:13.329173 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
7:11:13.329243 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.83
7:11:13.334460 INFO: Starting candidate selection
7:11:39.341096 INFO: Starting candidate scoring
7:11:49.136845 INFO: Finished candidate processing
7:11:49.137279 INFO: Collecting candidate features
7:11:49.413513 WARNING: intensity_correlation has 68 NaNs ( 0.06 % out of 122970)
7:11:49.414037 WARNING: height_correlation has 11 NaNs ( 0.01 % out of 122970)
7:11:49.422763 INFO: Collecting fragment features
7:11:49.503017 INFO: Finished candidate scoring
7:11:49.604496 INFO: performing precursor FDR with 47 features
7:11:49.604714 INFO: Decoy channel: -1
7:11:49.604759 INFO: competitive: True
7:11:49.667101 INFO: Setting torch num_threads to 2 for FDR classification task
7:11:49.701813 WARNING: dropped 38 target PSMs due to missing features
7:11:49.702105 WARNING: dropped 37 decoy PSMs due to missing features
7:11:49.778172 INFO: Estimating optimal hyperparameters - samples: 98,316, batch_size: 402, learning_rate: 3.13e-04
7:11:49.778757 INFO: Using random state 428026 for train-test-split
7:11:55.308078 INFO: Test AUC: 0.556
7:11:55.308651 INFO: Train AUC: 0.595
7:11:55.308702 INFO: AUC difference: 6.62%
7:11:55.308736 WARNING: AUC difference > 5%. This may indicate overfitting.
7:11:55.725535 INFO: Resetting torch num_threads to 128
7:11:55.738210 PROGRESS: === Extracted 122970 precursors and 1200371 fragments ===
7:11:55.740350 INFO: === FDR correction performed with classifier version 13 ===
7:11:55.756377 PROGRESS: ============================= Precursor FDR =============================
7:11:55.757334 PROGRESS: Total precursors accumulated: 22,623
7:11:55.757495 PROGRESS: Target precursors: 14,010 (61.93%)
7:11:55.757581 PROGRESS: Decoy precursors: 8,613 (38.07%)
7:11:55.757648 PROGRESS: 
7:11:55.757715 PROGRESS: Precursor Summary:
7:11:55.760874 PROGRESS: Channel   0:	 0.050 FDR:   355; 0.010 FDR:   264; 0.001 FDR:   224
7:11:55.761217 PROGRESS: 
7:11:55.761319 PROGRESS: Protein Summary:
7:11:55.763277 PROGRESS: Channel   0:	 0.050 FDR:   343; 0.010 FDR:   256; 0.001 FDR:   217
7:11:55.763435 PROGRESS: =========================================================================
7:11:55.768358 INFO: Target number of precursors reached.
7:11:55.870092 INFO: fragments_df: keeping 3387 of 1200371 [sum(precursor_idx_mask)=8391 sum(mass_error_mask)=1200359 stop_rank=3387
7:11:56.696326 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:11:56.883698 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:11:57.078942 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
7:11:59.077406 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:11:59.699032 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:11:59.700950 INFO: Using score_cutoff 40.80172534332275 (fac=0.99, q=1)
7:11:59.702465 INFO: Updating optimization_manager: fwhm_rt             : 2.8172197341918945 -> 2.8188114166259766
7:11:59.702916 INFO: Updating optimization_manager: fwhm_mobility       : 0.00825563259422779 -> 0.008251914754509926
7:11:59.703128 INFO: Updating optimization_manager: score_cutoff        : 36.06045463600159 -> 40.80172534332275
7:11:59.703340 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:11:59.718304 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:11:59.756141 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
7:11:59.768576 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:11:59.860109 INFO: === checking if optimization conditions were reached ===
7:11:59.861240 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
7:11:59.867286 INFO: Updating optimization_manager: mobility_error      : 0.07922692303938611 -> 0.06701878226679502
7:11:59.868196 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0670.
7:11:59.868515 INFO: ==============================================
7:11:59.868773 INFO: Starting optimization step 2.
7:11:59.869025 PROGRESS: === Extracting elution groups 0 to 24000 ===
7:11:59.869215 INFO: Using python extraction backend
7:11:59.869701 PROGRESS: Extracting batch of 47289 precursors
7:11:59.869894 INFO: === Search parameters used ===
7:11:59.870004 INFO: rt_error       : 114.95886318301656
7:11:59.870084 INFO: mobility_error : 0.06701878226679502
7:11:59.870169 INFO: num_candidates : 3
7:11:59.870248 INFO: ms1_error      : 15.0
7:11:59.870347 INFO: ms2_error      : 15.0
7:11:59.870431 INFO: fwhm_rt        : 2.8188114166259766
7:11:59.870506 INFO: quant_window   : 3
7:11:59.870580 INFO: ==============================================
7:11:59.926184 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
7:11:59.926699 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
7:11:59.926822 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
7:11:59.926857 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.83
7:11:59.929371 INFO: Starting candidate selection
7:12:23.764258 INFO: Starting candidate scoring
7:12:32.746010 INFO: Finished candidate processing
7:12:32.746315 INFO: Collecting candidate features
7:12:32.993591 WARNING: intensity_correlation has 75 NaNs ( 0.06 % out of 121725)
7:12:32.994092 WARNING: height_correlation has 10 NaNs ( 0.01 % out of 121725)
7:12:33.002055 INFO: Collecting fragment features
7:12:33.079828 INFO: Finished candidate scoring
7:12:33.166077 INFO: performing precursor FDR with 47 features
7:12:33.166308 INFO: Decoy channel: -1
7:12:33.166346 INFO: competitive: True
7:12:33.207236 INFO: Setting torch num_threads to 2 for FDR classification task
7:12:33.236936 WARNING: dropped 45 target PSMs due to missing features
7:12:33.237214 WARNING: dropped 35 decoy PSMs due to missing features
7:12:33.260035 INFO: Estimating optimal hyperparameters - samples: 97,316, batch_size: 398, learning_rate: 3.12e-04
7:12:33.260824 INFO: Using random state 428026 for train-test-split
7:12:38.971164 INFO: Test AUC: 0.554
7:12:38.971785 INFO: Train AUC: 0.592
7:12:38.971830 INFO: AUC difference: 6.45%
7:12:38.971859 WARNING: AUC difference > 5%. This may indicate overfitting.
7:12:39.419739 INFO: Resetting torch num_threads to 128
7:12:39.433321 PROGRESS: === Extracted 121725 precursors and 1182622 fragments ===
7:12:39.435528 INFO: === FDR correction performed with classifier version 13 ===
7:12:39.453760 PROGRESS: ============================= Precursor FDR =============================
7:12:39.454651 PROGRESS: Total precursors accumulated: 22,406
7:12:39.454754 PROGRESS: Target precursors: 13,733 (61.29%)
7:12:39.454841 PROGRESS: Decoy precursors: 8,673 (38.71%)
7:12:39.454920 PROGRESS: 
7:12:39.455011 PROGRESS: Precursor Summary:
7:12:39.458081 PROGRESS: Channel   0:	 0.050 FDR:   370; 0.010 FDR:   206; 0.001 FDR:   172
7:12:39.458294 PROGRESS: 
7:12:39.458381 PROGRESS: Protein Summary:
7:12:39.460224 PROGRESS: Channel   0:	 0.050 FDR:   361; 0.010 FDR:   200; 0.001 FDR:   167
7:12:39.460398 PROGRESS: =========================================================================
7:12:39.465314 INFO: Target number of precursors reached.
7:12:39.567310 INFO: fragments_df: keeping 2778 of 1182622 [sum(precursor_idx_mask)=6512 sum(mass_error_mask)=1182617 stop_rank=2778
7:12:40.399764 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
7:12:40.580843 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
7:12:40.759309 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
7:12:40.917788 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
7:12:41.396897 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
7:12:41.398976 INFO: Using score_cutoff 46.68074534797668 (fac=0.99, q=1)
7:12:41.400662 INFO: Updating optimization_manager: fwhm_rt             : 2.8188114166259766 -> 2.900386333465576
7:12:41.401243 INFO: Updating optimization_manager: fwhm_mobility       : 0.008251914754509926 -> 0.008815065957605839
7:12:41.401445 INFO: Updating optimization_manager: score_cutoff        : 40.80172534332275 -> 46.68074534797668
7:12:41.401632 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:12:41.416541 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:12:41.454244 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
7:12:41.467096 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:12:41.560164 INFO: === checking if optimization conditions were reached ===
7:12:41.561260 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
7:12:41.564648 INFO: Updating optimization_manager: mobility_error      : 0.06701878226679502 -> 0.1
7:12:41.565387 INFO: Updating optimization_manager: classifier_version  : 13 -> 14
7:12:41.565810 INFO: Updating optimization_manager: score_cutoff        : 46.68074534797668 -> 36.06045463600159
7:12:41.566238 INFO: Updating optimization_manager: fwhm_rt             : 2.900386333465576 -> 2.8172197341918945
7:12:41.566605 INFO: Updating optimization_manager: fwhm_mobility       : 0.008815065957605839 -> 0.00825563259422779
7:12:41.566920 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
7:12:41.567098 INFO: ==============================================
7:12:41.567301 PROGRESS: Optimization finished for mobility_error.
7:12:42.013577 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:12:42.035280 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:12:42.078154 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
7:12:42.093903 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:12:42.191657 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
7:12:42.193184 PROGRESS: ==============================================
7:12:42.193453 PROGRESS: ms2_error      : 15.0000
7:12:42.193615 PROGRESS: ms1_error      : 15.0000
7:12:42.193801 PROGRESS: rt_error       : 114.9589
7:12:42.193954 PROGRESS: mobility_error : 0.1000
7:12:42.194073 PROGRESS: ==============================================
7:12:42.209794 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
7:12:45.187285 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
7:12:56.654305 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
7:12:59.404669 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
7:13:33.136933 INFO: Using python extraction backend
7:13:33.139297 PROGRESS: Extracting batch of 11524154 precursors
7:13:33.139900 INFO: === Search parameters used ===
7:13:33.140104 INFO: rt_error       : 114.95886318301656
7:13:33.140213 INFO: mobility_error : 0.1
7:13:33.140304 INFO: num_candidates : 3
7:13:33.140390 INFO: ms1_error      : 15.0
7:13:33.140458 INFO: ms2_error      : 15.0
7:13:33.140543 INFO: fwhm_rt        : 2.8172197341918945
7:13:33.140641 INFO: quant_window   : 3
7:13:33.140760 INFO: ==============================================
7:13:41.179440 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
7:13:41.179996 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
7:13:41.180127 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
7:13:41.180158 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.83
7:13:41.187128 INFO: Starting candidate selection
8:28:31.084430 INFO: Removed 12310346 precursors with score below cutoff 36.06045463600159
8:28:34.785158 INFO: Starting candidate scoring
8:48:54.408391 INFO: Finished candidate processing
8:48:54.410153 INFO: Collecting candidate features
8:50:18.578212 WARNING: intensity_correlation has 10 NaNs ( 0.00 % out of 19746970)
8:50:20.539984 INFO: Collecting fragment features
8:51:03.911747 INFO: Finished candidate scoring
8:52:27.910277 INFO: === Performing FDR correction with classifier version 14 ===
8:52:27.914400 INFO: performing precursor FDR with 47 features
8:52:27.914577 INFO: Decoy channel: -1
8:52:27.914630 INFO: competitive: True
8:52:48.351408 INFO: Setting torch num_threads to 2 for FDR classification task
8:53:02.204896 WARNING: dropped 5 target PSMs due to missing features
8:53:02.206037 WARNING: dropped 5 decoy PSMs due to missing features
8:53:56.920779 INFO: Estimating optimal hyperparameters - samples: 15,797,568, batch_size: 4,096, learning_rate: 1.00e-03
8:53:57.162119 INFO: Using random state 281594 for train-test-split
9:06:56.558235 INFO: Test AUC: 0.556
9:06:56.558649 INFO: Train AUC: 0.557
9:06:56.558695 INFO: AUC difference: 0.27%
9:07:00.408851 INFO: Resetting torch num_threads to 128
9:07:00.939354 INFO: Removing fragments below FDR threshold
9:07:03.355012 PROGRESS: ============================= Precursor FDR =============================
9:07:03.355668 PROGRESS: Total precursors accumulated: 69,362
9:07:03.355766 PROGRESS: Target precursors: 68,676 (99.01%)
9:07:03.355850 PROGRESS: Decoy precursors: 686 (0.99%)
9:07:03.355913 PROGRESS: 
9:07:03.355972 PROGRESS: Precursor Summary:
9:07:03.382770 PROGRESS: Channel   0:	 0.050 FDR: 68,676; 0.010 FDR: 68,676; 0.001 FDR: 46,652
9:07:03.383104 PROGRESS: 
9:07:03.383216 PROGRESS: Protein Summary:
9:07:03.415807 PROGRESS: Channel   0:	 0.050 FDR: 11,266; 0.010 FDR: 11,266; 0.001 FDR: 8,850
9:07:03.416120 PROGRESS: =========================================================================
9:07:03.436269 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/psm.parquet
9:07:03.742472 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/frag.parquet
9:07:03.985661 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
9:07:04.904032 PROGRESS: Loading raw file 3/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506 
9:07:04.904238 INFO: Quantification results path: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant
9:07:04.904350 INFO: Creating folder /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/figures
9:07:04.904580 INFO: Initializing TimingManager
9:07:04.905150 INFO: Initializing RawFileManager
9:07:04.905316 INFO: Importing data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
9:07:04.905371 INFO: Using .d import for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
9:07:04.905414 INFO: Reading frame metadata for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
9:07:12.590219 INFO: Reading 39,128 frames with 2,897,842,446 detector events for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
9:08:39.179109 INFO: Indexing /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d...
9:08:39.181334 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
9:08:39.186439 INFO: Fetching mobility values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
9:08:39.186730 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
9:08:39.187150 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
9:08:39.188565 INFO: Fetching mz values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
9:08:39.230851 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
9:08:39.231334 INFO: Indexing quadrupole dimension
9:08:39.687417 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
9:08:39.687618 INFO: Transposing detector events
9:08:50.905645 INFO: Finished transposing data
9:08:50.971339 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
9:08:50.971975 INFO: RT (min)            : 0.0 - 70.0
9:08:50.972020 INFO: RT duration (sec)   : 4199.8
9:08:50.972044 INFO: RT duration (min)   : 70.0
9:08:50.972068 INFO: Cycle len (scans)   : 9
9:08:50.972088 INFO: Cycle len (sec)     : 0.97
9:08:50.972111 INFO: Number of cycles    : 4347
9:08:50.972131 INFO: MS2 range (m/z)     : 400.0 - 1000.0
9:08:50.972158 INFO: Creating DIA data object took: 106.06689262390137
9:08:53.229810 INFO: Initializing CalibrationManager
9:08:53.230189 INFO: Setting up calibration estimators ..
9:08:53.230263 INFO: Found 1 estimator(s) in calibration group 'fragment'
9:08:53.230360 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'}' ..
9:08:53.230477 INFO: Found 3 estimator(s) in calibration group 'precursor'
9:08:53.230549 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'}' ..
9:08:53.230617 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}}' ..
9:08:53.230687 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}}' ..
9:08:53.230753 INFO: Done setting up calibration estimators.
9:08:53.230910 INFO: Initializing OptimizationManager
9:08:53.231042 INFO: initial parameter: ms1_error = 30
9:08:53.231111 INFO: initial parameter: ms2_error = 30
9:08:53.231185 INFO: initial parameter: rt_error = 2099.8992935
9:08:53.231265 INFO: initial parameter: mobility_error = 0.1
9:08:53.231344 INFO: initial parameter: num_candidates = 1
9:08:53.231418 INFO: initial parameter: fwhm_rt = 5
9:08:53.231493 INFO: initial parameter: fwhm_mobility = 0.01
9:08:53.231568 INFO: initial parameter: score_cutoff = 0
9:08:53.231634 INFO: initial parameter: classifier_version = -1
9:08:53.231747 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
9:08:53.232034 INFO: FDRManager: loading saved state not requested, will be initialized.
9:08:53.232077 INFO: Initializing FDRManager
9:08:53.232140 INFO: Loading classifier store from /usr/local/lib/python3.10/site-packages/alphadia/constants/classifier
9:08:54.625375 PROGRESS: Initializing spectral library: 5,845,771 target precursors potentially observable (0 removed)
9:08:55.396481 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
9:08:55.397103 INFO: Updating optimization_manager: rt_error            : 2099.8992935 -> 2099.8992935
9:08:55.397226 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
9:08:55.397429 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
9:08:55.397538 PROGRESS: Starting initial search for precursors.
9:08:55.397636 INFO: Starting optimization step 0.
9:08:55.397716 PROGRESS: === Extracting elution groups 0 to 8000 ===
9:08:55.402926 INFO: Using python extraction backend
9:08:55.403151 PROGRESS: Extracting batch of 15766 precursors
9:08:55.403236 INFO: === Search parameters used ===
9:08:55.403295 INFO: rt_error       : 2099.8992935
9:08:55.403346 INFO: mobility_error : 0.1
9:08:55.403402 INFO: num_candidates : 1
9:08:55.403459 INFO: ms1_error      : 30
9:08:55.403532 INFO: ms2_error      : 30
9:08:55.403594 INFO: fwhm_rt        : 5
9:08:55.403642 INFO: quant_window   : 3
9:08:55.403691 INFO: ==============================================
9:08:55.406991 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
9:08:55.407050 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
9:08:55.407102 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
9:08:55.407135 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
9:08:55.408399 INFO: Starting candidate selection
9:10:31.964641 INFO: Starting candidate scoring
9:10:33.250817 INFO: Finished candidate processing
9:10:33.251759 INFO: Collecting candidate features
9:10:33.313504 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 15102)
9:10:33.318068 INFO: Collecting fragment features
9:10:33.332176 INFO: Finished candidate scoring
9:10:33.344173 INFO: performing precursor FDR with 47 features
9:10:33.344283 INFO: Decoy channel: -1
9:10:33.344316 INFO: competitive: True
9:10:33.350173 INFO: Setting torch num_threads to 2 for FDR classification task
9:10:33.353760 WARNING: dropped 1 decoy PSMs due to missing features
9:10:33.358304 INFO: Estimating optimal hyperparameters - samples: 12,080, batch_size: 128, learning_rate: 1.77e-04
9:10:33.359367 INFO: Using random state 630690 for train-test-split
9:10:34.881407 INFO: Test AUC: 0.540
9:10:34.881551 INFO: Train AUC: 0.589
9:10:34.881594 INFO: AUC difference: 8.41%
9:10:34.881619 WARNING: AUC difference > 5%. This may indicate overfitting.
9:10:35.160794 INFO: Resetting torch num_threads to 128
9:10:35.162892 PROGRESS: === Extracted 15102 precursors and 163449 fragments ===
9:10:35.164321 INFO: === FDR correction performed with classifier version -1 ===
9:10:35.167760 PROGRESS: ============================= Precursor FDR =============================
9:10:35.167905 PROGRESS: Total precursors accumulated: 7,730
9:10:35.167999 PROGRESS: Target precursors: 4,670 (60.41%)
9:10:35.168066 PROGRESS: Decoy precursors: 3,060 (39.59%)
9:10:35.168152 PROGRESS: 
9:10:35.168212 PROGRESS: Precursor Summary:
9:10:35.169285 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
9:10:35.169390 PROGRESS: 
9:10:35.169479 PROGRESS: Protein Summary:
9:10:35.170606 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
9:10:35.170714 PROGRESS: =========================================================================
9:10:35.170851 INFO: Target number of precursors not reached yet.
9:10:35.290709 INFO: Starting optimization step 1.
9:10:35.291103 PROGRESS: === Extracting elution groups 8000 to 24000 ===
9:10:35.291253 INFO: Using python extraction backend
9:10:35.291445 PROGRESS: Extracting batch of 31523 precursors
9:10:35.291563 INFO: === Search parameters used ===
9:10:35.291671 INFO: rt_error       : 2099.8992935
9:10:35.291758 INFO: mobility_error : 0.1
9:10:35.291838 INFO: num_candidates : 1
9:10:35.291918 INFO: ms1_error      : 30
9:10:35.291998 INFO: ms2_error      : 30
9:10:35.292076 INFO: fwhm_rt        : 5
9:10:35.292150 INFO: quant_window   : 3
9:10:35.292224 INFO: ==============================================
9:10:35.298711 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
9:10:35.298803 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
9:10:35.298847 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
9:10:35.298882 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
9:10:35.299647 INFO: Starting candidate selection
9:13:44.123500 INFO: Starting candidate scoring
9:13:46.400103 INFO: Finished candidate processing
9:13:46.400532 INFO: Collecting candidate features
9:13:46.479883 WARNING: intensity_correlation has 6 NaNs ( 0.02 % out of 30043)
9:13:46.480206 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 30043)
9:13:46.484657 INFO: Collecting fragment features
9:13:46.504437 INFO: Finished candidate scoring
9:13:46.536228 INFO: performing precursor FDR with 47 features
9:13:46.536400 INFO: Decoy channel: -1
9:13:46.536436 INFO: competitive: True
9:13:46.554293 INFO: Setting torch num_threads to 2 for FDR classification task
9:13:46.564171 WARNING: dropped 3 target PSMs due to missing features
9:13:46.564423 WARNING: dropped 4 decoy PSMs due to missing features
9:13:46.571846 INFO: Estimating optimal hyperparameters - samples: 36,110, batch_size: 147, learning_rate: 1.89e-04
9:13:46.572068 INFO: Using random state 371318 for train-test-split
9:13:50.102896 INFO: Test AUC: 0.551
9:13:50.103082 INFO: Train AUC: 0.598
9:13:50.103115 INFO: AUC difference: 7.88%
9:13:50.103139 WARNING: AUC difference > 5%. This may indicate overfitting.
9:13:50.388093 INFO: Resetting torch num_threads to 128
9:13:50.399745 PROGRESS: === Extracted 45145 precursors and 487905 fragments ===
9:13:50.400567 INFO: === FDR correction performed with classifier version -1 ===
9:13:50.405232 PROGRESS: ============================= Precursor FDR =============================
9:13:50.405395 PROGRESS: Total precursors accumulated: 23,114
9:13:50.405489 PROGRESS: Target precursors: 14,255 (61.67%)
9:13:50.405557 PROGRESS: Decoy precursors: 8,859 (38.33%)
9:13:50.405618 PROGRESS: 
9:13:50.405674 PROGRESS: Precursor Summary:
9:13:50.406935 PROGRESS: Channel   0:	 0.050 FDR:   163; 0.010 FDR:   108; 0.001 FDR:    21
9:13:50.407048 PROGRESS: 
9:13:50.407120 PROGRESS: Protein Summary:
9:13:50.408419 PROGRESS: Channel   0:	 0.050 FDR:   159; 0.010 FDR:   107; 0.001 FDR:    21
9:13:50.408535 PROGRESS: =========================================================================
9:13:50.408943 INFO: Target number of precursors not reached yet.
9:13:50.989925 INFO: Starting optimization step 2.
9:13:50.990294 PROGRESS: === Extracting elution groups 24000 to 56000 ===
9:13:50.990406 INFO: Using python extraction backend
9:13:50.990582 PROGRESS: Extracting batch of 63149 precursors
9:13:50.990676 INFO: === Search parameters used ===
9:13:50.990744 INFO: rt_error       : 2099.8992935
9:13:50.990801 INFO: mobility_error : 0.1
9:13:50.990858 INFO: num_candidates : 1
9:13:50.990920 INFO: ms1_error      : 30
9:13:50.990978 INFO: ms2_error      : 30
9:13:50.991031 INFO: fwhm_rt        : 5
9:13:50.991085 INFO: quant_window   : 3
9:13:50.991157 INFO: ==============================================
9:13:51.007422 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
9:13:51.007579 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
9:13:51.007615 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
9:13:51.007640 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
9:13:51.008530 INFO: Starting candidate selection
9:19:57.424442 INFO: Starting candidate scoring
9:20:02.147984 INFO: Finished candidate processing
9:20:02.148255 INFO: Collecting candidate features
9:20:02.273640 WARNING: intensity_correlation has 8 NaNs ( 0.01 % out of 60206)
9:20:02.273976 WARNING: height_correlation has 3 NaNs ( 0.00 % out of 60206)
9:20:02.279453 INFO: Collecting fragment features
9:20:02.318645 INFO: Finished candidate scoring
9:20:02.373235 INFO: performing precursor FDR with 47 features
9:20:02.373412 INFO: Decoy channel: -1
9:20:02.373466 INFO: competitive: True
9:20:02.416506 INFO: Setting torch num_threads to 2 for FDR classification task
9:20:02.441177 WARNING: dropped 10 target PSMs due to missing features
9:20:02.441352 WARNING: dropped 7 decoy PSMs due to missing features
9:20:02.456891 INFO: Estimating optimal hyperparameters - samples: 84,267, batch_size: 345, learning_rate: 2.90e-04
9:20:02.457230 INFO: Using random state 852641 for train-test-split
9:20:07.466063 INFO: Test AUC: 0.557
9:20:07.466232 INFO: Train AUC: 0.598
9:20:07.466264 INFO: AUC difference: 6.99%
9:20:07.466295 WARNING: AUC difference > 5%. This may indicate overfitting.
9:20:07.759460 INFO: Resetting torch num_threads to 128
9:20:07.784085 PROGRESS: === Extracted 105351 precursors and 1139924 fragments ===
9:20:07.784985 INFO: === FDR correction performed with classifier version -1 ===
9:20:07.803827 PROGRESS: ============================= Precursor FDR =============================
9:20:07.804034 PROGRESS: Total precursors accumulated: 53,929
9:20:07.804121 PROGRESS: Target precursors: 33,179 (61.52%)
9:20:07.804218 PROGRESS: Decoy precursors: 20,750 (38.48%)
9:20:07.804307 PROGRESS: 
9:20:07.804389 PROGRESS: Precursor Summary:
9:20:07.806138 PROGRESS: Channel   0:	 0.050 FDR:   383; 0.010 FDR:   269; 0.001 FDR:   152
9:20:07.806272 PROGRESS: 
9:20:07.806354 PROGRESS: Protein Summary:
9:20:07.808066 PROGRESS: Channel   0:	 0.050 FDR:   364; 0.010 FDR:   257; 0.001 FDR:   149
9:20:07.808190 PROGRESS: =========================================================================
9:20:07.809334 INFO: Target number of precursors reached.
9:20:07.902025 INFO: fragments_df: keeping 2519 of 1139924 [sum(precursor_idx_mask)=3082 sum(mass_error_mask)=1139924 stop_rank=2519
9:20:08.567381 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
9:20:08.700139 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
9:20:08.822796 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
9:20:08.945014 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
9:20:09.248894 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
9:20:09.249511 INFO: Using score_cutoff 55.45863032684326 (fac=0.99, q=1)
9:20:09.249936 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0848348140716553
9:20:09.250045 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010448433458805084
9:20:09.250135 INFO: Updating optimization_manager: score_cutoff        : 0 -> 55.45863032684326
9:20:09.250222 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:20:09.264853 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:20:09.330716 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:20:09.347036 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:20:09.498762 INFO: Updating optimization_manager: classifier_version  : -1 -> 2
9:20:09.499077 PROGRESS: Required number of precursors found. Starting search parameter optimization.
9:20:09.499211 INFO: Starting optimization step 3.
9:20:09.499309 PROGRESS: === Extracting elution groups 0 to 56000 ===
9:20:09.499419 INFO: Using python extraction backend
9:20:09.499608 PROGRESS: Extracting batch of 110438 precursors
9:20:09.499716 INFO: === Search parameters used ===
9:20:09.499791 INFO: rt_error       : 2099.8992935
9:20:09.499863 INFO: mobility_error : 0.1
9:20:09.499940 INFO: num_candidates : 3
9:20:09.500019 INFO: ms1_error      : 30
9:20:09.500095 INFO: ms2_error      : 30
9:20:09.500172 INFO: fwhm_rt        : 3.0848348140716553
9:20:09.500245 INFO: quant_window   : 3
9:20:09.500319 INFO: ==============================================
9:20:09.528617 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
9:20:09.528785 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
9:20:09.528849 INFO: FWHM in RT is 3.08 seconds, sigma is 0.68
9:20:09.528884 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.85
9:20:09.536430 INFO: Starting candidate selection
9:31:16.032150 INFO: Starting candidate scoring
9:31:35.028650 INFO: Finished candidate processing
9:31:35.028858 INFO: Collecting candidate features
9:31:35.523377 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 306136)
9:31:35.537580 INFO: Collecting fragment features
9:31:35.713869 INFO: Finished candidate scoring
9:31:35.858316 INFO: performing precursor FDR with 47 features
9:31:35.858490 INFO: Decoy channel: -1
9:31:35.858528 INFO: competitive: True
9:31:35.943063 INFO: Setting torch num_threads to 2 for FDR classification task
9:31:36.003125 WARNING: dropped 1 target PSMs due to missing features
9:31:36.003312 WARNING: dropped 2 decoy PSMs due to missing features
9:31:36.087653 INFO: Estimating optimal hyperparameters - samples: 244,906, batch_size: 1,003, learning_rate: 4.95e-04
9:31:36.088258 INFO: Using random state 424240 for train-test-split
9:31:44.049639 INFO: Test AUC: 0.564
9:31:44.049838 INFO: Train AUC: 0.591
9:31:44.049882 INFO: AUC difference: 4.69%
9:31:44.418863 INFO: Resetting torch num_threads to 128
9:31:44.427156 PROGRESS: === Extracted 306136 precursors and 3351691 fragments ===
9:31:44.427917 INFO: === FDR correction performed with classifier version 2 ===
9:31:44.437773 PROGRESS: ============================= Precursor FDR =============================
9:31:44.437975 PROGRESS: Total precursors accumulated: 54,916
9:31:44.438068 PROGRESS: Target precursors: 35,032 (63.79%)
9:31:44.438154 PROGRESS: Decoy precursors: 19,884 (36.21%)
9:31:44.438228 PROGRESS: 
9:31:44.438305 PROGRESS: Precursor Summary:
9:31:44.440004 PROGRESS: Channel   0:	 0.050 FDR:   386; 0.010 FDR:   312; 0.001 FDR:   230
9:31:44.440131 PROGRESS: 
9:31:44.440223 PROGRESS: Protein Summary:
9:31:44.441915 PROGRESS: Channel   0:	 0.050 FDR:   363; 0.010 FDR:   297; 0.001 FDR:   226
9:31:44.442041 PROGRESS: =========================================================================
9:31:44.443861 INFO: Target number of precursors reached.
9:31:44.694324 INFO: fragments_df: keeping 4706 of 3351691 [sum(precursor_idx_mask)=10136 sum(mass_error_mask)=3351691 stop_rank=4706
9:31:44.924734 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
9:31:45.058813 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
9:31:45.197176 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
9:31:45.337888 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
9:31:46.000753 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
9:31:46.001337 INFO: Using score_cutoff 49.4158718662262 (fac=0.99, q=1)
9:31:46.001741 INFO: Updating optimization_manager: fwhm_rt             : 3.0848348140716553 -> 3.0131313800811768
9:31:46.001857 INFO: Updating optimization_manager: fwhm_mobility       : 0.010448433458805084 -> 0.010052474215626717
9:31:46.001938 INFO: Updating optimization_manager: score_cutoff        : 55.45863032684326 -> 49.4158718662262
9:31:46.002028 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:31:46.017060 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:31:46.082878 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:31:46.098326 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:31:46.249569 INFO: === checking if optimization conditions were reached ===
9:31:46.252100 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
9:31:46.252238 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
9:31:46.252346 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
9:31:46.253491 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
9:31:46.253613 INFO: Updating optimization_manager: classifier_version  : 3 -> 3
9:31:46.253708 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
9:31:46.253814 INFO: ==============================================
9:31:46.253919 INFO: Starting optimization step 4.
9:31:46.254005 PROGRESS: === Extracting elution groups 0 to 56000 ===
9:31:46.254089 INFO: Using python extraction backend
9:31:46.254238 PROGRESS: Extracting batch of 110438 precursors
9:31:46.254341 INFO: === Search parameters used ===
9:31:46.254424 INFO: rt_error       : 2099.8992935
9:31:46.254498 INFO: mobility_error : 0.1
9:31:46.254561 INFO: num_candidates : 3
9:31:46.254622 INFO: ms1_error      : 15.0
9:31:46.254687 INFO: ms2_error      : 15.0
9:31:46.254749 INFO: fwhm_rt        : 3.0131313800811768
9:31:46.254817 INFO: quant_window   : 3
9:31:46.254886 INFO: ==============================================
9:31:46.283954 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
9:31:46.284121 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
9:31:46.284214 INFO: FWHM in RT is 3.01 seconds, sigma is 0.66
9:31:46.284247 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.66
9:31:46.285158 INFO: Starting candidate selection
9:46:40.092541 INFO: Starting candidate scoring
9:47:05.995586 INFO: Finished candidate processing
9:47:05.996021 INFO: Collecting candidate features
9:47:07.391029 WARNING: intensity_correlation has 7 NaNs ( 0.00 % out of 306141)
9:47:07.392270 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 306141)
9:47:07.410274 INFO: Collecting fragment features
9:47:07.821540 INFO: Finished candidate scoring
9:47:08.558462 INFO: performing precursor FDR with 47 features
9:47:08.558922 INFO: Decoy channel: -1
9:47:08.558992 INFO: competitive: True
9:47:08.847358 INFO: Setting torch num_threads to 2 for FDR classification task
9:47:08.993451 WARNING: dropped 5 target PSMs due to missing features
9:47:08.993831 WARNING: dropped 3 decoy PSMs due to missing features
9:47:09.187692 INFO: Estimating optimal hyperparameters - samples: 244,906, batch_size: 1,003, learning_rate: 4.95e-04
9:47:09.188645 INFO: Using random state 392500 for train-test-split
9:47:26.711090 INFO: Test AUC: 0.556
9:47:26.711741 INFO: Train AUC: 0.591
9:47:26.711798 INFO: AUC difference: 5.92%
9:47:26.711834 WARNING: AUC difference > 5%. This may indicate overfitting.
9:47:27.382335 INFO: Resetting torch num_threads to 128
9:47:27.447368 PROGRESS: === Extracted 306141 precursors and 3190440 fragments ===
9:47:27.452485 INFO: === FDR correction performed with classifier version 3 ===
9:47:27.527514 PROGRESS: ============================= Precursor FDR =============================
9:47:27.528966 PROGRESS: Total precursors accumulated: 54,883
9:47:27.529374 PROGRESS: Target precursors: 34,284 (62.47%)
9:47:27.529549 PROGRESS: Decoy precursors: 20,599 (37.53%)
9:47:27.529653 PROGRESS: 
9:47:27.529758 PROGRESS: Precursor Summary:
9:47:27.539596 PROGRESS: Channel   0:	 0.050 FDR:   548; 0.010 FDR:   416; 0.001 FDR:     0
9:47:27.540538 PROGRESS: 
9:47:27.540863 PROGRESS: Protein Summary:
9:47:27.548457 PROGRESS: Channel   0:	 0.050 FDR:   514; 0.010 FDR:   393; 0.001 FDR:     0
9:47:27.549580 PROGRESS: =========================================================================
9:47:27.565061 INFO: Target number of precursors reached.
9:47:27.878011 INFO: fragments_df: keeping 5000 of 3190440 [sum(precursor_idx_mask)=13353 sum(mass_error_mask)=3190437 stop_rank=5000
9:47:29.274166 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
9:47:29.519773 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
9:47:29.727820 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
9:47:29.944767 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
9:47:30.753836 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
9:47:30.755663 INFO: Using score_cutoff 42.557567974090574 (fac=0.99, q=1)
9:47:30.757134 INFO: Updating optimization_manager: fwhm_rt             : 3.0131313800811768 -> 2.8270912170410156
9:47:30.757463 INFO: Updating optimization_manager: fwhm_mobility       : 0.010052474215626717 -> 0.008510586805641651
9:47:30.757591 INFO: Updating optimization_manager: score_cutoff        : 49.4158718662262 -> 42.557567974090574
9:47:30.757725 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:47:30.777915 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:47:30.858719 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:47:30.880196 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:47:31.063644 INFO: === checking if optimization conditions were reached ===
9:47:31.068928 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
9:47:31.069396 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
9:47:31.069534 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
9:47:31.071261 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
9:47:31.071425 INFO: Updating optimization_manager: classifier_version  : 4 -> 4
9:47:31.071540 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
9:47:31.071642 INFO: ==============================================
9:47:31.071775 PROGRESS: Optimization finished for ms2_error, ms1_error.
9:47:31.772640 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
9:47:31.801959 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
9:47:31.889079 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
9:47:31.917223 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
9:47:32.161822 INFO: Starting optimization step 0.
9:47:32.163008 PROGRESS: === Extracting elution groups 0 to 56000 ===
9:47:32.163354 INFO: Using python extraction backend
9:47:32.164041 PROGRESS: Extracting batch of 110438 precursors
9:47:32.164367 INFO: === Search parameters used ===
9:47:32.164502 INFO: rt_error       : 2099.8992935
9:47:32.164672 INFO: mobility_error : 0.1
9:47:32.164773 INFO: num_candidates : 3
9:47:32.164926 INFO: ms1_error      : 15.0
9:47:32.165039 INFO: ms2_error      : 15.0
9:47:32.165174 INFO: fwhm_rt        : 2.8270912170410156
9:47:32.165314 INFO: quant_window   : 3
9:47:32.165441 INFO: ==============================================
9:47:32.296844 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
9:47:32.297899 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
9:47:32.298051 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
9:47:32.298096 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.95
9:47:32.302814 INFO: Starting candidate selection
10:12:29.885136 INFO: Starting candidate scoring
10:12:54.700820 INFO: Finished candidate processing
10:12:54.701138 INFO: Collecting candidate features
10:12:56.117144 WARNING: intensity_correlation has 6 NaNs ( 0.00 % out of 305895)
10:12:56.135791 INFO: Collecting fragment features
10:12:56.481278 INFO: Finished candidate scoring
10:12:57.193530 INFO: performing precursor FDR with 47 features
10:12:57.193988 INFO: Decoy channel: -1
10:12:57.194058 INFO: competitive: True
10:12:57.464673 INFO: Setting torch num_threads to 2 for FDR classification task
10:12:57.633815 WARNING: dropped 1 target PSMs due to missing features
10:12:57.634320 WARNING: dropped 5 decoy PSMs due to missing features
10:12:57.864456 INFO: Estimating optimal hyperparameters - samples: 244,711, batch_size: 1,002, learning_rate: 4.95e-04
10:12:57.865449 INFO: Using random state 127083 for train-test-split
10:13:15.997118 INFO: Test AUC: 0.561
10:13:15.997709 INFO: Train AUC: 0.599
10:13:15.997914 INFO: AUC difference: 6.27%
10:13:15.997961 WARNING: AUC difference > 5%. This may indicate overfitting.
10:13:16.647857 INFO: Resetting torch num_threads to 128
10:13:16.700783 PROGRESS: === Extracted 305895 precursors and 3178166 fragments ===
10:13:16.704332 INFO: === FDR correction performed with classifier version 4 ===
10:13:16.777688 PROGRESS: ============================= Precursor FDR =============================
10:13:16.779176 PROGRESS: Total precursors accumulated: 54,894
10:13:16.779669 PROGRESS: Target precursors: 34,546 (62.93%)
10:13:16.780118 PROGRESS: Decoy precursors: 20,348 (37.07%)
10:13:16.780348 PROGRESS: 
10:13:16.780471 PROGRESS: Precursor Summary:
10:13:16.792090 PROGRESS: Channel   0:	 0.050 FDR:   612; 0.010 FDR:   426; 0.001 FDR:   182
10:13:16.793274 PROGRESS: 
10:13:16.793607 PROGRESS: Protein Summary:
10:13:16.801991 PROGRESS: Channel   0:	 0.050 FDR:   567; 0.010 FDR:   399; 0.001 FDR:   177
10:13:16.803137 PROGRESS: =========================================================================
10:13:16.818849 INFO: Target number of precursors reached.
10:13:17.107538 INFO: fragments_df: keeping 5000 of 3178166 [sum(precursor_idx_mask)=13553 sum(mass_error_mask)=3178162 stop_rank=5000
10:13:18.566920 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
10:13:19.043712 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
10:13:19.307437 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
10:13:19.553801 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
10:13:20.457257 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
10:13:20.459513 INFO: Using score_cutoff 43.73520360946655 (fac=0.99, q=1)
10:13:20.461375 INFO: Updating optimization_manager: fwhm_rt             : 2.8270912170410156 -> 2.831956386566162
10:13:20.462016 INFO: Updating optimization_manager: fwhm_mobility       : 0.008510586805641651 -> 0.00852205790579319
10:13:20.462191 INFO: Updating optimization_manager: score_cutoff        : 42.557567974090574 -> 43.73520360946655
10:13:20.462399 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
10:13:20.486519 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
10:13:20.574581 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
10:13:20.601607 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
10:13:20.865953 INFO: === checking if optimization conditions were reached ===
10:13:20.867447 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
10:13:20.875680 INFO: Updating optimization_manager: rt_error            : 2099.8992935 -> 473.82687113494154
10:13:20.876719 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 473.8269.
10:13:20.877071 INFO: ==============================================
10:13:20.877263 INFO: Starting optimization step 1.
10:13:20.877424 PROGRESS: === Extracting elution groups 0 to 56000 ===
10:13:20.877617 INFO: Using python extraction backend
10:13:20.877946 PROGRESS: Extracting batch of 110438 precursors
10:13:20.878113 INFO: === Search parameters used ===
10:13:20.878217 INFO: rt_error       : 473.82687113494154
10:13:20.878313 INFO: mobility_error : 0.1
10:13:20.878402 INFO: num_candidates : 3
10:13:20.878497 INFO: ms1_error      : 15.0
10:13:20.878597 INFO: ms2_error      : 15.0
10:13:20.878701 INFO: fwhm_rt        : 2.831956386566162
10:13:20.878797 INFO: quant_window   : 3
10:13:20.878897 INFO: ==============================================
10:13:21.014005 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:13:21.014608 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:13:21.014804 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
10:13:21.014872 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.95
10:13:21.019062 INFO: Starting candidate selection
10:16:04.855958 INFO: Starting candidate scoring
10:16:15.685867 INFO: Finished candidate processing
10:16:15.686089 INFO: Collecting candidate features
10:16:16.325781 WARNING: intensity_correlation has 75 NaNs ( 0.03 % out of 297946)
10:16:16.326352 WARNING: height_correlation has 7 NaNs ( 0.00 % out of 297946)
10:16:16.340263 INFO: Collecting fragment features
10:16:16.605912 INFO: Finished candidate scoring
10:16:16.808203 INFO: performing precursor FDR with 47 features
10:16:16.808363 INFO: Decoy channel: -1
10:16:16.808392 INFO: competitive: True
10:16:16.908459 INFO: Setting torch num_threads to 2 for FDR classification task
10:16:16.968505 WARNING: dropped 46 target PSMs due to missing features
10:16:16.968696 WARNING: dropped 34 decoy PSMs due to missing features
10:16:17.087694 INFO: Estimating optimal hyperparameters - samples: 238,292, batch_size: 976, learning_rate: 4.88e-04
10:16:17.088448 INFO: Using random state 127083 for train-test-split
10:16:26.595544 INFO: Test AUC: 0.547
10:16:26.595750 INFO: Train AUC: 0.582
10:16:26.595783 INFO: AUC difference: 6.08%
10:16:26.595818 WARNING: AUC difference > 5%. This may indicate overfitting.
10:16:26.959877 INFO: Resetting torch num_threads to 128
10:16:26.967584 PROGRESS: === Extracted 297946 precursors and 3024018 fragments ===
10:16:26.968341 INFO: === FDR correction performed with classifier version 4 ===
10:16:26.978812 PROGRESS: ============================= Precursor FDR =============================
10:16:26.979015 PROGRESS: Total precursors accumulated: 54,211
10:16:26.979101 PROGRESS: Target precursors: 33,019 (60.91%)
10:16:26.979166 PROGRESS: Decoy precursors: 21,192 (39.09%)
10:16:26.979225 PROGRESS: 
10:16:26.979284 PROGRESS: Precursor Summary:
10:16:26.980984 PROGRESS: Channel   0:	 0.050 FDR:   678; 0.010 FDR:     1; 0.001 FDR:     1
10:16:26.981105 PROGRESS: 
10:16:26.981175 PROGRESS: Protein Summary:
10:16:26.982851 PROGRESS: Channel   0:	 0.050 FDR:   621; 0.010 FDR:     1; 0.001 FDR:     1
10:16:26.982972 PROGRESS: =========================================================================
10:16:26.984744 INFO: Target number of precursors not reached yet.
10:16:27.453054 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
10:16:27.470860 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
10:16:27.550199 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
10:16:27.574790 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
10:16:27.734820 INFO: === skipping optimization until target number of precursors are found ===
10:16:27.735199 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
10:16:27.735337 INFO: Starting optimization step 2.
10:16:27.735441 PROGRESS: === Extracting elution groups 56000 to 120000 ===
10:16:27.735545 INFO: Using python extraction backend
10:16:27.735707 PROGRESS: Extracting batch of 126145 precursors
10:16:27.735817 INFO: === Search parameters used ===
10:16:27.735888 INFO: rt_error       : 473.82687113494154
10:16:27.735961 INFO: mobility_error : 0.1
10:16:27.736038 INFO: num_candidates : 3
10:16:27.736108 INFO: ms1_error      : 15.0
10:16:27.736169 INFO: ms2_error      : 15.0
10:16:27.736232 INFO: fwhm_rt        : 2.831956386566162
10:16:27.736286 INFO: quant_window   : 3
10:16:27.736336 INFO: ==============================================
10:16:27.769033 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:16:27.769196 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:16:27.769252 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
10:16:27.769291 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.95
10:16:27.770290 INFO: Starting candidate selection
10:19:12.860063 INFO: Starting candidate scoring
10:19:24.752588 INFO: Finished candidate processing
10:19:24.752727 INFO: Collecting candidate features
10:19:25.324023 WARNING: intensity_correlation has 76 NaNs ( 0.02 % out of 340460)
10:19:25.324636 WARNING: height_correlation has 8 NaNs ( 0.00 % out of 340460)
10:19:25.339100 INFO: Collecting fragment features
10:19:25.560500 INFO: Finished candidate scoring
10:19:26.066081 INFO: performing precursor FDR with 47 features
10:19:26.066261 INFO: Decoy channel: -1
10:19:26.066302 INFO: competitive: True
10:19:26.370092 INFO: Setting torch num_threads to 2 for FDR classification task
10:19:26.495851 WARNING: dropped 92 target PSMs due to missing features
10:19:26.496042 WARNING: dropped 66 decoy PSMs due to missing features
10:19:26.865570 INFO: Estimating optimal hyperparameters - samples: 510,598, batch_size: 2,091, learning_rate: 7.14e-04
10:19:26.866850 INFO: Using random state 127083 for train-test-split
10:19:41.861784 INFO: Test AUC: 0.549
10:19:41.861960 INFO: Train AUC: 0.572
10:19:41.861994 INFO: AUC difference: 3.91%
10:19:42.312974 INFO: Resetting torch num_threads to 128
10:19:42.423412 PROGRESS: === Extracted 638406 precursors and 6479861 fragments ===
10:19:42.424431 INFO: === FDR correction performed with classifier version 4 ===
10:19:42.448815 PROGRESS: ============================= Precursor FDR =============================
10:19:42.449162 PROGRESS: Total precursors accumulated: 116,212
10:19:42.449245 PROGRESS: Target precursors: 69,519 (59.82%)
10:19:42.449314 PROGRESS: Decoy precursors: 46,693 (40.18%)
10:19:42.449383 PROGRESS: 
10:19:42.449442 PROGRESS: Precursor Summary:
10:19:42.451751 PROGRESS: Channel   0:	 0.050 FDR: 1,397; 0.010 FDR:   938; 0.001 FDR:     1
10:19:42.451870 PROGRESS: 
10:19:42.451944 PROGRESS: Protein Summary:
10:19:42.454228 PROGRESS: Channel   0:	 0.050 FDR: 1,198; 0.010 FDR:   814; 0.001 FDR:     1
10:19:42.454352 PROGRESS: =========================================================================
10:19:42.456371 INFO: Target number of precursors reached.
10:19:42.978694 INFO: fragments_df: keeping 5000 of 6479861 [sum(precursor_idx_mask)=29826 sum(mass_error_mask)=6479848 stop_rank=5000
10:19:43.214831 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
10:19:43.397636 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
10:19:43.580468 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
10:19:43.769304 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
10:19:45.746636 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
10:19:45.747208 INFO: Using score_cutoff 45.56583847732544 (fac=0.99, q=1)
10:19:45.747607 INFO: Updating optimization_manager: fwhm_rt             : 2.831956386566162 -> 2.8344287872314453
10:19:45.747699 INFO: Updating optimization_manager: fwhm_mobility       : 0.00852205790579319 -> 0.009049036540091038
10:19:45.747765 INFO: Updating optimization_manager: score_cutoff        : 43.73520360946655 -> 45.56583847732544
10:19:45.747841 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
10:19:45.761372 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
10:19:45.826810 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
10:19:45.841351 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
10:19:45.981068 INFO: === checking if optimization conditions were reached ===
10:19:45.981436 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
10:19:45.984338 INFO: Updating optimization_manager: rt_error            : 473.82687113494154 -> 173.56023828934312
10:19:45.984496 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 173.5602.
10:19:45.984604 INFO: ==============================================
10:19:45.984720 INFO: Starting optimization step 3.
10:19:45.984831 PROGRESS: === Extracting elution groups 0 to 56000 ===
10:19:45.984932 INFO: Using python extraction backend
10:19:45.985094 PROGRESS: Extracting batch of 110438 precursors
10:19:45.985196 INFO: === Search parameters used ===
10:19:45.985282 INFO: rt_error       : 173.56023828934312
10:19:45.985363 INFO: mobility_error : 0.1
10:19:45.985438 INFO: num_candidates : 3
10:19:45.985503 INFO: ms1_error      : 15.0
10:19:45.985569 INFO: ms2_error      : 15.0
10:19:45.985652 INFO: fwhm_rt        : 2.8344287872314453
10:19:45.985732 INFO: quant_window   : 3
10:19:45.985831 INFO: ==============================================
10:19:46.014067 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:19:46.014228 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:19:46.014285 INFO: FWHM in RT is 2.83 seconds, sigma is 0.62
10:19:46.014321 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.20
10:19:46.015219 INFO: Starting candidate selection
10:20:43.169260 INFO: Starting candidate scoring
10:20:53.894069 INFO: Finished candidate processing
10:20:53.894279 INFO: Collecting candidate features
10:20:54.531254 WARNING: intensity_correlation has 122 NaNs ( 0.04 % out of 293618)
10:20:54.531786 WARNING: height_correlation has 11 NaNs ( 0.00 % out of 293618)
10:20:54.544277 INFO: Collecting fragment features
10:20:54.785511 INFO: Finished candidate scoring
10:20:54.934005 INFO: performing precursor FDR with 47 features
10:20:54.934151 INFO: Decoy channel: -1
10:20:54.934183 INFO: competitive: True
10:20:55.015894 INFO: Setting torch num_threads to 2 for FDR classification task
10:20:55.073815 WARNING: dropped 68 target PSMs due to missing features
10:20:55.073986 WARNING: dropped 60 decoy PSMs due to missing features
10:20:55.154420 INFO: Estimating optimal hyperparameters - samples: 234,792, batch_size: 961, learning_rate: 4.84e-04
10:20:55.155155 INFO: Using random state 127083 for train-test-split
10:21:02.652989 INFO: Test AUC: 0.545
10:21:02.653194 INFO: Train AUC: 0.575
10:21:02.653239 INFO: AUC difference: 5.20%
10:21:02.653272 WARNING: AUC difference > 5%. This may indicate overfitting.
10:21:03.021035 INFO: Resetting torch num_threads to 128
10:21:03.029279 PROGRESS: === Extracted 293618 precursors and 2909805 fragments ===
10:21:03.030041 INFO: === FDR correction performed with classifier version 4 ===
10:21:03.040943 PROGRESS: ============================= Precursor FDR =============================
10:21:03.041121 PROGRESS: Total precursors accumulated: 53,719
10:21:03.041210 PROGRESS: Target precursors: 32,024 (59.61%)
10:21:03.041287 PROGRESS: Decoy precursors: 21,695 (40.39%)
10:21:03.041358 PROGRESS: 
10:21:03.041422 PROGRESS: Precursor Summary:
10:21:03.043371 PROGRESS: Channel   0:	 0.050 FDR:   810; 0.010 FDR:   589; 0.001 FDR:     0
10:21:03.043505 PROGRESS: 
10:21:03.043597 PROGRESS: Protein Summary:
10:21:03.045390 PROGRESS: Channel   0:	 0.050 FDR:   742; 0.010 FDR:   537; 0.001 FDR:     0
10:21:03.045506 PROGRESS: =========================================================================
10:21:03.051106 INFO: Target number of precursors reached.
10:21:03.275723 INFO: fragments_df: keeping 5000 of 2909805 [sum(precursor_idx_mask)=18344 sum(mass_error_mask)=2909799 stop_rank=5000
10:21:03.799814 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
10:21:03.961681 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
10:21:04.123257 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
10:21:04.287171 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
10:21:05.005031 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
10:21:05.005611 INFO: Using score_cutoff 40.52550362091065 (fac=0.99, q=1)
10:21:05.006023 INFO: Updating optimization_manager: fwhm_rt             : 2.8344287872314453 -> 2.844442367553711
10:21:05.006126 INFO: Updating optimization_manager: fwhm_mobility       : 0.009049036540091038 -> 0.00856353621929884
10:21:05.006198 INFO: Updating optimization_manager: score_cutoff        : 45.56583847732544 -> 40.52550362091065
10:21:05.006273 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
10:21:05.012766 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
10:21:05.040784 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
10:21:05.046972 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
10:21:05.105158 INFO: === checking if optimization conditions were reached ===
10:21:05.105522 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
10:21:05.108703 INFO: Updating optimization_manager: rt_error            : 173.56023828934312 -> 157.43541980318622
10:21:05.108842 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 157.4354.
10:21:05.108931 INFO: ==============================================
10:21:05.109021 INFO: Starting optimization step 4.
10:21:05.109100 PROGRESS: === Extracting elution groups 0 to 24000 ===
10:21:05.109185 INFO: Using python extraction backend
10:21:05.109348 PROGRESS: Extracting batch of 47289 precursors
10:21:05.109440 INFO: === Search parameters used ===
10:21:05.109511 INFO: rt_error       : 157.43541980318622
10:21:05.109575 INFO: mobility_error : 0.1
10:21:05.109637 INFO: num_candidates : 3
10:21:05.109698 INFO: ms1_error      : 15.0
10:21:05.109806 INFO: ms2_error      : 15.0
10:21:05.109872 INFO: fwhm_rt        : 2.844442367553711
10:21:05.109954 INFO: quant_window   : 3
10:21:05.110033 INFO: ==============================================
10:21:05.130378 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:21:05.130532 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:21:05.130614 INFO: FWHM in RT is 2.84 seconds, sigma is 0.63
10:21:05.130659 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.97
10:21:05.131534 INFO: Starting candidate selection
10:21:27.210893 INFO: Starting candidate scoring
10:21:31.914719 INFO: Finished candidate processing
10:21:31.914933 INFO: Collecting candidate features
10:21:32.170521 WARNING: intensity_correlation has 63 NaNs ( 0.05 % out of 125485)
10:21:32.170925 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 125485)
10:21:32.179505 INFO: Collecting fragment features
10:21:32.303979 INFO: Finished candidate scoring
10:21:32.370631 INFO: performing precursor FDR with 47 features
10:21:32.370777 INFO: Decoy channel: -1
10:21:32.370811 INFO: competitive: True
10:21:32.419147 INFO: Setting torch num_threads to 2 for FDR classification task
10:21:32.447677 WARNING: dropped 28 target PSMs due to missing features
10:21:32.447833 WARNING: dropped 39 decoy PSMs due to missing features
10:21:32.475080 INFO: Estimating optimal hyperparameters - samples: 100,334, batch_size: 410, learning_rate: 3.16e-04
10:21:32.475862 INFO: Using random state 127083 for train-test-split
10:21:37.495648 INFO: Test AUC: 0.539
10:21:37.495803 INFO: Train AUC: 0.598
10:21:37.495835 INFO: AUC difference: 9.77%
10:21:37.495866 WARNING: AUC difference > 5%. This may indicate overfitting.
10:21:37.817401 INFO: Resetting torch num_threads to 128
10:21:37.822577 PROGRESS: === Extracted 125485 precursors and 1239391 fragments ===
10:21:37.823318 INFO: === FDR correction performed with classifier version 4 ===
10:21:37.829108 PROGRESS: ============================= Precursor FDR =============================
10:21:37.829306 PROGRESS: Total precursors accumulated: 22,972
10:21:37.829400 PROGRESS: Target precursors: 14,178 (61.72%)
10:21:37.829472 PROGRESS: Decoy precursors: 8,794 (38.28%)
10:21:37.829540 PROGRESS: 
10:21:37.829597 PROGRESS: Precursor Summary:
10:21:37.831025 PROGRESS: Channel   0:	 0.050 FDR:   295; 0.010 FDR:   213; 0.001 FDR:   182
10:21:37.831140 PROGRESS: 
10:21:37.831210 PROGRESS: Protein Summary:
10:21:37.832632 PROGRESS: Channel   0:	 0.050 FDR:   284; 0.010 FDR:   205; 0.001 FDR:   177
10:21:37.832739 PROGRESS: =========================================================================
10:21:37.835905 INFO: Target number of precursors reached.
10:21:37.931992 INFO: fragments_df: keeping 2842 of 1239391 [sum(precursor_idx_mask)=6653 sum(mass_error_mask)=1239389 stop_rank=2842
10:21:38.456622 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
10:21:38.584509 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
10:21:38.715555 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
10:21:38.848298 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
10:21:39.255818 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
10:21:39.256414 INFO: Using score_cutoff 45.296786233520514 (fac=0.99, q=1)
10:21:39.256821 INFO: Updating optimization_manager: fwhm_rt             : 2.844442367553711 -> 2.862088441848755
10:21:39.256923 INFO: Updating optimization_manager: fwhm_mobility       : 0.00856353621929884 -> 0.008583473041653633
10:21:39.257004 INFO: Updating optimization_manager: score_cutoff        : 40.52550362091065 -> 45.296786233520514
10:21:39.257102 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
10:21:39.264133 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
10:21:39.293160 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
10:21:39.299597 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
10:21:39.359640 INFO: === checking if optimization conditions were reached ===
10:21:39.360015 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
10:21:39.362965 INFO: Updating optimization_manager: rt_error            : 157.43541980318622 -> 131.7852492999483
10:21:39.363106 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 131.7852.
10:21:39.363192 INFO: ==============================================
10:21:39.363290 INFO: Starting optimization step 5.
10:21:39.363420 PROGRESS: === Extracting elution groups 0 to 24000 ===
10:21:39.363534 INFO: Using python extraction backend
10:21:39.363718 PROGRESS: Extracting batch of 47289 precursors
10:21:39.363836 INFO: === Search parameters used ===
10:21:39.363907 INFO: rt_error       : 131.7852492999483
10:21:39.363971 INFO: mobility_error : 0.1
10:21:39.364067 INFO: num_candidates : 3
10:21:39.364153 INFO: ms1_error      : 15.0
10:21:39.364229 INFO: ms2_error      : 15.0
10:21:39.364322 INFO: fwhm_rt        : 2.862088441848755
10:21:39.364408 INFO: quant_window   : 3
10:21:39.364468 INFO: ==============================================
10:21:39.383743 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:21:39.383902 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:21:39.383955 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
10:21:39.383982 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.98
10:21:39.386771 INFO: Starting candidate selection
10:21:57.631958 INFO: Starting candidate scoring
10:22:03.325968 INFO: Finished candidate processing
10:22:03.326177 INFO: Collecting candidate features
10:22:03.534516 WARNING: intensity_correlation has 65 NaNs ( 0.05 % out of 125219)
10:22:03.534917 WARNING: height_correlation has 9 NaNs ( 0.01 % out of 125219)
10:22:03.543193 INFO: Collecting fragment features
10:22:03.622423 INFO: Finished candidate scoring
10:22:03.704318 INFO: performing precursor FDR with 47 features
10:22:03.704473 INFO: Decoy channel: -1
10:22:03.704500 INFO: competitive: True
10:22:03.747557 INFO: Setting torch num_threads to 2 for FDR classification task
10:22:03.773881 WARNING: dropped 33 target PSMs due to missing features
10:22:03.774054 WARNING: dropped 37 decoy PSMs due to missing features
10:22:03.805383 INFO: Estimating optimal hyperparameters - samples: 100,119, batch_size: 410, learning_rate: 3.16e-04
10:22:03.805915 INFO: Using random state 127083 for train-test-split
10:22:09.865638 INFO: Test AUC: 0.545
10:22:09.865904 INFO: Train AUC: 0.588
10:22:09.865951 INFO: AUC difference: 7.39%
10:22:09.865978 WARNING: AUC difference > 5%. This may indicate overfitting.
10:22:10.190090 INFO: Resetting torch num_threads to 128
10:22:10.193654 PROGRESS: === Extracted 125219 precursors and 1232388 fragments ===
10:22:10.194409 INFO: === FDR correction performed with classifier version 4 ===
10:22:10.198847 PROGRESS: ============================= Precursor FDR =============================
10:22:10.198994 PROGRESS: Total precursors accumulated: 22,947
10:22:10.199078 PROGRESS: Target precursors: 14,033 (61.15%)
10:22:10.199154 PROGRESS: Decoy precursors: 8,914 (38.85%)
10:22:10.199216 PROGRESS: 
10:22:10.199277 PROGRESS: Precursor Summary:
10:22:10.200621 PROGRESS: Channel   0:	 0.050 FDR:   305; 0.010 FDR:   210; 0.001 FDR:   180
10:22:10.200735 PROGRESS: 
10:22:10.200808 PROGRESS: Protein Summary:
10:22:10.202246 PROGRESS: Channel   0:	 0.050 FDR:   296; 0.010 FDR:   203; 0.001 FDR:   173
10:22:10.202360 PROGRESS: =========================================================================
10:22:10.203075 INFO: Target number of precursors reached.
10:22:10.297739 INFO: fragments_df: keeping 2822 of 1232388 [sum(precursor_idx_mask)=6455 sum(mass_error_mask)=1232384 stop_rank=2822
10:22:10.503845 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
10:22:10.613294 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
10:22:10.734453 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
10:22:10.867194 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
10:22:11.278433 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
10:22:11.279001 INFO: Using score_cutoff 45.37914207000732 (fac=0.99, q=1)
10:22:11.279379 INFO: Updating optimization_manager: fwhm_rt             : 2.862088441848755 -> 2.8677330017089844
10:22:11.279477 INFO: Updating optimization_manager: fwhm_mobility       : 0.008583473041653633 -> 0.008718881756067276
10:22:11.279545 INFO: Updating optimization_manager: score_cutoff        : 45.296786233520514 -> 45.37914207000732
10:22:11.279623 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
10:22:11.286475 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
10:22:11.315763 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
10:22:11.321966 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
10:22:11.383063 INFO: === checking if optimization conditions were reached ===
10:22:11.383391 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
10:22:11.385848 INFO: Updating optimization_manager: rt_error            : 131.7852492999483 -> 130.10261977357834
10:22:11.385982 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 130.1026.
10:22:11.386067 INFO: ==============================================
10:22:11.386157 INFO: Starting optimization step 6.
10:22:11.386253 PROGRESS: === Extracting elution groups 0 to 24000 ===
10:22:11.386336 INFO: Using python extraction backend
10:22:11.386500 PROGRESS: Extracting batch of 47289 precursors
10:22:11.386606 INFO: === Search parameters used ===
10:22:11.386695 INFO: rt_error       : 130.10261977357834
10:22:11.386775 INFO: mobility_error : 0.1
10:22:11.386848 INFO: num_candidates : 3
10:22:11.386907 INFO: ms1_error      : 15.0
10:22:11.386960 INFO: ms2_error      : 15.0
10:22:11.387020 INFO: fwhm_rt        : 2.8677330017089844
10:22:11.387082 INFO: quant_window   : 3
10:22:11.387149 INFO: ==============================================
10:22:11.400177 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:22:11.400309 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:22:11.400362 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
10:22:11.400397 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.04
10:22:11.401394 INFO: Starting candidate selection
10:22:29.598921 INFO: Starting candidate scoring
10:22:34.230172 INFO: Finished candidate processing
10:22:34.230355 INFO: Collecting candidate features
10:22:34.443405 WARNING: intensity_correlation has 61 NaNs ( 0.05 % out of 124691)
10:22:34.443795 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 124691)
10:22:34.451647 INFO: Collecting fragment features
10:22:34.537978 INFO: Finished candidate scoring
10:22:34.613421 INFO: performing precursor FDR with 47 features
10:22:34.613573 INFO: Decoy channel: -1
10:22:34.613611 INFO: competitive: True
10:22:34.650823 INFO: Setting torch num_threads to 2 for FDR classification task
10:22:34.677015 WARNING: dropped 32 target PSMs due to missing features
10:22:34.677184 WARNING: dropped 33 decoy PSMs due to missing features
10:22:34.701487 INFO: Estimating optimal hyperparameters - samples: 99,700, batch_size: 408, learning_rate: 3.16e-04
10:22:34.701931 INFO: Using random state 127083 for train-test-split
10:22:39.413217 INFO: Test AUC: 0.540
10:22:39.413373 INFO: Train AUC: 0.583
10:22:39.413409 INFO: AUC difference: 7.35%
10:22:39.413437 WARNING: AUC difference > 5%. This may indicate overfitting.
10:22:39.717937 INFO: Resetting torch num_threads to 128
10:22:39.721999 PROGRESS: === Extracted 124691 precursors and 1225451 fragments ===
10:22:39.722730 INFO: === FDR correction performed with classifier version 4 ===
10:22:39.726799 PROGRESS: ============================= Precursor FDR =============================
10:22:39.726963 PROGRESS: Total precursors accumulated: 22,841
10:22:39.727058 PROGRESS: Target precursors: 13,958 (61.11%)
10:22:39.727138 PROGRESS: Decoy precursors: 8,883 (38.89%)
10:22:39.727211 PROGRESS: 
10:22:39.727289 PROGRESS: Precursor Summary:
10:22:39.728629 PROGRESS: Channel   0:	 0.050 FDR:   323; 0.010 FDR:   235; 0.001 FDR:   188
10:22:39.728750 PROGRESS: 
10:22:39.728837 PROGRESS: Protein Summary:
10:22:39.730317 PROGRESS: Channel   0:	 0.050 FDR:   314; 0.010 FDR:   228; 0.001 FDR:   181
10:22:39.730441 PROGRESS: =========================================================================
10:22:39.731258 INFO: Target number of precursors reached.
10:22:39.828866 INFO: fragments_df: keeping 3030 of 1225451 [sum(precursor_idx_mask)=7198 sum(mass_error_mask)=1225448 stop_rank=3030
10:22:40.348702 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
10:22:40.476913 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
10:22:40.618377 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
10:22:40.752468 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
10:22:41.188864 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
10:22:41.189465 INFO: Using score_cutoff 34.565002088928225 (fac=0.99, q=1)
10:22:41.189887 INFO: Updating optimization_manager: fwhm_rt             : 2.8677330017089844 -> 2.844442367553711
10:22:41.190001 INFO: Updating optimization_manager: fwhm_mobility       : 0.008718881756067276 -> 0.008479557000100613
10:22:41.190090 INFO: Updating optimization_manager: score_cutoff        : 45.37914207000732 -> 34.565002088928225
10:22:41.190251 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
10:22:41.197317 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
10:22:41.226767 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
10:22:41.233237 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
10:22:41.293513 INFO: === checking if optimization conditions were reached ===
10:22:41.293872 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
10:22:41.295427 INFO: Updating optimization_manager: rt_error            : 130.10261977357834 -> 130.10261977357834
10:22:41.295604 INFO: Updating optimization_manager: classifier_version  : 4 -> 11
10:22:41.295747 INFO: Updating optimization_manager: score_cutoff        : 34.565002088928225 -> 34.565002088928225
10:22:41.295878 INFO: Updating optimization_manager: fwhm_rt             : 2.844442367553711 -> 2.844442367553711
10:22:41.296004 INFO: Updating optimization_manager: fwhm_mobility       : 0.008479557000100613 -> 0.008479557000100613
10:22:41.296128 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 130.1026 found after 6 searches.
10:22:41.296218 INFO: ==============================================
10:22:41.296315 PROGRESS: Optimization finished for rt_error.
10:22:41.482381 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
10:22:41.489930 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
10:22:41.519071 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
10:22:41.525589 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
10:22:41.591527 INFO: Starting optimization step 0.
10:22:41.591862 PROGRESS: === Extracting elution groups 0 to 24000 ===
10:22:41.591971 INFO: Using python extraction backend
10:22:41.592131 PROGRESS: Extracting batch of 47289 precursors
10:22:41.592240 INFO: === Search parameters used ===
10:22:41.592314 INFO: rt_error       : 130.10261977357834
10:22:41.592386 INFO: mobility_error : 0.1
10:22:41.592478 INFO: num_candidates : 3
10:22:41.592558 INFO: ms1_error      : 15.0
10:22:41.592632 INFO: ms2_error      : 15.0
10:22:41.592703 INFO: fwhm_rt        : 2.844442367553711
10:22:41.592782 INFO: quant_window   : 3
10:22:41.592850 INFO: ==============================================
10:22:41.605670 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:22:41.605799 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:22:41.605864 INFO: FWHM in RT is 2.84 seconds, sigma is 0.63
10:22:41.605902 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.93
10:22:41.606891 INFO: Starting candidate selection
10:22:59.635315 INFO: Starting candidate scoring
10:23:04.549246 INFO: Finished candidate processing
10:23:04.549462 INFO: Collecting candidate features
10:23:04.751655 WARNING: intensity_correlation has 63 NaNs ( 0.05 % out of 124964)
10:23:04.752049 WARNING: height_correlation has 9 NaNs ( 0.01 % out of 124964)
10:23:04.759754 INFO: Collecting fragment features
10:23:04.826358 INFO: Finished candidate scoring
10:23:04.886698 INFO: performing precursor FDR with 47 features
10:23:04.886859 INFO: Decoy channel: -1
10:23:04.886886 INFO: competitive: True
10:23:04.924185 INFO: Setting torch num_threads to 2 for FDR classification task
10:23:04.950720 WARNING: dropped 31 target PSMs due to missing features
10:23:04.950886 WARNING: dropped 36 decoy PSMs due to missing features
10:23:04.973651 INFO: Estimating optimal hyperparameters - samples: 99,917, batch_size: 409, learning_rate: 3.16e-04
10:23:04.974064 INFO: Using random state 119185 for train-test-split
10:23:09.859639 INFO: Test AUC: 0.564
10:23:09.859807 INFO: Train AUC: 0.628
10:23:09.859839 INFO: AUC difference: 10.29%
10:23:09.859872 WARNING: AUC difference > 5%. This may indicate overfitting.
10:23:10.156992 INFO: Resetting torch num_threads to 128
10:23:10.161043 PROGRESS: === Extracted 124964 precursors and 1228695 fragments ===
10:23:10.161684 INFO: === FDR correction performed with classifier version 11 ===
10:23:10.165912 PROGRESS: ============================= Precursor FDR =============================
10:23:10.166053 PROGRESS: Total precursors accumulated: 22,912
10:23:10.166131 PROGRESS: Target precursors: 14,945 (65.23%)
10:23:10.166197 PROGRESS: Decoy precursors: 7,967 (34.77%)
10:23:10.166254 PROGRESS: 
10:23:10.166310 PROGRESS: Precursor Summary:
10:23:10.167649 PROGRESS: Channel   0:	 0.050 FDR:   286; 0.010 FDR:   217; 0.001 FDR:    21
10:23:10.167783 PROGRESS: 
10:23:10.167906 PROGRESS: Protein Summary:
10:23:10.169337 PROGRESS: Channel   0:	 0.050 FDR:   276; 0.010 FDR:   209; 0.001 FDR:    21
10:23:10.169475 PROGRESS: =========================================================================
10:23:10.170307 INFO: Target number of precursors reached.
10:23:10.264964 INFO: fragments_df: keeping 2865 of 1228695 [sum(precursor_idx_mask)=6652 sum(mass_error_mask)=1228694 stop_rank=2865
10:23:10.449114 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
10:23:10.575216 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
10:23:10.707358 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
10:23:10.831273 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
10:23:11.241007 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
10:23:11.241552 INFO: Using score_cutoff 36.53454028930664 (fac=0.99, q=1)
10:23:11.241933 INFO: Updating optimization_manager: fwhm_rt             : 2.844442367553711 -> 2.8591086864471436
10:23:11.242031 INFO: Updating optimization_manager: fwhm_mobility       : 0.008479557000100613 -> 0.00856353621929884
10:23:11.242104 INFO: Updating optimization_manager: score_cutoff        : 34.565002088928225 -> 36.53454028930664
10:23:11.242173 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
10:23:11.249802 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
10:23:11.279162 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
10:23:11.285412 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
10:23:11.342054 INFO: === checking if optimization conditions were reached ===
10:23:11.342396 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
10:23:11.344528 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.09373869716834306
10:23:11.344649 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0937.
10:23:11.344741 INFO: ==============================================
10:23:11.344854 INFO: Starting optimization step 1.
10:23:11.344942 PROGRESS: === Extracting elution groups 0 to 24000 ===
10:23:11.345026 INFO: Using python extraction backend
10:23:11.345181 PROGRESS: Extracting batch of 47289 precursors
10:23:11.345273 INFO: === Search parameters used ===
10:23:11.345346 INFO: rt_error       : 130.10261977357834
10:23:11.345410 INFO: mobility_error : 0.09373869716834306
10:23:11.345474 INFO: num_candidates : 3
10:23:11.345538 INFO: ms1_error      : 15.0
10:23:11.345599 INFO: ms2_error      : 15.0
10:23:11.345667 INFO: fwhm_rt        : 2.8591086864471436
10:23:11.345733 INFO: quant_window   : 3
10:23:11.345829 INFO: ==============================================
10:23:11.358926 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:23:11.359073 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:23:11.359123 INFO: FWHM in RT is 2.86 seconds, sigma is 0.63
10:23:11.359148 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.97
10:23:11.362110 INFO: Starting candidate selection
10:23:27.545041 INFO: Starting candidate scoring
10:23:32.358892 INFO: Finished candidate processing
10:23:32.359106 INFO: Collecting candidate features
10:23:32.546458 WARNING: intensity_correlation has 63 NaNs ( 0.05 % out of 124182)
10:23:32.546836 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 124182)
10:23:32.554401 INFO: Collecting fragment features
10:23:32.620791 INFO: Finished candidate scoring
10:23:32.681398 INFO: performing precursor FDR with 47 features
10:23:32.681559 INFO: Decoy channel: -1
10:23:32.681587 INFO: competitive: True
10:23:32.718037 INFO: Setting torch num_threads to 2 for FDR classification task
10:23:32.744116 WARNING: dropped 34 target PSMs due to missing features
10:23:32.744291 WARNING: dropped 32 decoy PSMs due to missing features
10:23:32.764132 INFO: Estimating optimal hyperparameters - samples: 99,292, batch_size: 406, learning_rate: 3.15e-04
10:23:32.764519 INFO: Using random state 119185 for train-test-split
10:23:37.603793 INFO: Test AUC: 0.557
10:23:37.603955 INFO: Train AUC: 0.605
10:23:37.603987 INFO: AUC difference: 7.84%
10:23:37.604010 WARNING: AUC difference > 5%. This may indicate overfitting.
10:23:37.903610 INFO: Resetting torch num_threads to 128
10:23:37.907627 PROGRESS: === Extracted 124182 precursors and 1218135 fragments ===
10:23:37.908283 INFO: === FDR correction performed with classifier version 11 ===
10:23:37.912351 PROGRESS: ============================= Precursor FDR =============================
10:23:37.912489 PROGRESS: Total precursors accumulated: 22,768
10:23:37.912567 PROGRESS: Target precursors: 14,204 (62.39%)
10:23:37.912634 PROGRESS: Decoy precursors: 8,564 (37.61%)
10:23:37.912693 PROGRESS: 
10:23:37.912750 PROGRESS: Precursor Summary:
10:23:37.914114 PROGRESS: Channel   0:	 0.050 FDR:   351; 0.010 FDR:   221; 0.001 FDR:   152
10:23:37.914242 PROGRESS: 
10:23:37.914318 PROGRESS: Protein Summary:
10:23:37.915758 PROGRESS: Channel   0:	 0.050 FDR:   338; 0.010 FDR:   213; 0.001 FDR:   146
10:23:37.915866 PROGRESS: =========================================================================
10:23:37.916629 INFO: Target number of precursors reached.
10:23:38.008954 INFO: fragments_df: keeping 2852 of 1218135 [sum(precursor_idx_mask)=6766 sum(mass_error_mask)=1218133 stop_rank=2852
10:23:38.193511 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
10:23:38.320633 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
10:23:38.453275 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
10:23:38.573793 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
10:23:38.915092 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
10:23:38.915641 INFO: Using score_cutoff 34.366099342346196 (fac=0.99, q=1)
10:23:38.916013 INFO: Updating optimization_manager: fwhm_rt             : 2.8591086864471436 -> 2.8815648555755615
10:23:38.916108 INFO: Updating optimization_manager: fwhm_mobility       : 0.00856353621929884 -> 0.008583473041653633
10:23:38.916175 INFO: Updating optimization_manager: score_cutoff        : 36.53454028930664 -> 34.366099342346196
10:23:38.916247 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
10:23:38.923223 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
10:23:38.953182 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
10:23:38.959941 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
10:23:39.021764 INFO: === checking if optimization conditions were reached ===
10:23:39.022154 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
10:23:39.024792 INFO: Updating optimization_manager: mobility_error      : 0.09373869716834306 -> 0.0746658970145917
10:23:39.024929 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0747.
10:23:39.025022 INFO: ==============================================
10:23:39.025125 INFO: Starting optimization step 2.
10:23:39.025212 PROGRESS: === Extracting elution groups 0 to 24000 ===
10:23:39.025297 INFO: Using python extraction backend
10:23:39.025455 PROGRESS: Extracting batch of 47289 precursors
10:23:39.025549 INFO: === Search parameters used ===
10:23:39.025620 INFO: rt_error       : 130.10261977357834
10:23:39.025721 INFO: mobility_error : 0.0746658970145917
10:23:39.025800 INFO: num_candidates : 3
10:23:39.025869 INFO: ms1_error      : 15.0
10:23:39.025964 INFO: ms2_error      : 15.0
10:23:39.026041 INFO: fwhm_rt        : 2.8815648555755615
10:23:39.026106 INFO: quant_window   : 3
10:23:39.026168 INFO: ==============================================
10:23:39.043272 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:23:39.043403 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:23:39.043450 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
10:23:39.043508 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.98
10:23:39.044387 INFO: Starting candidate selection
10:23:52.602066 INFO: Starting candidate scoring
10:23:57.289521 INFO: Finished candidate processing
10:23:57.289721 INFO: Collecting candidate features
10:23:57.510591 WARNING: intensity_correlation has 68 NaNs ( 0.06 % out of 122572)
10:23:57.510999 WARNING: height_correlation has 12 NaNs ( 0.01 % out of 122572)
10:23:57.518973 INFO: Collecting fragment features
10:23:57.585516 INFO: Finished candidate scoring
10:23:57.652546 INFO: performing precursor FDR with 47 features
10:23:57.652704 INFO: Decoy channel: -1
10:23:57.652733 INFO: competitive: True
10:23:57.693536 INFO: Setting torch num_threads to 2 for FDR classification task
10:23:57.719815 WARNING: dropped 45 target PSMs due to missing features
10:23:57.719980 WARNING: dropped 29 decoy PSMs due to missing features
10:23:57.742130 INFO: Estimating optimal hyperparameters - samples: 97,998, batch_size: 401, learning_rate: 3.13e-04
10:23:57.742514 INFO: Using random state 119185 for train-test-split
10:24:02.567955 INFO: Test AUC: 0.560
10:24:02.568115 INFO: Train AUC: 0.626
10:24:02.568146 INFO: AUC difference: 10.52%
10:24:02.568171 WARNING: AUC difference > 5%. This may indicate overfitting.
10:24:02.867757 INFO: Resetting torch num_threads to 128
10:24:02.871686 PROGRESS: === Extracted 122572 precursors and 1195962 fragments ===
10:24:02.872323 INFO: === FDR correction performed with classifier version 11 ===
10:24:02.876416 PROGRESS: ============================= Precursor FDR =============================
10:24:02.876557 PROGRESS: Total precursors accumulated: 22,530
10:24:02.876641 PROGRESS: Target precursors: 14,663 (65.08%)
10:24:02.876704 PROGRESS: Decoy precursors: 7,867 (34.92%)
10:24:02.876768 PROGRESS: 
10:24:02.876825 PROGRESS: Precursor Summary:
10:24:02.878145 PROGRESS: Channel   0:	 0.050 FDR:   323; 0.010 FDR:   188; 0.001 FDR:   130
10:24:02.878257 PROGRESS: 
10:24:02.878328 PROGRESS: Protein Summary:
10:24:02.879757 PROGRESS: Channel   0:	 0.050 FDR:   310; 0.010 FDR:   181; 0.001 FDR:   127
10:24:02.879864 PROGRESS: =========================================================================
10:24:02.880621 INFO: Target number of precursors not reached yet.
10:24:03.137482 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
10:24:03.146959 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
10:24:03.187366 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
10:24:03.197550 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
10:24:03.282805 INFO: === skipping optimization until target number of precursors are found ===
10:24:03.283178 PROGRESS: === Optimization of mobility_error has been skipped 1 time(s); maximum number is 1 ===
10:24:03.283299 INFO: Starting optimization step 3.
10:24:03.283405 PROGRESS: === Extracting elution groups 24000 to 56000 ===
10:24:03.283518 INFO: Using python extraction backend
10:24:03.283684 PROGRESS: Extracting batch of 63149 precursors
10:24:03.283797 INFO: === Search parameters used ===
10:24:03.283884 INFO: rt_error       : 130.10261977357834
10:24:03.283963 INFO: mobility_error : 0.0746658970145917
10:24:03.284042 INFO: num_candidates : 3
10:24:03.284124 INFO: ms1_error      : 15.0
10:24:03.284198 INFO: ms2_error      : 15.0
10:24:03.284272 INFO: fwhm_rt        : 2.8815648555755615
10:24:03.284345 INFO: quant_window   : 3
10:24:03.284421 INFO: ==============================================
10:24:03.301210 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:24:03.301346 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:24:03.301426 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
10:24:03.301464 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.98
10:24:03.302413 INFO: Starting candidate selection
10:24:21.104413 INFO: Starting candidate scoring
10:24:27.450132 INFO: Finished candidate processing
10:24:27.450334 INFO: Collecting candidate features
10:24:27.772687 WARNING: intensity_correlation has 82 NaNs ( 0.05 % out of 163599)
10:24:27.773107 WARNING: height_correlation has 8 NaNs ( 0.00 % out of 163599)
10:24:27.782767 INFO: Collecting fragment features
10:24:27.919511 INFO: Finished candidate scoring
10:24:28.120088 INFO: performing precursor FDR with 47 features
10:24:28.120261 INFO: Decoy channel: -1
10:24:28.120289 INFO: competitive: True
10:24:28.239217 INFO: Setting torch num_threads to 2 for FDR classification task
10:24:28.304439 WARNING: dropped 93 target PSMs due to missing features
10:24:28.304610 WARNING: dropped 67 decoy PSMs due to missing features
10:24:28.441236 INFO: Estimating optimal hyperparameters - samples: 228,808, batch_size: 937, learning_rate: 4.78e-04
10:24:28.441884 INFO: Using random state 119185 for train-test-split
10:24:38.101906 INFO: Test AUC: 0.548
10:24:38.102080 INFO: Train AUC: 0.582
10:24:38.102113 INFO: AUC difference: 5.81%
10:24:38.102139 WARNING: AUC difference > 5%. This may indicate overfitting.
10:24:38.460976 INFO: Resetting torch num_threads to 128
10:24:38.517516 PROGRESS: === Extracted 286171 precursors and 2795188 fragments ===
10:24:38.518488 INFO: === FDR correction performed with classifier version 11 ===
10:24:38.530123 PROGRESS: ============================= Precursor FDR =============================
10:24:38.530370 PROGRESS: Total precursors accumulated: 52,601
10:24:38.530456 PROGRESS: Target precursors: 31,732 (60.33%)
10:24:38.530536 PROGRESS: Decoy precursors: 20,869 (39.67%)
10:24:38.530597 PROGRESS: 
10:24:38.530662 PROGRESS: Precursor Summary:
10:24:38.532367 PROGRESS: Channel   0:	 0.050 FDR:   753; 0.010 FDR:   516; 0.001 FDR:   428
10:24:38.532481 PROGRESS: 
10:24:38.532556 PROGRESS: Protein Summary:
10:24:38.534301 PROGRESS: Channel   0:	 0.050 FDR:   684; 0.010 FDR:   475; 0.001 FDR:   395
10:24:38.534416 PROGRESS: =========================================================================
10:24:38.535228 INFO: Target number of precursors reached.
10:24:38.763958 INFO: fragments_df: keeping 5000 of 2795188 [sum(precursor_idx_mask)=16179 sum(mass_error_mask)=2795182 stop_rank=5000
10:24:38.977792 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
10:24:39.136975 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
10:24:39.290959 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
10:24:39.449852 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
10:24:40.171322 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
10:24:40.171893 INFO: Using score_cutoff 41.93996547889709 (fac=0.99, q=1)
10:24:40.172287 INFO: Updating optimization_manager: fwhm_rt             : 2.8815648555755615 -> 2.837337017059326
10:24:40.172381 INFO: Updating optimization_manager: fwhm_mobility       : 0.008583473041653633 -> 0.008654424920678139
10:24:40.172451 INFO: Updating optimization_manager: score_cutoff        : 34.366099342346196 -> 41.93996547889709
10:24:40.172527 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
10:24:40.179451 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
10:24:40.208558 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
10:24:40.214989 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
10:24:40.276231 INFO: === checking if optimization conditions were reached ===
10:24:40.276579 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
10:24:40.277732 INFO: Updating optimization_manager: mobility_error      : 0.0746658970145917 -> 0.0746658970145917
10:24:40.277931 INFO: Updating optimization_manager: classifier_version  : 11 -> 15
10:24:40.278074 INFO: Updating optimization_manager: score_cutoff        : 41.93996547889709 -> 41.93996547889709
10:24:40.278223 INFO: Updating optimization_manager: fwhm_rt             : 2.837337017059326 -> 2.837337017059326
10:24:40.278353 INFO: Updating optimization_manager: fwhm_mobility       : 0.008654424920678139 -> 0.008654424920678139
10:24:40.278479 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0747 found after 3 searches.
10:24:40.278577 INFO: ==============================================
10:24:40.278687 PROGRESS: Optimization finished for mobility_error.
10:24:40.482121 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
10:24:40.489497 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
10:24:40.518366 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
10:24:40.524872 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
10:24:40.585864 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
10:24:40.586230 PROGRESS: ==============================================
10:24:40.586349 PROGRESS: ms2_error      : 15.0000
10:24:40.586445 PROGRESS: ms1_error      : 15.0000
10:24:40.586537 PROGRESS: rt_error       : 130.1026
10:24:40.586626 PROGRESS: mobility_error : 0.0747
10:24:40.586715 PROGRESS: ==============================================
10:24:40.589794 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
10:24:42.273475 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
10:24:50.237173 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
10:24:51.977657 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
10:25:09.006457 INFO: Using python extraction backend
10:25:09.006959 PROGRESS: Extracting batch of 11524154 precursors
10:25:09.007140 INFO: === Search parameters used ===
10:25:09.007246 INFO: rt_error       : 130.10261977357834
10:25:09.007313 INFO: mobility_error : 0.0746658970145917
10:25:09.007373 INFO: num_candidates : 3
10:25:09.007433 INFO: ms1_error      : 15.0
10:25:09.007494 INFO: ms2_error      : 15.0
10:25:09.007554 INFO: fwhm_rt        : 2.837337017059326
10:25:09.007609 INFO: quant_window   : 3
10:25:09.007663 INFO: ==============================================
10:25:11.815724 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
10:25:11.815912 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
10:25:11.815960 INFO: FWHM in RT is 2.84 seconds, sigma is 0.62
10:25:11.815987 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.01
10:25:11.817022 INFO: Starting candidate selection
11:35:26.443635 INFO: Removed 19974612 precursors with score below cutoff 41.93996547889709
11:35:29.680102 INFO: Starting candidate scoring
11:43:13.692879 INFO: Finished candidate processing
11:43:13.693201 INFO: Collecting candidate features
11:43:37.089114 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 11743838)
11:43:37.452772 INFO: Collecting fragment features
11:43:46.489847 INFO: Finished candidate scoring
11:43:58.635365 INFO: === Performing FDR correction with classifier version 15 ===
11:43:58.636663 INFO: performing precursor FDR with 47 features
11:43:58.636709 INFO: Decoy channel: -1
11:43:58.636740 INFO: competitive: True
11:44:02.335258 INFO: Setting torch num_threads to 2 for FDR classification task
11:44:04.135818 WARNING: dropped 1 target PSMs due to missing features
11:44:09.991866 INFO: Estimating optimal hyperparameters - samples: 9,395,069, batch_size: 4,096, learning_rate: 1.00e-03
11:44:10.017011 INFO: Using random state 583508 for train-test-split
11:47:46.769042 INFO: Test AUC: 0.558
11:47:46.769462 INFO: Train AUC: 0.560
11:47:46.769508 INFO: AUC difference: 0.26%
11:47:49.836832 INFO: Resetting torch num_threads to 128
11:47:50.243245 INFO: Removing fragments below FDR threshold
11:47:51.759259 PROGRESS: ============================= Precursor FDR =============================
11:47:51.759589 PROGRESS: Total precursors accumulated: 72,495
11:47:51.759690 PROGRESS: Target precursors: 71,778 (99.01%)
11:47:51.759765 PROGRESS: Decoy precursors: 717 (0.99%)
11:47:51.759826 PROGRESS: 
11:47:51.759881 PROGRESS: Precursor Summary:
11:47:51.785652 PROGRESS: Channel   0:	 0.050 FDR: 71,778; 0.010 FDR: 71,778; 0.001 FDR: 50,565
11:47:51.785977 PROGRESS: 
11:47:51.786062 PROGRESS: Protein Summary:
11:47:51.818987 PROGRESS: Channel   0:	 0.050 FDR: 11,360; 0.010 FDR: 11,360; 0.001 FDR: 9,015
11:47:51.819297 PROGRESS: =========================================================================
11:47:51.977543 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/psm.parquet
11:47:52.285439 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/frag.parquet
11:47:52.532527 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
11:47:53.167050 PROGRESS: Loading raw file 4/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496 
11:47:53.167256 INFO: Quantification results path: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant
11:47:53.167361 INFO: Creating folder /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/figures
11:47:53.167589 INFO: Initializing TimingManager
11:47:53.168089 INFO: Initializing RawFileManager
11:47:53.168255 INFO: Importing data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
11:47:53.168306 INFO: Using .d import for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
11:47:53.168351 INFO: Reading frame metadata for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
11:47:54.774603 INFO: Reading 39,128 frames with 2,751,035,867 detector events for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
11:50:05.206289 INFO: Indexing /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d...
11:50:05.208159 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
11:50:05.213249 INFO: Fetching mobility values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
11:50:05.213519 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
11:50:05.213981 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
11:50:05.215630 INFO: Fetching mz values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
11:50:05.238647 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
11:50:05.241925 INFO: Indexing quadrupole dimension
11:50:05.668105 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
11:50:05.668318 INFO: Transposing detector events
11:50:17.764465 INFO: Finished transposing data
11:50:17.829164 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
11:50:17.830017 INFO: RT (min)            : 0.0 - 70.0
11:50:17.830095 INFO: RT duration (sec)   : 4199.8
11:50:17.830144 INFO: RT duration (min)   : 70.0
11:50:17.830196 INFO: Cycle len (scans)   : 9
11:50:17.830244 INFO: Cycle len (sec)     : 0.97
11:50:17.830283 INFO: Number of cycles    : 4347
11:50:17.830339 INFO: MS2 range (m/z)     : 400.0 - 1000.0
11:50:17.830409 INFO: Creating DIA data object took: 144.6621971130371
11:50:20.186099 INFO: Initializing CalibrationManager
11:50:20.186483 INFO: Setting up calibration estimators ..
11:50:20.186561 INFO: Found 1 estimator(s) in calibration group 'fragment'
11:50:20.186656 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'}' ..
11:50:20.186811 INFO: Found 3 estimator(s) in calibration group 'precursor'
11:50:20.186894 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'}' ..
11:50:20.186974 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}}' ..
11:50:20.187059 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}}' ..
11:50:20.187138 INFO: Done setting up calibration estimators.
11:50:20.187278 INFO: Initializing OptimizationManager
11:50:20.187395 INFO: initial parameter: ms1_error = 30
11:50:20.187467 INFO: initial parameter: ms2_error = 30
11:50:20.187538 INFO: initial parameter: rt_error = 2099.891532
11:50:20.187602 INFO: initial parameter: mobility_error = 0.1
11:50:20.187661 INFO: initial parameter: num_candidates = 1
11:50:20.187728 INFO: initial parameter: fwhm_rt = 5
11:50:20.187799 INFO: initial parameter: fwhm_mobility = 0.01
11:50:20.187876 INFO: initial parameter: score_cutoff = 0
11:50:20.187951 INFO: initial parameter: classifier_version = -1
11:50:20.188063 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
11:50:20.188357 INFO: FDRManager: loading saved state not requested, will be initialized.
11:50:20.188396 INFO: Initializing FDRManager
11:50:20.188444 INFO: Loading classifier store from /usr/local/lib/python3.10/site-packages/alphadia/constants/classifier
11:50:21.637797 PROGRESS: Initializing spectral library: 5,845,771 target precursors potentially observable (0 removed)
11:50:22.558560 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
11:50:22.559171 INFO: Updating optimization_manager: rt_error            : 2099.891532 -> 2099.891532
11:50:22.559286 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
11:50:22.559501 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
11:50:22.559616 PROGRESS: Starting initial search for precursors.
11:50:22.559744 INFO: Starting optimization step 0.
11:50:22.559834 PROGRESS: === Extracting elution groups 0 to 8000 ===
11:50:22.559939 INFO: Using python extraction backend
11:50:22.560155 PROGRESS: Extracting batch of 15766 precursors
11:50:22.560255 INFO: === Search parameters used ===
11:50:22.560324 INFO: rt_error       : 2099.891532
11:50:22.560390 INFO: mobility_error : 0.1
11:50:22.560456 INFO: num_candidates : 1
11:50:22.560519 INFO: ms1_error      : 30
11:50:22.560596 INFO: ms2_error      : 30
11:50:22.560669 INFO: fwhm_rt        : 5
11:50:22.560741 INFO: quant_window   : 3
11:50:22.560801 INFO: ==============================================
11:50:22.564230 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:50:22.564286 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:50:22.564324 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
11:50:22.564358 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
11:50:22.566050 INFO: Starting candidate selection
11:51:54.255222 INFO: Starting candidate scoring
11:51:55.332242 INFO: Finished candidate processing
11:51:55.332464 INFO: Collecting candidate features
11:51:55.360712 WARNING: intensity_correlation has 3 NaNs ( 0.02 % out of 15055)
11:51:55.364911 INFO: Collecting fragment features
11:51:55.375671 INFO: Finished candidate scoring
11:51:55.383351 INFO: performing precursor FDR with 47 features
11:51:55.383462 INFO: Decoy channel: -1
11:51:55.383530 INFO: competitive: True
11:51:55.388057 INFO: Setting torch num_threads to 2 for FDR classification task
11:51:55.391533 WARNING: dropped 1 target PSMs due to missing features
11:51:55.391608 WARNING: dropped 2 decoy PSMs due to missing features
11:51:55.394542 INFO: Estimating optimal hyperparameters - samples: 12,041, batch_size: 128, learning_rate: 1.77e-04
11:51:55.395360 INFO: Using random state 709626 for train-test-split
11:51:56.607748 INFO: Test AUC: 0.539
11:51:56.607889 INFO: Train AUC: 0.590
11:51:56.607920 INFO: AUC difference: 8.65%
11:51:56.607943 WARNING: AUC difference > 5%. This may indicate overfitting.
11:51:56.865596 INFO: Resetting torch num_threads to 128
11:51:56.866866 PROGRESS: === Extracted 15055 precursors and 162661 fragments ===
11:51:56.867421 INFO: === FDR correction performed with classifier version -1 ===
11:51:56.868999 PROGRESS: ============================= Precursor FDR =============================
11:51:56.869117 PROGRESS: Total precursors accumulated: 7,712
11:51:56.869190 PROGRESS: Target precursors: 4,692 (60.84%)
11:51:56.869252 PROGRESS: Decoy precursors: 3,020 (39.16%)
11:51:56.869309 PROGRESS: 
11:51:56.869364 PROGRESS: Precursor Summary:
11:51:56.870394 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
11:51:56.870502 PROGRESS: 
11:51:56.870576 PROGRESS: Protein Summary:
11:51:56.871662 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
11:51:56.871762 PROGRESS: =========================================================================
11:51:56.871891 INFO: Target number of precursors not reached yet.
11:51:57.159196 INFO: Starting optimization step 1.
11:51:57.159547 PROGRESS: === Extracting elution groups 8000 to 24000 ===
11:51:57.159698 INFO: Using python extraction backend
11:51:57.159881 PROGRESS: Extracting batch of 31523 precursors
11:51:57.159997 INFO: === Search parameters used ===
11:51:57.160084 INFO: rt_error       : 2099.891532
11:51:57.160167 INFO: mobility_error : 0.1
11:51:57.160243 INFO: num_candidates : 1
11:51:57.160318 INFO: ms1_error      : 30
11:51:57.160389 INFO: ms2_error      : 30
11:51:57.160466 INFO: fwhm_rt        : 5
11:51:57.160535 INFO: quant_window   : 3
11:51:57.160609 INFO: ==============================================
11:51:57.167209 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:51:57.167301 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:51:57.167345 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
11:51:57.167377 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
11:51:57.168586 INFO: Starting candidate selection
11:54:59.395652 INFO: Starting candidate scoring
11:55:01.858263 INFO: Finished candidate processing
11:55:01.858454 INFO: Collecting candidate features
11:55:01.941403 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 29992)
11:55:01.941718 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 29992)
11:55:01.946270 INFO: Collecting fragment features
11:55:01.969533 INFO: Finished candidate scoring
11:55:02.005822 INFO: performing precursor FDR with 47 features
11:55:02.005991 INFO: Decoy channel: -1
11:55:02.006019 INFO: competitive: True
11:55:02.027177 INFO: Setting torch num_threads to 2 for FDR classification task
11:55:02.038037 WARNING: dropped 5 target PSMs due to missing features
11:55:02.038203 WARNING: dropped 5 decoy PSMs due to missing features
11:55:02.047028 INFO: Estimating optimal hyperparameters - samples: 36,029, batch_size: 147, learning_rate: 1.89e-04
11:55:02.047306 INFO: Using random state 261196 for train-test-split
11:55:06.198434 INFO: Test AUC: 0.566
11:55:06.198585 INFO: Train AUC: 0.594
11:55:06.198618 INFO: AUC difference: 4.78%
11:55:08.019349 INFO: Resetting torch num_threads to 128
11:55:08.027196 PROGRESS: === Extracted 45047 precursors and 485942 fragments ===
11:55:08.027927 INFO: === FDR correction performed with classifier version -1 ===
11:55:08.031935 PROGRESS: ============================= Precursor FDR =============================
11:55:08.032120 PROGRESS: Total precursors accumulated: 23,075
11:55:08.032212 PROGRESS: Target precursors: 14,173 (61.42%)
11:55:08.032292 PROGRESS: Decoy precursors: 8,902 (38.58%)
11:55:08.032353 PROGRESS: 
11:55:08.032409 PROGRESS: Precursor Summary:
11:55:08.033668 PROGRESS: Channel   0:	 0.050 FDR:    71; 0.010 FDR:     0; 0.001 FDR:     0
11:55:08.033793 PROGRESS: 
11:55:08.033873 PROGRESS: Protein Summary:
11:55:08.035144 PROGRESS: Channel   0:	 0.050 FDR:    70; 0.010 FDR:     0; 0.001 FDR:     0
11:55:08.035268 PROGRESS: =========================================================================
11:55:08.035690 INFO: Target number of precursors not reached yet.
11:55:08.797121 INFO: Starting optimization step 2.
11:55:08.797489 PROGRESS: === Extracting elution groups 24000 to 56000 ===
11:55:08.797598 INFO: Using python extraction backend
11:55:08.797784 PROGRESS: Extracting batch of 63149 precursors
11:55:08.797880 INFO: === Search parameters used ===
11:55:08.797943 INFO: rt_error       : 2099.891532
11:55:08.797998 INFO: mobility_error : 0.1
11:55:08.798057 INFO: num_candidates : 1
11:55:08.798107 INFO: ms1_error      : 30
11:55:08.798163 INFO: ms2_error      : 30
11:55:08.798211 INFO: fwhm_rt        : 5
11:55:08.798259 INFO: quant_window   : 3
11:55:08.798308 INFO: ==============================================
11:55:08.812280 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
11:55:08.812400 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
11:55:08.812431 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
11:55:08.812454 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
11:55:08.813199 INFO: Starting candidate selection
12:01:07.921308 INFO: Starting candidate scoring
12:01:12.214959 INFO: Finished candidate processing
12:01:12.215170 INFO: Collecting candidate features
12:01:12.362132 WARNING: intensity_correlation has 6 NaNs ( 0.01 % out of 60143)
12:01:12.362459 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 60143)
12:01:12.368632 INFO: Collecting fragment features
12:01:12.416422 INFO: Finished candidate scoring
12:01:12.506535 INFO: performing precursor FDR with 47 features
12:01:12.506705 INFO: Decoy channel: -1
12:01:12.506738 INFO: competitive: True
12:01:12.556269 INFO: Setting torch num_threads to 2 for FDR classification task
12:01:12.583828 WARNING: dropped 7 target PSMs due to missing features
12:01:12.583988 WARNING: dropped 10 decoy PSMs due to missing features
12:01:12.608954 INFO: Estimating optimal hyperparameters - samples: 84,138, batch_size: 344, learning_rate: 2.90e-04
12:01:12.609328 INFO: Using random state 904821 for train-test-split
12:01:18.391040 INFO: Test AUC: 0.560
12:01:18.391345 INFO: Train AUC: 0.598
12:01:18.391381 INFO: AUC difference: 6.23%
12:01:18.391409 WARNING: AUC difference > 5%. This may indicate overfitting.
12:01:18.694281 INFO: Resetting torch num_threads to 128
12:01:18.715743 PROGRESS: === Extracted 105190 precursors and 1135436 fragments ===
12:01:18.716717 INFO: === FDR correction performed with classifier version -1 ===
12:01:18.729038 PROGRESS: ============================= Precursor FDR =============================
12:01:18.729331 PROGRESS: Total precursors accumulated: 53,854
12:01:18.729424 PROGRESS: Target precursors: 33,101 (61.46%)
12:01:18.729511 PROGRESS: Decoy precursors: 20,753 (38.54%)
12:01:18.729588 PROGRESS: 
12:01:18.729669 PROGRESS: Precursor Summary:
12:01:18.731246 PROGRESS: Channel   0:	 0.050 FDR:   305; 0.010 FDR:     0; 0.001 FDR:     0
12:01:18.731370 PROGRESS: 
12:01:18.731457 PROGRESS: Protein Summary:
12:01:18.732983 PROGRESS: Channel   0:	 0.050 FDR:   294; 0.010 FDR:     0; 0.001 FDR:     0
12:01:18.733105 PROGRESS: =========================================================================
12:01:18.733991 INFO: Target number of precursors not reached yet.
12:01:19.729901 INFO: Starting optimization step 3.
12:01:19.730345 PROGRESS: === Extracting elution groups 56000 to 120000 ===
12:01:19.730500 INFO: Using python extraction backend
12:01:19.730707 PROGRESS: Extracting batch of 126145 precursors
12:01:19.730824 INFO: === Search parameters used ===
12:01:19.730917 INFO: rt_error       : 2099.891532
12:01:19.731003 INFO: mobility_error : 0.1
12:01:19.731080 INFO: num_candidates : 1
12:01:19.731148 INFO: ms1_error      : 30
12:01:19.731215 INFO: ms2_error      : 30
12:01:19.731281 INFO: fwhm_rt        : 5
12:01:19.731345 INFO: quant_window   : 3
12:01:19.731410 INFO: ==============================================
12:01:19.763854 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:01:19.764029 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:01:19.764074 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
12:01:19.764104 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
12:01:19.764992 INFO: Starting candidate selection
12:13:09.598943 INFO: Starting candidate scoring
12:13:16.911832 INFO: Finished candidate processing
12:13:16.912160 INFO: Collecting candidate features
12:13:17.157640 WARNING: intensity_correlation has 24 NaNs ( 0.02 % out of 120200)
12:13:17.158036 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 120200)
12:13:17.165145 INFO: Collecting fragment features
12:13:17.246742 INFO: Finished candidate scoring
12:13:17.383642 INFO: performing precursor FDR with 47 features
12:13:17.383847 INFO: Decoy channel: -1
12:13:17.383890 INFO: competitive: True
12:13:17.485258 INFO: Setting torch num_threads to 2 for FDR classification task
12:13:17.539721 WARNING: dropped 19 target PSMs due to missing features
12:13:17.539901 WARNING: dropped 24 decoy PSMs due to missing features
12:13:17.596776 INFO: Estimating optimal hyperparameters - samples: 180,277, batch_size: 738, learning_rate: 4.24e-04
12:13:17.597348 INFO: Using random state 61094 for train-test-split
12:13:24.829336 INFO: Test AUC: 0.559
12:13:24.829515 INFO: Train AUC: 0.587
12:13:24.829558 INFO: AUC difference: 4.77%
12:13:25.166985 INFO: Resetting torch num_threads to 128
12:13:25.370023 PROGRESS: === Extracted 225390 precursors and 2433188 fragments ===
12:13:25.371018 INFO: === FDR correction performed with classifier version -1 ===
12:13:25.397849 PROGRESS: ============================= Precursor FDR =============================
12:13:25.398203 PROGRESS: Total precursors accumulated: 115,421
12:13:25.398293 PROGRESS: Target precursors: 69,454 (60.17%)
12:13:25.398373 PROGRESS: Decoy precursors: 45,967 (39.83%)
12:13:25.398453 PROGRESS: 
12:13:25.398529 PROGRESS: Precursor Summary:
12:13:25.400822 PROGRESS: Channel   0:	 0.050 FDR:   901; 0.010 FDR:   644; 0.001 FDR:   527
12:13:25.400973 PROGRESS: 
12:13:25.401060 PROGRESS: Protein Summary:
12:13:25.403254 PROGRESS: Channel   0:	 0.050 FDR:   797; 0.010 FDR:   572; 0.001 FDR:   476
12:13:25.403381 PROGRESS: =========================================================================
12:13:25.407832 INFO: Target number of precursors reached.
12:13:25.609281 INFO: fragments_df: keeping 5000 of 2433188 [sum(precursor_idx_mask)=7354 sum(mass_error_mask)=2433185 stop_rank=5000
12:13:26.545192 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:13:26.698721 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:13:26.847049 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:13:27.001499 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:13:27.656100 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
12:13:27.656643 INFO: Using score_cutoff 54.279916901779174 (fac=0.99, q=1)
12:13:27.657060 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.128988742828369
12:13:27.657158 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010827498510479927
12:13:27.657230 INFO: Updating optimization_manager: score_cutoff        : 0 -> 54.279916901779174
12:13:27.657306 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:13:27.671436 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:13:27.746076 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:13:27.760047 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:13:27.916102 INFO: Updating optimization_manager: classifier_version  : -1 -> 3
12:13:27.916428 PROGRESS: Required number of precursors found. Starting search parameter optimization.
12:13:27.916546 INFO: Starting optimization step 4.
12:13:27.916633 PROGRESS: === Extracting elution groups 0 to 56000 ===
12:13:27.916718 INFO: Using python extraction backend
12:13:27.916861 PROGRESS: Extracting batch of 110438 precursors
12:13:27.916967 INFO: === Search parameters used ===
12:13:27.917031 INFO: rt_error       : 2099.891532
12:13:27.917087 INFO: mobility_error : 0.1
12:13:27.917137 INFO: num_candidates : 3
12:13:27.917192 INFO: ms1_error      : 30
12:13:27.917254 INFO: ms2_error      : 30
12:13:27.917316 INFO: fwhm_rt        : 3.128988742828369
12:13:27.917375 INFO: quant_window   : 3
12:13:27.917434 INFO: ==============================================
12:13:27.945498 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:13:27.945661 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:13:27.945710 INFO: FWHM in RT is 3.13 seconds, sigma is 0.69
12:13:27.945741 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 5.02
12:13:27.946724 INFO: Starting candidate selection
12:23:46.990553 INFO: Starting candidate scoring
12:24:05.516399 INFO: Finished candidate processing
12:24:05.516616 INFO: Collecting candidate features
12:24:06.293899 WARNING: intensity_correlation has 7 NaNs ( 0.00 % out of 305986)
12:24:06.307421 INFO: Collecting fragment features
12:24:06.588814 INFO: Finished candidate scoring
12:24:06.800239 INFO: performing precursor FDR with 47 features
12:24:06.800399 INFO: Decoy channel: -1
12:24:06.800432 INFO: competitive: True
12:24:06.896157 INFO: Setting torch num_threads to 2 for FDR classification task
12:24:06.959941 WARNING: dropped 4 target PSMs due to missing features
12:24:06.960108 WARNING: dropped 3 decoy PSMs due to missing features
12:24:07.048028 INFO: Estimating optimal hyperparameters - samples: 244,783, batch_size: 1,002, learning_rate: 4.95e-04
12:24:07.048722 INFO: Using random state 473053 for train-test-split
12:24:16.787202 INFO: Test AUC: 0.566
12:24:16.787556 INFO: Train AUC: 0.600
12:24:16.787592 INFO: AUC difference: 5.62%
12:24:16.787623 WARNING: AUC difference > 5%. This may indicate overfitting.
12:24:17.145424 INFO: Resetting torch num_threads to 128
12:24:17.154142 PROGRESS: === Extracted 305986 precursors and 3343531 fragments ===
12:24:17.154946 INFO: === FDR correction performed with classifier version 3 ===
12:24:17.165816 PROGRESS: ============================= Precursor FDR =============================
12:24:17.166016 PROGRESS: Total precursors accumulated: 54,874
12:24:17.166104 PROGRESS: Target precursors: 35,062 (63.90%)
12:24:17.166171 PROGRESS: Decoy precursors: 19,812 (36.10%)
12:24:17.166258 PROGRESS: 
12:24:17.166316 PROGRESS: Precursor Summary:
12:24:17.168092 PROGRESS: Channel   0:	 0.050 FDR:   431; 0.010 FDR:   305; 0.001 FDR:   245
12:24:17.168219 PROGRESS: 
12:24:17.168293 PROGRESS: Protein Summary:
12:24:17.170080 PROGRESS: Channel   0:	 0.050 FDR:   404; 0.010 FDR:   292; 0.001 FDR:   240
12:24:17.170207 PROGRESS: =========================================================================
12:24:17.181464 INFO: Target number of precursors reached.
12:24:17.434613 INFO: fragments_df: keeping 4636 of 3343531 [sum(precursor_idx_mask)=9967 sum(mass_error_mask)=3343531 stop_rank=4636
12:24:18.362808 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:24:18.491650 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:24:18.609586 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:24:18.735774 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:24:19.334296 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:24:19.334876 INFO: Using score_cutoff 50.1177690032959 (fac=0.99, q=1)
12:24:19.335293 INFO: Updating optimization_manager: fwhm_rt             : 3.128988742828369 -> 3.074986457824707
12:24:19.335389 INFO: Updating optimization_manager: fwhm_mobility       : 0.010827498510479927 -> 0.010393803007900715
12:24:19.335466 INFO: Updating optimization_manager: score_cutoff        : 54.279916901779174 -> 50.1177690032959
12:24:19.335537 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:24:19.351926 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:24:19.420289 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:24:19.437208 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:24:19.599329 INFO: === checking if optimization conditions were reached ===
12:24:19.602248 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
12:24:19.602389 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
12:24:19.602497 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
12:24:19.603836 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
12:24:19.603958 INFO: Updating optimization_manager: classifier_version  : 4 -> 4
12:24:19.604041 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
12:24:19.604117 INFO: ==============================================
12:24:19.604205 INFO: Starting optimization step 5.
12:24:19.604283 PROGRESS: === Extracting elution groups 0 to 56000 ===
12:24:19.604364 INFO: Using python extraction backend
12:24:19.604535 PROGRESS: Extracting batch of 110438 precursors
12:24:19.604627 INFO: === Search parameters used ===
12:24:19.604694 INFO: rt_error       : 2099.891532
12:24:19.604755 INFO: mobility_error : 0.1
12:24:19.604816 INFO: num_candidates : 3
12:24:19.604875 INFO: ms1_error      : 15.0
12:24:19.604934 INFO: ms2_error      : 15.0
12:24:19.604997 INFO: fwhm_rt        : 3.074986457824707
12:24:19.605056 INFO: quant_window   : 3
12:24:19.605115 INFO: ==============================================
12:24:19.646237 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:24:19.646395 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:24:19.646445 INFO: FWHM in RT is 3.07 seconds, sigma is 0.68
12:24:19.646471 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.82
12:24:19.647228 INFO: Starting candidate selection
12:33:47.787503 INFO: Starting candidate scoring
12:33:58.410148 INFO: Finished candidate processing
12:33:58.410565 INFO: Collecting candidate features
12:33:58.883521 WARNING: intensity_correlation has 10 NaNs ( 0.00 % out of 305698)
12:33:58.897632 INFO: Collecting fragment features
12:33:59.086196 INFO: Finished candidate scoring
12:33:59.248539 INFO: performing precursor FDR with 47 features
12:33:59.248706 INFO: Decoy channel: -1
12:33:59.248733 INFO: competitive: True
12:33:59.336402 INFO: Setting torch num_threads to 2 for FDR classification task
12:33:59.396795 WARNING: dropped 3 target PSMs due to missing features
12:33:59.397006 WARNING: dropped 7 decoy PSMs due to missing features
12:33:59.533415 INFO: Estimating optimal hyperparameters - samples: 244,550, batch_size: 1,001, learning_rate: 4.94e-04
12:33:59.534117 INFO: Using random state 784004 for train-test-split
12:34:07.627035 INFO: Test AUC: 0.561
12:34:07.627232 INFO: Train AUC: 0.599
12:34:07.627266 INFO: AUC difference: 6.35%
12:34:07.627292 WARNING: AUC difference > 5%. This may indicate overfitting.
12:34:07.987148 INFO: Resetting torch num_threads to 128
12:34:07.995043 PROGRESS: === Extracted 305698 precursors and 3179561 fragments ===
12:34:07.995782 INFO: === FDR correction performed with classifier version 4 ===
12:34:08.006442 PROGRESS: ============================= Precursor FDR =============================
12:34:08.006659 PROGRESS: Total precursors accumulated: 54,782
12:34:08.006747 PROGRESS: Target precursors: 34,746 (63.43%)
12:34:08.006814 PROGRESS: Decoy precursors: 20,036 (36.57%)
12:34:08.006889 PROGRESS: 
12:34:08.006946 PROGRESS: Precursor Summary:
12:34:08.008678 PROGRESS: Channel   0:	 0.050 FDR:   632; 0.010 FDR:   413; 0.001 FDR:   313
12:34:08.008802 PROGRESS: 
12:34:08.008874 PROGRESS: Protein Summary:
12:34:08.010629 PROGRESS: Channel   0:	 0.050 FDR:   592; 0.010 FDR:   387; 0.001 FDR:   305
12:34:08.010758 PROGRESS: =========================================================================
12:34:08.014900 INFO: Target number of precursors reached.
12:34:08.293794 INFO: fragments_df: keeping 5000 of 3179561 [sum(precursor_idx_mask)=12901 sum(mass_error_mask)=3179561 stop_rank=5000
12:34:09.220501 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:34:09.349474 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:34:09.472548 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:34:09.602285 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:34:10.250471 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:34:10.251032 INFO: Using score_cutoff 48.71214786071777 (fac=0.99, q=1)
12:34:10.251430 INFO: Updating optimization_manager: fwhm_rt             : 3.074986457824707 -> 2.8750956058502197
12:34:10.251531 INFO: Updating optimization_manager: fwhm_mobility       : 0.010393803007900715 -> 0.008923409506678581
12:34:10.251604 INFO: Updating optimization_manager: score_cutoff        : 50.1177690032959 -> 48.71214786071777
12:34:10.251675 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:34:10.265405 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:34:10.331242 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:34:10.346019 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:34:10.516358 INFO: === checking if optimization conditions were reached ===
12:34:10.518897 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
12:34:10.519035 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
12:34:10.519133 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
12:34:10.520304 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
12:34:10.520432 INFO: Updating optimization_manager: classifier_version  : 5 -> 5
12:34:10.520529 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
12:34:10.520620 INFO: ==============================================
12:34:10.520728 PROGRESS: Optimization finished for ms2_error, ms1_error.
12:34:10.897676 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:34:10.911971 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:34:10.978382 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:34:10.993160 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:34:11.142456 INFO: Starting optimization step 0.
12:34:11.142814 PROGRESS: === Extracting elution groups 0 to 56000 ===
12:34:11.142938 INFO: Using python extraction backend
12:34:11.143122 PROGRESS: Extracting batch of 110438 precursors
12:34:11.143243 INFO: === Search parameters used ===
12:34:11.143327 INFO: rt_error       : 2099.891532
12:34:11.143401 INFO: mobility_error : 0.1
12:34:11.143469 INFO: num_candidates : 3
12:34:11.143538 INFO: ms1_error      : 15.0
12:34:11.143602 INFO: ms2_error      : 15.0
12:34:11.143671 INFO: fwhm_rt        : 2.8750956058502197
12:34:11.143740 INFO: quant_window   : 3
12:34:11.143821 INFO: ==============================================
12:34:11.172360 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:34:11.172532 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:34:11.172620 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
12:34:11.172652 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.14
12:34:11.173721 INFO: Starting candidate selection
12:43:37.936158 INFO: Starting candidate scoring
12:43:48.454536 INFO: Finished candidate processing
12:43:48.454943 INFO: Collecting candidate features
12:43:49.277173 WARNING: intensity_correlation has 9 NaNs ( 0.00 % out of 304670)
12:43:49.277719 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 304670)
12:43:49.290516 INFO: Collecting fragment features
12:43:49.621148 INFO: Finished candidate scoring
12:43:49.913629 INFO: performing precursor FDR with 47 features
12:43:49.913793 INFO: Decoy channel: -1
12:43:49.913829 INFO: competitive: True
12:43:50.016182 INFO: Setting torch num_threads to 2 for FDR classification task
12:43:50.077867 WARNING: dropped 5 target PSMs due to missing features
12:43:50.078035 WARNING: dropped 5 decoy PSMs due to missing features
12:43:50.164290 INFO: Estimating optimal hyperparameters - samples: 243,728, batch_size: 998, learning_rate: 4.94e-04
12:43:50.164972 INFO: Using random state 877777 for train-test-split
12:43:59.883842 INFO: Test AUC: 0.567
12:43:59.883997 INFO: Train AUC: 0.611
12:43:59.884029 INFO: AUC difference: 7.27%
12:43:59.884053 WARNING: AUC difference > 5%. This may indicate overfitting.
12:44:00.244209 INFO: Resetting torch num_threads to 128
12:44:00.252223 PROGRESS: === Extracted 304670 precursors and 3159384 fragments ===
12:44:00.253078 INFO: === FDR correction performed with classifier version 5 ===
12:44:00.264190 PROGRESS: ============================= Precursor FDR =============================
12:44:00.264373 PROGRESS: Total precursors accumulated: 54,705
12:44:00.264450 PROGRESS: Target precursors: 35,312 (64.55%)
12:44:00.264532 PROGRESS: Decoy precursors: 19,393 (35.45%)
12:44:00.264610 PROGRESS: 
12:44:00.264697 PROGRESS: Precursor Summary:
12:44:00.266644 PROGRESS: Channel   0:	 0.050 FDR:   788; 0.010 FDR:   505; 0.001 FDR:   409
12:44:00.266792 PROGRESS: 
12:44:00.266872 PROGRESS: Protein Summary:
12:44:00.268840 PROGRESS: Channel   0:	 0.050 FDR:   737; 0.010 FDR:   474; 0.001 FDR:   385
12:44:00.268966 PROGRESS: =========================================================================
12:44:00.273339 INFO: Target number of precursors reached.
12:44:00.511410 INFO: fragments_df: keeping 5000 of 3159384 [sum(precursor_idx_mask)=15833 sum(mass_error_mask)=3159384 stop_rank=5000
12:44:02.645537 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:44:02.802392 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:44:02.956716 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:44:03.113520 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:44:03.839038 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:44:03.840480 INFO: Using score_cutoff 40.899712623596194 (fac=0.99, q=1)
12:44:03.841230 INFO: Updating optimization_manager: fwhm_rt             : 2.8750956058502197 -> 2.84663724899292
12:44:03.841328 INFO: Updating optimization_manager: fwhm_mobility       : 0.008923409506678581 -> 0.008652163669466972
12:44:03.841398 INFO: Updating optimization_manager: score_cutoff        : 48.71214786071777 -> 40.899712623596194
12:44:03.841488 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:44:03.849421 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:44:03.878650 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:44:03.885108 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:44:03.950212 INFO: === checking if optimization conditions were reached ===
12:44:03.950589 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
12:44:03.954151 INFO: Updating optimization_manager: rt_error            : 2099.891532 -> 619.5342841037498
12:44:03.954292 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 619.5343.
12:44:03.954385 INFO: ==============================================
12:44:03.954501 INFO: Starting optimization step 1.
12:44:03.954595 PROGRESS: === Extracting elution groups 0 to 24000 ===
12:44:03.954686 INFO: Using python extraction backend
12:44:03.954885 PROGRESS: Extracting batch of 47289 precursors
12:44:03.954998 INFO: === Search parameters used ===
12:44:03.955147 INFO: rt_error       : 619.5342841037498
12:44:03.955241 INFO: mobility_error : 0.1
12:44:03.955330 INFO: num_candidates : 3
12:44:03.955420 INFO: ms1_error      : 15.0
12:44:03.955507 INFO: ms2_error      : 15.0
12:44:03.955592 INFO: fwhm_rt        : 2.84663724899292
12:44:03.955677 INFO: quant_window   : 3
12:44:03.955762 INFO: ==============================================
12:44:04.004950 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:44:04.005164 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:44:04.005248 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
12:44:04.005297 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.01
12:44:04.006541 INFO: Starting candidate selection
12:45:20.164341 INFO: Starting candidate scoring
12:45:24.840531 INFO: Finished candidate processing
12:45:24.840749 INFO: Collecting candidate features
12:45:25.049666 WARNING: intensity_correlation has 28 NaNs ( 0.02 % out of 128045)
12:45:25.050112 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 128045)
12:45:25.058428 INFO: Collecting fragment features
12:45:25.137525 INFO: Finished candidate scoring
12:45:25.218867 INFO: performing precursor FDR with 47 features
12:45:25.219018 INFO: Decoy channel: -1
12:45:25.219046 INFO: competitive: True
12:45:25.262983 INFO: Setting torch num_threads to 2 for FDR classification task
12:45:25.290212 WARNING: dropped 19 target PSMs due to missing features
12:45:25.290370 WARNING: dropped 12 decoy PSMs due to missing features
12:45:25.322653 INFO: Estimating optimal hyperparameters - samples: 102,411, batch_size: 419, learning_rate: 3.20e-04
12:45:25.323123 INFO: Using random state 877777 for train-test-split
12:45:31.715657 INFO: Test AUC: 0.560
12:45:31.715817 INFO: Train AUC: 0.621
12:45:31.715852 INFO: AUC difference: 9.82%
12:45:31.715876 WARNING: AUC difference > 5%. This may indicate overfitting.
12:45:32.032100 INFO: Resetting torch num_threads to 128
12:45:32.035878 PROGRESS: === Extracted 128045 precursors and 1303119 fragments ===
12:45:32.036527 INFO: === FDR correction performed with classifier version 5 ===
12:45:32.041162 PROGRESS: ============================= Precursor FDR =============================
12:45:32.041301 PROGRESS: Total precursors accumulated: 23,267
12:45:32.041383 PROGRESS: Target precursors: 15,034 (64.62%)
12:45:32.041461 PROGRESS: Decoy precursors: 8,233 (35.38%)
12:45:32.041533 PROGRESS: 
12:45:32.041620 PROGRESS: Precursor Summary:
12:45:32.042991 PROGRESS: Channel   0:	 0.050 FDR:   322; 0.010 FDR:   180; 0.001 FDR:   170
12:45:32.043108 PROGRESS: 
12:45:32.043194 PROGRESS: Protein Summary:
12:45:32.044620 PROGRESS: Channel   0:	 0.050 FDR:   313; 0.010 FDR:   177; 0.001 FDR:   167
12:45:32.044737 PROGRESS: =========================================================================
12:45:32.051815 INFO: Target number of precursors not reached yet.
12:45:32.967307 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:45:32.976979 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:45:33.017769 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:45:33.027921 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:45:33.122642 INFO: === skipping optimization until target number of precursors are found ===
12:45:33.123044 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
12:45:33.123181 INFO: Starting optimization step 2.
12:45:33.123316 PROGRESS: === Extracting elution groups 24000 to 56000 ===
12:45:33.123428 INFO: Using python extraction backend
12:45:33.123624 PROGRESS: Extracting batch of 63149 precursors
12:45:33.123734 INFO: === Search parameters used ===
12:45:33.123806 INFO: rt_error       : 619.5342841037498
12:45:33.123894 INFO: mobility_error : 0.1
12:45:33.123960 INFO: num_candidates : 3
12:45:33.124023 INFO: ms1_error      : 15.0
12:45:33.124116 INFO: ms2_error      : 15.0
12:45:33.124201 INFO: fwhm_rt        : 2.84663724899292
12:45:33.124284 INFO: quant_window   : 3
12:45:33.124364 INFO: ==============================================
12:45:33.148940 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:45:33.149149 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:45:33.149221 INFO: FWHM in RT is 2.85 seconds, sigma is 0.63
12:45:33.149264 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.01
12:45:33.150266 INFO: Starting candidate selection
12:47:14.548747 INFO: Starting candidate scoring
12:47:20.430351 INFO: Finished candidate processing
12:47:20.430493 INFO: Collecting candidate features
12:47:20.723013 WARNING: intensity_correlation has 34 NaNs ( 0.02 % out of 170745)
12:47:20.723408 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 170745)
12:47:20.732713 INFO: Collecting fragment features
12:47:20.859025 INFO: Finished candidate scoring
12:47:21.090392 INFO: performing precursor FDR with 47 features
12:47:21.090562 INFO: Decoy channel: -1
12:47:21.090594 INFO: competitive: True
12:47:21.219868 INFO: Setting torch num_threads to 2 for FDR classification task
12:47:21.288618 WARNING: dropped 40 target PSMs due to missing features
12:47:21.288802 WARNING: dropped 26 decoy PSMs due to missing features
12:47:21.380874 INFO: Estimating optimal hyperparameters - samples: 238,979, batch_size: 978, learning_rate: 4.89e-04
12:47:21.381605 INFO: Using random state 877777 for train-test-split
12:47:30.794038 INFO: Test AUC: 0.558
12:47:30.794213 INFO: Train AUC: 0.602
12:47:30.794247 INFO: AUC difference: 7.25%
12:47:30.794272 WARNING: AUC difference > 5%. This may indicate overfitting.
12:47:31.152096 INFO: Resetting torch num_threads to 128
12:47:31.206072 PROGRESS: === Extracted 298790 precursors and 3042697 fragments ===
12:47:31.207114 INFO: === FDR correction performed with classifier version 5 ===
12:47:31.219704 PROGRESS: ============================= Precursor FDR =============================
12:47:31.219891 PROGRESS: Total precursors accumulated: 54,251
12:47:31.220006 PROGRESS: Target precursors: 34,256 (63.14%)
12:47:31.220097 PROGRESS: Decoy precursors: 19,995 (36.86%)
12:47:31.220180 PROGRESS: 
12:47:31.220267 PROGRESS: Precursor Summary:
12:47:31.222156 PROGRESS: Channel   0:	 0.050 FDR:   801; 0.010 FDR:   504; 0.001 FDR:   348
12:47:31.222293 PROGRESS: 
12:47:31.222388 PROGRESS: Protein Summary:
12:47:31.224231 PROGRESS: Channel   0:	 0.050 FDR:   740; 0.010 FDR:   473; 0.001 FDR:   334
12:47:31.224356 PROGRESS: =========================================================================
12:47:31.225734 INFO: Target number of precursors reached.
12:47:31.469642 INFO: fragments_df: keeping 5000 of 3042697 [sum(precursor_idx_mask)=15856 sum(mass_error_mask)=3042696 stop_rank=5000
12:47:32.184726 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:47:32.320771 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:47:32.460705 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:47:32.596110 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:47:33.250413 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:47:33.250986 INFO: Using score_cutoff 40.46679518280029 (fac=0.99, q=1)
12:47:33.251433 INFO: Updating optimization_manager: fwhm_rt             : 2.84663724899292 -> 2.879582166671753
12:47:33.251537 INFO: Updating optimization_manager: fwhm_mobility       : 0.008652163669466972 -> 0.008684265427291393
12:47:33.251617 INFO: Updating optimization_manager: score_cutoff        : 40.899712623596194 -> 40.46679518280029
12:47:33.251698 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:47:33.258498 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:47:33.287814 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:47:33.294211 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:47:33.356209 INFO: === checking if optimization conditions were reached ===
12:47:33.356619 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
12:47:33.359763 INFO: Updating optimization_manager: rt_error            : 619.5342841037498 -> 466.93591277543516
12:47:33.359918 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 466.9359.
12:47:33.360015 INFO: ==============================================
12:47:33.360120 INFO: Starting optimization step 3.
12:47:33.360213 PROGRESS: === Extracting elution groups 0 to 24000 ===
12:47:33.360319 INFO: Using python extraction backend
12:47:33.360505 PROGRESS: Extracting batch of 47289 precursors
12:47:33.360609 INFO: === Search parameters used ===
12:47:33.360682 INFO: rt_error       : 466.93591277543516
12:47:33.360748 INFO: mobility_error : 0.1
12:47:33.360811 INFO: num_candidates : 3
12:47:33.360872 INFO: ms1_error      : 15.0
12:47:33.360936 INFO: ms2_error      : 15.0
12:47:33.360999 INFO: fwhm_rt        : 2.879582166671753
12:47:33.361059 INFO: quant_window   : 3
12:47:33.361119 INFO: ==============================================
12:47:33.380098 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:47:33.380317 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:47:33.380388 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
12:47:33.380432 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.03
12:47:33.381616 INFO: Starting candidate selection
12:48:39.817825 INFO: Starting candidate scoring
12:48:44.171957 INFO: Finished candidate processing
12:48:44.172145 INFO: Collecting candidate features
12:48:44.373861 WARNING: intensity_correlation has 37 NaNs ( 0.03 % out of 126266)
12:48:44.374277 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 126266)
12:48:44.383113 INFO: Collecting fragment features
12:48:44.462535 INFO: Finished candidate scoring
12:48:44.540583 INFO: performing precursor FDR with 47 features
12:48:44.540736 INFO: Decoy channel: -1
12:48:44.540764 INFO: competitive: True
12:48:44.584423 INFO: Setting torch num_threads to 2 for FDR classification task
12:48:44.610895 WARNING: dropped 26 target PSMs due to missing features
12:48:44.611058 WARNING: dropped 16 decoy PSMs due to missing features
12:48:44.642462 INFO: Estimating optimal hyperparameters - samples: 100,979, batch_size: 413, learning_rate: 3.18e-04
12:48:44.642946 INFO: Using random state 877777 for train-test-split
12:48:50.239724 INFO: Test AUC: 0.556
12:48:50.239891 INFO: Train AUC: 0.618
12:48:50.239923 INFO: AUC difference: 9.99%
12:48:50.239947 WARNING: AUC difference > 5%. This may indicate overfitting.
12:48:50.555988 INFO: Resetting torch num_threads to 128
12:48:50.560456 PROGRESS: === Extracted 126266 precursors and 1277525 fragments ===
12:48:50.561148 INFO: === FDR correction performed with classifier version 5 ===
12:48:50.566013 PROGRESS: ============================= Precursor FDR =============================
12:48:50.566182 PROGRESS: Total precursors accumulated: 23,064
12:48:50.566289 PROGRESS: Target precursors: 14,878 (64.51%)
12:48:50.566379 PROGRESS: Decoy precursors: 8,186 (35.49%)
12:48:50.566465 PROGRESS: 
12:48:50.566540 PROGRESS: Precursor Summary:
12:48:50.567832 PROGRESS: Channel   0:	 0.050 FDR:   313; 0.010 FDR:   149; 0.001 FDR:   108
12:48:50.567940 PROGRESS: 
12:48:50.568008 PROGRESS: Protein Summary:
12:48:50.569355 PROGRESS: Channel   0:	 0.050 FDR:   304; 0.010 FDR:   147; 0.001 FDR:   107
12:48:50.569460 PROGRESS: =========================================================================
12:48:50.571694 INFO: Target number of precursors not reached yet.
12:48:50.946805 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:48:50.956635 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:48:50.997800 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:48:51.008114 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:48:51.098181 INFO: === skipping optimization until target number of precursors are found ===
12:48:51.098552 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
12:48:51.098683 INFO: Starting optimization step 4.
12:48:51.098778 PROGRESS: === Extracting elution groups 24000 to 56000 ===
12:48:51.098874 INFO: Using python extraction backend
12:48:51.099058 PROGRESS: Extracting batch of 63149 precursors
12:48:51.099174 INFO: === Search parameters used ===
12:48:51.099246 INFO: rt_error       : 466.93591277543516
12:48:51.099311 INFO: mobility_error : 0.1
12:48:51.099377 INFO: num_candidates : 3
12:48:51.099479 INFO: ms1_error      : 15.0
12:48:51.099552 INFO: ms2_error      : 15.0
12:48:51.099614 INFO: fwhm_rt        : 2.879582166671753
12:48:51.099698 INFO: quant_window   : 3
12:48:51.099760 INFO: ==============================================
12:48:51.126006 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:48:51.126269 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:48:51.126346 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
12:48:51.126394 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.03
12:48:51.128106 INFO: Starting candidate selection
12:50:20.432921 INFO: Starting candidate scoring
12:50:26.112589 INFO: Finished candidate processing
12:50:26.112794 INFO: Collecting candidate features
12:50:26.398133 WARNING: intensity_correlation has 46 NaNs ( 0.03 % out of 168486)
12:50:26.398543 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 168486)
12:50:26.407812 INFO: Collecting fragment features
12:50:26.508953 INFO: Finished candidate scoring
12:50:26.680234 INFO: performing precursor FDR with 47 features
12:50:26.680416 INFO: Decoy channel: -1
12:50:26.680445 INFO: competitive: True
12:50:26.788822 INFO: Setting torch num_threads to 2 for FDR classification task
12:50:26.847637 WARNING: dropped 53 target PSMs due to missing features
12:50:26.847803 WARNING: dropped 39 decoy PSMs due to missing features
12:50:26.931675 INFO: Estimating optimal hyperparameters - samples: 235,728, batch_size: 965, learning_rate: 4.85e-04
12:50:26.932336 INFO: Using random state 877777 for train-test-split
12:50:35.923968 INFO: Test AUC: 0.551
12:50:35.924134 INFO: Train AUC: 0.586
12:50:35.924167 INFO: AUC difference: 5.98%
12:50:35.924193 WARNING: AUC difference > 5%. This may indicate overfitting.
12:50:36.292229 INFO: Resetting torch num_threads to 128
12:50:36.349467 PROGRESS: === Extracted 294752 precursors and 2985203 fragments ===
12:50:36.350454 INFO: === FDR correction performed with classifier version 5 ===
12:50:36.362739 PROGRESS: ============================= Precursor FDR =============================
12:50:36.363002 PROGRESS: Total precursors accumulated: 53,772
12:50:36.363097 PROGRESS: Target precursors: 32,773 (60.95%)
12:50:36.363175 PROGRESS: Decoy precursors: 20,999 (39.05%)
12:50:36.363247 PROGRESS: 
12:50:36.363316 PROGRESS: Precursor Summary:
12:50:36.365060 PROGRESS: Channel   0:	 0.050 FDR:   742; 0.010 FDR:   534; 0.001 FDR:   366
12:50:36.365180 PROGRESS: 
12:50:36.365266 PROGRESS: Protein Summary:
12:50:36.367032 PROGRESS: Channel   0:	 0.050 FDR:   688; 0.010 FDR:   497; 0.001 FDR:   349
12:50:36.367154 PROGRESS: =========================================================================
12:50:36.367990 INFO: Target number of precursors reached.
12:50:36.606632 INFO: fragments_df: keeping 5000 of 2985203 [sum(precursor_idx_mask)=16608 sum(mass_error_mask)=2985200 stop_rank=5000
12:50:36.795029 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:50:36.938192 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:50:37.078904 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:50:37.206631 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:50:37.861876 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:50:37.862447 INFO: Using score_cutoff 42.58727684898376 (fac=0.99, q=1)
12:50:37.862864 INFO: Updating optimization_manager: fwhm_rt             : 2.879582166671753 -> 2.948381185531616
12:50:37.862962 INFO: Updating optimization_manager: fwhm_mobility       : 0.008684265427291393 -> 0.008667944930493832
12:50:37.863031 INFO: Updating optimization_manager: score_cutoff        : 40.46679518280029 -> 42.58727684898376
12:50:37.863104 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:50:37.870043 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:50:37.899432 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:50:37.906076 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:50:37.968117 INFO: === checking if optimization conditions were reached ===
12:50:37.968570 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
12:50:37.971900 INFO: Updating optimization_manager: rt_error            : 466.93591277543516 -> 361.9631190057719
12:50:37.972141 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 361.9631.
12:50:37.972269 INFO: ==============================================
12:50:37.972389 INFO: Starting optimization step 5.
12:50:37.972500 PROGRESS: === Extracting elution groups 0 to 24000 ===
12:50:37.972610 INFO: Using python extraction backend
12:50:37.972809 PROGRESS: Extracting batch of 47289 precursors
12:50:37.972927 INFO: === Search parameters used ===
12:50:37.973019 INFO: rt_error       : 361.9631190057719
12:50:37.973104 INFO: mobility_error : 0.1
12:50:37.973189 INFO: num_candidates : 3
12:50:37.973271 INFO: ms1_error      : 15.0
12:50:37.973351 INFO: ms2_error      : 15.0
12:50:37.973431 INFO: fwhm_rt        : 2.948381185531616
12:50:37.973511 INFO: quant_window   : 3
12:50:37.973591 INFO: ==============================================
12:50:37.992598 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:50:37.992828 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:50:37.992905 INFO: FWHM in RT is 2.95 seconds, sigma is 0.65
12:50:37.992951 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.02
12:50:37.996268 INFO: Starting candidate selection
12:51:26.629018 INFO: Starting candidate scoring
12:51:31.119321 INFO: Finished candidate processing
12:51:31.119532 INFO: Collecting candidate features
12:51:31.319381 WARNING: intensity_correlation has 38 NaNs ( 0.03 % out of 125521)
12:51:31.319791 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 125521)
12:51:31.327647 INFO: Collecting fragment features
12:51:31.396244 INFO: Finished candidate scoring
12:51:31.464581 INFO: performing precursor FDR with 47 features
12:51:31.464751 INFO: Decoy channel: -1
12:51:31.464779 INFO: competitive: True
12:51:31.509143 INFO: Setting torch num_threads to 2 for FDR classification task
12:51:31.535401 WARNING: dropped 21 target PSMs due to missing features
12:51:31.535566 WARNING: dropped 18 decoy PSMs due to missing features
12:51:31.567239 INFO: Estimating optimal hyperparameters - samples: 100,385, batch_size: 411, learning_rate: 3.17e-04
12:51:31.567657 INFO: Using random state 877777 for train-test-split
12:51:37.621120 INFO: Test AUC: 0.550
12:51:37.621337 INFO: Train AUC: 0.597
12:51:37.621373 INFO: AUC difference: 7.84%
12:51:37.621398 WARNING: AUC difference > 5%. This may indicate overfitting.
12:51:37.925907 INFO: Resetting torch num_threads to 128
12:51:37.929498 PROGRESS: === Extracted 125521 precursors and 1260529 fragments ===
12:51:37.930162 INFO: === FDR correction performed with classifier version 5 ===
12:51:37.934442 PROGRESS: ============================= Precursor FDR =============================
12:51:37.934592 PROGRESS: Total precursors accumulated: 22,937
12:51:37.934674 PROGRESS: Target precursors: 14,269 (62.21%)
12:51:37.934740 PROGRESS: Decoy precursors: 8,668 (37.79%)
12:51:37.934818 PROGRESS: 
12:51:37.934878 PROGRESS: Precursor Summary:
12:51:37.936136 PROGRESS: Channel   0:	 0.050 FDR:   350; 0.010 FDR:   220; 0.001 FDR:     0
12:51:37.936244 PROGRESS: 
12:51:37.936314 PROGRESS: Protein Summary:
12:51:37.937645 PROGRESS: Channel   0:	 0.050 FDR:   338; 0.010 FDR:   213; 0.001 FDR:     0
12:51:37.937760 PROGRESS: =========================================================================
12:51:37.939765 INFO: Target number of precursors reached.
12:51:38.036346 INFO: fragments_df: keeping 2904 of 1260529 [sum(precursor_idx_mask)=6856 sum(mass_error_mask)=1260524 stop_rank=2904
12:51:38.221251 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:51:38.326520 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:51:38.438244 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:51:38.556366 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:51:38.901500 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:51:38.902078 INFO: Using score_cutoff 42.19209926834106 (fac=0.99, q=1)
12:51:38.902471 INFO: Updating optimization_manager: fwhm_rt             : 2.948381185531616 -> 2.948381185531616
12:51:38.902568 INFO: Updating optimization_manager: fwhm_mobility       : 0.008667944930493832 -> 0.008629371412098408
12:51:38.902644 INFO: Updating optimization_manager: score_cutoff        : 42.58727684898376 -> 42.19209926834106
12:51:38.902726 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:51:38.910602 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:51:38.940842 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:51:38.947679 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:51:39.012686 INFO: === checking if optimization conditions were reached ===
12:51:39.013050 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
12:51:39.016037 INFO: Updating optimization_manager: rt_error            : 361.9631190057719 -> 237.47216022052282
12:51:39.016183 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 237.4722.
12:51:39.016288 INFO: ==============================================
12:51:39.016392 INFO: Starting optimization step 6.
12:51:39.016476 PROGRESS: === Extracting elution groups 0 to 24000 ===
12:51:39.016572 INFO: Using python extraction backend
12:51:39.016758 PROGRESS: Extracting batch of 47289 precursors
12:51:39.016858 INFO: === Search parameters used ===
12:51:39.016927 INFO: rt_error       : 237.47216022052282
12:51:39.016992 INFO: mobility_error : 0.1
12:51:39.017055 INFO: num_candidates : 3
12:51:39.017117 INFO: ms1_error      : 15.0
12:51:39.017178 INFO: ms2_error      : 15.0
12:51:39.017238 INFO: fwhm_rt        : 2.948381185531616
12:51:39.017299 INFO: quant_window   : 3
12:51:39.017361 INFO: ==============================================
12:51:39.036060 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:51:39.036214 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:51:39.036300 INFO: FWHM in RT is 2.95 seconds, sigma is 0.65
12:51:39.036330 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.00
12:51:39.037438 INFO: Starting candidate selection
12:52:10.675223 INFO: Starting candidate scoring
12:52:14.958740 INFO: Finished candidate processing
12:52:14.959013 INFO: Collecting candidate features
12:52:15.223193 WARNING: intensity_correlation has 51 NaNs ( 0.04 % out of 125487)
12:52:15.223587 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 125487)
12:52:15.231932 INFO: Collecting fragment features
12:52:15.323606 INFO: Finished candidate scoring
12:52:15.419790 INFO: performing precursor FDR with 47 features
12:52:15.419944 INFO: Decoy channel: -1
12:52:15.419976 INFO: competitive: True
12:52:15.462284 INFO: Setting torch num_threads to 2 for FDR classification task
12:52:15.488801 WARNING: dropped 28 target PSMs due to missing features
12:52:15.488968 WARNING: dropped 27 decoy PSMs due to missing features
12:52:15.519054 INFO: Estimating optimal hyperparameters - samples: 100,345, batch_size: 411, learning_rate: 3.17e-04
12:52:15.519513 INFO: Using random state 877777 for train-test-split
12:52:21.413331 INFO: Test AUC: 0.550
12:52:21.413480 INFO: Train AUC: 0.610
12:52:21.413512 INFO: AUC difference: 9.84%
12:52:21.413536 WARNING: AUC difference > 5%. This may indicate overfitting.
12:52:21.719430 INFO: Resetting torch num_threads to 128
12:52:21.728879 PROGRESS: === Extracted 125487 precursors and 1247491 fragments ===
12:52:21.729576 INFO: === FDR correction performed with classifier version 5 ===
12:52:21.734343 PROGRESS: ============================= Precursor FDR =============================
12:52:21.734513 PROGRESS: Total precursors accumulated: 22,978
12:52:21.734611 PROGRESS: Target precursors: 14,566 (63.39%)
12:52:21.734695 PROGRESS: Decoy precursors: 8,412 (36.61%)
12:52:21.734772 PROGRESS: 
12:52:21.734858 PROGRESS: Precursor Summary:
12:52:21.736218 PROGRESS: Channel   0:	 0.050 FDR:   363; 0.010 FDR:   240; 0.001 FDR:   147
12:52:21.736336 PROGRESS: 
12:52:21.736428 PROGRESS: Protein Summary:
12:52:21.737866 PROGRESS: Channel   0:	 0.050 FDR:   351; 0.010 FDR:   233; 0.001 FDR:   145
12:52:21.737974 PROGRESS: =========================================================================
12:52:21.739122 INFO: Target number of precursors reached.
12:52:21.839099 INFO: fragments_df: keeping 3101 of 1247491 [sum(precursor_idx_mask)=7323 sum(mass_error_mask)=1247488 stop_rank=3101
12:52:22.542015 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:52:22.668319 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:52:22.802552 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:52:22.921715 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:52:23.296160 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:52:23.296704 INFO: Using score_cutoff 36.048650537109374 (fac=0.99, q=1)
12:52:23.297086 INFO: Updating optimization_manager: fwhm_rt             : 2.948381185531616 -> 2.948381185531616
12:52:23.297175 INFO: Updating optimization_manager: fwhm_mobility       : 0.008629371412098408 -> 0.008629371412098408
12:52:23.297240 INFO: Updating optimization_manager: score_cutoff        : 42.19209926834106 -> 36.048650537109374
12:52:23.297309 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:52:23.304398 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:52:23.334258 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:52:23.340662 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:52:23.412983 INFO: === checking if optimization conditions were reached ===
12:52:23.413415 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
12:52:23.416445 INFO: Updating optimization_manager: rt_error            : 237.47216022052282 -> 181.72057326563856
12:52:23.416614 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 181.7206.
12:52:23.416728 INFO: ==============================================
12:52:23.416849 INFO: Starting optimization step 7.
12:52:23.416958 PROGRESS: === Extracting elution groups 0 to 24000 ===
12:52:23.417071 INFO: Using python extraction backend
12:52:23.417265 PROGRESS: Extracting batch of 47289 precursors
12:52:23.417382 INFO: === Search parameters used ===
12:52:23.417482 INFO: rt_error       : 181.72057326563856
12:52:23.417572 INFO: mobility_error : 0.1
12:52:23.417654 INFO: num_candidates : 3
12:52:23.417734 INFO: ms1_error      : 15.0
12:52:23.417831 INFO: ms2_error      : 15.0
12:52:23.417915 INFO: fwhm_rt        : 2.948381185531616
12:52:23.417994 INFO: quant_window   : 3
12:52:23.418077 INFO: ==============================================
12:52:23.436450 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:52:23.436674 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:52:23.436749 INFO: FWHM in RT is 2.95 seconds, sigma is 0.65
12:52:23.436795 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.00
12:52:23.437891 INFO: Starting candidate selection
12:52:47.209206 INFO: Starting candidate scoring
12:52:51.875980 INFO: Finished candidate processing
12:52:51.876141 INFO: Collecting candidate features
12:52:52.084213 WARNING: intensity_correlation has 56 NaNs ( 0.04 % out of 125272)
12:52:52.084586 WARNING: height_correlation has 5 NaNs ( 0.00 % out of 125272)
12:52:52.092566 INFO: Collecting fragment features
12:52:52.175183 INFO: Finished candidate scoring
12:52:52.249759 INFO: performing precursor FDR with 47 features
12:52:52.249898 INFO: Decoy channel: -1
12:52:52.249927 INFO: competitive: True
12:52:52.290920 INFO: Setting torch num_threads to 2 for FDR classification task
12:52:52.316476 WARNING: dropped 31 target PSMs due to missing features
12:52:52.316634 WARNING: dropped 28 decoy PSMs due to missing features
12:52:52.341354 INFO: Estimating optimal hyperparameters - samples: 100,170, batch_size: 410, learning_rate: 3.16e-04
12:52:52.341755 INFO: Using random state 877777 for train-test-split
12:52:58.038327 INFO: Test AUC: 0.547
12:52:58.038485 INFO: Train AUC: 0.610
12:52:58.038518 INFO: AUC difference: 10.30%
12:52:58.038548 WARNING: AUC difference > 5%. This may indicate overfitting.
12:52:58.349698 INFO: Resetting torch num_threads to 128
12:52:58.353659 PROGRESS: === Extracted 125272 precursors and 1236763 fragments ===
12:52:58.354281 INFO: === FDR correction performed with classifier version 5 ===
12:52:58.358225 PROGRESS: ============================= Precursor FDR =============================
12:52:58.358373 PROGRESS: Total precursors accumulated: 22,962
12:52:58.358450 PROGRESS: Target precursors: 14,545 (63.34%)
12:52:58.358514 PROGRESS: Decoy precursors: 8,417 (36.66%)
12:52:58.358590 PROGRESS: 
12:52:58.358650 PROGRESS: Precursor Summary:
12:52:58.359967 PROGRESS: Channel   0:	 0.050 FDR:   391; 0.010 FDR:   239; 0.001 FDR:   193
12:52:58.360079 PROGRESS: 
12:52:58.360150 PROGRESS: Protein Summary:
12:52:58.361563 PROGRESS: Channel   0:	 0.050 FDR:   378; 0.010 FDR:   231; 0.001 FDR:   187
12:52:58.361675 PROGRESS: =========================================================================
12:52:58.362421 INFO: Target number of precursors reached.
12:52:58.458385 INFO: fragments_df: keeping 3098 of 1236763 [sum(precursor_idx_mask)=7330 sum(mass_error_mask)=1236763 stop_rank=3098
12:52:58.807579 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:52:58.918906 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:52:59.032958 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:52:59.153944 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:52:59.526742 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:52:59.527275 INFO: Using score_cutoff 32.16528761901856 (fac=0.99, q=1)
12:52:59.527648 INFO: Updating optimization_manager: fwhm_rt             : 2.948381185531616 -> 2.9302210807800293
12:52:59.527742 INFO: Updating optimization_manager: fwhm_mobility       : 0.008629371412098408 -> 0.008490501902997494
12:52:59.527809 INFO: Updating optimization_manager: score_cutoff        : 36.048650537109374 -> 32.16528761901856
12:52:59.527879 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:52:59.535585 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:52:59.566006 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:52:59.572880 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:52:59.637187 INFO: === checking if optimization conditions were reached ===
12:52:59.637549 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
12:52:59.640567 INFO: Updating optimization_manager: rt_error            : 181.72057326563856 -> 161.93239637179022
12:52:59.640712 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 161.9324.
12:52:59.640815 INFO: ==============================================
12:52:59.640914 INFO: Starting optimization step 8.
12:52:59.641002 PROGRESS: === Extracting elution groups 0 to 24000 ===
12:52:59.641093 INFO: Using python extraction backend
12:52:59.641262 PROGRESS: Extracting batch of 47289 precursors
12:52:59.641357 INFO: === Search parameters used ===
12:52:59.641470 INFO: rt_error       : 161.93239637179022
12:52:59.641564 INFO: mobility_error : 0.1
12:52:59.641656 INFO: num_candidates : 3
12:52:59.641754 INFO: ms1_error      : 15.0
12:52:59.641848 INFO: ms2_error      : 15.0
12:52:59.641934 INFO: fwhm_rt        : 2.9302210807800293
12:52:59.642020 INFO: quant_window   : 3
12:52:59.642104 INFO: ==============================================
12:52:59.660717 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:52:59.660928 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:52:59.661000 INFO: FWHM in RT is 2.93 seconds, sigma is 0.64
12:52:59.661064 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.94
12:52:59.662231 INFO: Starting candidate selection
12:53:21.016067 INFO: Starting candidate scoring
12:53:26.719763 INFO: Finished candidate processing
12:53:26.719957 INFO: Collecting candidate features
12:53:26.928876 WARNING: intensity_correlation has 46 NaNs ( 0.04 % out of 124947)
12:53:26.929250 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 124947)
12:53:26.937330 INFO: Collecting fragment features
12:53:27.013244 INFO: Finished candidate scoring
12:53:27.082554 INFO: performing precursor FDR with 47 features
12:53:27.082696 INFO: Decoy channel: -1
12:53:27.082724 INFO: competitive: True
12:53:27.123497 INFO: Setting torch num_threads to 2 for FDR classification task
12:53:27.149226 WARNING: dropped 22 target PSMs due to missing features
12:53:27.149389 WARNING: dropped 30 decoy PSMs due to missing features
12:53:27.174975 INFO: Estimating optimal hyperparameters - samples: 99,916, batch_size: 409, learning_rate: 3.16e-04
12:53:27.175439 INFO: Using random state 877777 for train-test-split
12:53:32.970381 INFO: Test AUC: 0.547
12:53:32.970533 INFO: Train AUC: 0.610
12:53:32.970565 INFO: AUC difference: 10.29%
12:53:32.970591 WARNING: AUC difference > 5%. This may indicate overfitting.
12:53:33.278368 INFO: Resetting torch num_threads to 128
12:53:33.281938 PROGRESS: === Extracted 124947 precursors and 1228545 fragments ===
12:53:33.282575 INFO: === FDR correction performed with classifier version 5 ===
12:53:33.286659 PROGRESS: ============================= Precursor FDR =============================
12:53:33.286806 PROGRESS: Total precursors accumulated: 22,899
12:53:33.286885 PROGRESS: Target precursors: 14,607 (63.79%)
12:53:33.286950 PROGRESS: Decoy precursors: 8,292 (36.21%)
12:53:33.287029 PROGRESS: 
12:53:33.287113 PROGRESS: Precursor Summary:
12:53:33.288478 PROGRESS: Channel   0:	 0.050 FDR:   374; 0.010 FDR:   247; 0.001 FDR:   224
12:53:33.288587 PROGRESS: 
12:53:33.288658 PROGRESS: Protein Summary:
12:53:33.290123 PROGRESS: Channel   0:	 0.050 FDR:   360; 0.010 FDR:   240; 0.001 FDR:   217
12:53:33.290236 PROGRESS: =========================================================================
12:53:33.290908 INFO: Target number of precursors reached.
12:53:33.386161 INFO: fragments_df: keeping 3084 of 1228545 [sum(precursor_idx_mask)=7547 sum(mass_error_mask)=1228545 stop_rank=3084
12:53:33.570285 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:53:33.681645 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:53:33.796111 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:53:33.912724 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:53:34.282019 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:53:34.282581 INFO: Using score_cutoff 29.457504193496703 (fac=0.99, q=1)
12:53:34.282960 INFO: Updating optimization_manager: fwhm_rt             : 2.9302210807800293 -> 2.9228410720825195
12:53:34.283057 INFO: Updating optimization_manager: fwhm_mobility       : 0.008490501902997494 -> 0.008344557136297226
12:53:34.283127 INFO: Updating optimization_manager: score_cutoff        : 32.16528761901856 -> 29.457504193496703
12:53:34.283201 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:53:34.291038 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:53:34.321501 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:53:34.328361 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:53:34.393058 INFO: === checking if optimization conditions were reached ===
12:53:34.393405 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
12:53:34.396418 INFO: Updating optimization_manager: rt_error            : 161.93239637179022 -> 161.81511161609725
12:53:34.396566 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 161.8151.
12:53:34.396664 INFO: ==============================================
12:53:34.396815 INFO: Starting optimization step 9.
12:53:34.396929 PROGRESS: === Extracting elution groups 0 to 24000 ===
12:53:34.397046 INFO: Using python extraction backend
12:53:34.397244 PROGRESS: Extracting batch of 47289 precursors
12:53:34.397363 INFO: === Search parameters used ===
12:53:34.397456 INFO: rt_error       : 161.81511161609725
12:53:34.397544 INFO: mobility_error : 0.1
12:53:34.397638 INFO: num_candidates : 3
12:53:34.397724 INFO: ms1_error      : 15.0
12:53:34.397862 INFO: ms2_error      : 15.0
12:53:34.397956 INFO: fwhm_rt        : 2.9228410720825195
12:53:34.398039 INFO: quant_window   : 3
12:53:34.398122 INFO: ==============================================
12:53:34.416761 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:53:34.416926 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:53:34.416978 INFO: FWHM in RT is 2.92 seconds, sigma is 0.64
12:53:34.417008 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.87
12:53:34.418183 INFO: Starting candidate selection
12:53:55.374075 INFO: Starting candidate scoring
12:54:00.111167 INFO: Finished candidate processing
12:54:00.111369 INFO: Collecting candidate features
12:54:00.316408 WARNING: intensity_correlation has 56 NaNs ( 0.04 % out of 124971)
12:54:00.316854 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 124971)
12:54:00.324794 INFO: Collecting fragment features
12:54:00.394753 INFO: Finished candidate scoring
12:54:00.464898 INFO: performing precursor FDR with 47 features
12:54:00.465066 INFO: Decoy channel: -1
12:54:00.465101 INFO: competitive: True
12:54:00.515240 INFO: Setting torch num_threads to 2 for FDR classification task
12:54:00.541429 WARNING: dropped 32 target PSMs due to missing features
12:54:00.541591 WARNING: dropped 29 decoy PSMs due to missing features
12:54:00.574441 INFO: Estimating optimal hyperparameters - samples: 99,928, batch_size: 409, learning_rate: 3.16e-04
12:54:00.574821 INFO: Using random state 877777 for train-test-split
12:54:06.446832 INFO: Test AUC: 0.550
12:54:06.446988 INFO: Train AUC: 0.609
12:54:06.447020 INFO: AUC difference: 9.74%
12:54:06.447045 WARNING: AUC difference > 5%. This may indicate overfitting.
12:54:06.748074 INFO: Resetting torch num_threads to 128
12:54:06.751662 PROGRESS: === Extracted 124971 precursors and 1227966 fragments ===
12:54:06.752264 INFO: === FDR correction performed with classifier version 5 ===
12:54:06.756249 PROGRESS: ============================= Precursor FDR =============================
12:54:06.756419 PROGRESS: Total precursors accumulated: 22,892
12:54:06.756499 PROGRESS: Target precursors: 14,468 (63.20%)
12:54:06.756568 PROGRESS: Decoy precursors: 8,424 (36.80%)
12:54:06.756631 PROGRESS: 
12:54:06.756692 PROGRESS: Precursor Summary:
12:54:06.758046 PROGRESS: Channel   0:	 0.050 FDR:   429; 0.010 FDR:   269; 0.001 FDR:   243
12:54:06.758159 PROGRESS: 
12:54:06.758232 PROGRESS: Protein Summary:
12:54:06.759676 PROGRESS: Channel   0:	 0.050 FDR:   415; 0.010 FDR:   259; 0.001 FDR:   235
12:54:06.759786 PROGRESS: =========================================================================
12:54:06.760469 INFO: Target number of precursors reached.
12:54:06.855602 INFO: fragments_df: keeping 3359 of 1227966 [sum(precursor_idx_mask)=8267 sum(mass_error_mask)=1227966 stop_rank=3359
12:54:07.040375 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:54:07.156517 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:54:07.275727 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:54:07.392838 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:54:07.798502 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:54:07.799082 INFO: Using score_cutoff 39.18769300689697 (fac=0.99, q=1)
12:54:07.799451 INFO: Updating optimization_manager: fwhm_rt             : 2.9228410720825195 -> 2.889674663543701
12:54:07.799547 INFO: Updating optimization_manager: fwhm_mobility       : 0.008344557136297226 -> 0.008159670978784561
12:54:07.799616 INFO: Updating optimization_manager: score_cutoff        : 29.457504193496703 -> 39.18769300689697
12:54:07.799697 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:54:07.807301 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:54:07.837556 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:54:07.844666 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:54:07.910116 INFO: === checking if optimization conditions were reached ===
12:54:07.910465 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
12:54:07.912325 INFO: Updating optimization_manager: rt_error            : 161.81511161609725 -> 161.81511161609725
12:54:07.912543 INFO: Updating optimization_manager: classifier_version  : 5 -> 15
12:54:07.912680 INFO: Updating optimization_manager: score_cutoff        : 39.18769300689697 -> 39.18769300689697
12:54:07.912807 INFO: Updating optimization_manager: fwhm_rt             : 2.889674663543701 -> 2.889674663543701
12:54:07.912927 INFO: Updating optimization_manager: fwhm_mobility       : 0.008159670978784561 -> 0.008159670978784561
12:54:07.913049 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 161.8151 found after 8 searches.
12:54:07.913141 INFO: ==============================================
12:54:07.913237 PROGRESS: Optimization finished for rt_error.
12:54:08.106442 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:54:08.114211 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:54:08.144584 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:54:08.151294 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:54:08.211492 INFO: Starting optimization step 0.
12:54:08.211842 PROGRESS: === Extracting elution groups 0 to 24000 ===
12:54:08.211959 INFO: Using python extraction backend
12:54:08.212149 PROGRESS: Extracting batch of 47289 precursors
12:54:08.212256 INFO: === Search parameters used ===
12:54:08.212330 INFO: rt_error       : 161.81511161609725
12:54:08.212396 INFO: mobility_error : 0.1
12:54:08.212460 INFO: num_candidates : 3
12:54:08.212523 INFO: ms1_error      : 15.0
12:54:08.212584 INFO: ms2_error      : 15.0
12:54:08.212646 INFO: fwhm_rt        : 2.889674663543701
12:54:08.212705 INFO: quant_window   : 3
12:54:08.212766 INFO: ==============================================
12:54:08.231778 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:54:08.231942 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:54:08.231998 INFO: FWHM in RT is 2.89 seconds, sigma is 0.64
12:54:08.232028 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.78
12:54:08.233068 INFO: Starting candidate selection
12:54:29.431699 INFO: Starting candidate scoring
12:54:34.065208 INFO: Finished candidate processing
12:54:34.065341 INFO: Collecting candidate features
12:54:34.247515 WARNING: intensity_correlation has 48 NaNs ( 0.04 % out of 125013)
12:54:34.247912 WARNING: height_correlation has 4 NaNs ( 0.00 % out of 125013)
12:54:34.255943 INFO: Collecting fragment features
12:54:34.324130 INFO: Finished candidate scoring
12:54:34.387350 INFO: performing precursor FDR with 47 features
12:54:34.387515 INFO: Decoy channel: -1
12:54:34.387543 INFO: competitive: True
12:54:34.433477 INFO: Setting torch num_threads to 2 for FDR classification task
12:54:34.459365 WARNING: dropped 31 target PSMs due to missing features
12:54:34.459530 WARNING: dropped 20 decoy PSMs due to missing features
12:54:34.490096 INFO: Estimating optimal hyperparameters - samples: 99,969, batch_size: 409, learning_rate: 3.16e-04
12:54:34.490509 INFO: Using random state 292856 for train-test-split
12:54:40.587593 INFO: Test AUC: 0.575
12:54:40.587747 INFO: Train AUC: 0.630
12:54:40.587779 INFO: AUC difference: 8.80%
12:54:40.587812 WARNING: AUC difference > 5%. This may indicate overfitting.
12:54:40.888813 INFO: Resetting torch num_threads to 128
12:54:40.892363 PROGRESS: === Extracted 125013 precursors and 1228348 fragments ===
12:54:40.892976 INFO: === FDR correction performed with classifier version 15 ===
12:54:40.897478 PROGRESS: ============================= Precursor FDR =============================
12:54:40.897632 PROGRESS: Total precursors accumulated: 22,931
12:54:40.897715 PROGRESS: Target precursors: 15,225 (66.39%)
12:54:40.897795 PROGRESS: Decoy precursors: 7,706 (33.61%)
12:54:40.897860 PROGRESS: 
12:54:40.897922 PROGRESS: Precursor Summary:
12:54:40.899310 PROGRESS: Channel   0:	 0.050 FDR:   475; 0.010 FDR:   335; 0.001 FDR:   232
12:54:40.899420 PROGRESS: 
12:54:40.899487 PROGRESS: Protein Summary:
12:54:40.900969 PROGRESS: Channel   0:	 0.050 FDR:   458; 0.010 FDR:   326; 0.001 FDR:   226
12:54:40.901076 PROGRESS: =========================================================================
12:54:40.901779 INFO: Target number of precursors reached.
12:54:40.995769 INFO: fragments_df: keeping 3970 of 1228348 [sum(precursor_idx_mask)=9978 sum(mass_error_mask)=1228348 stop_rank=3970
12:54:41.181830 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:54:41.313146 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:54:41.442094 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:54:41.571180 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:54:42.066620 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:54:42.067165 INFO: Using score_cutoff 24.735968000793456 (fac=0.99, q=1)
12:54:42.067539 INFO: Updating optimization_manager: fwhm_rt             : 2.889674663543701 -> 2.88808012008667
12:54:42.067634 INFO: Updating optimization_manager: fwhm_mobility       : 0.008159670978784561 -> 0.0078039271757006645
12:54:42.067703 INFO: Updating optimization_manager: score_cutoff        : 39.18769300689697 -> 24.735968000793456
12:54:42.067782 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:54:42.075098 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:54:42.105066 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:54:42.111491 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:54:42.176484 INFO: === checking if optimization conditions were reached ===
12:54:42.176845 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
12:54:42.179417 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.08694743194301657
12:54:42.179557 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0869.
12:54:42.179650 INFO: ==============================================
12:54:42.179746 INFO: Starting optimization step 1.
12:54:42.179832 PROGRESS: === Extracting elution groups 0 to 24000 ===
12:54:42.179921 INFO: Using python extraction backend
12:54:42.180099 PROGRESS: Extracting batch of 47289 precursors
12:54:42.180192 INFO: === Search parameters used ===
12:54:42.180261 INFO: rt_error       : 161.81511161609725
12:54:42.180325 INFO: mobility_error : 0.08694743194301657
12:54:42.180387 INFO: num_candidates : 3
12:54:42.180451 INFO: ms1_error      : 15.0
12:54:42.180514 INFO: ms2_error      : 15.0
12:54:42.180573 INFO: fwhm_rt        : 2.88808012008667
12:54:42.180646 INFO: quant_window   : 3
12:54:42.180708 INFO: ==============================================
12:54:42.199884 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:54:42.200041 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:54:42.200104 INFO: FWHM in RT is 2.89 seconds, sigma is 0.63
12:54:42.200132 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.62
12:54:42.201109 INFO: Starting candidate selection
12:55:00.699118 INFO: Starting candidate scoring
12:55:05.194678 INFO: Finished candidate processing
12:55:05.194865 INFO: Collecting candidate features
12:55:05.423049 WARNING: intensity_correlation has 75 NaNs ( 0.06 % out of 123373)
12:55:05.423475 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 123373)
12:55:05.431506 INFO: Collecting fragment features
12:55:05.500566 INFO: Finished candidate scoring
12:55:05.568321 INFO: performing precursor FDR with 47 features
12:55:05.568500 INFO: Decoy channel: -1
12:55:05.568534 INFO: competitive: True
12:55:05.609423 INFO: Setting torch num_threads to 2 for FDR classification task
12:55:05.634902 WARNING: dropped 43 target PSMs due to missing features
12:55:05.635060 WARNING: dropped 37 decoy PSMs due to missing features
12:55:05.663745 INFO: Estimating optimal hyperparameters - samples: 98,634, batch_size: 404, learning_rate: 3.14e-04
12:55:05.664156 INFO: Using random state 292856 for train-test-split
12:55:11.726591 INFO: Test AUC: 0.570
12:55:11.726751 INFO: Train AUC: 0.629
12:55:11.726784 INFO: AUC difference: 9.46%
12:55:11.726809 WARNING: AUC difference > 5%. This may indicate overfitting.
12:55:12.024148 INFO: Resetting torch num_threads to 128
12:55:12.027850 PROGRESS: === Extracted 123373 precursors and 1209005 fragments ===
12:55:12.028494 INFO: === FDR correction performed with classifier version 15 ===
12:55:12.032522 PROGRESS: ============================= Precursor FDR =============================
12:55:12.032670 PROGRESS: Total precursors accumulated: 22,673
12:55:12.032764 PROGRESS: Target precursors: 14,924 (65.82%)
12:55:12.032831 PROGRESS: Decoy precursors: 7,749 (34.18%)
12:55:12.032910 PROGRESS: 
12:55:12.032976 PROGRESS: Precursor Summary:
12:55:12.034564 PROGRESS: Channel   0:	 0.050 FDR:   482; 0.010 FDR:   273; 0.001 FDR:   259
12:55:12.034680 PROGRESS: 
12:55:12.034755 PROGRESS: Protein Summary:
12:55:12.036204 PROGRESS: Channel   0:	 0.050 FDR:   465; 0.010 FDR:   263; 0.001 FDR:   250
12:55:12.036315 PROGRESS: =========================================================================
12:55:12.037044 INFO: Target number of precursors reached.
12:55:12.130232 INFO: fragments_df: keeping 3432 of 1209005 [sum(precursor_idx_mask)=8226 sum(mass_error_mask)=1209005 stop_rank=3432
12:55:12.318523 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:55:12.455095 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:55:12.597049 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:55:12.743623 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:55:13.203495 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:55:13.204050 INFO: Using score_cutoff 30.727134970092774 (fac=0.99, q=1)
12:55:13.204420 INFO: Updating optimization_manager: fwhm_rt             : 2.88808012008667 -> 2.878197193145752
12:55:13.204518 INFO: Updating optimization_manager: fwhm_mobility       : 0.0078039271757006645 -> 0.008176051080226898
12:55:13.204588 INFO: Updating optimization_manager: score_cutoff        : 24.735968000793456 -> 30.727134970092774
12:55:13.204668 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:55:13.212369 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:55:13.242805 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:55:13.249707 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:55:13.316784 INFO: === checking if optimization conditions were reached ===
12:55:13.317100 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
12:55:13.319443 INFO: Updating optimization_manager: mobility_error      : 0.08694743194301657 -> 0.06987021920391867
12:55:13.319567 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0699.
12:55:13.319648 INFO: ==============================================
12:55:13.319734 INFO: Starting optimization step 2.
12:55:13.319814 PROGRESS: === Extracting elution groups 0 to 24000 ===
12:55:13.319895 INFO: Using python extraction backend
12:55:13.320078 PROGRESS: Extracting batch of 47289 precursors
12:55:13.320183 INFO: === Search parameters used ===
12:55:13.320265 INFO: rt_error       : 161.81511161609725
12:55:13.320336 INFO: mobility_error : 0.06987021920391867
12:55:13.320414 INFO: num_candidates : 3
12:55:13.320481 INFO: ms1_error      : 15.0
12:55:13.320547 INFO: ms2_error      : 15.0
12:55:13.320623 INFO: fwhm_rt        : 2.878197193145752
12:55:13.320689 INFO: quant_window   : 3
12:55:13.320751 INFO: ==============================================
12:55:13.334391 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:55:13.334539 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:55:13.334594 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
12:55:13.334625 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
12:55:13.335474 INFO: Starting candidate selection
12:55:28.742639 INFO: Starting candidate scoring
12:55:33.376802 INFO: Finished candidate processing
12:55:33.376934 INFO: Collecting candidate features
12:55:33.554977 WARNING: intensity_correlation has 75 NaNs ( 0.06 % out of 121752)
12:55:33.555350 WARNING: height_correlation has 10 NaNs ( 0.01 % out of 121752)
12:55:33.563124 INFO: Collecting fragment features
12:55:33.631232 INFO: Finished candidate scoring
12:55:33.707206 INFO: performing precursor FDR with 47 features
12:55:33.707368 INFO: Decoy channel: -1
12:55:33.707397 INFO: competitive: True
12:55:33.747349 INFO: Setting torch num_threads to 2 for FDR classification task
12:55:33.772759 WARNING: dropped 43 target PSMs due to missing features
12:55:33.772920 WARNING: dropped 38 decoy PSMs due to missing features
12:55:33.798514 INFO: Estimating optimal hyperparameters - samples: 97,336, batch_size: 398, learning_rate: 3.12e-04
12:55:33.798921 INFO: Using random state 292856 for train-test-split
12:55:39.999506 INFO: Test AUC: 0.572
12:55:39.999663 INFO: Train AUC: 0.625
12:55:39.999697 INFO: AUC difference: 8.57%
12:55:39.999728 WARNING: AUC difference > 5%. This may indicate overfitting.
12:55:40.298445 INFO: Resetting torch num_threads to 128
12:55:40.302239 PROGRESS: === Extracted 121752 precursors and 1186827 fragments ===
12:55:40.302871 INFO: === FDR correction performed with classifier version 15 ===
12:55:40.306883 PROGRESS: ============================= Precursor FDR =============================
12:55:40.307026 PROGRESS: Total precursors accumulated: 22,454
12:55:40.307104 PROGRESS: Target precursors: 14,696 (65.45%)
12:55:40.307197 PROGRESS: Decoy precursors: 7,758 (34.55%)
12:55:40.307259 PROGRESS: 
12:55:40.307335 PROGRESS: Precursor Summary:
12:55:40.308728 PROGRESS: Channel   0:	 0.050 FDR:   517; 0.010 FDR:   320; 0.001 FDR:   194
12:55:40.308856 PROGRESS: 
12:55:40.308951 PROGRESS: Protein Summary:
12:55:40.310518 PROGRESS: Channel   0:	 0.050 FDR:   501; 0.010 FDR:   310; 0.001 FDR:   188
12:55:40.310655 PROGRESS: =========================================================================
12:55:40.311386 INFO: Target number of precursors reached.
12:55:40.404574 INFO: fragments_df: keeping 3791 of 1186827 [sum(precursor_idx_mask)=9642 sum(mass_error_mask)=1186827 stop_rank=3791
12:55:40.591605 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:55:40.721613 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:55:40.864448 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:55:41.000860 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:55:41.485735 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:55:41.486325 INFO: Using score_cutoff 30.882023628044127 (fac=0.99, q=1)
12:55:41.486695 INFO: Updating optimization_manager: fwhm_rt             : 2.878197193145752 -> 2.904594659805298
12:55:41.486788 INFO: Updating optimization_manager: fwhm_mobility       : 0.008176051080226898 -> 0.007871473208069801
12:55:41.486855 INFO: Updating optimization_manager: score_cutoff        : 30.727134970092774 -> 30.882023628044127
12:55:41.486928 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:55:41.494295 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:55:41.524385 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:55:41.531136 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:55:41.598351 INFO: === checking if optimization conditions were reached ===
12:55:41.598672 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
12:55:41.601156 INFO: Updating optimization_manager: mobility_error      : 0.06987021920391867 -> 0.057407845641076205
12:55:41.601289 PROGRESS: ❌ mobility_error : optimization incomplete after 3 search(es). Will search with parameter 0.0574.
12:55:41.601387 INFO: ==============================================
12:55:41.601495 INFO: Starting optimization step 3.
12:55:41.601593 PROGRESS: === Extracting elution groups 0 to 24000 ===
12:55:41.601690 INFO: Using python extraction backend
12:55:41.601876 PROGRESS: Extracting batch of 47289 precursors
12:55:41.601977 INFO: === Search parameters used ===
12:55:41.602050 INFO: rt_error       : 161.81511161609725
12:55:41.602126 INFO: mobility_error : 0.057407845641076205
12:55:41.602197 INFO: num_candidates : 3
12:55:41.602257 INFO: ms1_error      : 15.0
12:55:41.602314 INFO: ms2_error      : 15.0
12:55:41.602377 INFO: fwhm_rt        : 2.904594659805298
12:55:41.602443 INFO: quant_window   : 3
12:55:41.602506 INFO: ==============================================
12:55:41.616012 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:55:41.616155 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:55:41.616217 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
12:55:41.616248 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.65
12:55:41.617027 INFO: Starting candidate selection
12:55:53.823496 INFO: Starting candidate scoring
12:55:58.283585 INFO: Finished candidate processing
12:55:58.283789 INFO: Collecting candidate features
12:55:58.485673 WARNING: intensity_correlation has 65 NaNs ( 0.05 % out of 119567)
12:55:58.486076 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 119567)
12:55:58.493675 INFO: Collecting fragment features
12:55:58.565277 INFO: Finished candidate scoring
12:55:58.629045 INFO: performing precursor FDR with 47 features
12:55:58.629197 INFO: Decoy channel: -1
12:55:58.629224 INFO: competitive: True
12:55:58.668490 INFO: Setting torch num_threads to 2 for FDR classification task
12:55:58.694155 WARNING: dropped 39 target PSMs due to missing features
12:55:58.694331 WARNING: dropped 33 decoy PSMs due to missing features
12:55:58.715810 INFO: Estimating optimal hyperparameters - samples: 95,596, batch_size: 391, learning_rate: 3.09e-04
12:55:58.716220 INFO: Using random state 292856 for train-test-split
12:56:04.385029 INFO: Test AUC: 0.559
12:56:04.385193 INFO: Train AUC: 0.607
12:56:04.385225 INFO: AUC difference: 7.87%
12:56:04.385250 WARNING: AUC difference > 5%. This may indicate overfitting.
12:56:04.681665 INFO: Resetting torch num_threads to 128
12:56:04.685199 PROGRESS: === Extracted 119567 precursors and 1154664 fragments ===
12:56:04.685823 INFO: === FDR correction performed with classifier version 15 ===
12:56:04.689614 PROGRESS: ============================= Precursor FDR =============================
12:56:04.689764 PROGRESS: Total precursors accumulated: 22,048
12:56:04.689854 PROGRESS: Target precursors: 13,993 (63.47%)
12:56:04.689929 PROGRESS: Decoy precursors: 8,055 (36.53%)
12:56:04.689992 PROGRESS: 
12:56:04.690050 PROGRESS: Precursor Summary:
12:56:04.691355 PROGRESS: Channel   0:	 0.050 FDR:   466; 0.010 FDR:   234; 0.001 FDR:   129
12:56:04.691475 PROGRESS: 
12:56:04.691548 PROGRESS: Protein Summary:
12:56:04.692990 PROGRESS: Channel   0:	 0.050 FDR:   452; 0.010 FDR:   227; 0.001 FDR:   127
12:56:04.693099 PROGRESS: =========================================================================
12:56:04.693963 INFO: Target number of precursors reached.
12:56:04.784519 INFO: fragments_df: keeping 2977 of 1154664 [sum(precursor_idx_mask)=7167 sum(mass_error_mask)=1154655 stop_rank=2977
12:56:04.971207 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
12:56:05.082320 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
12:56:05.199160 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
12:56:05.309709 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
12:56:05.668721 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
12:56:05.669337 INFO: Using score_cutoff 39.88312657814026 (fac=0.99, q=1)
12:56:05.669709 INFO: Updating optimization_manager: fwhm_rt             : 2.904594659805298 -> 2.932662010192871
12:56:05.669812 INFO: Updating optimization_manager: fwhm_mobility       : 0.007871473208069801 -> 0.008488073945045471
12:56:05.669884 INFO: Updating optimization_manager: score_cutoff        : 30.882023628044127 -> 39.88312657814026
12:56:05.669989 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:56:05.677998 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:56:05.708340 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:56:05.715390 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:56:05.778311 INFO: === checking if optimization conditions were reached ===
12:56:05.778658 PROGRESS: === Optimization of mobility_error has been performed 4 time(s); minimum number is 2 ===
12:56:05.779775 INFO: Updating optimization_manager: mobility_error      : 0.057407845641076205 -> 0.1
12:56:05.779952 INFO: Updating optimization_manager: classifier_version  : 15 -> 16
12:56:05.780105 INFO: Updating optimization_manager: score_cutoff        : 39.88312657814026 -> 24.735968000793456
12:56:05.780246 INFO: Updating optimization_manager: fwhm_rt             : 2.932662010192871 -> 2.88808012008667
12:56:05.780380 INFO: Updating optimization_manager: fwhm_mobility       : 0.008488073945045471 -> 0.0078039271757006645
12:56:05.780516 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 4 searches.
12:56:05.780612 INFO: ==============================================
12:56:05.780722 PROGRESS: Optimization finished for mobility_error.
12:56:05.965465 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:56:05.973531 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:56:06.003773 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:56:06.010538 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:56:06.068698 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
12:56:06.069042 PROGRESS: ==============================================
12:56:06.069192 PROGRESS: ms2_error      : 15.0000
12:56:06.069289 PROGRESS: ms1_error      : 15.0000
12:56:06.069386 PROGRESS: rt_error       : 161.8151
12:56:06.069471 PROGRESS: mobility_error : 0.1000
12:56:06.069550 PROGRESS: ==============================================
12:56:06.071378 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
12:56:07.960832 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
12:56:15.958097 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
12:56:17.512108 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
12:56:40.613035 INFO: Using python extraction backend
12:56:40.613506 PROGRESS: Extracting batch of 11524154 precursors
12:56:40.613624 INFO: === Search parameters used ===
12:56:40.613700 INFO: rt_error       : 161.81511161609725
12:56:40.613777 INFO: mobility_error : 0.1
12:56:40.613853 INFO: num_candidates : 3
12:56:40.613915 INFO: ms1_error      : 15.0
12:56:40.613987 INFO: ms2_error      : 15.0
12:56:40.614045 INFO: fwhm_rt        : 2.88808012008667
12:56:40.614104 INFO: quant_window   : 3
12:56:40.614161 INFO: ==============================================
12:56:43.486544 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
12:56:43.486723 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
12:56:43.486771 INFO: FWHM in RT is 2.89 seconds, sigma is 0.63
12:56:43.486797 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.62
12:56:43.487679 INFO: Starting candidate selection
14:47:41.357536 INFO: Removed 4240332 precursors with score below cutoff 24.735968000793456
14:47:59.255993 INFO: Starting candidate scoring
15:18:44.008119 INFO: Finished candidate processing
15:18:44.008829 INFO: Collecting candidate features
15:19:29.527164 WARNING: intensity_correlation has 363 NaNs ( 0.00 % out of 27771346)
15:19:29.549812 WARNING: height_correlation has 7 NaNs ( 0.00 % out of 27771346)
15:19:30.432089 INFO: Collecting fragment features
15:19:50.827187 INFO: Finished candidate scoring
15:20:32.430582 INFO: === Performing FDR correction with classifier version 16 ===
15:20:32.431841 INFO: performing precursor FDR with 47 features
15:20:32.431901 INFO: Decoy channel: -1
15:20:32.431937 INFO: competitive: True
15:20:39.516503 INFO: Setting torch num_threads to 2 for FDR classification task
15:20:43.639441 WARNING: dropped 202 target PSMs due to missing features
15:20:43.639817 WARNING: dropped 165 decoy PSMs due to missing features
15:20:55.377644 INFO: Estimating optimal hyperparameters - samples: 22,216,783, batch_size: 4,096, learning_rate: 1.00e-03
15:20:55.604243 INFO: Using random state 574364 for train-test-split
15:29:41.446270 INFO: Test AUC: 0.560
15:29:41.446714 INFO: Train AUC: 0.561
15:29:41.446762 INFO: AUC difference: 0.10%
15:29:46.383241 INFO: Resetting torch num_threads to 128
15:29:47.409860 INFO: Removing fragments below FDR threshold
15:29:50.533880 PROGRESS: ============================= Precursor FDR =============================
15:29:50.534419 PROGRESS: Total precursors accumulated: 69,848
15:29:50.534513 PROGRESS: Target precursors: 69,157 (99.01%)
15:29:50.534582 PROGRESS: Decoy precursors: 691 (0.99%)
15:29:50.534651 PROGRESS: 
15:29:50.534708 PROGRESS: Precursor Summary:
15:29:50.563678 PROGRESS: Channel   0:	 0.050 FDR: 69,157; 0.010 FDR: 69,157; 0.001 FDR: 46,398
15:29:50.563975 PROGRESS: 
15:29:50.564077 PROGRESS: Protein Summary:
15:29:50.596612 PROGRESS: Channel   0:	 0.050 FDR: 11,179; 0.010 FDR: 11,179; 0.001 FDR: 8,631
15:29:50.596916 PROGRESS: =========================================================================
15:29:51.003614 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/psm.parquet
15:29:51.307925 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/frag.parquet
15:29:51.576648 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
15:29:52.857570 PROGRESS: Loading raw file 5/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502 
15:29:52.857790 INFO: Quantification results path: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant
15:29:52.857911 INFO: Creating folder /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/figures
15:29:52.858193 INFO: Initializing TimingManager
15:29:52.858939 INFO: Initializing RawFileManager
15:29:52.859108 INFO: Importing data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
15:29:52.859166 INFO: Using .d import for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
15:29:52.859211 INFO: Reading frame metadata for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
15:29:54.578688 INFO: Reading 39,128 frames with 2,766,418,119 detector events for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
15:31:15.993876 INFO: Indexing /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d...
15:31:15.995607 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
15:31:16.004269 INFO: Fetching mobility values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
15:31:16.004658 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
15:31:16.005120 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
15:31:16.006580 INFO: Fetching mz values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
15:31:16.049303 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
15:31:16.049742 INFO: Indexing quadrupole dimension
15:31:16.921972 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
15:31:16.922168 INFO: Transposing detector events
15:31:25.173458 INFO: Finished transposing data
15:31:25.238552 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
15:31:25.239342 INFO: RT (min)            : 0.0 - 70.0
15:31:25.239392 INFO: RT duration (sec)   : 4199.9
15:31:25.239427 INFO: RT duration (min)   : 70.0
15:31:25.239456 INFO: Cycle len (scans)   : 9
15:31:25.239486 INFO: Cycle len (sec)     : 0.97
15:31:25.239515 INFO: Number of cycles    : 4347
15:31:25.239542 INFO: MS2 range (m/z)     : 400.0 - 1000.0
15:31:25.239594 INFO: Creating DIA data object took: 92.380526304245
15:31:29.844635 INFO: Initializing CalibrationManager
15:31:29.845018 INFO: Setting up calibration estimators ..
15:31:29.845104 INFO: Found 1 estimator(s) in calibration group 'fragment'
15:31:29.845202 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'}' ..
15:31:29.845340 INFO: Found 3 estimator(s) in calibration group 'precursor'
15:31:29.845418 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'}' ..
15:31:29.845491 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}}' ..
15:31:29.845567 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}}' ..
15:31:29.845630 INFO: Done setting up calibration estimators.
15:31:29.845783 INFO: Initializing OptimizationManager
15:31:29.845908 INFO: initial parameter: ms1_error = 30
15:31:29.845980 INFO: initial parameter: ms2_error = 30
15:31:29.846043 INFO: initial parameter: rt_error = 2099.9331315
15:31:29.846102 INFO: initial parameter: mobility_error = 0.1
15:31:29.846153 INFO: initial parameter: num_candidates = 1
15:31:29.846203 INFO: initial parameter: fwhm_rt = 5
15:31:29.846254 INFO: initial parameter: fwhm_mobility = 0.01
15:31:29.846307 INFO: initial parameter: score_cutoff = 0
15:31:29.846363 INFO: initial parameter: classifier_version = -1
15:31:29.846449 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
15:31:29.846755 INFO: FDRManager: loading saved state not requested, will be initialized.
15:31:29.846799 INFO: Initializing FDRManager
15:31:29.846849 INFO: Loading classifier store from /usr/local/lib/python3.10/site-packages/alphadia/constants/classifier
15:31:31.560320 PROGRESS: Initializing spectral library: 5,845,771 target precursors potentially observable (0 removed)
15:31:32.959338 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
15:31:32.959976 INFO: Updating optimization_manager: rt_error            : 2099.9331315 -> 2099.9331315
15:31:32.960101 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
15:31:32.960313 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
15:31:32.960424 PROGRESS: Starting initial search for precursors.
15:31:32.960532 INFO: Starting optimization step 0.
15:31:32.960630 PROGRESS: === Extracting elution groups 0 to 8000 ===
15:31:32.960722 INFO: Using python extraction backend
15:31:32.960930 PROGRESS: Extracting batch of 15766 precursors
15:31:32.961015 INFO: === Search parameters used ===
15:31:32.961073 INFO: rt_error       : 2099.9331315
15:31:32.961127 INFO: mobility_error : 0.1
15:31:32.961179 INFO: num_candidates : 1
15:31:32.961230 INFO: ms1_error      : 30
15:31:32.961278 INFO: ms2_error      : 30
15:31:32.961328 INFO: fwhm_rt        : 5
15:31:32.961375 INFO: quant_window   : 3
15:31:32.961426 INFO: ==============================================
15:31:32.964699 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:31:32.964760 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:31:32.964809 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
15:31:32.964834 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
15:31:32.966349 INFO: Starting candidate selection
15:33:05.571854 INFO: Starting candidate scoring
15:33:06.538152 INFO: Finished candidate processing
15:33:06.538353 INFO: Collecting candidate features
15:33:06.598052 WARNING: intensity_correlation has 1 NaNs ( 0.01 % out of 15031)
15:33:06.605480 INFO: Collecting fragment features
15:33:06.618451 INFO: Finished candidate scoring
15:33:06.628263 INFO: performing precursor FDR with 47 features
15:33:06.628373 INFO: Decoy channel: -1
15:33:06.628407 INFO: competitive: True
15:33:06.634124 INFO: Setting torch num_threads to 2 for FDR classification task
15:33:06.637866 WARNING: dropped 1 decoy PSMs due to missing features
15:33:06.642395 INFO: Estimating optimal hyperparameters - samples: 12,024, batch_size: 128, learning_rate: 1.77e-04
15:33:06.643494 INFO: Using random state 522155 for train-test-split
15:33:08.188783 INFO: Test AUC: 0.542
15:33:08.188949 INFO: Train AUC: 0.576
15:33:08.188987 INFO: AUC difference: 5.88%
15:33:08.189012 WARNING: AUC difference > 5%. This may indicate overfitting.
15:33:08.472434 INFO: Resetting torch num_threads to 128
15:33:08.473926 PROGRESS: === Extracted 15031 precursors and 162701 fragments ===
15:33:08.474631 INFO: === FDR correction performed with classifier version -1 ===
15:33:08.476390 PROGRESS: ============================= Precursor FDR =============================
15:33:08.476510 PROGRESS: Total precursors accumulated: 7,699
15:33:08.476587 PROGRESS: Target precursors: 4,867 (63.22%)
15:33:08.476653 PROGRESS: Decoy precursors: 2,832 (36.78%)
15:33:08.476720 PROGRESS: 
15:33:08.476782 PROGRESS: Precursor Summary:
15:33:08.478613 PROGRESS: Channel   0:	 0.050 FDR: 2,086; 0.010 FDR: 2,086; 0.001 FDR: 2,086
15:33:08.478732 PROGRESS: 
15:33:08.478812 PROGRESS: Protein Summary:
15:33:08.481267 PROGRESS: Channel   0:	 0.050 FDR: 1,960; 0.010 FDR: 1,960; 0.001 FDR: 1,960
15:33:08.481382 PROGRESS: =========================================================================
15:33:08.481539 INFO: Target number of precursors reached.
15:33:08.500976 INFO: fragments_df: keeping 5000 of 162701 [sum(precursor_idx_mask)=22284 sum(mass_error_mask)=162701 stop_rank=5000
15:33:08.868716 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:33:09.176700 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:33:09.492202 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:33:09.802644 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:33:10.521716 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
15:33:10.522392 INFO: Using score_cutoff 15.008996921539307 (fac=0.99, q=1)
15:33:10.522849 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.407287120819092
15:33:10.522947 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.008338863030076027
15:33:10.523015 INFO: Updating optimization_manager: score_cutoff        : 0 -> 15.008996921539307
15:33:10.523089 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:33:10.526137 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:33:10.535952 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:33:10.538574 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:33:10.560516 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
15:33:10.560746 PROGRESS: Required number of precursors found. Starting search parameter optimization.
15:33:10.560888 INFO: Starting optimization step 1.
15:33:10.560990 PROGRESS: === Extracting elution groups 0 to 8000 ===
15:33:10.561098 INFO: Using python extraction backend
15:33:10.561286 PROGRESS: Extracting batch of 15766 precursors
15:33:10.561385 INFO: === Search parameters used ===
15:33:10.561461 INFO: rt_error       : 2099.9331315
15:33:10.561536 INFO: mobility_error : 0.1
15:33:10.561611 INFO: num_candidates : 3
15:33:10.561682 INFO: ms1_error      : 30
15:33:10.561779 INFO: ms2_error      : 30
15:33:10.561888 INFO: fwhm_rt        : 3.407287120819092
15:33:10.561966 INFO: quant_window   : 3
15:33:10.562033 INFO: ==============================================
15:33:10.567866 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:33:10.567939 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:33:10.568016 INFO: FWHM in RT is 3.41 seconds, sigma is 0.75
15:33:10.568055 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.87
15:33:10.569148 INFO: Starting candidate selection
15:34:56.504877 INFO: Starting candidate scoring
15:34:59.460251 INFO: Finished candidate processing
15:34:59.460377 INFO: Collecting candidate features
15:34:59.525496 INFO: Collecting fragment features
15:34:59.551272 INFO: Finished candidate scoring
15:34:59.571443 INFO: performing precursor FDR with 47 features
15:34:59.571593 INFO: Decoy channel: -1
15:34:59.571624 INFO: competitive: True
15:34:59.585256 INFO: Setting torch num_threads to 2 for FDR classification task
15:34:59.597639 INFO: Estimating optimal hyperparameters - samples: 35,099, batch_size: 143, learning_rate: 1.87e-04
15:34:59.597880 INFO: Using random state 555939 for train-test-split
15:35:03.045899 INFO: Test AUC: 0.561
15:35:03.046062 INFO: Train AUC: 0.594
15:35:03.046101 INFO: AUC difference: 5.47%
15:35:03.046126 WARNING: AUC difference > 5%. This may indicate overfitting.
15:35:03.321883 INFO: Resetting torch num_threads to 128
15:35:03.323956 PROGRESS: === Extracted 43874 precursors and 479265 fragments ===
15:35:03.324610 INFO: === FDR correction performed with classifier version 0 ===
15:35:03.326250 PROGRESS: ============================= Precursor FDR =============================
15:35:03.326398 PROGRESS: Total precursors accumulated: 7,869
15:35:03.326477 PROGRESS: Target precursors: 5,401 (68.64%)
15:35:03.326540 PROGRESS: Decoy precursors: 2,468 (31.36%)
15:35:03.326602 PROGRESS: 
15:35:03.326667 PROGRESS: Precursor Summary:
15:35:03.328553 PROGRESS: Channel   0:	 0.050 FDR: 2,517; 0.010 FDR: 2,517; 0.001 FDR: 2,517
15:35:03.328687 PROGRESS: 
15:35:03.328758 PROGRESS: Protein Summary:
15:35:03.331415 PROGRESS: Channel   0:	 0.050 FDR: 2,313; 0.010 FDR: 2,313; 0.001 FDR: 2,313
15:35:03.331537 PROGRESS: =========================================================================
15:35:03.332009 INFO: Target number of precursors reached.
15:35:03.393074 INFO: fragments_df: keeping 5000 of 479265 [sum(precursor_idx_mask)=78116 sum(mass_error_mask)=479265 stop_rank=5000
15:35:03.502484 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:35:03.804733 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:35:04.115468 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:35:04.423994 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:35:05.072562 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:35:05.073141 INFO: Using score_cutoff 32.022453048706055 (fac=0.99, q=1)
15:35:05.073589 INFO: Updating optimization_manager: fwhm_rt             : 3.407287120819092 -> 3.3614823818206787
15:35:05.073686 INFO: Updating optimization_manager: fwhm_mobility       : 0.008338863030076027 -> 0.007728668861091137
15:35:05.073771 INFO: Updating optimization_manager: score_cutoff        : 15.008996921539307 -> 32.022453048706055
15:35:05.073857 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:35:05.076751 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:35:05.086539 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:35:05.089106 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:35:05.109262 INFO: === checking if optimization conditions were reached ===
15:35:05.111222 INFO: Updating optimization_manager: ms2_error           : 30 -> 17.341824175765858
15:35:05.111389 INFO: Updating optimization_manager: classifier_version  : 0 -> 1
15:35:05.111492 PROGRESS: ❌ ms2_error      : 17.3418 > 15.0000 or insufficient steps taken.
15:35:05.112909 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
15:35:05.113035 INFO: Updating optimization_manager: classifier_version  : 1 -> 1
15:35:05.113129 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
15:35:05.113226 INFO: ==============================================
15:35:05.113340 INFO: Starting optimization step 2.
15:35:05.113436 PROGRESS: === Extracting elution groups 0 to 8000 ===
15:35:05.113535 INFO: Using python extraction backend
15:35:05.113719 PROGRESS: Extracting batch of 15766 precursors
15:35:05.113840 INFO: === Search parameters used ===
15:35:05.113926 INFO: rt_error       : 2099.9331315
15:35:05.114001 INFO: mobility_error : 0.1
15:35:05.114066 INFO: num_candidates : 3
15:35:05.114132 INFO: ms1_error      : 15.0
15:35:05.114203 INFO: ms2_error      : 17.341824175765858
15:35:05.114271 INFO: fwhm_rt        : 3.3614823818206787
15:35:05.114346 INFO: quant_window   : 3
15:35:05.114417 INFO: ==============================================
15:35:05.119873 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:35:05.119942 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:35:05.119997 INFO: FWHM in RT is 3.36 seconds, sigma is 0.74
15:35:05.120033 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.58
15:35:05.125870 INFO: Starting candidate selection
15:36:50.872133 INFO: Starting candidate scoring
15:36:52.890022 INFO: Finished candidate processing
15:36:52.890214 INFO: Collecting candidate features
15:36:52.978157 INFO: Collecting fragment features
15:36:53.003451 INFO: Finished candidate scoring
15:36:53.029921 INFO: performing precursor FDR with 47 features
15:36:53.030064 INFO: Decoy channel: -1
15:36:53.030095 INFO: competitive: True
15:36:53.042658 INFO: Setting torch num_threads to 2 for FDR classification task
15:36:53.055107 INFO: Estimating optimal hyperparameters - samples: 35,158, batch_size: 144, learning_rate: 1.88e-04
15:36:53.055360 INFO: Using random state 348235 for train-test-split
15:36:56.376174 INFO: Test AUC: 0.564
15:36:56.376325 INFO: Train AUC: 0.599
15:36:56.376356 INFO: AUC difference: 5.72%
15:36:56.376382 WARNING: AUC difference > 5%. This may indicate overfitting.
15:36:56.649781 INFO: Resetting torch num_threads to 128
15:36:56.651621 PROGRESS: === Extracted 43948 precursors and 459952 fragments ===
15:36:56.652213 INFO: === FDR correction performed with classifier version 1 ===
15:36:56.653741 PROGRESS: ============================= Precursor FDR =============================
15:36:56.653867 PROGRESS: Total precursors accumulated: 7,885
15:36:56.653946 PROGRESS: Target precursors: 5,472 (69.40%)
15:36:56.654013 PROGRESS: Decoy precursors: 2,413 (30.60%)
15:36:56.654075 PROGRESS: 
15:36:56.654134 PROGRESS: Precursor Summary:
15:36:56.656163 PROGRESS: Channel   0:	 0.050 FDR: 3,079; 0.010 FDR: 3,079; 0.001 FDR: 3,079
15:36:56.656280 PROGRESS: 
15:36:56.656353 PROGRESS: Protein Summary:
15:36:56.659249 PROGRESS: Channel   0:	 0.050 FDR: 2,810; 0.010 FDR: 2,810; 0.001 FDR: 2,810
15:36:56.659382 PROGRESS: =========================================================================
15:36:56.659750 INFO: Target number of precursors reached.
15:36:56.722260 INFO: fragments_df: keeping 5000 of 459952 [sum(precursor_idx_mask)=91511 sum(mass_error_mask)=459952 stop_rank=5000
15:36:56.829641 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:36:57.272553 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:36:57.698048 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:36:58.070481 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:36:58.718344 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:36:58.718906 INFO: Using score_cutoff 25.117027325820924 (fac=0.99, q=1)
15:36:58.719352 INFO: Updating optimization_manager: fwhm_rt             : 3.3614823818206787 -> 2.8969619274139404
15:36:58.719447 INFO: Updating optimization_manager: fwhm_mobility       : 0.007728668861091137 -> 0.006009127479046583
15:36:58.719517 INFO: Updating optimization_manager: score_cutoff        : 32.022453048706055 -> 25.117027325820924
15:36:58.719590 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:36:58.722372 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:36:58.731949 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:36:58.734424 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:36:58.754369 INFO: === checking if optimization conditions were reached ===
15:36:58.756601 INFO: Updating optimization_manager: ms2_error           : 17.341824175765858 -> 15.0
15:36:58.756741 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
15:36:58.756835 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
15:36:58.758601 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
15:36:58.758734 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
15:36:58.758827 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
15:36:58.758902 INFO: ==============================================
15:36:58.758992 PROGRESS: Optimization finished for ms2_error, ms1_error.
15:36:58.869967 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:36:58.873116 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:36:58.882748 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:36:58.885222 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:36:58.904947 INFO: Starting optimization step 0.
15:36:58.905132 PROGRESS: === Extracting elution groups 0 to 8000 ===
15:36:58.905244 INFO: Using python extraction backend
15:36:58.905419 PROGRESS: Extracting batch of 15766 precursors
15:36:58.905523 INFO: === Search parameters used ===
15:36:58.905603 INFO: rt_error       : 2099.9331315
15:36:58.905679 INFO: mobility_error : 0.1
15:36:58.905763 INFO: num_candidates : 3
15:36:58.905847 INFO: ms1_error      : 15.0
15:36:58.905933 INFO: ms2_error      : 15.0
15:36:58.906004 INFO: fwhm_rt        : 2.8969619274139404
15:36:58.906071 INFO: quant_window   : 3
15:36:58.906148 INFO: ==============================================
15:36:58.910406 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:36:58.910482 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:36:58.910546 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
15:36:58.910582 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.79
15:36:58.911581 INFO: Starting candidate selection
15:38:36.152933 INFO: Starting candidate scoring
15:38:38.147068 INFO: Finished candidate processing
15:38:38.147288 INFO: Collecting candidate features
15:38:38.236761 INFO: Collecting fragment features
15:38:38.262481 INFO: Finished candidate scoring
15:38:38.283389 INFO: performing precursor FDR with 47 features
15:38:38.283540 INFO: Decoy channel: -1
15:38:38.283568 INFO: competitive: True
15:38:38.296468 INFO: Setting torch num_threads to 2 for FDR classification task
15:38:38.308054 INFO: Estimating optimal hyperparameters - samples: 35,177, batch_size: 144, learning_rate: 1.88e-04
15:38:38.308267 INFO: Using random state 894657 for train-test-split
15:38:41.771415 INFO: Test AUC: 0.572
15:38:41.771567 INFO: Train AUC: 0.616
15:38:41.771600 INFO: AUC difference: 7.19%
15:38:41.771647 WARNING: AUC difference > 5%. This may indicate overfitting.
15:38:42.045320 INFO: Resetting torch num_threads to 128
15:38:42.047217 PROGRESS: === Extracted 43972 precursors and 454005 fragments ===
15:38:42.047864 INFO: === FDR correction performed with classifier version 2 ===
15:38:42.049451 PROGRESS: ============================= Precursor FDR =============================
15:38:42.049567 PROGRESS: Total precursors accumulated: 7,891
15:38:42.049649 PROGRESS: Target precursors: 5,577 (70.68%)
15:38:42.049714 PROGRESS: Decoy precursors: 2,314 (29.32%)
15:38:42.049784 PROGRESS: 
15:38:42.049843 PROGRESS: Precursor Summary:
15:38:42.051889 PROGRESS: Channel   0:	 0.050 FDR: 3,017; 0.010 FDR: 3,017; 0.001 FDR: 3,017
15:38:42.052011 PROGRESS: 
15:38:42.052081 PROGRESS: Protein Summary:
15:38:42.055024 PROGRESS: Channel   0:	 0.050 FDR: 2,768; 0.010 FDR: 2,768; 0.001 FDR: 2,768
15:38:42.055148 PROGRESS: =========================================================================
15:38:42.055554 INFO: Target number of precursors reached.
15:38:42.116754 INFO: fragments_df: keeping 5000 of 454005 [sum(precursor_idx_mask)=88731 sum(mass_error_mask)=454005 stop_rank=5000
15:38:42.223707 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:38:42.658720 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:38:43.093100 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:38:43.528183 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:38:44.240746 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:38:44.241333 INFO: Using score_cutoff 26.430480587768553 (fac=0.99, q=1)
15:38:44.241822 INFO: Updating optimization_manager: fwhm_rt             : 2.8969619274139404 -> 2.883049726486206
15:38:44.241925 INFO: Updating optimization_manager: fwhm_mobility       : 0.006009127479046583 -> 0.005683925002813339
15:38:44.241993 INFO: Updating optimization_manager: score_cutoff        : 25.117027325820924 -> 26.430480587768553
15:38:44.242074 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:38:44.244960 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:38:44.254459 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:38:44.256996 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:38:44.276414 INFO: === checking if optimization conditions were reached ===
15:38:44.276598 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
15:38:44.280151 INFO: Updating optimization_manager: rt_error            : 2099.9331315 -> 1447.3434741630715
15:38:44.280282 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 1447.3435.
15:38:44.280364 INFO: ==============================================
15:38:44.280447 INFO: Starting optimization step 1.
15:38:44.280520 PROGRESS: === Extracting elution groups 0 to 8000 ===
15:38:44.280593 INFO: Using python extraction backend
15:38:44.280728 PROGRESS: Extracting batch of 15766 precursors
15:38:44.280806 INFO: === Search parameters used ===
15:38:44.280865 INFO: rt_error       : 1447.3434741630715
15:38:44.280921 INFO: mobility_error : 0.1
15:38:44.280975 INFO: num_candidates : 3
15:38:44.281026 INFO: ms1_error      : 15.0
15:38:44.281076 INFO: ms2_error      : 15.0
15:38:44.281125 INFO: fwhm_rt        : 2.883049726486206
15:38:44.281184 INFO: quant_window   : 3
15:38:44.281239 INFO: ==============================================
15:38:44.286027 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:38:44.286093 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:38:44.286131 INFO: FWHM in RT is 2.88 seconds, sigma is 0.63
15:38:44.286156 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.64
15:38:44.287074 INFO: Starting candidate selection
15:39:55.669590 INFO: Starting candidate scoring
15:39:57.539798 INFO: Finished candidate processing
15:39:57.540028 INFO: Collecting candidate features
15:39:57.615644 INFO: Collecting fragment features
15:39:57.644398 INFO: Finished candidate scoring
15:39:57.668314 INFO: performing precursor FDR with 47 features
15:39:57.668468 INFO: Decoy channel: -1
15:39:57.668494 INFO: competitive: True
15:39:57.683298 INFO: Setting torch num_threads to 2 for FDR classification task
15:39:57.696766 INFO: Estimating optimal hyperparameters - samples: 35,179, batch_size: 144, learning_rate: 1.88e-04
15:39:57.697058 INFO: Using random state 894657 for train-test-split
15:40:01.871051 INFO: Test AUC: 0.572
15:40:01.871213 INFO: Train AUC: 0.613
15:40:01.871246 INFO: AUC difference: 6.70%
15:40:01.871271 WARNING: AUC difference > 5%. This may indicate overfitting.
15:40:03.927881 INFO: Resetting torch num_threads to 128
15:40:03.929838 PROGRESS: === Extracted 43974 precursors and 453054 fragments ===
15:40:03.930536 INFO: === FDR correction performed with classifier version 2 ===
15:40:03.932474 PROGRESS: ============================= Precursor FDR =============================
15:40:03.932599 PROGRESS: Total precursors accumulated: 7,896
15:40:03.932675 PROGRESS: Target precursors: 5,544 (70.21%)
15:40:03.932745 PROGRESS: Decoy precursors: 2,352 (29.79%)
15:40:03.932808 PROGRESS: 
15:40:03.932869 PROGRESS: Precursor Summary:
15:40:03.935113 PROGRESS: Channel   0:	 0.050 FDR: 3,132; 0.010 FDR: 3,132; 0.001 FDR: 3,132
15:40:03.935237 PROGRESS: 
15:40:03.935312 PROGRESS: Protein Summary:
15:40:03.938452 PROGRESS: Channel   0:	 0.050 FDR: 2,842; 0.010 FDR: 2,842; 0.001 FDR: 2,842
15:40:03.938573 PROGRESS: =========================================================================
15:40:03.938915 INFO: Target number of precursors reached.
15:40:04.004560 INFO: fragments_df: keeping 5000 of 453054 [sum(precursor_idx_mask)=91350 sum(mass_error_mask)=453054 stop_rank=5000
15:40:04.134169 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:40:04.541603 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:40:04.939663 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:40:05.326413 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:40:05.994315 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:40:05.994905 INFO: Using score_cutoff 24.290463034629823 (fac=0.99, q=1)
15:40:05.995385 INFO: Updating optimization_manager: fwhm_rt             : 2.883049726486206 -> 2.72538423538208
15:40:05.995483 INFO: Updating optimization_manager: fwhm_mobility       : 0.005683925002813339 -> 0.005371004343032837
15:40:05.995548 INFO: Updating optimization_manager: score_cutoff        : 26.430480587768553 -> 24.290463034629823
15:40:05.995620 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:40:05.998674 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:40:06.008503 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:40:06.010978 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:40:06.031876 INFO: === checking if optimization conditions were reached ===
15:40:06.032120 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
15:40:06.036420 INFO: Updating optimization_manager: rt_error            : 1447.3434741630715 -> 1287.8920239913527
15:40:06.036565 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 1287.8920.
15:40:06.036660 INFO: ==============================================
15:40:06.036758 INFO: Starting optimization step 2.
15:40:06.036843 PROGRESS: === Extracting elution groups 0 to 8000 ===
15:40:06.036930 INFO: Using python extraction backend
15:40:06.037106 PROGRESS: Extracting batch of 15766 precursors
15:40:06.037217 INFO: === Search parameters used ===
15:40:06.037292 INFO: rt_error       : 1287.8920239913527
15:40:06.037354 INFO: mobility_error : 0.1
15:40:06.037416 INFO: num_candidates : 3
15:40:06.037477 INFO: ms1_error      : 15.0
15:40:06.037535 INFO: ms2_error      : 15.0
15:40:06.037594 INFO: fwhm_rt        : 2.72538423538208
15:40:06.037658 INFO: quant_window   : 3
15:40:06.037719 INFO: ==============================================
15:40:06.045421 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:40:06.045495 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:40:06.045540 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
15:40:06.045566 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.49
15:40:06.046540 INFO: Starting candidate selection
15:41:18.921481 INFO: Starting candidate scoring
15:41:20.719423 INFO: Finished candidate processing
15:41:20.719623 INFO: Collecting candidate features
15:41:20.793034 INFO: Collecting fragment features
15:41:20.826097 INFO: Finished candidate scoring
15:41:20.851744 INFO: performing precursor FDR with 47 features
15:41:20.851893 INFO: Decoy channel: -1
15:41:20.851921 INFO: competitive: True
15:41:20.868743 INFO: Setting torch num_threads to 2 for FDR classification task
15:41:20.883667 INFO: Estimating optimal hyperparameters - samples: 35,180, batch_size: 144, learning_rate: 1.88e-04
15:41:20.883977 INFO: Using random state 894657 for train-test-split
15:41:24.682579 INFO: Test AUC: 0.578
15:41:24.682722 INFO: Train AUC: 0.610
15:41:24.682756 INFO: AUC difference: 5.14%
15:41:24.682781 WARNING: AUC difference > 5%. This may indicate overfitting.
15:41:24.963995 INFO: Resetting torch num_threads to 128
15:41:24.965821 PROGRESS: === Extracted 43976 precursors and 452473 fragments ===
15:41:24.966472 INFO: === FDR correction performed with classifier version 2 ===
15:41:24.968349 PROGRESS: ============================= Precursor FDR =============================
15:41:24.968476 PROGRESS: Total precursors accumulated: 7,902
15:41:24.968553 PROGRESS: Target precursors: 5,195 (65.74%)
15:41:24.968618 PROGRESS: Decoy precursors: 2,707 (34.26%)
15:41:24.968678 PROGRESS: 
15:41:24.968742 PROGRESS: Precursor Summary:
15:41:24.969848 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
15:41:24.969957 PROGRESS: 
15:41:24.970030 PROGRESS: Protein Summary:
15:41:24.971197 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
15:41:24.971311 PROGRESS: =========================================================================
15:41:24.971706 INFO: Target number of precursors not reached yet.
15:41:25.563418 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:41:25.569255 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:41:25.587623 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:41:25.595618 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:41:25.637355 INFO: === skipping optimization until target number of precursors are found ===
15:41:25.637695 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
15:41:25.637829 INFO: Starting optimization step 3.
15:41:25.637918 PROGRESS: === Extracting elution groups 8000 to 24000 ===
15:41:25.638026 INFO: Using python extraction backend
15:41:25.638245 PROGRESS: Extracting batch of 31523 precursors
15:41:25.638361 INFO: === Search parameters used ===
15:41:25.638441 INFO: rt_error       : 1287.8920239913527
15:41:25.638514 INFO: mobility_error : 0.1
15:41:25.638592 INFO: num_candidates : 3
15:41:25.638674 INFO: ms1_error      : 15.0
15:41:25.638749 INFO: ms2_error      : 15.0
15:41:25.638823 INFO: fwhm_rt        : 2.72538423538208
15:41:25.638897 INFO: quant_window   : 3
15:41:25.638968 INFO: ==============================================
15:41:25.647895 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:41:25.648013 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:41:25.648080 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
15:41:25.648115 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.49
15:41:25.649012 INFO: Starting candidate selection
15:43:49.089079 INFO: Starting candidate scoring
15:43:52.294910 INFO: Finished candidate processing
15:43:52.295126 INFO: Collecting candidate features
15:43:52.437446 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 87825)
15:43:52.444575 INFO: Collecting fragment features
15:43:52.493094 INFO: Finished candidate scoring
15:43:52.563277 INFO: performing precursor FDR with 47 features
15:43:52.563465 INFO: Decoy channel: -1
15:43:52.563493 INFO: competitive: True
15:43:52.609859 INFO: Setting torch num_threads to 2 for FDR classification task
15:43:52.636343 WARNING: dropped 1 target PSMs due to missing features
15:43:52.636519 WARNING: dropped 1 decoy PSMs due to missing features
15:43:52.661522 INFO: Estimating optimal hyperparameters - samples: 105,439, batch_size: 431, learning_rate: 3.24e-04
15:43:52.661976 INFO: Using random state 894657 for train-test-split
15:43:59.075474 INFO: Test AUC: 0.552
15:43:59.076079 INFO: Train AUC: 0.593
15:43:59.076138 INFO: AUC difference: 6.95%
15:43:59.076167 WARNING: AUC difference > 5%. This may indicate overfitting.
15:43:59.391625 INFO: Resetting torch num_threads to 128
15:43:59.416852 PROGRESS: === Extracted 131801 precursors and 1355224 fragments ===
15:43:59.417860 INFO: === FDR correction performed with classifier version 2 ===
15:43:59.424544 PROGRESS: ============================= Precursor FDR =============================
15:43:59.424711 PROGRESS: Total precursors accumulated: 23,686
15:43:59.424796 PROGRESS: Target precursors: 15,121 (63.84%)
15:43:59.424865 PROGRESS: Decoy precursors: 8,565 (36.16%)
15:43:59.424926 PROGRESS: 
15:43:59.424984 PROGRESS: Precursor Summary:
15:43:59.428465 PROGRESS: Channel   0:	 0.050 FDR: 4,524; 0.010 FDR: 4,524; 0.001 FDR: 4,524
15:43:59.428603 PROGRESS: 
15:43:59.428681 PROGRESS: Protein Summary:
15:43:59.432831 PROGRESS: Channel   0:	 0.050 FDR: 3,968; 0.010 FDR: 3,968; 0.001 FDR: 3,968
15:43:59.432957 PROGRESS: =========================================================================
15:43:59.433604 INFO: Target number of precursors reached.
15:43:59.583994 INFO: fragments_df: keeping 5000 of 1355224 [sum(precursor_idx_mask)=130079 sum(mass_error_mask)=1355224 stop_rank=5000
15:44:00.073002 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:44:00.726309 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:44:01.389900 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:44:02.036086 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:44:02.768095 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:44:02.768708 INFO: Using score_cutoff 24.47476797924042 (fac=0.99, q=1)
15:44:02.769221 INFO: Updating optimization_manager: fwhm_rt             : 2.72538423538208 -> 2.8173022270202637
15:44:02.769324 INFO: Updating optimization_manager: fwhm_mobility       : 0.005371004343032837 -> 0.005231023766100407
15:44:02.769398 INFO: Updating optimization_manager: score_cutoff        : 24.290463034629823 -> 24.47476797924042
15:44:02.769470 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:44:02.772279 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:44:02.782144 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:44:02.784515 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:44:02.804185 INFO: === checking if optimization conditions were reached ===
15:44:02.804422 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
15:44:02.806109 INFO: Updating optimization_manager: rt_error            : 1287.8920239913527 -> 1447.3434741630715
15:44:02.806296 INFO: Updating optimization_manager: classifier_version  : 2 -> 4
15:44:02.806434 INFO: Updating optimization_manager: score_cutoff        : 24.47476797924042 -> 24.290463034629823
15:44:02.806559 INFO: Updating optimization_manager: fwhm_rt             : 2.8173022270202637 -> 2.72538423538208
15:44:02.806675 INFO: Updating optimization_manager: fwhm_mobility       : 0.005231023766100407 -> 0.005371004343032837
15:44:02.806802 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 1447.3435 found after 3 searches.
15:44:02.806894 INFO: ==============================================
15:44:02.806989 PROGRESS: Optimization finished for rt_error.
15:44:03.019072 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:44:03.022195 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:44:03.031886 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:44:03.034249 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:44:03.052802 INFO: Starting optimization step 0.
15:44:03.053017 PROGRESS: === Extracting elution groups 0 to 8000 ===
15:44:03.053114 INFO: Using python extraction backend
15:44:03.053294 PROGRESS: Extracting batch of 15766 precursors
15:44:03.053390 INFO: === Search parameters used ===
15:44:03.053462 INFO: rt_error       : 1447.3434741630715
15:44:03.053535 INFO: mobility_error : 0.1
15:44:03.053591 INFO: num_candidates : 3
15:44:03.053645 INFO: ms1_error      : 15.0
15:44:03.053709 INFO: ms2_error      : 15.0
15:44:03.053791 INFO: fwhm_rt        : 2.72538423538208
15:44:03.053876 INFO: quant_window   : 3
15:44:03.053952 INFO: ==============================================
15:44:03.059084 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:44:03.059153 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:44:03.059203 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
15:44:03.059238 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.49
15:44:03.060053 INFO: Starting candidate selection
15:45:11.584095 INFO: Starting candidate scoring
15:45:13.356328 INFO: Finished candidate processing
15:45:13.356570 INFO: Collecting candidate features
15:45:13.454268 INFO: Collecting fragment features
15:45:13.484741 INFO: Finished candidate scoring
15:45:13.507613 INFO: performing precursor FDR with 47 features
15:45:13.507773 INFO: Decoy channel: -1
15:45:13.507818 INFO: competitive: True
15:45:13.521156 INFO: Setting torch num_threads to 2 for FDR classification task
15:45:13.533326 INFO: Estimating optimal hyperparameters - samples: 35,293, batch_size: 144, learning_rate: 1.88e-04
15:45:13.533595 INFO: Using random state 688177 for train-test-split
15:45:17.755985 INFO: Test AUC: 0.571
15:45:17.756141 INFO: Train AUC: 0.636
15:45:17.756173 INFO: AUC difference: 10.27%
15:45:17.756197 WARNING: AUC difference > 5%. This may indicate overfitting.
15:45:18.036285 INFO: Resetting torch num_threads to 128
15:45:18.038200 PROGRESS: === Extracted 44117 precursors and 453699 fragments ===
15:45:18.038867 INFO: === FDR correction performed with classifier version 4 ===
15:45:18.040464 PROGRESS: ============================= Precursor FDR =============================
15:45:18.040582 PROGRESS: Total precursors accumulated: 7,910
15:45:18.040667 PROGRESS: Target precursors: 5,605 (70.86%)
15:45:18.040735 PROGRESS: Decoy precursors: 2,305 (29.14%)
15:45:18.040796 PROGRESS: 
15:45:18.040852 PROGRESS: Precursor Summary:
15:45:18.042876 PROGRESS: Channel   0:	 0.050 FDR: 2,825; 0.010 FDR: 2,825; 0.001 FDR: 2,825
15:45:18.043023 PROGRESS: 
15:45:18.043095 PROGRESS: Protein Summary:
15:45:18.045987 PROGRESS: Channel   0:	 0.050 FDR: 2,595; 0.010 FDR: 2,595; 0.001 FDR: 2,595
15:45:18.046117 PROGRESS: =========================================================================
15:45:18.047455 INFO: Target number of precursors reached.
15:45:18.107264 INFO: fragments_df: keeping 5000 of 453699 [sum(precursor_idx_mask)=81763 sum(mass_error_mask)=453699 stop_rank=5000
15:45:18.413290 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:45:18.781904 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:45:19.135139 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:45:19.493226 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:45:20.152612 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:45:20.153200 INFO: Using score_cutoff 23.172624069213864 (fac=0.99, q=1)
15:45:20.153660 INFO: Updating optimization_manager: fwhm_rt             : 2.72538423538208 -> 2.6852104663848877
15:45:20.153767 INFO: Updating optimization_manager: fwhm_mobility       : 0.005371004343032837 -> 0.0050796084105968475
15:45:20.153846 INFO: Updating optimization_manager: score_cutoff        : 24.290463034629823 -> 23.172624069213864
15:45:20.153923 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:45:20.156870 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:45:20.166462 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:45:20.168793 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:45:20.188149 INFO: === checking if optimization conditions were reached ===
15:45:20.188363 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
15:45:20.190523 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.10241402946063118
15:45:20.190670 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.1024.
15:45:20.190772 INFO: ==============================================
15:45:20.190873 INFO: Starting optimization step 1.
15:45:20.190972 PROGRESS: === Extracting elution groups 0 to 8000 ===
15:45:20.191063 INFO: Using python extraction backend
15:45:20.191221 PROGRESS: Extracting batch of 15766 precursors
15:45:20.191314 INFO: === Search parameters used ===
15:45:20.191392 INFO: rt_error       : 1447.3434741630715
15:45:20.191459 INFO: mobility_error : 0.10241402946063118
15:45:20.191525 INFO: num_candidates : 3
15:45:20.191600 INFO: ms1_error      : 15.0
15:45:20.191662 INFO: ms2_error      : 15.0
15:45:20.191724 INFO: fwhm_rt        : 2.6852104663848877
15:45:20.191810 INFO: quant_window   : 3
15:45:20.191894 INFO: ==============================================
15:45:20.196561 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:45:20.196622 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:45:20.196673 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
15:45:20.196708 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.36
15:45:20.197678 INFO: Starting candidate selection
15:46:30.038495 INFO: Starting candidate scoring
15:46:31.962811 INFO: Finished candidate processing
15:46:31.963086 INFO: Collecting candidate features
15:46:32.056732 INFO: Collecting fragment features
15:46:32.082946 INFO: Finished candidate scoring
15:46:32.104091 INFO: performing precursor FDR with 47 features
15:46:32.104231 INFO: Decoy channel: -1
15:46:32.104258 INFO: competitive: True
15:46:32.118716 INFO: Setting torch num_threads to 2 for FDR classification task
15:46:32.130890 INFO: Estimating optimal hyperparameters - samples: 35,276, batch_size: 144, learning_rate: 1.88e-04
15:46:32.131163 INFO: Using random state 688177 for train-test-split
15:46:35.516270 INFO: Test AUC: 0.598
15:46:35.516441 INFO: Train AUC: 0.624
15:46:35.516485 INFO: AUC difference: 4.10%
15:46:35.807051 INFO: Resetting torch num_threads to 128
15:46:35.809201 PROGRESS: === Extracted 44096 precursors and 453588 fragments ===
15:46:35.809864 INFO: === FDR correction performed with classifier version 4 ===
15:46:35.811503 PROGRESS: ============================= Precursor FDR =============================
15:46:35.811622 PROGRESS: Total precursors accumulated: 7,919
15:46:35.811696 PROGRESS: Target precursors: 5,498 (69.43%)
15:46:35.811759 PROGRESS: Decoy precursors: 2,421 (30.57%)
15:46:35.811817 PROGRESS: 
15:46:35.811874 PROGRESS: Precursor Summary:
15:46:35.813824 PROGRESS: Channel   0:	 0.050 FDR: 2,734; 0.010 FDR: 2,734; 0.001 FDR: 2,734
15:46:35.813945 PROGRESS: 
15:46:35.814018 PROGRESS: Protein Summary:
15:46:35.820464 PROGRESS: Channel   0:	 0.050 FDR: 2,523; 0.010 FDR: 2,523; 0.001 FDR: 2,523
15:46:35.820605 PROGRESS: =========================================================================
15:46:35.821315 INFO: Target number of precursors reached.
15:46:35.879998 INFO: fragments_df: keeping 5000 of 453588 [sum(precursor_idx_mask)=81127 sum(mass_error_mask)=453588 stop_rank=5000
15:46:35.983034 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:46:36.380008 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:46:36.722244 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:46:37.062971 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:46:37.714805 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:46:37.715400 INFO: Using score_cutoff 26.259431976699826 (fac=0.99, q=1)
15:46:37.715831 INFO: Updating optimization_manager: fwhm_rt             : 2.6852104663848877 -> 2.869400978088379
15:46:37.715924 INFO: Updating optimization_manager: fwhm_mobility       : 0.0050796084105968475 -> 0.005527076311409473
15:46:37.715989 INFO: Updating optimization_manager: score_cutoff        : 23.172624069213864 -> 26.259431976699826
15:46:37.716063 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:46:37.718879 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:46:37.728436 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:46:37.730886 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:46:37.750078 INFO: === checking if optimization conditions were reached ===
15:46:37.750271 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
15:46:37.752503 INFO: Updating optimization_manager: mobility_error      : 0.10241402946063118 -> 0.10804521810246097
15:46:37.752627 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.1080.
15:46:37.752731 INFO: ==============================================
15:46:37.752839 INFO: Starting optimization step 2.
15:46:37.752932 PROGRESS: === Extracting elution groups 0 to 8000 ===
15:46:37.753031 INFO: Using python extraction backend
15:46:37.753222 PROGRESS: Extracting batch of 15766 precursors
15:46:37.753324 INFO: === Search parameters used ===
15:46:37.753406 INFO: rt_error       : 1447.3434741630715
15:46:37.753477 INFO: mobility_error : 0.10804521810246097
15:46:37.753541 INFO: num_candidates : 3
15:46:37.753604 INFO: ms1_error      : 15.0
15:46:37.753669 INFO: ms2_error      : 15.0
15:46:37.753756 INFO: fwhm_rt        : 2.869400978088379
15:46:37.753834 INFO: quant_window   : 3
15:46:37.753906 INFO: ==============================================
15:46:37.759060 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:46:37.759126 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:46:37.759182 INFO: FWHM in RT is 2.87 seconds, sigma is 0.63
15:46:37.759216 INFO: FWHM in mobility is 0.006 1/K_0, sigma is 2.56
15:46:37.760178 INFO: Starting candidate selection
15:47:51.013806 INFO: Starting candidate scoring
15:47:52.932141 INFO: Finished candidate processing
15:47:52.932525 INFO: Collecting candidate features
15:47:53.046205 INFO: Collecting fragment features
15:47:53.075843 INFO: Finished candidate scoring
15:47:53.099988 INFO: performing precursor FDR with 47 features
15:47:53.100147 INFO: Decoy channel: -1
15:47:53.100181 INFO: competitive: True
15:47:53.116560 INFO: Setting torch num_threads to 2 for FDR classification task
15:47:53.131702 INFO: Estimating optimal hyperparameters - samples: 35,283, batch_size: 144, learning_rate: 1.88e-04
15:47:53.132012 INFO: Using random state 688177 for train-test-split
15:47:56.955473 INFO: Test AUC: 0.580
15:47:56.955646 INFO: Train AUC: 0.633
15:47:56.955681 INFO: AUC difference: 8.43%
15:47:56.955710 WARNING: AUC difference > 5%. This may indicate overfitting.
15:47:57.238346 INFO: Resetting torch num_threads to 128
15:47:57.240346 PROGRESS: === Extracted 44104 precursors and 455525 fragments ===
15:47:57.240998 INFO: === FDR correction performed with classifier version 4 ===
15:47:57.242649 PROGRESS: ============================= Precursor FDR =============================
15:47:57.242769 PROGRESS: Total precursors accumulated: 7,917
15:47:57.242848 PROGRESS: Target precursors: 5,369 (67.82%)
15:47:57.242914 PROGRESS: Decoy precursors: 2,548 (32.18%)
15:47:57.242975 PROGRESS: 
15:47:57.243033 PROGRESS: Precursor Summary:
15:47:57.244727 PROGRESS: Channel   0:	 0.050 FDR: 1,899; 0.010 FDR: 1,899; 0.001 FDR: 1,899
15:47:57.244839 PROGRESS: 
15:47:57.244925 PROGRESS: Protein Summary:
15:47:57.247204 PROGRESS: Channel   0:	 0.050 FDR: 1,795; 0.010 FDR: 1,795; 0.001 FDR: 1,795
15:47:57.247329 PROGRESS: =========================================================================
15:47:57.247774 INFO: Target number of precursors reached.
15:47:57.299788 INFO: fragments_df: keeping 5000 of 455525 [sum(precursor_idx_mask)=55095 sum(mass_error_mask)=455525 stop_rank=5000
15:47:57.402915 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
15:47:57.694707 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
15:47:57.977623 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
15:47:58.257620 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
15:47:58.976887 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
15:47:58.977468 INFO: Using score_cutoff 25.484771591949464 (fac=0.99, q=1)
15:47:58.977915 INFO: Updating optimization_manager: fwhm_rt             : 2.869400978088379 -> 2.751535177230835
15:47:58.978018 INFO: Updating optimization_manager: fwhm_mobility       : 0.005527076311409473 -> 0.0052187517285346985
15:47:58.978085 INFO: Updating optimization_manager: score_cutoff        : 26.259431976699826 -> 25.484771591949464
15:47:58.978161 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:47:58.981150 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:47:58.990774 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:47:58.993335 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:47:59.013981 INFO: === checking if optimization conditions were reached ===
15:47:59.014179 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
15:47:59.015263 INFO: Updating optimization_manager: mobility_error      : 0.10804521810246097 -> 0.1
15:47:59.015428 INFO: Updating optimization_manager: classifier_version  : 4 -> 7
15:47:59.015569 INFO: Updating optimization_manager: score_cutoff        : 25.484771591949464 -> 23.172624069213864
15:47:59.015698 INFO: Updating optimization_manager: fwhm_rt             : 2.751535177230835 -> 2.6852104663848877
15:47:59.015820 INFO: Updating optimization_manager: fwhm_mobility       : 0.0052187517285346985 -> 0.0050796084105968475
15:47:59.015952 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
15:47:59.016057 INFO: ==============================================
15:47:59.016168 PROGRESS: Optimization finished for mobility_error.
15:47:59.118274 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:47:59.121573 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:47:59.131187 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:47:59.133781 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:47:59.154553 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
15:47:59.154786 PROGRESS: ==============================================
15:47:59.154893 PROGRESS: ms2_error      : 15.0000
15:47:59.155018 PROGRESS: ms1_error      : 15.0000
15:47:59.155093 PROGRESS: rt_error       : 1447.3435
15:47:59.155159 PROGRESS: mobility_error : 0.1000
15:47:59.155223 PROGRESS: ==============================================
15:47:59.156929 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
15:48:00.623155 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
15:48:07.287573 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
15:48:08.741363 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
15:48:28.540152 INFO: Using python extraction backend
15:48:28.541200 PROGRESS: Extracting batch of 11524154 precursors
15:48:28.541390 INFO: === Search parameters used ===
15:48:28.541474 INFO: rt_error       : 1447.3434741630715
15:48:28.541544 INFO: mobility_error : 0.1
15:48:28.541618 INFO: num_candidates : 3
15:48:28.541679 INFO: ms1_error      : 15.0
15:48:28.541781 INFO: ms2_error      : 15.0
15:48:28.541873 INFO: fwhm_rt        : 2.6852104663848877
15:48:28.541940 INFO: quant_window   : 3
15:48:28.542011 INFO: ==============================================
15:48:32.448942 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
15:48:32.449126 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
15:48:32.449186 INFO: FWHM in RT is 2.69 seconds, sigma is 0.59
15:48:32.449211 INFO: FWHM in mobility is 0.005 1/K_0, sigma is 2.36
15:48:32.450728 INFO: Starting candidate selection
1 day, 5:10:43.338815 INFO: Removed 400051 precursors with score below cutoff 23.172624069213864
1 day, 5:10:46.627059 INFO: Starting candidate scoring
1 day, 5:27:52.185250 INFO: Finished candidate processing
1 day, 5:27:52.187173 INFO: Collecting candidate features
1 day, 5:28:43.244874 WARNING: intensity_correlation has 66 NaNs ( 0.00 % out of 31784998)
1 day, 5:28:43.271255 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 31784998)
1 day, 5:28:44.296038 INFO: Collecting fragment features
1 day, 5:29:06.229237 INFO: Finished candidate scoring
1 day, 5:29:47.798463 INFO: === Performing FDR correction with classifier version 7 ===
1 day, 5:29:47.799799 INFO: performing precursor FDR with 47 features
1 day, 5:29:47.799861 INFO: Decoy channel: -1
1 day, 5:29:47.799894 INFO: competitive: True
1 day, 5:29:57.265198 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:30:02.643388 WARNING: dropped 42 target PSMs due to missing features
1 day, 5:30:02.643589 WARNING: dropped 25 decoy PSMs due to missing features
1 day, 5:30:16.583580 INFO: Estimating optimal hyperparameters - samples: 25,427,944, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 5:30:16.642657 INFO: Using random state 874955 for train-test-split
1 day, 5:40:26.749526 INFO: Test AUC: 0.571
1 day, 5:40:26.750019 INFO: Train AUC: 0.572
1 day, 5:40:26.750067 INFO: AUC difference: 0.11%
1 day, 5:40:32.159929 INFO: Resetting torch num_threads to 128
1 day, 5:40:33.193375 INFO: Removing fragments below FDR threshold
1 day, 5:40:36.174553 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:40:36.174934 PROGRESS: Total precursors accumulated: 59,255
1 day, 5:40:36.175040 PROGRESS: Target precursors: 58,669 (99.01%)
1 day, 5:40:36.175127 PROGRESS: Decoy precursors: 586 (0.99%)
1 day, 5:40:36.175203 PROGRESS: 
1 day, 5:40:36.175276 PROGRESS: Precursor Summary:
1 day, 5:40:36.196153 PROGRESS: Channel   0:	 0.050 FDR: 58,669; 0.010 FDR: 58,669; 0.001 FDR: 36,464
1 day, 5:40:36.196477 PROGRESS: 
1 day, 5:40:36.196555 PROGRESS: Protein Summary:
1 day, 5:40:36.222228 PROGRESS: Channel   0:	 0.050 FDR: 9,641; 0.010 FDR: 9,641; 0.001 FDR: 7,338
1 day, 5:40:36.222517 PROGRESS: =========================================================================
1 day, 5:40:36.564023 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/psm.parquet
1 day, 5:40:36.910223 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/frag.parquet
1 day, 5:40:37.135777 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 5:40:37.904087 PROGRESS: Loading raw file 6/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508 
1 day, 5:40:37.904282 INFO: Quantification results path: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant
1 day, 5:40:37.904398 INFO: Creating folder /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/figures
1 day, 5:40:37.904691 INFO: Initializing TimingManager
1 day, 5:40:37.905224 INFO: Initializing RawFileManager
1 day, 5:40:37.905386 INFO: Importing data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 5:40:37.905444 INFO: Using .d import for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 5:40:37.905511 INFO: Reading frame metadata for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 5:40:39.718399 INFO: Reading 39,129 frames with 2,804,178,635 detector events for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 5:41:36.500500 INFO: Indexing /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d...
1 day, 5:41:36.502916 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 5:41:36.510935 INFO: Fetching mobility values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 5:41:36.511208 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 5:41:36.511592 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 5:41:36.512784 INFO: Fetching mz values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 5:41:36.545939 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 5:41:36.546234 INFO: Indexing quadrupole dimension
1 day, 5:41:37.426187 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 5:41:37.426420 INFO: Transposing detector events
1 day, 5:41:46.179755 INFO: Finished transposing data
1 day, 5:41:46.245292 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 5:41:46.246268 INFO: RT (min)            : 0.0 - 70.0
1 day, 5:41:46.246351 INFO: RT duration (sec)   : 4199.8
1 day, 5:41:46.246412 INFO: RT duration (min)   : 70.0
1 day, 5:41:46.246467 INFO: Cycle len (scans)   : 9
1 day, 5:41:46.246496 INFO: Cycle len (sec)     : 0.97
1 day, 5:41:46.246524 INFO: Number of cycles    : 4347
1 day, 5:41:46.246552 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 5:41:46.246600 INFO: Creating DIA data object took: 68.3412549495697
1 day, 5:41:48.417095 INFO: Initializing CalibrationManager
1 day, 5:41:48.417537 INFO: Setting up calibration estimators ..
1 day, 5:41:48.417665 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 5:41:48.417811 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, 5:41:48.417964 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 5:41:48.418067 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, 5:41:48.418160 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, 5:41:48.418261 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, 5:41:48.418341 INFO: Done setting up calibration estimators.
1 day, 5:41:48.418589 INFO: Initializing OptimizationManager
1 day, 5:41:48.418732 INFO: initial parameter: ms1_error = 30
1 day, 5:41:48.418807 INFO: initial parameter: ms2_error = 30
1 day, 5:41:48.418888 INFO: initial parameter: rt_error = 2099.9231665
1 day, 5:41:48.418965 INFO: initial parameter: mobility_error = 0.1
1 day, 5:41:48.419055 INFO: initial parameter: num_candidates = 1
1 day, 5:41:48.419126 INFO: initial parameter: fwhm_rt = 5
1 day, 5:41:48.419193 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 5:41:48.419255 INFO: initial parameter: score_cutoff = 0
1 day, 5:41:48.419313 INFO: initial parameter: classifier_version = -1
1 day, 5:41:48.419407 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 5:41:48.419716 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 5:41:48.419756 INFO: Initializing FDRManager
1 day, 5:41:48.419817 INFO: Loading classifier store from /usr/local/lib/python3.10/site-packages/alphadia/constants/classifier
1 day, 5:41:49.985778 PROGRESS: Initializing spectral library: 5,845,771 target precursors potentially observable (0 removed)
1 day, 5:41:51.391776 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 5:41:51.392515 INFO: Updating optimization_manager: rt_error            : 2099.9231665 -> 2099.9231665
1 day, 5:41:51.392647 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 5:41:51.392871 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 5:41:51.393003 PROGRESS: Starting initial search for precursors.
1 day, 5:41:51.393131 INFO: Starting optimization step 0.
1 day, 5:41:51.393234 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 5:41:51.393331 INFO: Using python extraction backend
1 day, 5:41:51.393560 PROGRESS: Extracting batch of 15766 precursors
1 day, 5:41:51.393655 INFO: === Search parameters used ===
1 day, 5:41:51.393724 INFO: rt_error       : 2099.9231665
1 day, 5:41:51.393800 INFO: mobility_error : 0.1
1 day, 5:41:51.393874 INFO: num_candidates : 1
1 day, 5:41:51.393934 INFO: ms1_error      : 30
1 day, 5:41:51.393995 INFO: ms2_error      : 30
1 day, 5:41:51.394048 INFO: fwhm_rt        : 5
1 day, 5:41:51.394106 INFO: quant_window   : 3
1 day, 5:41:51.394162 INFO: ==============================================
1 day, 5:41:51.397247 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:41:51.397305 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:41:51.397343 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 5:41:51.397367 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 5:41:51.398677 INFO: Starting candidate selection
1 day, 5:43:24.885771 INFO: Starting candidate scoring
1 day, 5:43:26.107667 INFO: Finished candidate processing
1 day, 5:43:26.107922 INFO: Collecting candidate features
1 day, 5:43:26.163388 WARNING: intensity_correlation has 3 NaNs ( 0.02 % out of 15041)
1 day, 5:43:26.170429 INFO: Collecting fragment features
1 day, 5:43:26.183679 INFO: Finished candidate scoring
1 day, 5:43:26.192441 INFO: performing precursor FDR with 47 features
1 day, 5:43:26.192585 INFO: Decoy channel: -1
1 day, 5:43:26.192619 INFO: competitive: True
1 day, 5:43:26.199106 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:43:26.202801 WARNING: dropped 3 target PSMs due to missing features
1 day, 5:43:26.206109 INFO: Estimating optimal hyperparameters - samples: 12,030, batch_size: 128, learning_rate: 1.77e-04
1 day, 5:43:26.206984 INFO: Using random state 145194 for train-test-split
1 day, 5:43:27.458138 INFO: Test AUC: 0.545
1 day, 5:43:27.458318 INFO: Train AUC: 0.583
1 day, 5:43:27.458352 INFO: AUC difference: 6.53%
1 day, 5:43:27.458377 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 5:43:27.724640 INFO: Resetting torch num_threads to 128
1 day, 5:43:27.725950 PROGRESS: === Extracted 15041 precursors and 162842 fragments ===
1 day, 5:43:27.726542 INFO: === FDR correction performed with classifier version -1 ===
1 day, 5:43:27.728054 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:43:27.728183 PROGRESS: Total precursors accumulated: 7,705
1 day, 5:43:27.728259 PROGRESS: Target precursors: 4,857 (63.04%)
1 day, 5:43:27.728328 PROGRESS: Decoy precursors: 2,848 (36.96%)
1 day, 5:43:27.728404 PROGRESS: 
1 day, 5:43:27.728466 PROGRESS: Precursor Summary:
1 day, 5:43:27.729978 PROGRESS: Channel   0:	 0.050 FDR: 1,789; 0.010 FDR: 1,789; 0.001 FDR:     1
1 day, 5:43:27.730104 PROGRESS: 
1 day, 5:43:27.730177 PROGRESS: Protein Summary:
1 day, 5:43:27.732065 PROGRESS: Channel   0:	 0.050 FDR: 1,689; 0.010 FDR: 1,689; 0.001 FDR:     1
1 day, 5:43:27.732176 PROGRESS: =========================================================================
1 day, 5:43:27.732303 INFO: Target number of precursors reached.
1 day, 5:43:27.750211 INFO: fragments_df: keeping 4088 of 162842 [sum(precursor_idx_mask)=19059 sum(mass_error_mask)=162842 stop_rank=4088
1 day, 5:43:27.867107 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 5:43:28.103331 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 5:43:28.341615 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 5:43:28.578654 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 5:43:29.080181 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 5:43:29.080749 INFO: Using score_cutoff 12.314838609695434 (fac=0.99, q=1)
1 day, 5:43:29.081201 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.239382743835449
1 day, 5:43:29.081303 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.00783432088792324
1 day, 5:43:29.081377 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.314838609695434
1 day, 5:43:29.081454 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 5:43:29.084230 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 5:43:29.093924 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 5:43:29.096319 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 5:43:29.117045 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
1 day, 5:43:29.117235 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 5:43:29.117354 INFO: Starting optimization step 1.
1 day, 5:43:29.117438 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 5:43:29.117522 INFO: Using python extraction backend
1 day, 5:43:29.117675 PROGRESS: Extracting batch of 15766 precursors
1 day, 5:43:29.117777 INFO: === Search parameters used ===
1 day, 5:43:29.117852 INFO: rt_error       : 2099.9231665
1 day, 5:43:29.117954 INFO: mobility_error : 0.1
1 day, 5:43:29.118019 INFO: num_candidates : 3
1 day, 5:43:29.118099 INFO: ms1_error      : 30
1 day, 5:43:29.118159 INFO: ms2_error      : 30
1 day, 5:43:29.118235 INFO: fwhm_rt        : 3.239382743835449
1 day, 5:43:29.118294 INFO: quant_window   : 3
1 day, 5:43:29.118350 INFO: ==============================================
1 day, 5:43:29.125155 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:43:29.125234 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:43:29.125305 INFO: FWHM in RT is 3.24 seconds, sigma is 0.71
1 day, 5:43:29.125334 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.63
1 day, 5:43:29.126434 INFO: Starting candidate selection
1 day, 5:45:19.801020 INFO: Starting candidate scoring
1 day, 5:45:22.733330 INFO: Finished candidate processing
1 day, 5:45:22.733521 INFO: Collecting candidate features
1 day, 5:45:22.835564 INFO: Collecting fragment features
1 day, 5:45:22.861640 INFO: Finished candidate scoring
1 day, 5:45:22.880798 INFO: performing precursor FDR with 47 features
1 day, 5:45:22.880943 INFO: Decoy channel: -1
1 day, 5:45:22.880980 INFO: competitive: True
1 day, 5:45:22.895024 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:45:22.907226 INFO: Estimating optimal hyperparameters - samples: 35,085, batch_size: 143, learning_rate: 1.87e-04
1 day, 5:45:22.907497 INFO: Using random state 981032 for train-test-split
1 day, 5:45:26.374929 INFO: Test AUC: 0.564
1 day, 5:45:26.375051 INFO: Train AUC: 0.595
1 day, 5:45:26.375084 INFO: AUC difference: 5.27%
1 day, 5:45:26.375109 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 5:45:26.650116 INFO: Resetting torch num_threads to 128
1 day, 5:45:26.651933 PROGRESS: === Extracted 43857 precursors and 478878 fragments ===
1 day, 5:45:26.652537 INFO: === FDR correction performed with classifier version 0 ===
1 day, 5:45:26.654173 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:45:26.654296 PROGRESS: Total precursors accumulated: 7,875
1 day, 5:45:26.654373 PROGRESS: Target precursors: 4,959 (62.97%)
1 day, 5:45:26.654441 PROGRESS: Decoy precursors: 2,916 (37.03%)
1 day, 5:45:26.654502 PROGRESS: 
1 day, 5:45:26.654558 PROGRESS: Precursor Summary:
1 day, 5:45:26.655586 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 5:45:26.655688 PROGRESS: 
1 day, 5:45:26.655754 PROGRESS: Protein Summary:
1 day, 5:45:26.656832 PROGRESS: Channel   0:	 0.050 FDR:     0; 0.010 FDR:     0; 0.001 FDR:     0
1 day, 5:45:26.656933 PROGRESS: =========================================================================
1 day, 5:45:26.657312 INFO: Target number of precursors not reached yet.
1 day, 5:45:26.903808 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 5:45:26.908945 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 5:45:26.927367 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 5:45:26.931511 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 5:45:26.972816 INFO: === skipping optimization until target number of precursors are found ===
1 day, 5:45:26.973145 INFO: Starting optimization step 2.
1 day, 5:45:26.973237 PROGRESS: === Extracting elution groups 8000 to 24000 ===
1 day, 5:45:26.973340 INFO: Using python extraction backend
1 day, 5:45:26.973488 PROGRESS: Extracting batch of 31523 precursors
1 day, 5:45:26.973578 INFO: === Search parameters used ===
1 day, 5:45:26.973637 INFO: rt_error       : 2099.9231665
1 day, 5:45:26.973723 INFO: mobility_error : 0.1
1 day, 5:45:26.973804 INFO: num_candidates : 3
1 day, 5:45:26.973886 INFO: ms1_error      : 30
1 day, 5:45:26.973959 INFO: ms2_error      : 30
1 day, 5:45:26.974026 INFO: fwhm_rt        : 3.239382743835449
1 day, 5:45:26.974091 INFO: quant_window   : 3
1 day, 5:45:26.974151 INFO: ==============================================
1 day, 5:45:26.982183 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:45:26.982291 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:45:26.982340 INFO: FWHM in RT is 3.24 seconds, sigma is 0.71
1 day, 5:45:26.982371 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.63
1 day, 5:45:26.983578 INFO: Starting candidate selection
1 day, 5:49:03.228410 INFO: Starting candidate scoring
1 day, 5:49:09.501795 INFO: Finished candidate processing
1 day, 5:49:09.502009 INFO: Collecting candidate features
1 day, 5:49:09.620021 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 87552)
1 day, 5:49:09.626919 INFO: Collecting fragment features
1 day, 5:49:09.674278 INFO: Finished candidate scoring
1 day, 5:49:09.755084 INFO: performing precursor FDR with 47 features
1 day, 5:49:09.755255 INFO: Decoy channel: -1
1 day, 5:49:09.755288 INFO: competitive: True
1 day, 5:49:09.798446 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:49:09.819158 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 5:49:09.843493 INFO: Estimating optimal hyperparameters - samples: 105,126, batch_size: 430, learning_rate: 3.24e-04
1 day, 5:49:09.843864 INFO: Using random state 981032 for train-test-split
1 day, 5:49:14.850494 INFO: Test AUC: 0.562
1 day, 5:49:14.850660 INFO: Train AUC: 0.594
1 day, 5:49:14.850695 INFO: AUC difference: 5.41%
1 day, 5:49:14.850720 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 5:49:15.158926 INFO: Resetting torch num_threads to 128
1 day, 5:49:15.218936 PROGRESS: === Extracted 131409 precursors and 1433466 fragments ===
1 day, 5:49:15.219827 INFO: === FDR correction performed with classifier version 0 ===
1 day, 5:49:15.224888 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:49:15.225025 PROGRESS: Total precursors accumulated: 23,610
1 day, 5:49:15.225116 PROGRESS: Target precursors: 14,829 (62.81%)
1 day, 5:49:15.225181 PROGRESS: Decoy precursors: 8,781 (37.19%)
1 day, 5:49:15.225242 PROGRESS: 
1 day, 5:49:15.225303 PROGRESS: Precursor Summary:
1 day, 5:49:15.226509 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
1 day, 5:49:15.226617 PROGRESS: 
1 day, 5:49:15.226690 PROGRESS: Protein Summary:
1 day, 5:49:15.227927 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
1 day, 5:49:15.228039 PROGRESS: =========================================================================
1 day, 5:49:15.228491 INFO: Target number of precursors not reached yet.
1 day, 5:49:15.544070 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 5:49:15.553971 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 5:49:15.590576 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 5:49:15.600606 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 5:49:15.688966 INFO: === skipping optimization until target number of precursors are found ===
1 day, 5:49:15.689396 INFO: Starting optimization step 3.
1 day, 5:49:15.689531 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1 day, 5:49:15.689718 INFO: Using python extraction backend
1 day, 5:49:15.690039 PROGRESS: Extracting batch of 63149 precursors
1 day, 5:49:15.690170 INFO: === Search parameters used ===
1 day, 5:49:15.690245 INFO: rt_error       : 2099.9231665
1 day, 5:49:15.690311 INFO: mobility_error : 0.1
1 day, 5:49:15.690379 INFO: num_candidates : 3
1 day, 5:49:15.690442 INFO: ms1_error      : 30
1 day, 5:49:15.690507 INFO: ms2_error      : 30
1 day, 5:49:15.690569 INFO: fwhm_rt        : 3.239382743835449
1 day, 5:49:15.690633 INFO: quant_window   : 3
1 day, 5:49:15.690692 INFO: ==============================================
1 day, 5:49:15.711576 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:49:15.711730 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:49:15.711790 INFO: FWHM in RT is 3.24 seconds, sigma is 0.71
1 day, 5:49:15.711824 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.63
1 day, 5:49:15.717897 INFO: Starting candidate selection
1 day, 5:56:17.341642 INFO: Starting candidate scoring
1 day, 5:56:28.663728 INFO: Finished candidate processing
1 day, 5:56:28.663938 INFO: Collecting candidate features
1 day, 5:56:28.939770 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 175265)
1 day, 5:56:28.949232 INFO: Collecting fragment features
1 day, 5:56:29.046679 INFO: Finished candidate scoring
1 day, 5:56:29.293257 INFO: performing precursor FDR with 47 features
1 day, 5:56:29.293511 INFO: Decoy channel: -1
1 day, 5:56:29.293543 INFO: competitive: True
1 day, 5:56:29.393637 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 5:56:29.438001 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 5:56:29.526960 INFO: Estimating optimal hyperparameters - samples: 245,336, batch_size: 1,004, learning_rate: 4.95e-04
1 day, 5:56:29.527718 INFO: Using random state 981032 for train-test-split
1 day, 5:56:37.054889 INFO: Test AUC: 0.559
1 day, 5:56:37.055068 INFO: Train AUC: 0.588
1 day, 5:56:37.055104 INFO: AUC difference: 4.88%
1 day, 5:56:37.416755 INFO: Resetting torch num_threads to 128
1 day, 5:56:37.459986 PROGRESS: === Extracted 306674 precursors and 3347291 fragments ===
1 day, 5:56:37.460993 INFO: === FDR correction performed with classifier version 0 ===
1 day, 5:56:37.471780 PROGRESS: ============================= Precursor FDR =============================
1 day, 5:56:37.472055 PROGRESS: Total precursors accumulated: 55,074
1 day, 5:56:37.472153 PROGRESS: Target precursors: 34,250 (62.19%)
1 day, 5:56:37.472239 PROGRESS: Decoy precursors: 20,824 (37.81%)
1 day, 5:56:37.472337 PROGRESS: 
1 day, 5:56:37.472412 PROGRESS: Precursor Summary:
1 day, 5:56:37.473974 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
1 day, 5:56:37.474099 PROGRESS: 
1 day, 5:56:37.474182 PROGRESS: Protein Summary:
1 day, 5:56:37.475592 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
1 day, 5:56:37.475703 PROGRESS: =========================================================================
1 day, 5:56:37.476584 INFO: Target number of precursors not reached yet.
1 day, 5:56:37.782224 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 5:56:37.797366 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 5:56:37.869544 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 5:56:37.885550 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 5:56:38.059701 INFO: === skipping optimization until target number of precursors are found ===
1 day, 5:56:38.060091 INFO: Starting optimization step 4.
1 day, 5:56:38.060196 PROGRESS: === Extracting elution groups 56000 to 120000 ===
1 day, 5:56:38.060320 INFO: Using python extraction backend
1 day, 5:56:38.060550 PROGRESS: Extracting batch of 126145 precursors
1 day, 5:56:38.060666 INFO: === Search parameters used ===
1 day, 5:56:38.060760 INFO: rt_error       : 2099.9231665
1 day, 5:56:38.060843 INFO: mobility_error : 0.1
1 day, 5:56:38.060917 INFO: num_candidates : 3
1 day, 5:56:38.060999 INFO: ms1_error      : 30
1 day, 5:56:38.061067 INFO: ms2_error      : 30
1 day, 5:56:38.061126 INFO: fwhm_rt        : 3.239382743835449
1 day, 5:56:38.061190 INFO: quant_window   : 3
1 day, 5:56:38.061252 INFO: ==============================================
1 day, 5:56:38.090105 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 5:56:38.090252 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 5:56:38.090325 INFO: FWHM in RT is 3.24 seconds, sigma is 0.71
1 day, 5:56:38.090364 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.63
1 day, 5:56:38.091383 INFO: Starting candidate selection
1 day, 6:10:41.670008 INFO: Starting candidate scoring
1 day, 6:11:01.834728 INFO: Finished candidate processing
1 day, 6:11:01.835139 INFO: Collecting candidate features
1 day, 6:11:02.419692 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 350166)
1 day, 6:11:02.435700 INFO: Collecting fragment features
1 day, 6:11:02.620611 INFO: Finished candidate scoring
1 day, 6:11:02.931418 INFO: performing precursor FDR with 47 features
1 day, 6:11:02.931596 INFO: Decoy channel: -1
1 day, 6:11:02.931629 INFO: competitive: True
1 day, 6:11:03.145518 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 6:11:03.256706 WARNING: dropped 3 target PSMs due to missing features
1 day, 6:11:03.256890 WARNING: dropped 4 decoy PSMs due to missing features
1 day, 6:11:03.485393 INFO: Estimating optimal hyperparameters - samples: 525,466, batch_size: 2,152, learning_rate: 7.25e-04
1 day, 6:11:03.486314 INFO: Using random state 981032 for train-test-split
1 day, 6:11:16.508576 INFO: Test AUC: 0.567
1 day, 6:11:16.508795 INFO: Train AUC: 0.581
1 day, 6:11:16.508833 INFO: AUC difference: 2.54%
1 day, 6:11:16.982469 INFO: Resetting torch num_threads to 128
1 day, 6:11:17.152987 PROGRESS: === Extracted 656840 precursors and 7166817 fragments ===
1 day, 6:11:17.154088 INFO: === FDR correction performed with classifier version 0 ===
1 day, 6:11:17.175803 PROGRESS: ============================= Precursor FDR =============================
1 day, 6:11:17.176161 PROGRESS: Total precursors accumulated: 118,046
1 day, 6:11:17.176270 PROGRESS: Target precursors: 73,429 (62.20%)
1 day, 6:11:17.176347 PROGRESS: Decoy precursors: 44,617 (37.80%)
1 day, 6:11:17.176417 PROGRESS: 
1 day, 6:11:17.176477 PROGRESS: Precursor Summary:
1 day, 6:11:17.178630 PROGRESS: Channel   0:	 0.050 FDR:   883; 0.010 FDR:   548; 0.001 FDR:     3
1 day, 6:11:17.178750 PROGRESS: 
1 day, 6:11:17.178823 PROGRESS: Protein Summary:
1 day, 6:11:17.180765 PROGRESS: Channel   0:	 0.050 FDR:   784; 0.010 FDR:   491; 0.001 FDR:     3
1 day, 6:11:17.180893 PROGRESS: =========================================================================
1 day, 6:11:17.182831 INFO: Target number of precursors reached.
1 day, 6:11:17.766279 INFO: fragments_df: keeping 5000 of 7166817 [sum(precursor_idx_mask)=17909 sum(mass_error_mask)=7166817 stop_rank=5000
1 day, 6:11:18.226817 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:11:18.383765 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:11:18.542906 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:11:18.679385 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:11:19.328418 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 6:11:19.328984 INFO: Using score_cutoff 54.989937474060056 (fac=0.99, q=1)
1 day, 6:11:19.329399 INFO: Updating optimization_manager: fwhm_rt             : 3.239382743835449 -> 3.0508995056152344
1 day, 6:11:19.329491 INFO: Updating optimization_manager: fwhm_mobility       : 0.00783432088792324 -> 0.010625982657074928
1 day, 6:11:19.329555 INFO: Updating optimization_manager: score_cutoff        : 12.314838609695434 -> 54.989937474060056
1 day, 6:11:19.329627 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:11:19.344929 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:11:19.411794 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:11:19.428790 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:11:19.584836 INFO: === checking if optimization conditions were reached ===
1 day, 6:11:19.587770 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 6:11:19.587915 INFO: Updating optimization_manager: classifier_version  : 0 -> 4
1 day, 6:11:19.588008 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 6:11:19.589390 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 6:11:19.589520 INFO: Updating optimization_manager: classifier_version  : 4 -> 4
1 day, 6:11:19.589616 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 6:11:19.589699 INFO: ==============================================
1 day, 6:11:19.589850 INFO: Starting optimization step 5.
1 day, 6:11:19.589943 PROGRESS: === Extracting elution groups 0 to 56000 ===
1 day, 6:11:19.590062 INFO: Using python extraction backend
1 day, 6:11:19.590250 PROGRESS: Extracting batch of 110438 precursors
1 day, 6:11:19.590348 INFO: === Search parameters used ===
1 day, 6:11:19.590419 INFO: rt_error       : 2099.9231665
1 day, 6:11:19.590483 INFO: mobility_error : 0.1
1 day, 6:11:19.590548 INFO: num_candidates : 3
1 day, 6:11:19.590613 INFO: ms1_error      : 15.0
1 day, 6:11:19.590698 INFO: ms2_error      : 15.0
1 day, 6:11:19.590780 INFO: fwhm_rt        : 3.0508995056152344
1 day, 6:11:19.590859 INFO: quant_window   : 3
1 day, 6:11:19.590939 INFO: ==============================================
1 day, 6:11:19.628358 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 6:11:19.628511 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 6:11:19.628561 INFO: FWHM in RT is 3.05 seconds, sigma is 0.67
1 day, 6:11:19.628588 INFO: FWHM in mobility is 0.011 1/K_0, sigma is 4.93
1 day, 6:11:19.629341 INFO: Starting candidate selection
1 day, 6:21:14.510162 INFO: Starting candidate scoring
1 day, 6:21:26.063573 INFO: Finished candidate processing
1 day, 6:21:26.063720 INFO: Collecting candidate features
1 day, 6:21:26.652553 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 305907)
1 day, 6:21:26.653108 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 305907)
1 day, 6:21:26.666048 INFO: Collecting fragment features
1 day, 6:21:26.879654 INFO: Finished candidate scoring
1 day, 6:21:27.054157 INFO: performing precursor FDR with 47 features
1 day, 6:21:27.054316 INFO: Decoy channel: -1
1 day, 6:21:27.054348 INFO: competitive: True
1 day, 6:21:27.140186 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 6:21:27.194987 WARNING: dropped 2 target PSMs due to missing features
1 day, 6:21:27.195161 WARNING: dropped 2 decoy PSMs due to missing features
1 day, 6:21:27.279453 INFO: Estimating optimal hyperparameters - samples: 244,722, batch_size: 1,002, learning_rate: 4.95e-04
1 day, 6:21:27.280243 INFO: Using random state 844549 for train-test-split
1 day, 6:21:34.907500 INFO: Test AUC: 0.558
1 day, 6:21:34.907790 INFO: Train AUC: 0.587
1 day, 6:21:34.907825 INFO: AUC difference: 4.99%
1 day, 6:21:35.274831 INFO: Resetting torch num_threads to 128
1 day, 6:21:35.281697 PROGRESS: === Extracted 305907 precursors and 3191721 fragments ===
1 day, 6:21:35.282493 INFO: === FDR correction performed with classifier version 4 ===
1 day, 6:21:35.293205 PROGRESS: ============================= Precursor FDR =============================
1 day, 6:21:35.293416 PROGRESS: Total precursors accumulated: 54,822
1 day, 6:21:35.293512 PROGRESS: Target precursors: 34,087 (62.18%)
1 day, 6:21:35.293595 PROGRESS: Decoy precursors: 20,735 (37.82%)
1 day, 6:21:35.293673 PROGRESS: 
1 day, 6:21:35.293765 PROGRESS: Precursor Summary:
1 day, 6:21:35.295494 PROGRESS: Channel   0:	 0.050 FDR:   628; 0.010 FDR:   417; 0.001 FDR:   356
1 day, 6:21:35.295612 PROGRESS: 
1 day, 6:21:35.295691 PROGRESS: Protein Summary:
1 day, 6:21:35.297426 PROGRESS: Channel   0:	 0.050 FDR:   584; 0.010 FDR:   389; 0.001 FDR:   331
1 day, 6:21:35.297543 PROGRESS: =========================================================================
1 day, 6:21:35.342247 INFO: Target number of precursors reached.
1 day, 6:21:35.584289 INFO: fragments_df: keeping 5000 of 3191721 [sum(precursor_idx_mask)=13395 sum(mass_error_mask)=3191721 stop_rank=5000
1 day, 6:21:36.557279 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:21:36.711264 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:21:36.850923 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:21:37.001308 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:21:37.716463 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 6:21:37.717017 INFO: Using score_cutoff 48.034386845397954 (fac=0.99, q=1)
1 day, 6:21:37.717407 INFO: Updating optimization_manager: fwhm_rt             : 3.0508995056152344 -> 2.9108266830444336
1 day, 6:21:37.717501 INFO: Updating optimization_manager: fwhm_mobility       : 0.010625982657074928 -> 0.00899641402065754
1 day, 6:21:37.717567 INFO: Updating optimization_manager: score_cutoff        : 54.989937474060056 -> 48.034386845397954
1 day, 6:21:37.717635 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:21:37.731609 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:21:37.798189 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:21:37.814904 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:21:37.983351 INFO: === checking if optimization conditions were reached ===
1 day, 6:21:37.985913 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 6:21:37.986050 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
1 day, 6:21:37.986149 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 6:21:37.987307 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 6:21:37.987428 INFO: Updating optimization_manager: classifier_version  : 5 -> 5
1 day, 6:21:37.987518 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 6:21:37.987611 INFO: ==============================================
1 day, 6:21:37.987715 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 6:21:38.277287 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:21:38.291388 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:21:38.359216 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:21:38.374658 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:21:38.522535 INFO: Starting optimization step 0.
1 day, 6:21:38.522861 PROGRESS: === Extracting elution groups 0 to 56000 ===
1 day, 6:21:38.522968 INFO: Using python extraction backend
1 day, 6:21:38.523142 PROGRESS: Extracting batch of 110438 precursors
1 day, 6:21:38.523263 INFO: === Search parameters used ===
1 day, 6:21:38.523340 INFO: rt_error       : 2099.9231665
1 day, 6:21:38.523411 INFO: mobility_error : 0.1
1 day, 6:21:38.523480 INFO: num_candidates : 3
1 day, 6:21:38.523543 INFO: ms1_error      : 15.0
1 day, 6:21:38.523607 INFO: ms2_error      : 15.0
1 day, 6:21:38.523673 INFO: fwhm_rt        : 2.9108266830444336
1 day, 6:21:38.523739 INFO: quant_window   : 3
1 day, 6:21:38.523802 INFO: ==============================================
1 day, 6:21:38.553775 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 6:21:38.553940 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 6:21:38.554000 INFO: FWHM in RT is 2.91 seconds, sigma is 0.64
1 day, 6:21:38.554062 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.17
1 day, 6:21:38.554996 INFO: Starting candidate selection
1 day, 6:31:14.694294 INFO: Starting candidate scoring
1 day, 6:31:25.531192 INFO: Finished candidate processing
1 day, 6:31:25.531338 INFO: Collecting candidate features
1 day, 6:31:26.304004 WARNING: intensity_correlation has 5 NaNs ( 0.00 % out of 306322)
1 day, 6:31:26.318095 INFO: Collecting fragment features
1 day, 6:31:26.755977 INFO: Finished candidate scoring
1 day, 6:31:27.014107 INFO: performing precursor FDR with 47 features
1 day, 6:31:27.014265 INFO: Decoy channel: -1
1 day, 6:31:27.014298 INFO: competitive: True
1 day, 6:31:27.137928 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 6:31:27.204794 WARNING: dropped 2 target PSMs due to missing features
1 day, 6:31:27.204965 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 6:31:27.389192 INFO: Estimating optimal hyperparameters - samples: 245,053, batch_size: 1,003, learning_rate: 4.95e-04
1 day, 6:31:27.389971 INFO: Using random state 632602 for train-test-split
1 day, 6:31:36.316998 INFO: Test AUC: 0.565
1 day, 6:31:36.317169 INFO: Train AUC: 0.600
1 day, 6:31:36.317203 INFO: AUC difference: 5.90%
1 day, 6:31:36.317228 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 6:31:36.678174 INFO: Resetting torch num_threads to 128
1 day, 6:31:36.684927 PROGRESS: === Extracted 306322 precursors and 3188023 fragments ===
1 day, 6:31:36.685690 INFO: === FDR correction performed with classifier version 5 ===
1 day, 6:31:36.695451 PROGRESS: ============================= Precursor FDR =============================
1 day, 6:31:36.695640 PROGRESS: Total precursors accumulated: 54,906
1 day, 6:31:36.695726 PROGRESS: Target precursors: 34,776 (63.34%)
1 day, 6:31:36.695797 PROGRESS: Decoy precursors: 20,130 (36.66%)
1 day, 6:31:36.695879 PROGRESS: 
1 day, 6:31:36.695946 PROGRESS: Precursor Summary:
1 day, 6:31:36.697664 PROGRESS: Channel   0:	 0.050 FDR:   713; 0.010 FDR:   472; 0.001 FDR:   306
1 day, 6:31:36.697798 PROGRESS: 
1 day, 6:31:36.697877 PROGRESS: Protein Summary:
1 day, 6:31:36.699617 PROGRESS: Channel   0:	 0.050 FDR:   664; 0.010 FDR:   437; 0.001 FDR:   291
1 day, 6:31:36.699731 PROGRESS: =========================================================================
1 day, 6:31:36.701836 INFO: Target number of precursors reached.
1 day, 6:31:37.004179 INFO: fragments_df: keeping 5000 of 3188023 [sum(precursor_idx_mask)=14974 sum(mass_error_mask)=3188023 stop_rank=5000
1 day, 6:31:37.708634 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:31:37.856037 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:31:38.004476 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:31:38.156391 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:31:38.874291 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 6:31:38.874879 INFO: Using score_cutoff 47.1958058921814 (fac=0.99, q=1)
1 day, 6:31:38.875280 INFO: Updating optimization_manager: fwhm_rt             : 2.9108266830444336 -> 2.915755271911621
1 day, 6:31:38.875375 INFO: Updating optimization_manager: fwhm_mobility       : 0.00899641402065754 -> 0.008955556899309158
1 day, 6:31:38.875442 INFO: Updating optimization_manager: score_cutoff        : 48.034386845397954 -> 47.1958058921814
1 day, 6:31:38.875510 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:31:38.882234 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:31:38.914813 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:31:38.921242 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:31:38.980411 INFO: === checking if optimization conditions were reached ===
1 day, 6:31:38.980802 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 6:31:38.983310 INFO: Updating optimization_manager: rt_error            : 2099.9231665 -> 620.3961098650736
1 day, 6:31:38.983478 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 620.3961.
1 day, 6:31:38.983585 INFO: ==============================================
1 day, 6:31:38.983735 INFO: Starting optimization step 1.
1 day, 6:31:38.983837 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 6:31:38.983937 INFO: Using python extraction backend
1 day, 6:31:38.984108 PROGRESS: Extracting batch of 47289 precursors
1 day, 6:31:38.984214 INFO: === Search parameters used ===
1 day, 6:31:38.984296 INFO: rt_error       : 620.3961098650736
1 day, 6:31:38.984373 INFO: mobility_error : 0.1
1 day, 6:31:38.984455 INFO: num_candidates : 3
1 day, 6:31:38.984536 INFO: ms1_error      : 15.0
1 day, 6:31:38.984606 INFO: ms2_error      : 15.0
1 day, 6:31:38.984677 INFO: fwhm_rt        : 2.915755271911621
1 day, 6:31:38.984746 INFO: quant_window   : 3
1 day, 6:31:38.984818 INFO: ==============================================
1 day, 6:31:39.035582 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 6:31:39.035726 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 6:31:39.035784 INFO: FWHM in RT is 2.92 seconds, sigma is 0.64
1 day, 6:31:39.035816 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.15
1 day, 6:31:39.036784 INFO: Starting candidate selection
1 day, 6:32:54.741037 INFO: Starting candidate scoring
1 day, 6:32:59.349475 INFO: Finished candidate processing
1 day, 6:32:59.349718 INFO: Collecting candidate features
1 day, 6:32:59.527714 WARNING: intensity_correlation has 34 NaNs ( 0.03 % out of 127938)
1 day, 6:32:59.528101 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 127938)
1 day, 6:32:59.535779 INFO: Collecting fragment features
1 day, 6:32:59.609086 INFO: Finished candidate scoring
1 day, 6:32:59.672656 INFO: performing precursor FDR with 47 features
1 day, 6:32:59.672803 INFO: Decoy channel: -1
1 day, 6:32:59.672834 INFO: competitive: True
1 day, 6:32:59.709621 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 6:32:59.733935 WARNING: dropped 17 target PSMs due to missing features
1 day, 6:32:59.734099 WARNING: dropped 18 decoy PSMs due to missing features
1 day, 6:32:59.760107 INFO: Estimating optimal hyperparameters - samples: 102,322, batch_size: 419, learning_rate: 3.20e-04
1 day, 6:32:59.760551 INFO: Using random state 632602 for train-test-split
1 day, 6:33:05.185726 INFO: Test AUC: 0.548
1 day, 6:33:05.185980 INFO: Train AUC: 0.592
1 day, 6:33:05.186024 INFO: AUC difference: 7.46%
1 day, 6:33:05.186051 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 6:33:05.485142 INFO: Resetting torch num_threads to 128
1 day, 6:33:05.488572 PROGRESS: === Extracted 127938 precursors and 1309223 fragments ===
1 day, 6:33:05.489213 INFO: === FDR correction performed with classifier version 5 ===
1 day, 6:33:05.493124 PROGRESS: ============================= Precursor FDR =============================
1 day, 6:33:05.493276 PROGRESS: Total precursors accumulated: 23,239
1 day, 6:33:05.493377 PROGRESS: Target precursors: 14,391 (61.93%)
1 day, 6:33:05.493447 PROGRESS: Decoy precursors: 8,848 (38.07%)
1 day, 6:33:05.493520 PROGRESS: 
1 day, 6:33:05.493578 PROGRESS: Precursor Summary:
1 day, 6:33:05.494863 PROGRESS: Channel   0:	 0.050 FDR:   257; 0.010 FDR:   128; 0.001 FDR:     0
1 day, 6:33:05.494990 PROGRESS: 
1 day, 6:33:05.495066 PROGRESS: Protein Summary:
1 day, 6:33:05.496425 PROGRESS: Channel   0:	 0.050 FDR:   252; 0.010 FDR:   127; 0.001 FDR:     0
1 day, 6:33:05.496553 PROGRESS: =========================================================================
1 day, 6:33:05.509968 INFO: Target number of precursors not reached yet.
1 day, 6:33:05.874547 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:33:05.882924 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:33:05.920609 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:33:05.929286 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:33:06.005487 INFO: === skipping optimization until target number of precursors are found ===
1 day, 6:33:06.005882 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1 day, 6:33:06.006017 INFO: Starting optimization step 2.
1 day, 6:33:06.006114 PROGRESS: === Extracting elution groups 24000 to 56000 ===
1 day, 6:33:06.006204 INFO: Using python extraction backend
1 day, 6:33:06.006357 PROGRESS: Extracting batch of 63149 precursors
1 day, 6:33:06.006468 INFO: === Search parameters used ===
1 day, 6:33:06.006546 INFO: rt_error       : 620.3961098650736
1 day, 6:33:06.006634 INFO: mobility_error : 0.1
1 day, 6:33:06.006711 INFO: num_candidates : 3
1 day, 6:33:06.006782 INFO: ms1_error      : 15.0
1 day, 6:33:06.006840 INFO: ms2_error      : 15.0
1 day, 6:33:06.006906 INFO: fwhm_rt        : 2.915755271911621
1 day, 6:33:06.006977 INFO: quant_window   : 3
1 day, 6:33:06.007051 INFO: ==============================================
1 day, 6:33:06.022838 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 6:33:06.022989 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 6:33:06.023047 INFO: FWHM in RT is 2.92 seconds, sigma is 0.64
1 day, 6:33:06.023081 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.15
1 day, 6:33:06.024159 INFO: Starting candidate selection
1 day, 6:34:47.340773 INFO: Starting candidate scoring
1 day, 6:34:53.459518 INFO: Finished candidate processing
1 day, 6:34:53.459736 INFO: Collecting candidate features
1 day, 6:34:53.725973 WARNING: intensity_correlation has 40 NaNs ( 0.02 % out of 170874)
1 day, 6:34:53.726403 WARNING: height_correlation has 5 NaNs ( 0.00 % out of 170874)
1 day, 6:34:53.735428 INFO: Collecting fragment features
1 day, 6:34:53.831281 INFO: Finished candidate scoring
1 day, 6:34:54.017261 INFO: performing precursor FDR with 47 features
1 day, 6:34:54.017445 INFO: Decoy channel: -1
1 day, 6:34:54.017479 INFO: competitive: True
1 day, 6:34:54.128506 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 6:34:54.189209 WARNING: dropped 38 target PSMs due to missing features
1 day, 6:34:54.189380 WARNING: dropped 40 decoy PSMs due to missing features
1 day, 6:34:54.323390 INFO: Estimating optimal hyperparameters - samples: 238,987, batch_size: 978, learning_rate: 4.89e-04
1 day, 6:34:54.324014 INFO: Using random state 632602 for train-test-split
1 day, 6:35:02.050715 INFO: Test AUC: 0.553
1 day, 6:35:02.050910 INFO: Train AUC: 0.585
1 day, 6:35:02.050944 INFO: AUC difference: 5.51%
1 day, 6:35:02.050975 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 6:35:04.141409 INFO: Resetting torch num_threads to 128
1 day, 6:35:04.257910 PROGRESS: === Extracted 298812 precursors and 3058341 fragments ===
1 day, 6:35:04.258971 INFO: === FDR correction performed with classifier version 5 ===
1 day, 6:35:04.272381 PROGRESS: ============================= Precursor FDR =============================
1 day, 6:35:04.272656 PROGRESS: Total precursors accumulated: 54,248
1 day, 6:35:04.272763 PROGRESS: Target precursors: 33,171 (61.15%)
1 day, 6:35:04.272843 PROGRESS: Decoy precursors: 21,077 (38.85%)
1 day, 6:35:04.272914 PROGRESS: 
1 day, 6:35:04.272987 PROGRESS: Precursor Summary:
1 day, 6:35:04.274780 PROGRESS: Channel   0:	 0.050 FDR:   710; 0.010 FDR:   430; 0.001 FDR:     2
1 day, 6:35:04.274906 PROGRESS: 
1 day, 6:35:04.274993 PROGRESS: Protein Summary:
1 day, 6:35:04.276712 PROGRESS: Channel   0:	 0.050 FDR:   662; 0.010 FDR:   402; 0.001 FDR:     2
1 day, 6:35:04.276829 PROGRESS: =========================================================================
1 day, 6:35:04.277717 INFO: Target number of precursors reached.
1 day, 6:35:04.536282 INFO: fragments_df: keeping 5000 of 3058341 [sum(precursor_idx_mask)=13711 sum(mass_error_mask)=3058338 stop_rank=5000
1 day, 6:35:04.989739 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:35:05.137816 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:35:05.279016 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:35:05.428373 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:35:06.146795 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 6:35:06.147352 INFO: Using score_cutoff 43.8959335144043 (fac=0.99, q=1)
1 day, 6:35:06.147725 INFO: Updating optimization_manager: fwhm_rt             : 2.915755271911621 -> 2.9153850078582764
1 day, 6:35:06.147819 INFO: Updating optimization_manager: fwhm_mobility       : 0.008955556899309158 -> 0.008898468688130379
1 day, 6:35:06.147885 INFO: Updating optimization_manager: score_cutoff        : 47.1958058921814 -> 43.8959335144043
1 day, 6:35:06.147961 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:35:06.161820 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:35:06.229739 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:35:06.244826 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:35:06.393262 INFO: === checking if optimization conditions were reached ===
1 day, 6:35:06.393616 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 6:35:06.396251 INFO: Updating optimization_manager: rt_error            : 620.3961098650736 -> 372.2734255568859
1 day, 6:35:06.396403 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 372.2734.
1 day, 6:35:06.396501 INFO: ==============================================
1 day, 6:35:06.396612 INFO: Starting optimization step 3.
1 day, 6:35:06.396702 PROGRESS: === Extracting elution groups 0 to 56000 ===
1 day, 6:35:06.396789 INFO: Using python extraction backend
1 day, 6:35:06.396957 PROGRESS: Extracting batch of 110438 precursors
1 day, 6:35:06.397056 INFO: === Search parameters used ===
1 day, 6:35:06.397137 INFO: rt_error       : 372.2734255568859
1 day, 6:35:06.397214 INFO: mobility_error : 0.1
1 day, 6:35:06.397293 INFO: num_candidates : 3
1 day, 6:35:06.397366 INFO: ms1_error      : 15.0
1 day, 6:35:06.397443 INFO: ms2_error      : 15.0
1 day, 6:35:06.397518 INFO: fwhm_rt        : 2.9153850078582764
1 day, 6:35:06.397584 INFO: quant_window   : 3
1 day, 6:35:06.397653 INFO: ==============================================
1 day, 6:35:06.432091 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 6:35:06.432229 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 6:35:06.432320 INFO: FWHM in RT is 2.92 seconds, sigma is 0.64
1 day, 6:35:06.432355 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 4.13
1 day, 6:35:06.434219 INFO: Starting candidate selection
1 day, 6:36:57.251461 INFO: Starting candidate scoring
1 day, 6:37:09.560599 INFO: Finished candidate processing
1 day, 6:37:09.560883 INFO: Collecting candidate features
1 day, 6:37:10.165868 WARNING: intensity_correlation has 91 NaNs ( 0.03 % out of 294378)
1 day, 6:37:10.166424 WARNING: height_correlation has 10 NaNs ( 0.00 % out of 294378)
1 day, 6:37:10.179456 INFO: Collecting fragment features
1 day, 6:37:10.551088 INFO: Finished candidate scoring
1 day, 6:37:10.709605 INFO: performing precursor FDR with 47 features
1 day, 6:37:10.709766 INFO: Decoy channel: -1
1 day, 6:37:10.709803 INFO: competitive: True
1 day, 6:37:10.799700 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 6:37:10.862298 WARNING: dropped 54 target PSMs due to missing features
1 day, 6:37:10.862462 WARNING: dropped 45 decoy PSMs due to missing features
1 day, 6:37:10.947895 INFO: Estimating optimal hyperparameters - samples: 235,423, batch_size: 964, learning_rate: 4.85e-04
1 day, 6:37:10.948561 INFO: Using random state 632602 for train-test-split
1 day, 6:37:18.541760 INFO: Test AUC: 0.553
1 day, 6:37:18.541925 INFO: Train AUC: 0.590
1 day, 6:37:18.541957 INFO: AUC difference: 6.22%
1 day, 6:37:18.541988 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 6:37:18.905206 INFO: Resetting torch num_threads to 128
1 day, 6:37:18.913506 PROGRESS: === Extracted 294378 precursors and 2974414 fragments ===
1 day, 6:37:18.914268 INFO: === FDR correction performed with classifier version 5 ===
1 day, 6:37:18.926271 PROGRESS: ============================= Precursor FDR =============================
1 day, 6:37:18.926500 PROGRESS: Total precursors accumulated: 53,724
1 day, 6:37:18.926585 PROGRESS: Target precursors: 33,141 (61.69%)
1 day, 6:37:18.926677 PROGRESS: Decoy precursors: 20,583 (38.31%)
1 day, 6:37:18.926793 PROGRESS: 
1 day, 6:37:18.926861 PROGRESS: Precursor Summary:
1 day, 6:37:18.928723 PROGRESS: Channel   0:	 0.050 FDR:   765; 0.010 FDR:   506; 0.001 FDR:     0
1 day, 6:37:18.928845 PROGRESS: 
1 day, 6:37:18.928924 PROGRESS: Protein Summary:
1 day, 6:37:18.930738 PROGRESS: Channel   0:	 0.050 FDR:   711; 0.010 FDR:   473; 0.001 FDR:     0
1 day, 6:37:18.930863 PROGRESS: =========================================================================
1 day, 6:37:18.935434 INFO: Target number of precursors reached.
1 day, 6:37:19.156464 INFO: fragments_df: keeping 5000 of 2974414 [sum(precursor_idx_mask)=16002 sum(mass_error_mask)=2974412 stop_rank=5000
1 day, 6:37:19.728130 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:37:19.882199 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:37:20.042775 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:37:20.199175 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:37:20.919582 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 6:37:20.920154 INFO: Using score_cutoff 42.365477519989014 (fac=0.99, q=1)
1 day, 6:37:20.920540 INFO: Updating optimization_manager: fwhm_rt             : 2.9153850078582764 -> 2.9389443397521973
1 day, 6:37:20.920635 INFO: Updating optimization_manager: fwhm_mobility       : 0.008898468688130379 -> 0.0085927564650774
1 day, 6:37:20.920705 INFO: Updating optimization_manager: score_cutoff        : 43.8959335144043 -> 42.365477519989014
1 day, 6:37:20.920785 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:37:20.927116 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:37:20.955684 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:37:20.962051 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:37:21.018606 INFO: === checking if optimization conditions were reached ===
1 day, 6:37:21.018986 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 6:37:21.022161 INFO: Updating optimization_manager: rt_error            : 372.2734255568859 -> 216.21085726476124
1 day, 6:37:21.022316 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 216.2109.
1 day, 6:37:21.022409 INFO: ==============================================
1 day, 6:37:21.022506 INFO: Starting optimization step 4.
1 day, 6:37:21.022592 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 6:37:21.022697 INFO: Using python extraction backend
1 day, 6:37:21.022864 PROGRESS: Extracting batch of 47289 precursors
1 day, 6:37:21.022957 INFO: === Search parameters used ===
1 day, 6:37:21.023025 INFO: rt_error       : 216.21085726476124
1 day, 6:37:21.023090 INFO: mobility_error : 0.1
1 day, 6:37:21.023151 INFO: num_candidates : 3
1 day, 6:37:21.023213 INFO: ms1_error      : 15.0
1 day, 6:37:21.023273 INFO: ms2_error      : 15.0
1 day, 6:37:21.023332 INFO: fwhm_rt        : 2.9389443397521973
1 day, 6:37:21.023391 INFO: quant_window   : 3
1 day, 6:37:21.023450 INFO: ==============================================
1 day, 6:37:21.040631 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 6:37:21.040743 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 6:37:21.040821 INFO: FWHM in RT is 2.94 seconds, sigma is 0.65
1 day, 6:37:21.040852 INFO: FWHM in mobility is 0.009 1/K_0, sigma is 3.99
1 day, 6:37:21.041956 INFO: Starting candidate selection
1 day, 6:37:48.416747 INFO: Starting candidate scoring
1 day, 6:37:52.931959 INFO: Finished candidate processing
1 day, 6:37:52.932159 INFO: Collecting candidate features
1 day, 6:37:53.146774 WARNING: intensity_correlation has 56 NaNs ( 0.04 % out of 125620)
1 day, 6:37:53.147166 WARNING: height_correlation has 8 NaNs ( 0.01 % out of 125620)
1 day, 6:37:53.155444 INFO: Collecting fragment features
1 day, 6:37:53.240086 INFO: Finished candidate scoring
1 day, 6:37:53.318024 INFO: performing precursor FDR with 47 features
1 day, 6:37:53.318191 INFO: Decoy channel: -1
1 day, 6:37:53.318219 INFO: competitive: True
1 day, 6:37:53.363561 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 6:37:53.390777 WARNING: dropped 32 target PSMs due to missing features
1 day, 6:37:53.390951 WARNING: dropped 29 decoy PSMs due to missing features
1 day, 6:37:53.423654 INFO: Estimating optimal hyperparameters - samples: 100,447, batch_size: 411, learning_rate: 3.17e-04
1 day, 6:37:53.424124 INFO: Using random state 632602 for train-test-split
1 day, 6:37:59.667745 INFO: Test AUC: 0.548
1 day, 6:37:59.667915 INFO: Train AUC: 0.600
1 day, 6:37:59.667949 INFO: AUC difference: 8.76%
1 day, 6:37:59.667974 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 6:37:59.983943 INFO: Resetting torch num_threads to 128
1 day, 6:37:59.987568 PROGRESS: === Extracted 125620 precursors and 1247450 fragments ===
1 day, 6:37:59.988232 INFO: === FDR correction performed with classifier version 5 ===
1 day, 6:37:59.992493 PROGRESS: ============================= Precursor FDR =============================
1 day, 6:37:59.992645 PROGRESS: Total precursors accumulated: 23,052
1 day, 6:37:59.992729 PROGRESS: Target precursors: 14,354 (62.27%)
1 day, 6:37:59.992794 PROGRESS: Decoy precursors: 8,698 (37.73%)
1 day, 6:37:59.992855 PROGRESS: 
1 day, 6:37:59.992911 PROGRESS: Precursor Summary:
1 day, 6:37:59.994400 PROGRESS: Channel   0:	 0.050 FDR:   373; 0.010 FDR:   226; 0.001 FDR:   163
1 day, 6:37:59.994524 PROGRESS: 
1 day, 6:37:59.994596 PROGRESS: Protein Summary:
1 day, 6:37:59.996088 PROGRESS: Channel   0:	 0.050 FDR:   362; 0.010 FDR:   219; 0.001 FDR:   160
1 day, 6:37:59.996201 PROGRESS: =========================================================================
1 day, 6:37:59.998113 INFO: Target number of precursors reached.
1 day, 6:38:00.095468 INFO: fragments_df: keeping 3007 of 1247450 [sum(precursor_idx_mask)=7084 sum(mass_error_mask)=1247449 stop_rank=3007
1 day, 6:38:00.304457 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:38:00.436373 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:38:00.578778 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:38:00.716100 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:38:01.150906 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 6:38:01.151509 INFO: Using score_cutoff 36.61883651733398 (fac=0.99, q=1)
1 day, 6:38:01.151889 INFO: Updating optimization_manager: fwhm_rt             : 2.9389443397521973 -> 2.923719882965088
1 day, 6:38:01.152004 INFO: Updating optimization_manager: fwhm_mobility       : 0.0085927564650774 -> 0.0082301190122962
1 day, 6:38:01.152077 INFO: Updating optimization_manager: score_cutoff        : 42.365477519989014 -> 36.61883651733398
1 day, 6:38:01.152148 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:38:01.159647 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:38:01.188915 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:38:01.195315 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:38:01.255419 INFO: === checking if optimization conditions were reached ===
1 day, 6:38:01.255753 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 6:38:01.258385 INFO: Updating optimization_manager: rt_error            : 216.21085726476124 -> 163.39830197669878
1 day, 6:38:01.258512 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 163.3983.
1 day, 6:38:01.258611 INFO: ==============================================
1 day, 6:38:01.258757 INFO: Starting optimization step 5.
1 day, 6:38:01.258854 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 6:38:01.258943 INFO: Using python extraction backend
1 day, 6:38:01.259103 PROGRESS: Extracting batch of 47289 precursors
1 day, 6:38:01.259197 INFO: === Search parameters used ===
1 day, 6:38:01.259269 INFO: rt_error       : 163.39830197669878
1 day, 6:38:01.259335 INFO: mobility_error : 0.1
1 day, 6:38:01.259402 INFO: num_candidates : 3
1 day, 6:38:01.259475 INFO: ms1_error      : 15.0
1 day, 6:38:01.259542 INFO: ms2_error      : 15.0
1 day, 6:38:01.259607 INFO: fwhm_rt        : 2.923719882965088
1 day, 6:38:01.259669 INFO: quant_window   : 3
1 day, 6:38:01.259732 INFO: ==============================================
1 day, 6:38:01.272594 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 6:38:01.272713 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 6:38:01.272769 INFO: FWHM in RT is 2.92 seconds, sigma is 0.64
1 day, 6:38:01.272802 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 6:38:01.273670 INFO: Starting candidate selection
1 day, 6:38:23.560708 INFO: Starting candidate scoring
1 day, 6:38:28.370260 INFO: Finished candidate processing
1 day, 6:38:28.370467 INFO: Collecting candidate features
1 day, 6:38:28.572054 WARNING: intensity_correlation has 55 NaNs ( 0.04 % out of 125355)
1 day, 6:38:28.572555 WARNING: height_correlation has 7 NaNs ( 0.01 % out of 125355)
1 day, 6:38:28.584022 INFO: Collecting fragment features
1 day, 6:38:28.655009 INFO: Finished candidate scoring
1 day, 6:38:28.714800 INFO: performing precursor FDR with 47 features
1 day, 6:38:28.714956 INFO: Decoy channel: -1
1 day, 6:38:28.714985 INFO: competitive: True
1 day, 6:38:28.754392 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 6:38:28.781674 WARNING: dropped 26 target PSMs due to missing features
1 day, 6:38:28.781849 WARNING: dropped 32 decoy PSMs due to missing features
1 day, 6:38:28.806355 INFO: Estimating optimal hyperparameters - samples: 100,237, batch_size: 410, learning_rate: 3.16e-04
1 day, 6:38:28.806807 INFO: Using random state 632602 for train-test-split
1 day, 6:38:34.017904 INFO: Test AUC: 0.550
1 day, 6:38:34.018083 INFO: Train AUC: 0.601
1 day, 6:38:34.018117 INFO: AUC difference: 8.41%
1 day, 6:38:34.018149 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 6:38:34.328541 INFO: Resetting torch num_threads to 128
1 day, 6:38:34.332538 PROGRESS: === Extracted 125355 precursors and 1235581 fragments ===
1 day, 6:38:34.333170 INFO: === FDR correction performed with classifier version 5 ===
1 day, 6:38:34.337407 PROGRESS: ============================= Precursor FDR =============================
1 day, 6:38:34.337565 PROGRESS: Total precursors accumulated: 23,020
1 day, 6:38:34.337658 PROGRESS: Target precursors: 14,408 (62.59%)
1 day, 6:38:34.337762 PROGRESS: Decoy precursors: 8,612 (37.41%)
1 day, 6:38:34.337858 PROGRESS: 
1 day, 6:38:34.337929 PROGRESS: Precursor Summary:
1 day, 6:38:34.339262 PROGRESS: Channel   0:	 0.050 FDR:   365; 0.010 FDR:   219; 0.001 FDR:   148
1 day, 6:38:34.339387 PROGRESS: 
1 day, 6:38:34.339481 PROGRESS: Protein Summary:
1 day, 6:38:34.340932 PROGRESS: Channel   0:	 0.050 FDR:   356; 0.010 FDR:   213; 0.001 FDR:   146
1 day, 6:38:34.341053 PROGRESS: =========================================================================
1 day, 6:38:34.341862 INFO: Target number of precursors reached.
1 day, 6:38:34.435870 INFO: fragments_df: keeping 2875 of 1235581 [sum(precursor_idx_mask)=6802 sum(mass_error_mask)=1235580 stop_rank=2875
1 day, 6:38:34.622570 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:38:34.732479 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:38:34.850024 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:38:34.983486 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:38:35.363190 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 6:38:35.363740 INFO: Using score_cutoff 38.8396787612915 (fac=0.99, q=1)
1 day, 6:38:35.364105 INFO: Updating optimization_manager: fwhm_rt             : 2.923719882965088 -> 2.9353721141815186
1 day, 6:38:35.364199 INFO: Updating optimization_manager: fwhm_mobility       : 0.0082301190122962 -> 0.008440511301159859
1 day, 6:38:35.364266 INFO: Updating optimization_manager: score_cutoff        : 36.61883651733398 -> 38.8396787612915
1 day, 6:38:35.364344 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:38:35.371904 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:38:35.401171 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:38:35.407951 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:38:35.466098 INFO: === checking if optimization conditions were reached ===
1 day, 6:38:35.466418 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 6:38:35.468868 INFO: Updating optimization_manager: rt_error            : 163.39830197669878 -> 162.32241579151378
1 day, 6:38:35.468986 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 162.3224.
1 day, 6:38:35.469068 INFO: ==============================================
1 day, 6:38:35.469152 INFO: Starting optimization step 6.
1 day, 6:38:35.469237 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 6:38:35.469316 INFO: Using python extraction backend
1 day, 6:38:35.469453 PROGRESS: Extracting batch of 47289 precursors
1 day, 6:38:35.469530 INFO: === Search parameters used ===
1 day, 6:38:35.469590 INFO: rt_error       : 162.32241579151378
1 day, 6:38:35.469646 INFO: mobility_error : 0.1
1 day, 6:38:35.469704 INFO: num_candidates : 3
1 day, 6:38:35.469774 INFO: ms1_error      : 15.0
1 day, 6:38:35.469839 INFO: ms2_error      : 15.0
1 day, 6:38:35.469896 INFO: fwhm_rt        : 2.9353721141815186
1 day, 6:38:35.469947 INFO: quant_window   : 3
1 day, 6:38:35.469999 INFO: ==============================================
1 day, 6:38:35.482367 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 6:38:35.482477 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 6:38:35.482524 INFO: FWHM in RT is 2.94 seconds, sigma is 0.65
1 day, 6:38:35.482555 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.92
1 day, 6:38:35.483509 INFO: Starting candidate selection
1 day, 6:38:58.086987 INFO: Starting candidate scoring
1 day, 6:39:02.715745 INFO: Finished candidate processing
1 day, 6:39:02.715949 INFO: Collecting candidate features
1 day, 6:39:02.918250 WARNING: intensity_correlation has 51 NaNs ( 0.04 % out of 125101)
1 day, 6:39:02.918662 WARNING: height_correlation has 6 NaNs ( 0.00 % out of 125101)
1 day, 6:39:02.926927 INFO: Collecting fragment features
1 day, 6:39:02.992977 INFO: Finished candidate scoring
1 day, 6:39:03.054176 INFO: performing precursor FDR with 47 features
1 day, 6:39:03.054334 INFO: Decoy channel: -1
1 day, 6:39:03.054361 INFO: competitive: True
1 day, 6:39:03.093028 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 6:39:03.120257 WARNING: dropped 30 target PSMs due to missing features
1 day, 6:39:03.120425 WARNING: dropped 26 decoy PSMs due to missing features
1 day, 6:39:03.153322 INFO: Estimating optimal hyperparameters - samples: 100,036, batch_size: 409, learning_rate: 3.16e-04
1 day, 6:39:03.153738 INFO: Using random state 632602 for train-test-split
1 day, 6:39:08.379266 INFO: Test AUC: 0.553
1 day, 6:39:08.379426 INFO: Train AUC: 0.600
1 day, 6:39:08.379459 INFO: AUC difference: 7.82%
1 day, 6:39:08.379483 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 6:39:08.687171 INFO: Resetting torch num_threads to 128
1 day, 6:39:08.691234 PROGRESS: === Extracted 125101 precursors and 1233694 fragments ===
1 day, 6:39:08.691889 INFO: === FDR correction performed with classifier version 5 ===
1 day, 6:39:08.695886 PROGRESS: ============================= Precursor FDR =============================
1 day, 6:39:08.696055 PROGRESS: Total precursors accumulated: 22,961
1 day, 6:39:08.696134 PROGRESS: Target precursors: 14,306 (62.31%)
1 day, 6:39:08.696202 PROGRESS: Decoy precursors: 8,655 (37.69%)
1 day, 6:39:08.696275 PROGRESS: 
1 day, 6:39:08.696335 PROGRESS: Precursor Summary:
1 day, 6:39:08.697675 PROGRESS: Channel   0:	 0.050 FDR:   389; 0.010 FDR:   244; 0.001 FDR:   171
1 day, 6:39:08.697810 PROGRESS: 
1 day, 6:39:08.697907 PROGRESS: Protein Summary:
1 day, 6:39:08.699357 PROGRESS: Channel   0:	 0.050 FDR:   380; 0.010 FDR:   237; 0.001 FDR:   167
1 day, 6:39:08.699468 PROGRESS: =========================================================================
1 day, 6:39:08.700227 INFO: Target number of precursors reached.
1 day, 6:39:08.795314 INFO: fragments_df: keeping 3179 of 1233694 [sum(precursor_idx_mask)=7578 sum(mass_error_mask)=1233694 stop_rank=3179
1 day, 6:39:08.981052 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:39:09.103106 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:39:09.222113 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:39:09.337514 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:39:09.718035 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 6:39:09.718619 INFO: Using score_cutoff 38.408564623260496 (fac=0.99, q=1)
1 day, 6:39:09.718995 INFO: Updating optimization_manager: fwhm_rt             : 2.9353721141815186 -> 2.9297969341278076
1 day, 6:39:09.719098 INFO: Updating optimization_manager: fwhm_mobility       : 0.008440511301159859 -> 0.008376887068152428
1 day, 6:39:09.719181 INFO: Updating optimization_manager: score_cutoff        : 38.8396787612915 -> 38.408564623260496
1 day, 6:39:09.719263 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:39:09.726313 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:39:09.755652 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:39:09.761878 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:39:09.819876 INFO: === checking if optimization conditions were reached ===
1 day, 6:39:09.820216 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 6:39:09.821732 INFO: Updating optimization_manager: rt_error            : 162.32241579151378 -> 162.32241579151378
1 day, 6:39:09.821908 INFO: Updating optimization_manager: classifier_version  : 5 -> 12
1 day, 6:39:09.822039 INFO: Updating optimization_manager: score_cutoff        : 38.408564623260496 -> 38.408564623260496
1 day, 6:39:09.822162 INFO: Updating optimization_manager: fwhm_rt             : 2.9297969341278076 -> 2.9297969341278076
1 day, 6:39:09.822281 INFO: Updating optimization_manager: fwhm_mobility       : 0.008376887068152428 -> 0.008376887068152428
1 day, 6:39:09.822426 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 162.3224 found after 6 searches.
1 day, 6:39:09.822512 INFO: ==============================================
1 day, 6:39:09.822603 PROGRESS: Optimization finished for rt_error.
1 day, 6:39:10.004298 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:39:10.011828 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:39:10.041045 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:39:10.047372 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:39:10.104836 INFO: Starting optimization step 0.
1 day, 6:39:10.105179 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 6:39:10.105293 INFO: Using python extraction backend
1 day, 6:39:10.105469 PROGRESS: Extracting batch of 47289 precursors
1 day, 6:39:10.105572 INFO: === Search parameters used ===
1 day, 6:39:10.105664 INFO: rt_error       : 162.32241579151378
1 day, 6:39:10.105736 INFO: mobility_error : 0.1
1 day, 6:39:10.105831 INFO: num_candidates : 3
1 day, 6:39:10.105914 INFO: ms1_error      : 15.0
1 day, 6:39:10.105990 INFO: ms2_error      : 15.0
1 day, 6:39:10.106060 INFO: fwhm_rt        : 2.9297969341278076
1 day, 6:39:10.106133 INFO: quant_window   : 3
1 day, 6:39:10.106203 INFO: ==============================================
1 day, 6:39:10.119802 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 6:39:10.119948 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 6:39:10.120001 INFO: FWHM in RT is 2.93 seconds, sigma is 0.64
1 day, 6:39:10.120040 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.89
1 day, 6:39:10.121047 INFO: Starting candidate selection
1 day, 6:39:32.795972 INFO: Starting candidate scoring
1 day, 6:39:37.454406 INFO: Finished candidate processing
1 day, 6:39:37.454616 INFO: Collecting candidate features
1 day, 6:39:37.657776 WARNING: intensity_correlation has 53 NaNs ( 0.04 % out of 124613)
1 day, 6:39:37.658168 WARNING: height_correlation has 5 NaNs ( 0.00 % out of 124613)
1 day, 6:39:37.666040 INFO: Collecting fragment features
1 day, 6:39:37.733179 INFO: Finished candidate scoring
1 day, 6:39:37.793804 INFO: performing precursor FDR with 47 features
1 day, 6:39:37.793954 INFO: Decoy channel: -1
1 day, 6:39:37.793982 INFO: competitive: True
1 day, 6:39:37.833137 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 6:39:37.859176 WARNING: dropped 34 target PSMs due to missing features
1 day, 6:39:37.859341 WARNING: dropped 23 decoy PSMs due to missing features
1 day, 6:39:37.890375 INFO: Estimating optimal hyperparameters - samples: 99,644, batch_size: 408, learning_rate: 3.16e-04
1 day, 6:39:37.890792 INFO: Using random state 270283 for train-test-split
1 day, 6:39:42.923045 INFO: Test AUC: 0.562
1 day, 6:39:42.923200 INFO: Train AUC: 0.621
1 day, 6:39:42.923234 INFO: AUC difference: 9.58%
1 day, 6:39:42.923258 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 6:39:43.213421 INFO: Resetting torch num_threads to 128
1 day, 6:39:43.217401 PROGRESS: === Extracted 124613 precursors and 1229157 fragments ===
1 day, 6:39:43.218074 INFO: === FDR correction performed with classifier version 12 ===
1 day, 6:39:43.222192 PROGRESS: ============================= Precursor FDR =============================
1 day, 6:39:43.222330 PROGRESS: Total precursors accumulated: 22,867
1 day, 6:39:43.222425 PROGRESS: Target precursors: 14,799 (64.72%)
1 day, 6:39:43.222493 PROGRESS: Decoy precursors: 8,068 (35.28%)
1 day, 6:39:43.222555 PROGRESS: 
1 day, 6:39:43.222615 PROGRESS: Precursor Summary:
1 day, 6:39:43.224012 PROGRESS: Channel   0:	 0.050 FDR:   407; 0.010 FDR:   242; 0.001 FDR:   204
1 day, 6:39:43.224127 PROGRESS: 
1 day, 6:39:43.224203 PROGRESS: Protein Summary:
1 day, 6:39:43.225696 PROGRESS: Channel   0:	 0.050 FDR:   397; 0.010 FDR:   235; 0.001 FDR:   198
1 day, 6:39:43.225818 PROGRESS: =========================================================================
1 day, 6:39:43.226581 INFO: Target number of precursors reached.
1 day, 6:39:43.319318 INFO: fragments_df: keeping 3162 of 1229157 [sum(precursor_idx_mask)=7480 sum(mass_error_mask)=1229157 stop_rank=3162
1 day, 6:39:43.503853 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:39:43.616148 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:39:43.733493 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:39:43.851722 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:39:44.291596 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 6:39:44.292178 INFO: Using score_cutoff 30.768488932228088 (fac=0.99, q=1)
1 day, 6:39:44.292539 INFO: Updating optimization_manager: fwhm_rt             : 2.9297969341278076 -> 2.948765516281128
1 day, 6:39:44.292635 INFO: Updating optimization_manager: fwhm_mobility       : 0.008376887068152428 -> 0.008376887068152428
1 day, 6:39:44.292702 INFO: Updating optimization_manager: score_cutoff        : 38.408564623260496 -> 30.768488932228088
1 day, 6:39:44.292773 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:39:44.299706 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:39:44.328637 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:39:44.334685 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:39:44.393354 INFO: === checking if optimization conditions were reached ===
1 day, 6:39:44.393686 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 6:39:44.395804 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07332792472079297
1 day, 6:39:44.395947 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0733.
1 day, 6:39:44.396033 INFO: ==============================================
1 day, 6:39:44.396129 INFO: Starting optimization step 1.
1 day, 6:39:44.396206 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 6:39:44.396303 INFO: Using python extraction backend
1 day, 6:39:44.396461 PROGRESS: Extracting batch of 47289 precursors
1 day, 6:39:44.396558 INFO: === Search parameters used ===
1 day, 6:39:44.396633 INFO: rt_error       : 162.32241579151378
1 day, 6:39:44.396707 INFO: mobility_error : 0.07332792472079297
1 day, 6:39:44.396771 INFO: num_candidates : 3
1 day, 6:39:44.396835 INFO: ms1_error      : 15.0
1 day, 6:39:44.396902 INFO: ms2_error      : 15.0
1 day, 6:39:44.396965 INFO: fwhm_rt        : 2.948765516281128
1 day, 6:39:44.397029 INFO: quant_window   : 3
1 day, 6:39:44.397087 INFO: ==============================================
1 day, 6:39:44.409644 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 6:39:44.409742 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 6:39:44.409793 INFO: FWHM in RT is 2.95 seconds, sigma is 0.65
1 day, 6:39:44.409825 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.89
1 day, 6:39:44.417869 INFO: Starting candidate selection
1 day, 6:40:00.191185 INFO: Starting candidate scoring
1 day, 6:40:04.933178 INFO: Finished candidate processing
1 day, 6:40:04.933398 INFO: Collecting candidate features
1 day, 6:40:05.148338 WARNING: intensity_correlation has 62 NaNs ( 0.05 % out of 122424)
1 day, 6:40:05.148729 WARNING: height_correlation has 11 NaNs ( 0.01 % out of 122424)
1 day, 6:40:05.156610 INFO: Collecting fragment features
1 day, 6:40:05.223196 INFO: Finished candidate scoring
1 day, 6:40:05.285957 INFO: performing precursor FDR with 47 features
1 day, 6:40:05.286103 INFO: Decoy channel: -1
1 day, 6:40:05.286129 INFO: competitive: True
1 day, 6:40:05.324367 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 6:40:05.349988 WARNING: dropped 41 target PSMs due to missing features
1 day, 6:40:05.350156 WARNING: dropped 30 decoy PSMs due to missing features
1 day, 6:40:05.371752 INFO: Estimating optimal hyperparameters - samples: 97,882, batch_size: 400, learning_rate: 3.13e-04
1 day, 6:40:05.372193 INFO: Using random state 270283 for train-test-split
1 day, 6:40:10.465026 INFO: Test AUC: 0.565
1 day, 6:40:10.465187 INFO: Train AUC: 0.598
1 day, 6:40:10.465218 INFO: AUC difference: 5.43%
1 day, 6:40:10.465241 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 6:40:10.767279 INFO: Resetting torch num_threads to 128
1 day, 6:40:10.771224 PROGRESS: === Extracted 122424 precursors and 1194371 fragments ===
1 day, 6:40:10.771887 INFO: === FDR correction performed with classifier version 12 ===
1 day, 6:40:10.775823 PROGRESS: ============================= Precursor FDR =============================
1 day, 6:40:10.775972 PROGRESS: Total precursors accumulated: 22,565
1 day, 6:40:10.776055 PROGRESS: Target precursors: 14,185 (62.86%)
1 day, 6:40:10.776124 PROGRESS: Decoy precursors: 8,380 (37.14%)
1 day, 6:40:10.776196 PROGRESS: 
1 day, 6:40:10.776255 PROGRESS: Precursor Summary:
1 day, 6:40:10.777588 PROGRESS: Channel   0:	 0.050 FDR:   376; 0.010 FDR:   246; 0.001 FDR:   193
1 day, 6:40:10.777699 PROGRESS: 
1 day, 6:40:10.777784 PROGRESS: Protein Summary:
1 day, 6:40:10.779212 PROGRESS: Channel   0:	 0.050 FDR:   366; 0.010 FDR:   239; 0.001 FDR:   188
1 day, 6:40:10.779325 PROGRESS: =========================================================================
1 day, 6:40:10.780088 INFO: Target number of precursors reached.
1 day, 6:40:10.872212 INFO: fragments_df: keeping 3224 of 1194371 [sum(precursor_idx_mask)=7657 sum(mass_error_mask)=1194366 stop_rank=3224
1 day, 6:40:11.058390 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:40:11.187713 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:40:11.325292 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:40:11.463063 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:40:11.916119 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 6:40:11.916739 INFO: Using score_cutoff 36.81261981010437 (fac=0.99, q=1)
1 day, 6:40:11.917122 INFO: Updating optimization_manager: fwhm_rt             : 2.948765516281128 -> 2.901212215423584
1 day, 6:40:11.917230 INFO: Updating optimization_manager: fwhm_mobility       : 0.008376887068152428 -> 0.008162545040249825
1 day, 6:40:11.917313 INFO: Updating optimization_manager: score_cutoff        : 30.768488932228088 -> 36.81261981010437
1 day, 6:40:11.917403 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:40:11.924636 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:40:11.953632 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:40:11.960033 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:40:12.018340 INFO: === checking if optimization conditions were reached ===
1 day, 6:40:12.018683 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 6:40:12.020879 INFO: Updating optimization_manager: mobility_error      : 0.07332792472079297 -> 0.0628567307929472
1 day, 6:40:12.021021 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0629.
1 day, 6:40:12.021130 INFO: ==============================================
1 day, 6:40:12.021242 INFO: Starting optimization step 2.
1 day, 6:40:12.021343 PROGRESS: === Extracting elution groups 0 to 24000 ===
1 day, 6:40:12.021444 INFO: Using python extraction backend
1 day, 6:40:12.021611 PROGRESS: Extracting batch of 47289 precursors
1 day, 6:40:12.021718 INFO: === Search parameters used ===
1 day, 6:40:12.021819 INFO: rt_error       : 162.32241579151378
1 day, 6:40:12.021904 INFO: mobility_error : 0.0628567307929472
1 day, 6:40:12.021982 INFO: num_candidates : 3
1 day, 6:40:12.022061 INFO: ms1_error      : 15.0
1 day, 6:40:12.022139 INFO: ms2_error      : 15.0
1 day, 6:40:12.022210 INFO: fwhm_rt        : 2.901212215423584
1 day, 6:40:12.022276 INFO: quant_window   : 3
1 day, 6:40:12.022354 INFO: ==============================================
1 day, 6:40:12.034782 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 6:40:12.034889 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 6:40:12.034949 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
1 day, 6:40:12.034989 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 6:40:12.036024 INFO: Starting candidate selection
1 day, 6:40:25.410798 INFO: Starting candidate scoring
1 day, 6:40:30.014102 INFO: Finished candidate processing
1 day, 6:40:30.014327 INFO: Collecting candidate features
1 day, 6:40:30.229322 WARNING: intensity_correlation has 73 NaNs ( 0.06 % out of 120461)
1 day, 6:40:30.229707 WARNING: height_correlation has 11 NaNs ( 0.01 % out of 120461)
1 day, 6:40:30.237560 INFO: Collecting fragment features
1 day, 6:40:30.303548 INFO: Finished candidate scoring
1 day, 6:40:30.369051 INFO: performing precursor FDR with 47 features
1 day, 6:40:30.369207 INFO: Decoy channel: -1
1 day, 6:40:30.369236 INFO: competitive: True
1 day, 6:40:30.406189 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 6:40:30.431852 WARNING: dropped 45 target PSMs due to missing features
1 day, 6:40:30.432019 WARNING: dropped 36 decoy PSMs due to missing features
1 day, 6:40:30.453164 INFO: Estimating optimal hyperparameters - samples: 96,304, batch_size: 394, learning_rate: 3.10e-04
1 day, 6:40:30.453564 INFO: Using random state 270283 for train-test-split
1 day, 6:40:35.702774 INFO: Test AUC: 0.561
1 day, 6:40:35.702906 INFO: Train AUC: 0.608
1 day, 6:40:35.702938 INFO: AUC difference: 7.72%
1 day, 6:40:35.702963 WARNING: AUC difference > 5%. This may indicate overfitting.
1 day, 6:40:36.001832 INFO: Resetting torch num_threads to 128
1 day, 6:40:36.005702 PROGRESS: === Extracted 120461 precursors and 1171978 fragments ===
1 day, 6:40:36.006372 INFO: === FDR correction performed with classifier version 12 ===
1 day, 6:40:36.010425 PROGRESS: ============================= Precursor FDR =============================
1 day, 6:40:36.010584 PROGRESS: Total precursors accumulated: 22,189
1 day, 6:40:36.010677 PROGRESS: Target precursors: 14,153 (63.78%)
1 day, 6:40:36.010771 PROGRESS: Decoy precursors: 8,036 (36.22%)
1 day, 6:40:36.010842 PROGRESS: 
1 day, 6:40:36.010901 PROGRESS: Precursor Summary:
1 day, 6:40:36.012161 PROGRESS: Channel   0:	 0.050 FDR:   368; 0.010 FDR:   222; 0.001 FDR:     0
1 day, 6:40:36.012279 PROGRESS: 
1 day, 6:40:36.012351 PROGRESS: Protein Summary:
1 day, 6:40:36.013710 PROGRESS: Channel   0:	 0.050 FDR:   360; 0.010 FDR:   215; 0.001 FDR:     0
1 day, 6:40:36.013839 PROGRESS: =========================================================================
1 day, 6:40:36.014591 INFO: Target number of precursors reached.
1 day, 6:40:36.104127 INFO: fragments_df: keeping 2995 of 1171978 [sum(precursor_idx_mask)=7051 sum(mass_error_mask)=1171974 stop_rank=2995
1 day, 6:40:36.288068 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:40:36.424584 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:40:36.555696 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:40:36.665906 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:40:37.022523 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 6:40:37.023089 INFO: Using score_cutoff 39.12769053382873 (fac=0.99, q=1)
1 day, 6:40:37.023463 INFO: Updating optimization_manager: fwhm_rt             : 2.901212215423584 -> 2.927356719970703
1 day, 6:40:37.023558 INFO: Updating optimization_manager: fwhm_mobility       : 0.008162545040249825 -> 0.008347845636308193
1 day, 6:40:37.023630 INFO: Updating optimization_manager: score_cutoff        : 36.81261981010437 -> 39.12769053382873
1 day, 6:40:37.023700 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:40:37.031242 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:40:37.060294 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:40:37.067001 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:40:37.126089 INFO: === checking if optimization conditions were reached ===
1 day, 6:40:37.126413 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 6:40:37.127513 INFO: Updating optimization_manager: mobility_error      : 0.0628567307929472 -> 0.07332792472079297
1 day, 6:40:37.127683 INFO: Updating optimization_manager: classifier_version  : 12 -> 14
1 day, 6:40:37.127811 INFO: Updating optimization_manager: score_cutoff        : 39.12769053382873 -> 36.81261981010437
1 day, 6:40:37.127932 INFO: Updating optimization_manager: fwhm_rt             : 2.927356719970703 -> 2.901212215423584
1 day, 6:40:37.128047 INFO: Updating optimization_manager: fwhm_mobility       : 0.008347845636308193 -> 0.008162545040249825
1 day, 6:40:37.128167 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0733 found after 3 searches.
1 day, 6:40:37.128256 INFO: ==============================================
1 day, 6:40:37.128343 PROGRESS: Optimization finished for mobility_error.
1 day, 6:40:37.309755 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:40:37.317843 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:40:37.346879 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:40:37.353601 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:40:37.410462 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 6:40:37.410790 PROGRESS: ==============================================
1 day, 6:40:37.410900 PROGRESS: ms2_error      : 15.0000
1 day, 6:40:37.410983 PROGRESS: ms1_error      : 15.0000
1 day, 6:40:37.411061 PROGRESS: rt_error       : 162.3224
1 day, 6:40:37.411132 PROGRESS: mobility_error : 0.0733
1 day, 6:40:37.411201 PROGRESS: ==============================================
1 day, 6:40:37.413247 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 6:40:39.137254 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 6:40:46.365618 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 6:40:47.846427 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 6:41:03.600093 INFO: Using python extraction backend
1 day, 6:41:03.600576 PROGRESS: Extracting batch of 11524154 precursors
1 day, 6:41:03.600711 INFO: === Search parameters used ===
1 day, 6:41:03.600790 INFO: rt_error       : 162.32241579151378
1 day, 6:41:03.600872 INFO: mobility_error : 0.07332792472079297
1 day, 6:41:03.600949 INFO: num_candidates : 3
1 day, 6:41:03.601011 INFO: ms1_error      : 15.0
1 day, 6:41:03.601069 INFO: ms2_error      : 15.0
1 day, 6:41:03.601125 INFO: fwhm_rt        : 2.901212215423584
1 day, 6:41:03.601179 INFO: quant_window   : 3
1 day, 6:41:03.601253 INFO: ==============================================
1 day, 6:41:06.277766 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 6:41:06.277950 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 6:41:06.277997 INFO: FWHM in RT is 2.90 seconds, sigma is 0.64
1 day, 6:41:06.278024 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 6:41:06.278861 INFO: Starting candidate selection
1 day, 7:37:15.865528 INFO: Removed 13210667 precursors with score below cutoff 36.81261981010437
1 day, 7:37:19.584734 INFO: Starting candidate scoring
1 day, 7:48:15.014575 INFO: Finished candidate processing
1 day, 7:48:15.015343 INFO: Collecting candidate features
1 day, 7:48:47.124733 WARNING: intensity_correlation has 7 NaNs ( 0.00 % out of 18360585)
1 day, 7:48:47.721304 INFO: Collecting fragment features
1 day, 7:49:00.723780 INFO: Finished candidate scoring
1 day, 7:49:16.170741 INFO: === Performing FDR correction with classifier version 14 ===
1 day, 7:49:16.171529 INFO: performing precursor FDR with 47 features
1 day, 7:49:16.171572 INFO: Decoy channel: -1
1 day, 7:49:16.171603 INFO: competitive: True
1 day, 7:49:19.760763 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 7:49:22.572213 WARNING: dropped 4 target PSMs due to missing features
1 day, 7:49:22.572412 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 7:49:31.388359 INFO: Estimating optimal hyperparameters - samples: 14,688,462, batch_size: 4,096, learning_rate: 1.00e-03
1 day, 7:49:31.434685 INFO: Using random state 581186 for train-test-split
1 day, 7:55:40.047163 INFO: Test AUC: 0.558
1 day, 7:55:40.047418 INFO: Train AUC: 0.559
1 day, 7:55:40.047459 INFO: AUC difference: 0.15%
1 day, 7:55:43.939156 INFO: Resetting torch num_threads to 128
1 day, 7:55:44.427216 INFO: Removing fragments below FDR threshold
1 day, 7:55:46.733021 PROGRESS: ============================= Precursor FDR =============================
1 day, 7:55:46.733361 PROGRESS: Total precursors accumulated: 70,936
1 day, 7:55:46.733447 PROGRESS: Target precursors: 70,234 (99.01%)
1 day, 7:55:46.733517 PROGRESS: Decoy precursors: 702 (0.99%)
1 day, 7:55:46.733577 PROGRESS: 
1 day, 7:55:46.733639 PROGRESS: Precursor Summary:
1 day, 7:55:46.763520 PROGRESS: Channel   0:	 0.050 FDR: 70,234; 0.010 FDR: 70,234; 0.001 FDR: 47,115
1 day, 7:55:46.763843 PROGRESS: 
1 day, 7:55:46.763951 PROGRESS: Protein Summary:
1 day, 7:55:46.800186 PROGRESS: Channel   0:	 0.050 FDR: 11,176; 0.010 FDR: 11,176; 0.001 FDR: 8,589
1 day, 7:55:46.800492 PROGRESS: =========================================================================
1 day, 7:55:47.063463 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/psm.parquet
1 day, 7:55:47.354420 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/frag.parquet
1 day, 7:55:47.606967 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 7:56:15.548860 PROGRESS: Processing search outputs
1 day, 7:56:15.549009 PROGRESS: === Performing protein grouping and FDR ===
1 day, 7:56:15.549062 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 7:56:15.629381 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 7:56:15.699488 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 7:56:15.737987 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 7:56:15.784069 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 7:56:15.822399 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 7:56:15.896574 INFO: Performing protein inference
1 day, 7:56:16.375775 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
1 day, 7:56:44.842005 INFO: Performing protein FDR
1 day, 7:56:51.718267 INFO: Normalizing q-values using 14,422 targets and 2,869 decoys
1 day, 7:56:51.722269 INFO: Test AUC: 0.881
1 day, 7:56:51.722340 INFO: Train AUC: 0.882
1 day, 7:56:51.722380 INFO: AUC difference: 0.09%
1 day, 7:56:52.326874 INFO: ================ Protein FDR =================
1 day, 7:56:52.327073 INFO: Unique protein groups in output
1 day, 7:56:52.327107 INFO:   1% protein FDR: 8,980
1 day, 7:56:52.327140 INFO: 
1 day, 7:56:52.327165 INFO: Unique precursor in output
1 day, 7:56:52.327186 INFO:   1% protein FDR: 91,740
1 day, 7:56:52.327206 INFO: ================================================
1 day, 7:56:52.379885 PROGRESS: Building search statistics
1 day, 7:56:52.494231 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/optimization_manager.pkl
1 day, 7:56:52.494598 INFO: Initializing OptimizationManager
1 day, 7:56:52.494997 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/calibration_manager.pkl
1 day, 7:56:52.495102 INFO: Initializing CalibrationManager
1 day, 7:56:52.495333 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/raw_file_manager.pkl
1 day, 7:56:52.495420 INFO: Initializing RawFileManager
1 day, 7:56:52.523307 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/optimization_manager.pkl
1 day, 7:56:52.523744 INFO: Initializing OptimizationManager
1 day, 7:56:52.524040 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/calibration_manager.pkl
1 day, 7:56:52.524132 INFO: Initializing CalibrationManager
1 day, 7:56:52.524498 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/raw_file_manager.pkl
1 day, 7:56:52.524600 INFO: Initializing RawFileManager
1 day, 7:56:52.553818 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/optimization_manager.pkl
1 day, 7:56:52.554057 INFO: Initializing OptimizationManager
1 day, 7:56:52.554317 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/calibration_manager.pkl
1 day, 7:56:52.554403 INFO: Initializing CalibrationManager
1 day, 7:56:52.554632 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/raw_file_manager.pkl
1 day, 7:56:52.554719 INFO: Initializing RawFileManager
1 day, 7:56:52.583409 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/optimization_manager.pkl
1 day, 7:56:52.583679 INFO: Initializing OptimizationManager
1 day, 7:56:52.583992 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/calibration_manager.pkl
1 day, 7:56:52.584084 INFO: Initializing CalibrationManager
1 day, 7:56:52.584307 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/raw_file_manager.pkl
1 day, 7:56:52.584397 INFO: Initializing RawFileManager
1 day, 7:56:52.617104 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/optimization_manager.pkl
1 day, 7:56:52.617345 INFO: Initializing OptimizationManager
1 day, 7:56:52.617629 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/calibration_manager.pkl
1 day, 7:56:52.617713 INFO: Initializing CalibrationManager
1 day, 7:56:52.617967 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/raw_file_manager.pkl
1 day, 7:56:52.618061 INFO: Initializing RawFileManager
1 day, 7:56:52.647268 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/optimization_manager.pkl
1 day, 7:56:52.647513 INFO: Initializing OptimizationManager
1 day, 7:56:52.647851 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/calibration_manager.pkl
1 day, 7:56:52.647943 INFO: Initializing CalibrationManager
1 day, 7:56:52.648173 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/raw_file_manager.pkl
1 day, 7:56:52.648267 INFO: Initializing RawFileManager
1 day, 7:56:52.650968 INFO: Writing stat output to disk
1 day, 7:56:52.651050 INFO: Saving /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/stat.tsv to disk
1 day, 7:56:52.657860 PROGRESS: Building internal statistics
1 day, 7:56:52.658471 INFO: Loaded TimingManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/timing_manager.pkl
1 day, 7:56:52.658525 INFO: Initializing TimingManager
1 day, 7:56:52.659121 INFO: Loaded TimingManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/timing_manager.pkl
1 day, 7:56:52.659170 INFO: Initializing TimingManager
1 day, 7:56:52.659420 INFO: Loaded TimingManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/timing_manager.pkl
1 day, 7:56:52.659464 INFO: Initializing TimingManager
1 day, 7:56:52.659677 INFO: Loaded TimingManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/timing_manager.pkl
1 day, 7:56:52.659716 INFO: Initializing TimingManager
1 day, 7:56:52.659917 INFO: Loaded TimingManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/timing_manager.pkl
1 day, 7:56:52.659958 INFO: Initializing TimingManager
1 day, 7:56:52.660161 INFO: Loaded TimingManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/timing_manager.pkl
1 day, 7:56:52.660202 INFO: Initializing TimingManager
1 day, 7:56:52.660753 INFO: Writing internal output to disk
1 day, 7:56:52.660800 INFO: Saving /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/internal.tsv to disk
1 day, 7:56:52.721640 INFO: Performing label free quantification
1 day, 7:56:52.721888 INFO: Accumulating fragment data
1 day, 7:56:52.721967 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 7:56:52.925148 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 7:56:54.021416 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 7:56:55.070878 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 7:56:56.194085 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 7:56:57.315126 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 7:56:58.704529 INFO: Performing label free quantification on the precursor level
1 day, 7:56:58.704719 INFO: Filtering fragments by quality
1 day, 7:56:58.981482 INFO: Performing label-free quantification with directlfq normalization
1 day, 7:56:59.402367 INFO: Applying directLFQ normalization
1 day, 7:57:00.429812 INFO: 91740 lfq-groups total
1 day, 7:59:11.679405 INFO: using 100 processes
1 day, 7:59:11.856075 INFO: lfq-object 0
1 day, 7:59:11.979305 INFO: lfq-object 100
1 day, 7:59:12.020023 INFO: lfq-object 300
1 day, 7:59:12.059060 INFO: lfq-object 500
1 day, 7:59:12.101627 INFO: lfq-object 200
1 day, 7:59:12.116432 INFO: lfq-object 700
1 day, 7:59:12.148366 INFO: lfq-object 400
1 day, 7:59:12.185764 INFO: lfq-object 600
1 day, 7:59:12.239167 INFO: lfq-object 800
1 day, 7:59:12.274902 INFO: lfq-object 1000
1 day, 7:59:12.345983 INFO: lfq-object 1200
1 day, 7:59:12.360858 INFO: lfq-object 900
1 day, 7:59:12.397389 INFO: lfq-object 1100
1 day, 7:59:12.466787 INFO: lfq-object 1400
1 day, 7:59:12.470554 INFO: lfq-object 1300
1 day, 7:59:12.591039 INFO: lfq-object 1500
1 day, 7:59:12.693988 INFO: lfq-object 1700
1 day, 7:59:12.712729 INFO: lfq-object 1600
1 day, 7:59:12.816704 INFO: lfq-object 1800
1 day, 7:59:12.842384 INFO: lfq-object 1900
1 day, 7:59:12.918400 INFO: lfq-object 2100
1 day, 7:59:12.965829 INFO: lfq-object 2000
1 day, 7:59:12.973480 INFO: lfq-object 2300
1 day, 7:59:13.046389 INFO: lfq-object 2200
1 day, 7:59:13.095493 INFO: lfq-object 2400
1 day, 7:59:13.179576 INFO: lfq-object 2600
1 day, 7:59:13.218827 INFO: lfq-object 2500
1 day, 7:59:13.221326 INFO: lfq-object 2800
1 day, 7:59:13.301689 INFO: lfq-object 2700
1 day, 7:59:13.311583 INFO: lfq-object 3000
1 day, 7:59:13.343434 INFO: lfq-object 2900
1 day, 7:59:13.433940 INFO: lfq-object 3100
1 day, 7:59:13.551611 INFO: lfq-object 3300
1 day, 7:59:13.556315 INFO: lfq-object 3200
1 day, 7:59:13.644093 INFO: lfq-object 3500
1 day, 7:59:13.671418 INFO: lfq-object 3400
1 day, 7:59:13.766343 INFO: lfq-object 3600
1 day, 7:59:17.058399 INFO: lfq-object 3700
1 day, 7:59:17.184532 INFO: lfq-object 3800
1 day, 7:59:17.279010 INFO: lfq-object 4000
1 day, 7:59:17.313059 INFO: lfq-object 3900
1 day, 7:59:17.320025 INFO: lfq-object 4200
1 day, 7:59:17.355555 INFO: lfq-object 4400
1 day, 7:59:17.393979 INFO: lfq-object 4600
1 day, 7:59:17.397372 INFO: lfq-object 4100
1 day, 7:59:17.439984 INFO: lfq-object 4300
1 day, 7:59:17.480445 INFO: lfq-object 4500
1 day, 7:59:17.523472 INFO: lfq-object 4700
1 day, 7:59:17.603505 INFO: lfq-object 4900
1 day, 7:59:17.644328 INFO: lfq-object 4800
1 day, 7:59:17.691321 INFO: lfq-object 5100
1 day, 7:59:17.721558 INFO: lfq-object 5000
1 day, 7:59:17.791706 INFO: lfq-object 5300
1 day, 7:59:17.809871 INFO: lfq-object 5200
1 day, 7:59:17.913310 INFO: lfq-object 5400
1 day, 7:59:18.007967 INFO: lfq-object 5600
1 day, 7:59:18.035013 INFO: lfq-object 5500
1 day, 7:59:18.087495 INFO: lfq-object 5800
1 day, 7:59:18.134057 INFO: lfq-object 5700
1 day, 7:59:18.168368 INFO: lfq-object 6000
1 day, 7:59:18.208236 INFO: lfq-object 5900
1 day, 7:59:18.293978 INFO: lfq-object 6100
1 day, 7:59:18.350706 INFO: lfq-object 6300
1 day, 7:59:18.382377 INFO: lfq-object 6500
1 day, 7:59:18.416643 INFO: lfq-object 6200
1 day, 7:59:18.480115 INFO: lfq-object 6400
1 day, 7:59:18.503134 INFO: lfq-object 6700
1 day, 7:59:18.506607 INFO: lfq-object 6600
1 day, 7:59:18.564936 INFO: lfq-object 6900
1 day, 7:59:18.624163 INFO: lfq-object 6800
1 day, 7:59:18.699754 INFO: lfq-object 7000
1 day, 7:59:18.796097 INFO: lfq-object 7200
1 day, 7:59:18.821494 INFO: lfq-object 7100
1 day, 7:59:18.844453 INFO: lfq-object 7400
1 day, 7:59:18.917399 INFO: lfq-object 7300
1 day, 7:59:18.973611 INFO: lfq-object 7500
1 day, 7:59:18.974121 INFO: lfq-object 7600
1 day, 7:59:19.095835 INFO: lfq-object 7700
1 day, 7:59:19.162049 INFO: lfq-object 7900
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1 day, 8:03:48.133890 INFO: Performing label free quantification on the pg level
1 day, 8:03:48.134371 INFO: Filtering fragments by quality
1 day, 8:03:48.462145 INFO: Performing label-free quantification with directlfq normalization
1 day, 8:03:48.651170 INFO: Applying directLFQ normalization
1 day, 8:03:48.848440 INFO: 8980 lfq-groups total
1 day, 8:05:43.111960 INFO: using 100 processes
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1 day, 8:05:50.390555 INFO: lfq-object 8600
1 day, 8:05:50.518211 INFO: lfq-object 8800
1 day, 8:05:50.565475 INFO: lfq-object 8900
1 day, 8:05:55.601960 INFO: Writing psm output to disk
1 day, 8:05:55.677798 INFO: Saving /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/precursors.parquet to disk
1 day, 8:05:56.478783 INFO: Writing precursor output to disk
1 day, 8:05:56.481443 INFO: Saving /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/precursor.matrix.parquet to disk
1 day, 8:05:56.556086 INFO: Writing peptide output to disk
1 day, 8:05:56.561499 INFO: Saving /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/peptide.matrix.parquet to disk
1 day, 8:05:56.631032 INFO: Writing pg output to disk
1 day, 8:05:56.634032 INFO: Saving /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/pg.matrix.parquet to disk
1 day, 8:05:56.702679 PROGRESS: Building MBR spectral library
1 day, 8:05:56.702914 INFO: Running MbrLibraryBuilder
1 day, 8:06:00.745772 INFO: MBR spectral library contains 91,740 precursors, 8,980 proteins
1 day, 8:06:00.745957 INFO: Writing MBR spectral library to disk
1 day, 8:06:02.073283 PROGRESS: =================== Search step 'library' finished ===================
1 day, 8:06:03.193640 INFO: =================== Running step 'mbr' ===================
1 day, 8:06:03.198470 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 15.0, 'target_ms2_tolerance': 15.0}})
1 day, 8:06:03.198680 INFO: loading default config from /usr/local/lib/python3.10/site-packages/alphadia/constants/default.yaml
1 day, 8:06:03.215260 INFO: loading additional config provided via CLI
1 day, 8:06:03.215348 INFO: loading additional config provided via CLI parameters
1 day, 8:06:03.215781 INFO: Updating config with 'user defined'
1 day, 8:06:03.215856 INFO: Updating config with 'user defined (cli)'
1 day, 8:06:03.215898 INFO: loading default config from /usr/local/lib/python3.10/site-packages/alphadia/constants/default_python.yaml
1 day, 8:06:03.217026 INFO: updating config with user defined values: [{'calibration': {'batch_size': 8000, 'optimization_lock_target': 200, 'min_steps': 2}, 'optimization': {'rt_error': {'automatic_update_percentile_range': 0.99, 'automatic_update_factor': 1.1, 'maximal_decrease': 0.2, 'favour_narrower_optimum': True, 'maximum_decrease_from_maximum': 0.1}}}, {'raw_paths': ['/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d'], 'fasta_paths': ['/public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta'], 'output_directory': '/home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest', 'general': {'thread_count': 100, 'mbr_step_enabled': True, 'transfer_step_enabled': False}, 'library_prediction': {'enabled': True, 'enzyme': 'trypsin/p', 'missed_cleavages': 1, 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M', 'max_var_mod_num': 1, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [400.0, 1000.0], 'fragment_mz': [100.0, 1700.0]}, 'search': {'target_ms1_tolerance': 15, 'target_ms2_tolerance': 15, 'extraction_backend': 'python'}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins'}, 'search_output': {'normalize_directlfq': True}}, {'raw_paths': ['/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d', '/public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d']}, {'fasta_paths': [], 'fdr': {'inference_strategy': 'library'}, 'search': {'target_ms1_tolerance': 15.0, 'target_ms2_tolerance': 15.0}, 'quant_directory': None, 'library_prediction': {'enabled': False}, 'transfer_library': {'enabled': False}, 'transfer_learning': {'enabled': False}, 'library_path': '/home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/speclib.mbr.hdf', 'output_directory': '/home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest'}]
1 day, 8:06:03.217299 INFO: Updating config with 'default_python'
1 day, 8:06:03.217344 INFO: Updating config with 'user defined'
1 day, 8:06:03.217392 INFO: Updating config with 'user defined (cli)'
1 day, 8:06:03.217415 INFO: Updating config with 'multistep search'
1 day, 8:06:03.217464 INFO: ├──version: None
1 day, 8:06:03.217489 INFO: ├──workflow_name: None
1 day, 8:06:03.217515 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest [multistep search, default: None][0m
1 day, 8:06:03.217536 INFO: [32;20m├──library_path: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/speclib.mbr.hdf [multistep search, default: None][0m
1 day, 8:06:03.217557 INFO: ├──raw_paths:
1 day, 8:06:03.217576 INFO: │   [32;20m- /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d [user defined (cli), default: None][0m
1 day, 8:06:03.217596 INFO: │   [32;20m- /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d [user defined (cli), default: None][0m
1 day, 8:06:03.217616 INFO: │   [32;20m- /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d [user defined (cli), default: None][0m
1 day, 8:06:03.217642 INFO: │   [32;20m- /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d [user defined (cli), default: None][0m
1 day, 8:06:03.217669 INFO: │   [32;20m- /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d [user defined (cli), default: None][0m
1 day, 8:06:03.217692 INFO: │   [32;20m- /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d [user defined (cli), default: None][0m
1 day, 8:06:03.217712 INFO: ├──fasta_paths:
1 day, 8:06:03.217731 INFO: ├──quant_directory: None
1 day, 8:06:03.217768 INFO: ├──general
1 day, 8:06:03.217799 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
1 day, 8:06:03.217820 INFO: │   ├──transfer_step_enabled: False
1 day, 8:06:03.217841 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
1 day, 8:06:03.217863 INFO: │   ├──reuse_calibration: False
1 day, 8:06:03.217882 INFO: │   ├──reuse_quant: False
1 day, 8:06:03.217901 INFO: │   ├──log_level: INFO
1 day, 8:06:03.217921 INFO: │   ├──use_gpu: True
1 day, 8:06:03.217941 INFO: │   ├──save_figures: True
1 day, 8:06:03.217962 INFO: │   ├──save_library: True
1 day, 8:06:03.217980 INFO: │   ├──save_flat_library: False
1 day, 8:06:03.217999 INFO: │   ├──input_library_type: base
1 day, 8:06:03.218026 INFO: │   ├──save_mbr_library: True
1 day, 8:06:03.218045 INFO: │   ├──random_state: None
1 day, 8:06:03.218076 INFO: │   └──fail_fast: False
1 day, 8:06:03.218102 INFO: ├──library_loading
1 day, 8:06:03.218126 INFO: │   └──drop_decoys: False
1 day, 8:06:03.218149 INFO: ├──library_prediction
1 day, 8:06:03.218174 INFO: │   ├──enabled: False
1 day, 8:06:03.218197 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
1 day, 8:06:03.218218 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
1 day, 8:06:03.218240 INFO: │   [32;20m├──variable_modifications: Oxidation@M [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
1 day, 8:06:03.218262 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
1 day, 8:06:03.218286 INFO: │   ├──missed_cleavages: 1
1 day, 8:06:03.218304 INFO: │   ├──precursor_len:
1 day, 8:06:03.218324 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
1 day, 8:06:03.218352 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
1 day, 8:06:03.218374 INFO: │   ├──precursor_charge:
1 day, 8:06:03.218395 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
1 day, 8:06:03.218419 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
1 day, 8:06:03.218441 INFO: │   ├──precursor_mz:
1 day, 8:06:03.218463 INFO: │   │   - 400.0
1 day, 8:06:03.218482 INFO: │   │   [32;20m- 1000.0 [user defined, default: 1200][0m
1 day, 8:06:03.218507 INFO: │   ├──fragment_mz:
1 day, 8:06:03.218532 INFO: │   │   [32;20m- 100.0 [user defined, default: 200][0m
1 day, 8:06:03.218552 INFO: │   │   [32;20m- 1700.0 [user defined, default: 2000][0m
1 day, 8:06:03.218572 INFO: │   ├──nce: 25.0
1 day, 8:06:03.218591 INFO: │   ├──fragment_types:
1 day, 8:06:03.218614 INFO: │   │   - b
1 day, 8:06:03.218634 INFO: │   │   - y
1 day, 8:06:03.218656 INFO: │   ├──max_fragment_charge: 2
1 day, 8:06:03.218674 INFO: │   ├──instrument: Lumos
1 day, 8:06:03.218694 INFO: │   ├──peptdeep_model_path: None
1 day, 8:06:03.218719 INFO: │   ├──peptdeep_model_type: generic
1 day, 8:06:03.218739 INFO: │   ├──predict_charge: False
1 day, 8:06:03.218762 INFO: │   └──min_charge_probability: 0.1
1 day, 8:06:03.218781 INFO: ├──custom_modifications:
1 day, 8:06:03.218804 INFO: │   ├──name: Dimethyl:d12@K
1 day, 8:06:03.218824 INFO: │   └──composition: H(-2)2H(8)13C(2)
1 day, 8:06:03.218843 INFO: │   ├──name: Dimethyl:d12@Any_N-term
1 day, 8:06:03.218864 INFO: │   └──composition: H(-2)2H(8)13C(2)
1 day, 8:06:03.218895 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
1 day, 8:06:03.218913 INFO: │   └──composition: H(-2)2H(8)13C(2)
1 day, 8:06:03.218932 INFO: │   ├──name: mTRAQ:d12@K
1 day, 8:06:03.218950 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
1 day, 8:06:03.218978 INFO: │   ├──name: mTRAQ:d12@Any_N-term
1 day, 8:06:03.218999 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
1 day, 8:06:03.219021 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
1 day, 8:06:03.219039 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
1 day, 8:06:03.219069 INFO: │   ├──name: Label:13C(12)@K
1 day, 8:06:03.219088 INFO: │   └──composition: C(12)
1 day, 8:06:03.219106 INFO: ├──search
1 day, 8:06:03.219128 INFO: │   [32;20m├──extraction_backend: python [user defined, default: rust][0m
1 day, 8:06:03.219153 INFO: │   [32;20m├──target_ms1_tolerance: 15.0 [multistep search, default: 5][0m
1 day, 8:06:03.219174 INFO: │   [32;20m├──target_ms2_tolerance: 15.0 [multistep search, default: 10][0m
1 day, 8:06:03.219198 INFO: │   ├──target_rt_tolerance: 0.0
1 day, 8:06:03.219218 INFO: │   ├──target_mobility_tolerance: 0.0
1 day, 8:06:03.219237 INFO: │   ├──quant_window: 3
1 day, 8:06:03.219257 INFO: │   ├──target_num_candidates: 3
1 day, 8:06:03.219281 INFO: │   ├──channel_filter: 
1 day, 8:06:03.219300 INFO: │   ├──compete_for_fragments: True
1 day, 8:06:03.219319 INFO: │   ├──top_k_fragments_selection: 12
1 day, 8:06:03.219338 INFO: │   ├──top_k_fragments_scoring: 12
1 day, 8:06:03.219364 INFO: │   ├──min_fragment_intensity: 0.01
1 day, 8:06:03.219383 INFO: │   ├──optimized_peak_group_score: False
1 day, 8:06:03.219405 INFO: │   ├──exclude_shared_ions: True
1 day, 8:06:03.219433 INFO: │   ├──quant_all: True
1 day, 8:06:03.219454 INFO: │   └──experimental_xic: True
1 day, 8:06:03.219479 INFO: ├──calibration
1 day, 8:06:03.219509 INFO: │   [32;20m├──batch_size: 8000 [default_python, default: 1000][0m
1 day, 8:06:03.219528 INFO: │   [32;20m├──optimization_lock_target: 200 [default_python, default: 1000][0m
1 day, 8:06:03.219549 INFO: │   ├──max_steps: 20
1 day, 8:06:03.219575 INFO: │   [32;20m├──min_steps: 2 [default_python, default: 5][0m
1 day, 8:06:03.219604 INFO: │   ├──max_skips: 1
1 day, 8:06:03.219640 INFO: │   ├──max_fragments: 5000
1 day, 8:06:03.219672 INFO: │   └──min_correlation: 0.7
1 day, 8:06:03.219702 INFO: ├──search_initial
1 day, 8:06:03.219733 INFO: │   ├──num_candidates: 1
1 day, 8:06:03.219763 INFO: │   ├──ms1_tolerance: 30
1 day, 8:06:03.219795 INFO: │   ├──ms2_tolerance: 30
1 day, 8:06:03.219826 INFO: │   ├──mobility_tolerance: 0.1
1 day, 8:06:03.219857 INFO: │   └──rt_tolerance: 0.5
1 day, 8:06:03.219887 INFO: ├──library_multiplexing
1 day, 8:06:03.219918 INFO: │   ├──enabled: False
1 day, 8:06:03.219950 INFO: │   ├──input_channel: 0
1 day, 8:06:03.219980 INFO: │   └──multiplex_mapping:
1 day, 8:06:03.220007 INFO: ├──multiplexing
1 day, 8:06:03.220037 INFO: │   ├──enabled: False
1 day, 8:06:03.220066 INFO: │   ├──target_channels: 4,8
1 day, 8:06:03.220093 INFO: │   ├──decoy_channel: 12
1 day, 8:06:03.220124 INFO: │   ├──reference_channel: 0
1 day, 8:06:03.220156 INFO: │   └──competitive_scoring: True
1 day, 8:06:03.220184 INFO: ├──fdr
1 day, 8:06:03.220214 INFO: │   ├──fdr: 0.01
1 day, 8:06:03.220242 INFO: │   ├──group_level: proteins
1 day, 8:06:03.220269 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
1 day, 8:06:03.220299 INFO: │   ├──competitive_scoring: True
1 day, 8:06:03.220334 INFO: │   ├──keep_decoys: False
1 day, 8:06:03.220363 INFO: │   ├──keep_decoys_in_mbr_library: False
1 day, 8:06:03.220392 INFO: │   ├──channel_wise_fdr: False
1 day, 8:06:03.220419 INFO: │   └──enable_nn_hyperparameter_tuning: True
1 day, 8:06:03.220448 INFO: ├──search_output
1 day, 8:06:03.220478 INFO: │   ├──file_format: parquet
1 day, 8:06:03.220505 INFO: │   ├──precursor_level_lfq: True
1 day, 8:06:03.220534 INFO: │   ├──peptide_level_lfq: True
1 day, 8:06:03.220570 INFO: │   ├──save_fragment_quant_matrix: False
1 day, 8:06:03.220597 INFO: │   ├──min_k_fragments: 12
1 day, 8:06:03.220626 INFO: │   ├──min_correlation: 0.9
1 day, 8:06:03.220662 INFO: │   ├──num_samples_quadratic: 50
1 day, 8:06:03.220691 INFO: │   ├──min_nonnan: 3
1 day, 8:06:03.220725 INFO: │   ├──normalization_method: directlfq
1 day, 8:06:03.220753 INFO: │   └──normalize_directlfq: True
1 day, 8:06:03.220779 INFO: ├──optimization
1 day, 8:06:03.220808 INFO: │   ├──order_of_optimization: None
1 day, 8:06:03.220836 INFO: │   ├──ms2_error
1 day, 8:06:03.220869 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1 day, 8:06:03.220896 INFO: │   │   ├──targeted_update_factor: 1.0
1 day, 8:06:03.220918 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1 day, 8:06:03.220946 INFO: │   │   ├──automatic_update_factor: 1.1
1 day, 8:06:03.220972 INFO: │   │   ├──try_narrower_values: True
1 day, 8:06:03.221000 INFO: │   │   ├──maximal_decrease: 0.5
1 day, 8:06:03.221030 INFO: │   │   ├──favour_narrower_optimum: False
1 day, 8:06:03.221059 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1 day, 8:06:03.221084 INFO: │   ├──ms1_error
1 day, 8:06:03.221110 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1 day, 8:06:03.221131 INFO: │   │   ├──targeted_update_factor: 1.0
1 day, 8:06:03.221150 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1 day, 8:06:03.221179 INFO: │   │   ├──automatic_update_factor: 1.1
1 day, 8:06:03.221208 INFO: │   │   ├──try_narrower_values: False
1 day, 8:06:03.221239 INFO: │   │   ├──maximal_decrease: 0.2
1 day, 8:06:03.221267 INFO: │   │   ├──favour_narrower_optimum: False
1 day, 8:06:03.221301 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1 day, 8:06:03.221328 INFO: │   ├──mobility_error
1 day, 8:06:03.221358 INFO: │   │   ├──targeted_update_percentile_range: 0.95
1 day, 8:06:03.221387 INFO: │   │   ├──targeted_update_factor: 1.0
1 day, 8:06:03.221424 INFO: │   │   ├──automatic_update_percentile_range: 0.99
1 day, 8:06:03.221453 INFO: │   │   ├──automatic_update_factor: 1.1
1 day, 8:06:03.221481 INFO: │   │   ├──try_narrower_values: False
1 day, 8:06:03.221513 INFO: │   │   ├──maximal_decrease: 0.2
1 day, 8:06:03.221542 INFO: │   │   ├──favour_narrower_optimum: False
1 day, 8:06:03.221573 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
1 day, 8:06:03.221604 INFO: │   └──rt_error
1 day, 8:06:03.221634 INFO: │       ├──targeted_update_percentile_range: 0.95
1 day, 8:06:03.221659 INFO: │       ├──targeted_update_factor: 1.0
1 day, 8:06:03.221688 INFO: │       [32;20m├──automatic_update_percentile_range: 0.99 [default_python, default: 0.999][0m
1 day, 8:06:03.221709 INFO: │       [32;20m├──automatic_update_factor: 1.1 [default_python, default: 1.5][0m
1 day, 8:06:03.221727 INFO: │       ├──try_narrower_values: True
1 day, 8:06:03.221756 INFO: │       [32;20m├──maximal_decrease: 0.2 [default_python, default: 0.1][0m
1 day, 8:06:03.221786 INFO: │       [32;20m├──favour_narrower_optimum: True [default_python, default: False][0m
1 day, 8:06:03.221817 INFO: │       [32;20m└──maximum_decrease_from_maximum: 0.1 [default_python, default: 0.5][0m
1 day, 8:06:03.221843 INFO: ├──optimization_manager
1 day, 8:06:03.221865 INFO: │   ├──fwhm_rt: 5
1 day, 8:06:03.221884 INFO: │   ├──fwhm_mobility: 0.01
1 day, 8:06:03.221906 INFO: │   └──score_cutoff: 0
1 day, 8:06:03.221931 INFO: ├──transfer_library
1 day, 8:06:03.221959 INFO: │   ├──enabled: False
1 day, 8:06:03.221982 INFO: │   ├──fragment_types:
1 day, 8:06:03.222013 INFO: │   │   - b
1 day, 8:06:03.222035 INFO: │   │   - y
1 day, 8:06:03.222061 INFO: │   ├──max_charge: 2
1 day, 8:06:03.222090 INFO: │   ├──top_k_samples: 3
1 day, 8:06:03.222113 INFO: │   ├──norm_delta_max: True
1 day, 8:06:03.222140 INFO: │   ├──precursor_correlation_cutoff: 0.5
1 day, 8:06:03.222172 INFO: │   └──fragment_correlation_ratio: 0.75
1 day, 8:06:03.222194 INFO: └──transfer_learning
1 day, 8:06:03.222221 INFO:     ├──enabled: False
1 day, 8:06:03.222245 INFO:     ├──batch_size: 2000
1 day, 8:06:03.222268 INFO:     ├──max_lr: 0.0001
1 day, 8:06:03.222294 INFO:     ├──train_fraction: 0.7
1 day, 8:06:03.222319 INFO:     ├──validation_fraction: 0.2
1 day, 8:06:03.222344 INFO:     ├──test_fraction: 0.1
1 day, 8:06:03.222372 INFO:     ├──test_interval: 1
1 day, 8:06:03.222399 INFO:     ├──lr_patience: 3
1 day, 8:06:03.222418 INFO:     ├──epochs: 51
1 day, 8:06:03.222445 INFO:     ├──warmup_epochs: 5
1 day, 8:06:03.222472 INFO:     ├──nce: 25
1 day, 8:06:03.222494 INFO:     └──instrument: Lumos
1 day, 8:06:03.229918 INFO: Registering 7 custom modifications
1 day, 8:06:03.252826 INFO: Searching 6 files:
1 day, 8:06:03.252908 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 8:06:03.252933 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 8:06:03.252953 INFO:   ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 8:06:03.252972 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 8:06:03.252989 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 8:06:03.253008 INFO:   ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 8:06:03.253030 INFO: Using 0 fasta files:
1 day, 8:06:03.253050 INFO: Using library: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/speclib.mbr.hdf
1 day, 8:06:03.253069 INFO: Saving output to: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest
1 day, 8:06:03.253099 PROGRESS: Loading spectral library
1 day, 8:06:03.253137 PROGRESS: Loading library (type: base) from disk..
1 day, 8:06:03.253186 INFO: Running DynamicLoader
1 day, 8:06:03.253280 INFO: Loading .hdf library from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/library/speclib.mbr.hdf
1 day, 8:06:03.743714 INFO: Running PrecursorInitializer
1 day, 8:06:03.744270 INFO: Channel column already present, skipping initialization
1 day, 8:06:03.744318 INFO: Elution group indices already present, skipping initialization
1 day, 8:06:03.744346 INFO: Precursor indices already present, skipping initialization
1 day, 8:06:03.744375 INFO: Running AnnotateFasta
1 day, 8:06:03.754908 INFO: Running IsotopeGenerator
1 day, 8:06:03.755230 INFO: Isotope information already present, skipping isotope generation
1 day, 8:06:03.755266 INFO: Running RTNormalization
1 day, 8:06:03.759428 INFO: Saving library to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/speclib.hdf
1 day, 8:06:04.364510 INFO: Running DecoyGenerator
1 day, 8:06:09.724839 INFO: Running FlattenLibrary
1 day, 8:06:11.116122 INFO: Running InitFlatColumns
1 day, 8:06:11.121760 INFO: Running LogFlatLibraryStats
1 day, 8:06:11.121909 INFO: ============ Library Stats ============
1 day, 8:06:11.121946 INFO: Number of precursors: 183,466
1 day, 8:06:11.160220 INFO: 	thereof targets:91,740
1 day, 8:06:11.160393 INFO: 	thereof decoys: 91,726
1 day, 8:06:11.162166 INFO: Number of elution groups: 91,740
1 day, 8:06:11.162248 INFO: 	average size: 2.00
1 day, 8:06:11.174136 INFO: Number of proteins: 8,980
1 day, 8:06:11.175036 INFO: Number of channels: 1 ([0])
1 day, 8:06:11.175133 INFO: Isotopes Distribution for 4 isotopes
1 day, 8:06:11.175162 INFO: =======================================
1 day, 8:06:11.175242 PROGRESS: =================== Starting Search Workflows for step mbr ===================
1 day, 8:06:11.175311 PROGRESS: Loading raw file 1/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494 
1 day, 8:06:11.175370 INFO: Quantification results path: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant
1 day, 8:06:11.175587 INFO: Creating folder /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/figures
1 day, 8:06:11.175881 INFO: Initializing TimingManager
1 day, 8:06:11.176359 INFO: Initializing RawFileManager
1 day, 8:06:11.176500 INFO: Importing data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 8:06:11.176546 INFO: Using .d import for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 8:06:11.176580 INFO: Reading frame metadata for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 8:06:12.001984 INFO: Reading 39,128 frames with 2,835,410,867 detector events for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 8:06:31.409009 INFO: Indexing /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d...
1 day, 8:06:31.411156 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 8:06:31.412921 INFO: Fetching mobility values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 8:06:31.413141 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 8:06:31.413546 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 8:06:31.414978 INFO: Fetching mz values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 8:06:31.441930 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 8:06:31.442255 INFO: Indexing quadrupole dimension
1 day, 8:06:31.982547 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 8:06:31.982710 INFO: Transposing detector events
1 day, 8:06:41.255609 INFO: Finished transposing data
1 day, 8:06:41.306688 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494.d
1 day, 8:06:41.307460 INFO: RT (min)            : 0.0 - 70.0
1 day, 8:06:41.307539 INFO: RT duration (sec)   : 4199.9
1 day, 8:06:41.307573 INFO: RT duration (min)   : 70.0
1 day, 8:06:41.307600 INFO: Cycle len (scans)   : 9
1 day, 8:06:41.307625 INFO: Cycle len (sec)     : 0.97
1 day, 8:06:41.307654 INFO: Number of cycles    : 4347
1 day, 8:06:41.307678 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 8:06:41.307719 INFO: Creating DIA data object took: 30.13124370574951
1 day, 8:06:41.340854 INFO: Initializing CalibrationManager
1 day, 8:06:41.341269 INFO: Setting up calibration estimators ..
1 day, 8:06:41.341367 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 8:06:41.341468 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, 8:06:41.341588 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 8:06:41.341663 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, 8:06:41.341740 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, 8:06:41.341881 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, 8:06:41.341987 INFO: Done setting up calibration estimators.
1 day, 8:06:41.342141 INFO: Initializing OptimizationManager
1 day, 8:06:41.342271 INFO: initial parameter: ms1_error = 30
1 day, 8:06:41.342341 INFO: initial parameter: ms2_error = 30
1 day, 8:06:41.342414 INFO: initial parameter: rt_error = 2099.928159
1 day, 8:06:41.342488 INFO: initial parameter: mobility_error = 0.1
1 day, 8:06:41.342561 INFO: initial parameter: num_candidates = 1
1 day, 8:06:41.342630 INFO: initial parameter: fwhm_rt = 5
1 day, 8:06:41.342697 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 8:06:41.342757 INFO: initial parameter: score_cutoff = 0
1 day, 8:06:41.342822 INFO: initial parameter: classifier_version = -1
1 day, 8:06:41.342920 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 8:06:41.343205 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 8:06:41.343246 INFO: Initializing FDRManager
1 day, 8:06:41.343301 INFO: Loading classifier store from /usr/local/lib/python3.10/site-packages/alphadia/constants/classifier
1 day, 8:06:41.372447 PROGRESS: Initializing spectral library: 91,740 target precursors potentially observable (0 removed)
1 day, 8:06:41.404395 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 8:06:41.405049 INFO: Updating optimization_manager: rt_error            : 2099.928159 -> 2099.928159
1 day, 8:06:41.405177 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 8:06:41.405413 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 8:06:41.405665 PROGRESS: Starting initial search for precursors.
1 day, 8:06:41.405809 INFO: Starting optimization step 0.
1 day, 8:06:41.405912 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:06:41.406014 INFO: Using python extraction backend
1 day, 8:06:41.406232 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:06:41.406334 INFO: === Search parameters used ===
1 day, 8:06:41.406410 INFO: rt_error       : 2099.928159
1 day, 8:06:41.406482 INFO: mobility_error : 0.1
1 day, 8:06:41.406552 INFO: num_candidates : 1
1 day, 8:06:41.406616 INFO: ms1_error      : 30
1 day, 8:06:41.406684 INFO: ms2_error      : 30
1 day, 8:06:41.406756 INFO: fwhm_rt        : 5
1 day, 8:06:41.406818 INFO: quant_window   : 3
1 day, 8:06:41.406875 INFO: ==============================================
1 day, 8:06:41.409702 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:06:41.409771 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:06:41.409819 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 8:06:41.409851 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 8:06:41.414735 INFO: Starting candidate selection
1 day, 8:08:15.126631 INFO: Starting candidate scoring
1 day, 8:08:16.544963 INFO: Finished candidate processing
1 day, 8:08:16.545155 INFO: Collecting candidate features
1 day, 8:08:16.613915 INFO: Collecting fragment features
1 day, 8:08:16.629468 INFO: Finished candidate scoring
1 day, 8:08:16.639701 INFO: performing precursor FDR with 47 features
1 day, 8:08:16.639823 INFO: Decoy channel: -1
1 day, 8:08:16.639856 INFO: competitive: True
1 day, 8:08:16.644878 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:08:16.654256 INFO: Estimating optimal hyperparameters - samples: 12,694, batch_size: 128, learning_rate: 1.77e-04
1 day, 8:08:16.655434 INFO: Using random state 947853 for train-test-split
1 day, 8:08:18.037992 INFO: Test AUC: 0.824
1 day, 8:08:18.038147 INFO: Train AUC: 0.838
1 day, 8:08:18.038180 INFO: AUC difference: 1.59%
1 day, 8:08:18.339595 INFO: Resetting torch num_threads to 128
1 day, 8:08:18.340825 PROGRESS: === Extracted 15868 precursors and 179899 fragments ===
1 day, 8:08:18.341689 INFO: === FDR correction performed with classifier version -1 ===
1 day, 8:08:18.343339 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:08:18.343475 PROGRESS: Total precursors accumulated: 7,995
1 day, 8:08:18.343566 PROGRESS: Target precursors: 6,705 (83.86%)
1 day, 8:08:18.343657 PROGRESS: Decoy precursors: 1,290 (16.14%)
1 day, 8:08:18.343730 PROGRESS: 
1 day, 8:08:18.343805 PROGRESS: Precursor Summary:
1 day, 8:08:18.346380 PROGRESS: Channel   0:	 0.050 FDR: 5,007; 0.010 FDR: 4,272; 0.001 FDR: 3,419
1 day, 8:08:18.346514 PROGRESS: 
1 day, 8:08:18.346603 PROGRESS: Protein Summary:
1 day, 8:08:18.350035 PROGRESS: Channel   0:	 0.050 FDR: 3,071; 0.010 FDR: 2,702; 0.001 FDR: 2,288
1 day, 8:08:18.350166 PROGRESS: =========================================================================
1 day, 8:08:18.350313 INFO: Target number of precursors reached.
1 day, 8:08:18.380205 INFO: fragments_df: keeping 5000 of 179899 [sum(precursor_idx_mask)=48527 sum(mass_error_mask)=179899 stop_rank=5000
1 day, 8:08:18.404277 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:08:19.024720 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:08:19.652511 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:08:20.266940 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:08:20.986794 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 8:08:20.987415 INFO: Using score_cutoff 48.92625428123474 (fac=0.99, q=1)
1 day, 8:08:20.987987 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.154878616333008
1 day, 8:08:20.988100 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010458160191774368
1 day, 8:08:20.988183 INFO: Updating optimization_manager: score_cutoff        : 0 -> 48.92625428123474
1 day, 8:08:20.988280 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:08:20.991182 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:08:21.000746 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:08:21.003198 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:08:21.024868 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
1 day, 8:08:21.025171 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 8:08:21.025349 INFO: Starting optimization step 1.
1 day, 8:08:21.025477 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:08:21.025603 INFO: Using python extraction backend
1 day, 8:08:21.025828 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:08:21.025964 INFO: === Search parameters used ===
1 day, 8:08:21.026069 INFO: rt_error       : 2099.928159
1 day, 8:08:21.026160 INFO: mobility_error : 0.1
1 day, 8:08:21.026248 INFO: num_candidates : 3
1 day, 8:08:21.026336 INFO: ms1_error      : 30
1 day, 8:08:21.026424 INFO: ms2_error      : 30
1 day, 8:08:21.026511 INFO: fwhm_rt        : 3.154878616333008
1 day, 8:08:21.026595 INFO: quant_window   : 3
1 day, 8:08:21.026678 INFO: ==============================================
1 day, 8:08:21.034454 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:08:21.034575 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:08:21.034651 INFO: FWHM in RT is 3.15 seconds, sigma is 0.69
1 day, 8:08:21.034701 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.85
1 day, 8:08:21.035509 INFO: Starting candidate selection
1 day, 8:10:03.300764 INFO: Starting candidate scoring
1 day, 8:10:06.673143 INFO: Finished candidate processing
1 day, 8:10:06.673341 INFO: Collecting candidate features
1 day, 8:10:06.765867 INFO: Collecting fragment features
1 day, 8:10:06.792450 INFO: Finished candidate scoring
1 day, 8:10:06.815831 INFO: performing precursor FDR with 47 features
1 day, 8:10:06.815975 INFO: Decoy channel: -1
1 day, 8:10:06.816004 INFO: competitive: True
1 day, 8:10:06.830380 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:10:06.843641 INFO: Estimating optimal hyperparameters - samples: 36,050, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:10:06.843909 INFO: Using random state 140512 for train-test-split
1 day, 8:10:10.325885 INFO: Test AUC: 0.710
1 day, 8:10:10.326032 INFO: Train AUC: 0.723
1 day, 8:10:10.326098 INFO: AUC difference: 1.81%
1 day, 8:10:10.615003 INFO: Resetting torch num_threads to 128
1 day, 8:10:10.616511 PROGRESS: === Extracted 45063 precursors and 510301 fragments ===
1 day, 8:10:10.617079 INFO: === FDR correction performed with classifier version 0 ===
1 day, 8:10:10.618652 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:10:10.618773 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:10:10.618856 PROGRESS: Target precursors: 7,072 (88.40%)
1 day, 8:10:10.618932 PROGRESS: Decoy precursors: 928 (11.60%)
1 day, 8:10:10.619001 PROGRESS: 
1 day, 8:10:10.619068 PROGRESS: Precursor Summary:
1 day, 8:10:10.621788 PROGRESS: Channel   0:	 0.050 FDR: 5,948; 0.010 FDR: 5,205; 0.001 FDR: 4,249
1 day, 8:10:10.621928 PROGRESS: 
1 day, 8:10:10.622001 PROGRESS: Protein Summary:
1 day, 8:10:10.625854 PROGRESS: Channel   0:	 0.050 FDR: 3,525; 0.010 FDR: 3,158; 0.001 FDR: 2,706
1 day, 8:10:10.625981 PROGRESS: =========================================================================
1 day, 8:10:10.626276 INFO: Target number of precursors reached.
1 day, 8:10:10.719849 INFO: fragments_df: keeping 5000 of 510301 [sum(precursor_idx_mask)=168616 sum(mass_error_mask)=510301 stop_rank=5000
1 day, 8:10:10.740052 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:10:11.505252 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:10:12.278404 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:10:13.044890 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:10:13.763505 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:10:13.764112 INFO: Using score_cutoff 48.10367763061523 (fac=0.99, q=1)
1 day, 8:10:13.764632 INFO: Updating optimization_manager: fwhm_rt             : 3.154878616333008 -> 3.0971648693084717
1 day, 8:10:13.764731 INFO: Updating optimization_manager: fwhm_mobility       : 0.010458160191774368 -> 0.010071085765957832
1 day, 8:10:13.764806 INFO: Updating optimization_manager: score_cutoff        : 48.92625428123474 -> 48.10367763061523
1 day, 8:10:13.764892 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:10:13.767750 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:10:13.777057 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:10:13.779507 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:10:13.799760 INFO: === checking if optimization conditions were reached ===
1 day, 8:10:13.802501 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 8:10:13.802655 INFO: Updating optimization_manager: classifier_version  : 0 -> 1
1 day, 8:10:13.802758 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 8:10:13.804909 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 8:10:13.805051 INFO: Updating optimization_manager: classifier_version  : 1 -> 1
1 day, 8:10:13.805141 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 8:10:13.805223 INFO: ==============================================
1 day, 8:10:13.805318 INFO: Starting optimization step 2.
1 day, 8:10:13.805405 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:10:13.805492 INFO: Using python extraction backend
1 day, 8:10:13.805653 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:10:13.805785 INFO: === Search parameters used ===
1 day, 8:10:13.805887 INFO: rt_error       : 2099.928159
1 day, 8:10:13.805987 INFO: mobility_error : 0.1
1 day, 8:10:13.806078 INFO: num_candidates : 3
1 day, 8:10:13.806158 INFO: ms1_error      : 15.0
1 day, 8:10:13.806241 INFO: ms2_error      : 15.0
1 day, 8:10:13.806319 INFO: fwhm_rt        : 3.0971648693084717
1 day, 8:10:13.806411 INFO: quant_window   : 3
1 day, 8:10:13.806497 INFO: ==============================================
1 day, 8:10:13.812673 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:10:13.812798 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:10:13.812876 INFO: FWHM in RT is 3.10 seconds, sigma is 0.68
1 day, 8:10:13.812923 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.67
1 day, 8:10:13.813636 INFO: Starting candidate selection
1 day, 8:11:46.777879 INFO: Starting candidate scoring
1 day, 8:11:49.027646 INFO: Finished candidate processing
1 day, 8:11:49.027842 INFO: Collecting candidate features
1 day, 8:11:49.123571 INFO: Collecting fragment features
1 day, 8:11:49.152418 INFO: Finished candidate scoring
1 day, 8:11:49.177321 INFO: performing precursor FDR with 47 features
1 day, 8:11:49.177479 INFO: Decoy channel: -1
1 day, 8:11:49.177508 INFO: competitive: True
1 day, 8:11:49.193979 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:11:49.208771 INFO: Estimating optimal hyperparameters - samples: 36,161, batch_size: 148, learning_rate: 1.90e-04
1 day, 8:11:49.209064 INFO: Using random state 5216 for train-test-split
1 day, 8:11:53.526460 INFO: Test AUC: 0.733
1 day, 8:11:53.526620 INFO: Train AUC: 0.751
1 day, 8:11:53.526652 INFO: AUC difference: 2.29%
1 day, 8:11:53.815708 INFO: Resetting torch num_threads to 128
1 day, 8:11:53.817413 PROGRESS: === Extracted 45202 precursors and 498539 fragments ===
1 day, 8:11:53.818008 INFO: === FDR correction performed with classifier version 1 ===
1 day, 8:11:53.819615 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:11:53.819737 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:11:53.819810 PROGRESS: Target precursors: 7,467 (93.34%)
1 day, 8:11:53.819875 PROGRESS: Decoy precursors: 533 (6.66%)
1 day, 8:11:53.819931 PROGRESS: 
1 day, 8:11:53.819987 PROGRESS: Precursor Summary:
1 day, 8:11:53.823182 PROGRESS: Channel   0:	 0.050 FDR: 7,173; 0.010 FDR: 6,519; 0.001 FDR: 5,732
1 day, 8:11:53.823319 PROGRESS: 
1 day, 8:11:53.823401 PROGRESS: Protein Summary:
1 day, 8:11:53.828152 PROGRESS: Channel   0:	 0.050 FDR: 4,070; 0.010 FDR: 3,764; 0.001 FDR: 3,421
1 day, 8:11:53.828289 PROGRESS: =========================================================================
1 day, 8:11:53.828603 INFO: Target number of precursors reached.
1 day, 8:11:53.936861 INFO: fragments_df: keeping 5000 of 498539 [sum(precursor_idx_mask)=206136 sum(mass_error_mask)=498539 stop_rank=5000
1 day, 8:11:53.958856 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:11:54.936831 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:11:55.920795 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:11:56.876436 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:11:57.539377 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:11:57.540035 INFO: Using score_cutoff 40.965813809967045 (fac=0.99, q=1)
1 day, 8:11:57.540580 INFO: Updating optimization_manager: fwhm_rt             : 3.0971648693084717 -> 2.813917636871338
1 day, 8:11:57.540676 INFO: Updating optimization_manager: fwhm_mobility       : 0.010071085765957832 -> 0.008283855393528938
1 day, 8:11:57.540747 INFO: Updating optimization_manager: score_cutoff        : 48.10367763061523 -> 40.965813809967045
1 day, 8:11:57.540821 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:11:57.543804 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:11:57.553187 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:11:57.555519 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:11:57.575943 INFO: === checking if optimization conditions were reached ===
1 day, 8:11:57.577965 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 8:11:57.578089 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
1 day, 8:11:57.578166 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 8:11:57.580157 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 8:11:57.580271 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
1 day, 8:11:57.580356 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 8:11:57.580421 INFO: ==============================================
1 day, 8:11:57.580495 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 8:11:57.603084 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:11:57.606033 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:11:57.615624 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:11:57.618098 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:11:57.639635 INFO: Starting optimization step 0.
1 day, 8:11:57.639807 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:11:57.639901 INFO: Using python extraction backend
1 day, 8:11:57.640051 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:11:57.640137 INFO: === Search parameters used ===
1 day, 8:11:57.640193 INFO: rt_error       : 2099.928159
1 day, 8:11:57.640243 INFO: mobility_error : 0.1
1 day, 8:11:57.640292 INFO: num_candidates : 3
1 day, 8:11:57.640338 INFO: ms1_error      : 15.0
1 day, 8:11:57.640401 INFO: ms2_error      : 15.0
1 day, 8:11:57.640463 INFO: fwhm_rt        : 2.813917636871338
1 day, 8:11:57.640529 INFO: quant_window   : 3
1 day, 8:11:57.640587 INFO: ==============================================
1 day, 8:11:57.645367 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:11:57.645431 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:11:57.645497 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1 day, 8:11:57.645528 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.84
1 day, 8:11:57.646393 INFO: Starting candidate selection
1 day, 8:13:28.697822 INFO: Starting candidate scoring
1 day, 8:13:30.734198 INFO: Finished candidate processing
1 day, 8:13:30.734321 INFO: Collecting candidate features
1 day, 8:13:30.819543 INFO: Collecting fragment features
1 day, 8:13:30.856077 INFO: Finished candidate scoring
1 day, 8:13:30.879007 INFO: performing precursor FDR with 47 features
1 day, 8:13:30.879167 INFO: Decoy channel: -1
1 day, 8:13:30.879199 INFO: competitive: True
1 day, 8:13:30.893035 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:13:30.905791 INFO: Estimating optimal hyperparameters - samples: 36,099, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:13:30.906041 INFO: Using random state 601924 for train-test-split
1 day, 8:13:34.462965 INFO: Test AUC: 0.751
1 day, 8:13:34.463129 INFO: Train AUC: 0.765
1 day, 8:13:34.463166 INFO: AUC difference: 1.74%
1 day, 8:13:34.752524 INFO: Resetting torch num_threads to 128
1 day, 8:13:34.754309 PROGRESS: === Extracted 45124 precursors and 498133 fragments ===
1 day, 8:13:34.755018 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:13:34.757138 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:13:34.757330 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:13:34.757434 PROGRESS: Target precursors: 7,482 (93.53%)
1 day, 8:13:34.757520 PROGRESS: Decoy precursors: 518 (6.48%)
1 day, 8:13:34.757605 PROGRESS: 
1 day, 8:13:34.757681 PROGRESS: Precursor Summary:
1 day, 8:13:34.760921 PROGRESS: Channel   0:	 0.050 FDR: 7,172; 0.010 FDR: 6,525; 0.001 FDR: 5,889
1 day, 8:13:34.761062 PROGRESS: 
1 day, 8:13:34.761159 PROGRESS: Protein Summary:
1 day, 8:13:34.765691 PROGRESS: Channel   0:	 0.050 FDR: 4,069; 0.010 FDR: 3,761; 0.001 FDR: 3,486
1 day, 8:13:34.765849 PROGRESS: =========================================================================
1 day, 8:13:34.766193 INFO: Target number of precursors reached.
1 day, 8:13:34.872737 INFO: fragments_df: keeping 5000 of 498133 [sum(precursor_idx_mask)=205960 sum(mass_error_mask)=498133 stop_rank=5000
1 day, 8:13:34.901046 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:13:35.889405 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:13:36.861810 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:13:37.813657 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:13:38.469077 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:13:38.469686 INFO: Using score_cutoff 40.982638417053224 (fac=0.99, q=1)
1 day, 8:13:38.470211 INFO: Updating optimization_manager: fwhm_rt             : 2.813917636871338 -> 2.8220560550689697
1 day, 8:13:38.470307 INFO: Updating optimization_manager: fwhm_mobility       : 0.008283855393528938 -> 0.008223069831728935
1 day, 8:13:38.470372 INFO: Updating optimization_manager: score_cutoff        : 40.965813809967045 -> 40.982638417053224
1 day, 8:13:38.470449 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:13:38.473396 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:13:38.483188 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:13:38.485790 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:13:38.507224 INFO: === checking if optimization conditions were reached ===
1 day, 8:13:38.507489 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 8:13:38.513557 INFO: Updating optimization_manager: rt_error            : 2099.928159 -> 373.6212473154493
1 day, 8:13:38.513711 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 373.6212.
1 day, 8:13:38.513821 INFO: ==============================================
1 day, 8:13:38.513918 INFO: Starting optimization step 1.
1 day, 8:13:38.514001 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:13:38.514085 INFO: Using python extraction backend
1 day, 8:13:38.514243 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:13:38.514333 INFO: === Search parameters used ===
1 day, 8:13:38.514406 INFO: rt_error       : 373.6212473154493
1 day, 8:13:38.514502 INFO: mobility_error : 0.1
1 day, 8:13:38.514590 INFO: num_candidates : 3
1 day, 8:13:38.514673 INFO: ms1_error      : 15.0
1 day, 8:13:38.514755 INFO: ms2_error      : 15.0
1 day, 8:13:38.514835 INFO: fwhm_rt        : 2.8220560550689697
1 day, 8:13:38.514922 INFO: quant_window   : 3
1 day, 8:13:38.515005 INFO: ==============================================
1 day, 8:13:38.521278 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:13:38.521390 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:13:38.521456 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 8:13:38.521505 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.81
1 day, 8:13:38.522302 INFO: Starting candidate selection
1 day, 8:13:57.784816 INFO: Starting candidate scoring
1 day, 8:13:59.668880 INFO: Finished candidate processing
1 day, 8:13:59.669111 INFO: Collecting candidate features
1 day, 8:13:59.777847 INFO: Collecting fragment features
1 day, 8:13:59.808937 INFO: Finished candidate scoring
1 day, 8:13:59.841968 INFO: performing precursor FDR with 47 features
1 day, 8:13:59.842130 INFO: Decoy channel: -1
1 day, 8:13:59.842165 INFO: competitive: True
1 day, 8:13:59.858534 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:13:59.873593 INFO: Estimating optimal hyperparameters - samples: 35,939, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:13:59.873888 INFO: Using random state 601924 for train-test-split
1 day, 8:14:04.222785 INFO: Test AUC: 0.752
1 day, 8:14:04.223008 INFO: Train AUC: 0.774
1 day, 8:14:04.223053 INFO: AUC difference: 2.80%
1 day, 8:14:04.518273 INFO: Resetting torch num_threads to 128
1 day, 8:14:04.519985 PROGRESS: === Extracted 44924 precursors and 490782 fragments ===
1 day, 8:14:04.520631 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:14:04.522322 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:14:04.522434 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:14:04.522508 PROGRESS: Target precursors: 7,565 (94.56%)
1 day, 8:14:04.522570 PROGRESS: Decoy precursors: 435 (5.44%)
1 day, 8:14:04.522636 PROGRESS: 
1 day, 8:14:04.522693 PROGRESS: Precursor Summary:
1 day, 8:14:04.525942 PROGRESS: Channel   0:	 0.050 FDR: 7,461; 0.010 FDR: 6,888; 0.001 FDR: 5,813
1 day, 8:14:04.526072 PROGRESS: 
1 day, 8:14:04.526141 PROGRESS: Protein Summary:
1 day, 8:14:04.531129 PROGRESS: Channel   0:	 0.050 FDR: 4,184; 0.010 FDR: 3,928; 0.001 FDR: 3,451
1 day, 8:14:04.531255 PROGRESS: =========================================================================
1 day, 8:14:04.531672 INFO: Target number of precursors reached.
1 day, 8:14:04.642615 INFO: fragments_df: keeping 5000 of 490782 [sum(precursor_idx_mask)=215367 sum(mass_error_mask)=490782 stop_rank=5000
1 day, 8:14:04.666050 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:14:05.703091 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:14:06.768503 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:14:07.807042 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:14:08.464851 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:14:08.465515 INFO: Using score_cutoff 38.75554462280274 (fac=0.99, q=1)
1 day, 8:14:08.466111 INFO: Updating optimization_manager: fwhm_rt             : 2.8220560550689697 -> 2.8083720207214355
1 day, 8:14:08.466211 INFO: Updating optimization_manager: fwhm_mobility       : 0.008223069831728935 -> 0.008101003244519234
1 day, 8:14:08.466274 INFO: Updating optimization_manager: score_cutoff        : 40.982638417053224 -> 38.75554462280274
1 day, 8:14:08.466348 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:14:08.469551 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:14:08.479570 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:14:08.482185 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:14:08.504908 INFO: === checking if optimization conditions were reached ===
1 day, 8:14:08.505116 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 8:14:08.511192 INFO: Updating optimization_manager: rt_error            : 373.6212473154493 -> 115.10157438915363
1 day, 8:14:08.511326 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 115.1016.
1 day, 8:14:08.511406 INFO: ==============================================
1 day, 8:14:08.511511 INFO: Starting optimization step 2.
1 day, 8:14:08.511606 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:14:08.511706 INFO: Using python extraction backend
1 day, 8:14:08.511932 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:14:08.512062 INFO: === Search parameters used ===
1 day, 8:14:08.512145 INFO: rt_error       : 115.10157438915363
1 day, 8:14:08.512221 INFO: mobility_error : 0.1
1 day, 8:14:08.512291 INFO: num_candidates : 3
1 day, 8:14:08.512361 INFO: ms1_error      : 15.0
1 day, 8:14:08.512429 INFO: ms2_error      : 15.0
1 day, 8:14:08.512500 INFO: fwhm_rt        : 2.8083720207214355
1 day, 8:14:08.512567 INFO: quant_window   : 3
1 day, 8:14:08.512635 INFO: ==============================================
1 day, 8:14:08.517692 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:14:08.517768 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:14:08.517830 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1 day, 8:14:08.517867 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.76
1 day, 8:14:08.518650 INFO: Starting candidate selection
1 day, 8:14:16.577254 INFO: Starting candidate scoring
1 day, 8:14:18.447620 INFO: Finished candidate processing
1 day, 8:14:18.447809 INFO: Collecting candidate features
1 day, 8:14:18.535273 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 44850)
1 day, 8:14:18.540652 INFO: Collecting fragment features
1 day, 8:14:18.565870 INFO: Finished candidate scoring
1 day, 8:14:18.585930 INFO: performing precursor FDR with 47 features
1 day, 8:14:18.586081 INFO: Decoy channel: -1
1 day, 8:14:18.586138 INFO: competitive: True
1 day, 8:14:18.599284 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:14:18.607434 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:14:18.607575 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 8:14:18.614844 INFO: Estimating optimal hyperparameters - samples: 35,878, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:14:18.615100 INFO: Using random state 601924 for train-test-split
1 day, 8:14:22.046274 INFO: Test AUC: 0.778
1 day, 8:14:22.046471 INFO: Train AUC: 0.785
1 day, 8:14:22.046512 INFO: AUC difference: 0.80%
1 day, 8:14:22.331707 INFO: Resetting torch num_threads to 128
1 day, 8:14:22.333180 PROGRESS: === Extracted 44850 precursors and 482014 fragments ===
1 day, 8:14:22.333784 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:14:22.335298 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:14:22.335409 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:14:22.335491 PROGRESS: Target precursors: 7,749 (96.86%)
1 day, 8:14:22.335559 PROGRESS: Decoy precursors: 251 (3.14%)
1 day, 8:14:22.335622 PROGRESS: 
1 day, 8:14:22.335690 PROGRESS: Precursor Summary:
1 day, 8:14:22.338718 PROGRESS: Channel   0:	 0.050 FDR: 7,749; 0.010 FDR: 7,400; 0.001 FDR: 6,743
1 day, 8:14:22.338838 PROGRESS: 
1 day, 8:14:22.338924 PROGRESS: Protein Summary:
1 day, 8:14:22.343660 PROGRESS: Channel   0:	 0.050 FDR: 4,304; 0.010 FDR: 4,164; 0.001 FDR: 3,889
1 day, 8:14:22.343793 PROGRESS: =========================================================================
1 day, 8:14:22.344053 INFO: Target number of precursors reached.
1 day, 8:14:22.450466 INFO: fragments_df: keeping 5000 of 482014 [sum(precursor_idx_mask)=229144 sum(mass_error_mask)=482014 stop_rank=5000
1 day, 8:14:22.467502 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:14:23.676625 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:14:24.916998 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:14:26.130834 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:14:26.844375 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:14:26.844995 INFO: Using score_cutoff 37.089828684997556 (fac=0.99, q=1)
1 day, 8:14:26.845515 INFO: Updating optimization_manager: fwhm_rt             : 2.8083720207214355 -> 2.7936277389526367
1 day, 8:14:26.845612 INFO: Updating optimization_manager: fwhm_mobility       : 0.008101003244519234 -> 0.007913539186120033
1 day, 8:14:26.845680 INFO: Updating optimization_manager: score_cutoff        : 38.75554462280274 -> 37.089828684997556
1 day, 8:14:26.845762 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:14:26.848841 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:14:26.858997 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:14:26.861418 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:14:26.882097 INFO: === checking if optimization conditions were reached ===
1 day, 8:14:26.882304 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 8:14:26.889195 INFO: Updating optimization_manager: rt_error            : 115.10157438915363 -> 24.34605384388391
1 day, 8:14:26.889384 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 24.3461.
1 day, 8:14:26.889484 INFO: ==============================================
1 day, 8:14:26.889580 INFO: Starting optimization step 3.
1 day, 8:14:26.889664 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:14:26.889833 INFO: Using python extraction backend
1 day, 8:14:26.890034 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:14:26.890158 INFO: === Search parameters used ===
1 day, 8:14:26.890254 INFO: rt_error       : 24.34605384388391
1 day, 8:14:26.890346 INFO: mobility_error : 0.1
1 day, 8:14:26.890436 INFO: num_candidates : 3
1 day, 8:14:26.890537 INFO: ms1_error      : 15.0
1 day, 8:14:26.890624 INFO: ms2_error      : 15.0
1 day, 8:14:26.890707 INFO: fwhm_rt        : 2.7936277389526367
1 day, 8:14:26.890789 INFO: quant_window   : 3
1 day, 8:14:26.890870 INFO: ==============================================
1 day, 8:14:26.898120 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:14:26.898240 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:14:26.898305 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1 day, 8:14:26.898348 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.67
1 day, 8:14:26.917932 INFO: Starting candidate selection
1 day, 8:14:29.060449 INFO: Starting candidate scoring
1 day, 8:14:30.858089 INFO: Finished candidate processing
1 day, 8:14:30.858308 INFO: Collecting candidate features
1 day, 8:14:30.959295 WARNING: intensity_correlation has 6 NaNs ( 0.01 % out of 44705)
1 day, 8:14:30.964551 INFO: Collecting fragment features
1 day, 8:14:30.990256 INFO: Finished candidate scoring
1 day, 8:14:31.009723 INFO: performing precursor FDR with 47 features
1 day, 8:14:31.009898 INFO: Decoy channel: -1
1 day, 8:14:31.009926 INFO: competitive: True
1 day, 8:14:31.021668 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:14:31.029723 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:14:31.029881 WARNING: dropped 5 decoy PSMs due to missing features
1 day, 8:14:31.036436 INFO: Estimating optimal hyperparameters - samples: 35,759, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:14:31.036656 INFO: Using random state 601924 for train-test-split
1 day, 8:14:34.460751 INFO: Test AUC: 0.813
1 day, 8:14:34.460918 INFO: Train AUC: 0.816
1 day, 8:14:34.460951 INFO: AUC difference: 0.39%
1 day, 8:14:34.737972 INFO: Resetting torch num_threads to 128
1 day, 8:14:34.739408 PROGRESS: === Extracted 44705 precursors and 472938 fragments ===
1 day, 8:14:34.740001 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:14:34.741452 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:14:34.741558 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:14:34.741629 PROGRESS: Target precursors: 7,852 (98.15%)
1 day, 8:14:34.741698 PROGRESS: Decoy precursors: 148 (1.85%)
1 day, 8:14:34.741773 PROGRESS: 
1 day, 8:14:34.741832 PROGRESS: Precursor Summary:
1 day, 8:14:34.744959 PROGRESS: Channel   0:	 0.050 FDR: 7,852; 0.010 FDR: 7,722; 0.001 FDR: 7,279
1 day, 8:14:34.745071 PROGRESS: 
1 day, 8:14:34.745142 PROGRESS: Protein Summary:
1 day, 8:14:34.750041 PROGRESS: Channel   0:	 0.050 FDR: 4,344; 0.010 FDR: 4,291; 0.001 FDR: 4,105
1 day, 8:14:34.750170 PROGRESS: =========================================================================
1 day, 8:14:34.750543 INFO: Target number of precursors reached.
1 day, 8:14:34.858527 INFO: fragments_df: keeping 5000 of 472938 [sum(precursor_idx_mask)=236289 sum(mass_error_mask)=472938 stop_rank=5000
1 day, 8:14:34.882597 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:14:36.165104 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:14:37.455378 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:14:40.337571 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:14:41.065962 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:14:41.066638 INFO: Using score_cutoff 33.61778776016235 (fac=0.99, q=1)
1 day, 8:14:41.067229 INFO: Updating optimization_manager: fwhm_rt             : 2.7936277389526367 -> 2.772231101989746
1 day, 8:14:41.067326 INFO: Updating optimization_manager: fwhm_mobility       : 0.007913539186120033 -> 0.007796559017151594
1 day, 8:14:41.067394 INFO: Updating optimization_manager: score_cutoff        : 37.089828684997556 -> 33.61778776016235
1 day, 8:14:41.067492 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:14:41.070634 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:14:41.080527 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:14:41.083095 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:14:41.103486 INFO: === checking if optimization conditions were reached ===
1 day, 8:14:41.103734 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 8:14:41.110957 INFO: Updating optimization_manager: rt_error            : 24.34605384388391 -> 17.947403399913604
1 day, 8:14:41.111113 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 17.9474.
1 day, 8:14:41.111211 INFO: ==============================================
1 day, 8:14:41.111310 INFO: Starting optimization step 4.
1 day, 8:14:41.111422 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:14:41.111549 INFO: Using python extraction backend
1 day, 8:14:41.111799 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:14:41.111901 INFO: === Search parameters used ===
1 day, 8:14:41.111970 INFO: rt_error       : 17.947403399913604
1 day, 8:14:41.112033 INFO: mobility_error : 0.1
1 day, 8:14:41.112098 INFO: num_candidates : 3
1 day, 8:14:41.112161 INFO: ms1_error      : 15.0
1 day, 8:14:41.112224 INFO: ms2_error      : 15.0
1 day, 8:14:41.112326 INFO: fwhm_rt        : 2.772231101989746
1 day, 8:14:41.112420 INFO: quant_window   : 3
1 day, 8:14:41.112513 INFO: ==============================================
1 day, 8:14:41.122227 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:14:41.122339 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:14:41.122406 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 8:14:41.122457 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.62
1 day, 8:14:41.123453 INFO: Starting candidate selection
1 day, 8:14:43.071499 INFO: Starting candidate scoring
1 day, 8:14:44.953324 INFO: Finished candidate processing
1 day, 8:14:44.953544 INFO: Collecting candidate features
1 day, 8:14:45.018671 WARNING: intensity_correlation has 5 NaNs ( 0.01 % out of 44601)
1 day, 8:14:45.024105 INFO: Collecting fragment features
1 day, 8:14:45.049855 INFO: Finished candidate scoring
1 day, 8:14:45.072925 INFO: performing precursor FDR with 47 features
1 day, 8:14:45.073081 INFO: Decoy channel: -1
1 day, 8:14:45.073109 INFO: competitive: True
1 day, 8:14:45.085653 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:14:45.093695 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:14:45.093863 WARNING: dropped 4 decoy PSMs due to missing features
1 day, 8:14:45.100349 INFO: Estimating optimal hyperparameters - samples: 35,676, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:14:45.100578 INFO: Using random state 601924 for train-test-split
1 day, 8:14:48.521525 INFO: Test AUC: 0.816
1 day, 8:14:48.521680 INFO: Train AUC: 0.831
1 day, 8:14:48.521715 INFO: AUC difference: 1.84%
1 day, 8:14:48.799609 INFO: Resetting torch num_threads to 128
1 day, 8:14:48.801049 PROGRESS: === Extracted 44601 precursors and 469790 fragments ===
1 day, 8:14:48.801619 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:14:48.803057 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:14:48.803170 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:14:48.803241 PROGRESS: Target precursors: 7,852 (98.15%)
1 day, 8:14:48.803302 PROGRESS: Decoy precursors: 148 (1.85%)
1 day, 8:14:48.803363 PROGRESS: 
1 day, 8:14:48.803419 PROGRESS: Precursor Summary:
1 day, 8:14:48.806588 PROGRESS: Channel   0:	 0.050 FDR: 7,852; 0.010 FDR: 7,694; 0.001 FDR: 7,242
1 day, 8:14:48.806712 PROGRESS: 
1 day, 8:14:48.806782 PROGRESS: Protein Summary:
1 day, 8:14:48.811663 PROGRESS: Channel   0:	 0.050 FDR: 4,335; 0.010 FDR: 4,278; 0.001 FDR: 4,094
1 day, 8:14:48.811795 PROGRESS: =========================================================================
1 day, 8:14:48.812067 INFO: Target number of precursors reached.
1 day, 8:14:48.921182 INFO: fragments_df: keeping 5000 of 469790 [sum(precursor_idx_mask)=234915 sum(mass_error_mask)=469790 stop_rank=5000
1 day, 8:14:48.938952 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:14:50.154505 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:14:51.414087 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:14:52.681232 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:14:53.385986 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:14:53.386595 INFO: Using score_cutoff 33.8050156036377 (fac=0.99, q=1)
1 day, 8:14:53.387171 INFO: Updating optimization_manager: fwhm_rt             : 2.772231101989746 -> 2.771760940551758
1 day, 8:14:53.387266 INFO: Updating optimization_manager: fwhm_mobility       : 0.007796559017151594 -> 0.007808406837284565
1 day, 8:14:53.387332 INFO: Updating optimization_manager: score_cutoff        : 33.61778776016235 -> 33.8050156036377
1 day, 8:14:53.387413 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:14:53.390394 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:14:53.400205 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:14:53.402768 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:14:53.423206 INFO: === checking if optimization conditions were reached ===
1 day, 8:14:53.423429 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 8:14:53.430523 INFO: Updating optimization_manager: rt_error            : 17.947403399913604 -> 16.46494146117545
1 day, 8:14:53.430682 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 16.4649.
1 day, 8:14:53.430815 INFO: ==============================================
1 day, 8:14:53.430940 INFO: Starting optimization step 5.
1 day, 8:14:53.431051 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:14:53.431163 INFO: Using python extraction backend
1 day, 8:14:53.431347 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:14:53.431470 INFO: === Search parameters used ===
1 day, 8:14:53.431584 INFO: rt_error       : 16.46494146117545
1 day, 8:14:53.431679 INFO: mobility_error : 0.1
1 day, 8:14:53.431767 INFO: num_candidates : 3
1 day, 8:14:53.431857 INFO: ms1_error      : 15.0
1 day, 8:14:53.431943 INFO: ms2_error      : 15.0
1 day, 8:14:53.432032 INFO: fwhm_rt        : 2.771760940551758
1 day, 8:14:53.432117 INFO: quant_window   : 3
1 day, 8:14:53.432206 INFO: ==============================================
1 day, 8:14:53.438013 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:14:53.438117 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:14:53.438185 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 8:14:53.438239 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.62
1 day, 8:14:53.439376 INFO: Starting candidate selection
1 day, 8:14:55.261647 INFO: Starting candidate scoring
1 day, 8:14:57.011609 INFO: Finished candidate processing
1 day, 8:14:57.011802 INFO: Collecting candidate features
1 day, 8:14:57.069392 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 44589)
1 day, 8:14:57.074768 INFO: Collecting fragment features
1 day, 8:14:57.099394 INFO: Finished candidate scoring
1 day, 8:14:57.119218 INFO: performing precursor FDR with 47 features
1 day, 8:14:57.119371 INFO: Decoy channel: -1
1 day, 8:14:57.119399 INFO: competitive: True
1 day, 8:14:57.131179 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:14:57.138840 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:14:57.138970 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 8:14:57.145555 INFO: Estimating optimal hyperparameters - samples: 35,665, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:14:57.145739 INFO: Using random state 601924 for train-test-split
1 day, 8:15:00.605563 INFO: Test AUC: 0.824
1 day, 8:15:00.605726 INFO: Train AUC: 0.830
1 day, 8:15:00.605773 INFO: AUC difference: 0.77%
1 day, 8:15:00.888091 INFO: Resetting torch num_threads to 128
1 day, 8:15:00.889518 PROGRESS: === Extracted 44589 precursors and 469640 fragments ===
1 day, 8:15:00.890089 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:15:00.891604 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:15:00.891711 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:15:00.891800 PROGRESS: Target precursors: 7,864 (98.30%)
1 day, 8:15:00.891885 PROGRESS: Decoy precursors: 136 (1.70%)
1 day, 8:15:00.891962 PROGRESS: 
1 day, 8:15:00.892033 PROGRESS: Precursor Summary:
1 day, 8:15:00.895427 PROGRESS: Channel   0:	 0.050 FDR: 7,864; 0.010 FDR: 7,735; 0.001 FDR: 7,362
1 day, 8:15:00.895564 PROGRESS: 
1 day, 8:15:00.895651 PROGRESS: Protein Summary:
1 day, 8:15:00.900675 PROGRESS: Channel   0:	 0.050 FDR: 4,338; 0.010 FDR: 4,299; 0.001 FDR: 4,143
1 day, 8:15:00.900815 PROGRESS: =========================================================================
1 day, 8:15:00.901078 INFO: Target number of precursors reached.
1 day, 8:15:01.009056 INFO: fragments_df: keeping 5000 of 469640 [sum(precursor_idx_mask)=236215 sum(mass_error_mask)=469640 stop_rank=5000
1 day, 8:15:01.026197 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:15:02.321459 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:15:03.619860 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:15:04.918898 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:15:05.643576 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:15:05.644197 INFO: Using score_cutoff 33.47183542098999 (fac=0.99, q=1)
1 day, 8:15:05.644734 INFO: Updating optimization_manager: fwhm_rt             : 2.771760940551758 -> 2.7735908031463623
1 day, 8:15:05.644827 INFO: Updating optimization_manager: fwhm_mobility       : 0.007808406837284565 -> 0.007805380504578352
1 day, 8:15:05.644890 INFO: Updating optimization_manager: score_cutoff        : 33.8050156036377 -> 33.47183542098999
1 day, 8:15:05.644956 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:15:05.647839 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:15:05.657698 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:15:05.660196 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:15:05.680953 INFO: === checking if optimization conditions were reached ===
1 day, 8:15:05.681170 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 8:15:05.688270 INFO: Updating optimization_manager: rt_error            : 16.46494146117545 -> 17.33161350705042
1 day, 8:15:05.688424 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 17.3316.
1 day, 8:15:05.688552 INFO: ==============================================
1 day, 8:15:05.688647 INFO: Starting optimization step 6.
1 day, 8:15:05.688731 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:15:05.688814 INFO: Using python extraction backend
1 day, 8:15:05.689024 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:15:05.689144 INFO: === Search parameters used ===
1 day, 8:15:05.689236 INFO: rt_error       : 17.33161350705042
1 day, 8:15:05.689324 INFO: mobility_error : 0.1
1 day, 8:15:05.689406 INFO: num_candidates : 3
1 day, 8:15:05.689486 INFO: ms1_error      : 15.0
1 day, 8:15:05.689565 INFO: ms2_error      : 15.0
1 day, 8:15:05.689645 INFO: fwhm_rt        : 2.7735908031463623
1 day, 8:15:05.689735 INFO: quant_window   : 3
1 day, 8:15:05.689835 INFO: ==============================================
1 day, 8:15:05.695551 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:15:05.695661 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:15:05.695723 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 8:15:05.695780 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.62
1 day, 8:15:05.696751 INFO: Starting candidate selection
1 day, 8:15:07.563522 INFO: Starting candidate scoring
1 day, 8:15:09.381334 INFO: Finished candidate processing
1 day, 8:15:09.381563 INFO: Collecting candidate features
1 day, 8:15:09.472191 WARNING: intensity_correlation has 6 NaNs ( 0.01 % out of 44599)
1 day, 8:15:09.479100 INFO: Collecting fragment features
1 day, 8:15:09.504959 INFO: Finished candidate scoring
1 day, 8:15:09.524968 INFO: performing precursor FDR with 47 features
1 day, 8:15:09.525135 INFO: Decoy channel: -1
1 day, 8:15:09.525162 INFO: competitive: True
1 day, 8:15:09.537256 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:15:09.544992 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:15:09.545137 WARNING: dropped 5 decoy PSMs due to missing features
1 day, 8:15:09.551897 INFO: Estimating optimal hyperparameters - samples: 35,674, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:15:09.552123 INFO: Using random state 601924 for train-test-split
1 day, 8:15:13.038793 INFO: Test AUC: 0.820
1 day, 8:15:13.038944 INFO: Train AUC: 0.832
1 day, 8:15:13.038977 INFO: AUC difference: 1.41%
1 day, 8:15:13.317801 INFO: Resetting torch num_threads to 128
1 day, 8:15:13.319237 PROGRESS: === Extracted 44599 precursors and 469819 fragments ===
1 day, 8:15:13.319782 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:15:13.321278 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:15:13.321388 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:15:13.321459 PROGRESS: Target precursors: 7,866 (98.32%)
1 day, 8:15:13.321524 PROGRESS: Decoy precursors: 134 (1.68%)
1 day, 8:15:13.321585 PROGRESS: 
1 day, 8:15:13.321649 PROGRESS: Precursor Summary:
1 day, 8:15:13.324907 PROGRESS: Channel   0:	 0.050 FDR: 7,866; 0.010 FDR: 7,727; 0.001 FDR: 7,241
1 day, 8:15:13.325026 PROGRESS: 
1 day, 8:15:13.325095 PROGRESS: Protein Summary:
1 day, 8:15:13.329881 PROGRESS: Channel   0:	 0.050 FDR: 4,351; 0.010 FDR: 4,302; 0.001 FDR: 4,086
1 day, 8:15:13.330001 PROGRESS: =========================================================================
1 day, 8:15:13.330234 INFO: Target number of precursors reached.
1 day, 8:15:13.437613 INFO: fragments_df: keeping 5000 of 469819 [sum(precursor_idx_mask)=235927 sum(mass_error_mask)=469819 stop_rank=5000
1 day, 8:15:13.454370 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:15:14.741534 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:15:16.034922 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:15:17.325388 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:15:18.047661 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:15:18.048307 INFO: Using score_cutoff 33.15260128326416 (fac=0.99, q=1)
1 day, 8:15:18.048830 INFO: Updating optimization_manager: fwhm_rt             : 2.7735908031463623 -> 2.7689671516418457
1 day, 8:15:18.048925 INFO: Updating optimization_manager: fwhm_mobility       : 0.007805380504578352 -> 0.007773791905492544
1 day, 8:15:18.048992 INFO: Updating optimization_manager: score_cutoff        : 33.47183542098999 -> 33.15260128326416
1 day, 8:15:18.049065 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:15:18.051973 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:15:18.061718 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:15:18.064268 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:15:18.085079 INFO: === checking if optimization conditions were reached ===
1 day, 8:15:18.085310 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 8:15:18.092298 INFO: Updating optimization_manager: rt_error            : 17.33161350705042 -> 16.637109778765083
1 day, 8:15:18.092457 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 16.6371.
1 day, 8:15:18.092590 INFO: ==============================================
1 day, 8:15:18.092733 INFO: Starting optimization step 7.
1 day, 8:15:18.092844 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:15:18.092950 INFO: Using python extraction backend
1 day, 8:15:18.093161 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:15:18.093283 INFO: === Search parameters used ===
1 day, 8:15:18.093382 INFO: rt_error       : 16.637109778765083
1 day, 8:15:18.093471 INFO: mobility_error : 0.1
1 day, 8:15:18.093554 INFO: num_candidates : 3
1 day, 8:15:18.093662 INFO: ms1_error      : 15.0
1 day, 8:15:18.093758 INFO: ms2_error      : 15.0
1 day, 8:15:18.093854 INFO: fwhm_rt        : 2.7689671516418457
1 day, 8:15:18.093943 INFO: quant_window   : 3
1 day, 8:15:18.094020 INFO: ==============================================
1 day, 8:15:18.099799 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:15:18.099908 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:15:18.099972 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 8:15:18.100020 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.61
1 day, 8:15:18.100936 INFO: Starting candidate selection
1 day, 8:15:19.980794 INFO: Starting candidate scoring
1 day, 8:15:21.767620 INFO: Finished candidate processing
1 day, 8:15:21.767773 INFO: Collecting candidate features
1 day, 8:15:21.826031 WARNING: intensity_correlation has 9 NaNs ( 0.02 % out of 44576)
1 day, 8:15:21.831336 INFO: Collecting fragment features
1 day, 8:15:21.857462 INFO: Finished candidate scoring
1 day, 8:15:21.876231 INFO: performing precursor FDR with 47 features
1 day, 8:15:21.876383 INFO: Decoy channel: -1
1 day, 8:15:21.876411 INFO: competitive: True
1 day, 8:15:21.887726 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:15:21.895242 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:15:21.895384 WARNING: dropped 8 decoy PSMs due to missing features
1 day, 8:15:21.901194 INFO: Estimating optimal hyperparameters - samples: 35,653, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:15:21.901370 INFO: Using random state 601924 for train-test-split
1 day, 8:15:25.302529 INFO: Test AUC: 0.816
1 day, 8:15:25.302678 INFO: Train AUC: 0.832
1 day, 8:15:25.302711 INFO: AUC difference: 1.89%
1 day, 8:15:25.585690 INFO: Resetting torch num_threads to 128
1 day, 8:15:25.587161 PROGRESS: === Extracted 44576 precursors and 469579 fragments ===
1 day, 8:15:25.587759 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:15:25.589210 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:15:25.589314 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:15:25.589387 PROGRESS: Target precursors: 7,865 (98.31%)
1 day, 8:15:25.589450 PROGRESS: Decoy precursors: 135 (1.69%)
1 day, 8:15:25.589506 PROGRESS: 
1 day, 8:15:25.589561 PROGRESS: Precursor Summary:
1 day, 8:15:25.592752 PROGRESS: Channel   0:	 0.050 FDR: 7,865; 0.010 FDR: 7,753; 0.001 FDR: 7,256
1 day, 8:15:25.592871 PROGRESS: 
1 day, 8:15:25.592940 PROGRESS: Protein Summary:
1 day, 8:15:25.597777 PROGRESS: Channel   0:	 0.050 FDR: 4,346; 0.010 FDR: 4,304; 0.001 FDR: 4,098
1 day, 8:15:25.597897 PROGRESS: =========================================================================
1 day, 8:15:25.598176 INFO: Target number of precursors reached.
1 day, 8:15:25.705934 INFO: fragments_df: keeping 5000 of 469579 [sum(precursor_idx_mask)=236648 sum(mass_error_mask)=469579 stop_rank=5000
1 day, 8:15:25.722542 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:15:27.018385 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:15:28.320500 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:15:29.618194 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:15:30.338189 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:15:30.338849 INFO: Using score_cutoff 33.04757919616699 (fac=0.99, q=1)
1 day, 8:15:30.339402 INFO: Updating optimization_manager: fwhm_rt             : 2.7689671516418457 -> 2.767432451248169
1 day, 8:15:30.339505 INFO: Updating optimization_manager: fwhm_mobility       : 0.007773791905492544 -> 0.007762253284454346
1 day, 8:15:30.339568 INFO: Updating optimization_manager: score_cutoff        : 33.15260128326416 -> 33.04757919616699
1 day, 8:15:30.339635 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:15:30.342644 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:15:30.352528 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:15:30.355094 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:15:30.377143 INFO: === checking if optimization conditions were reached ===
1 day, 8:15:30.377343 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1 day, 8:15:30.378951 INFO: Updating optimization_manager: rt_error            : 16.637109778765083 -> 16.46494146117545
1 day, 8:15:30.379132 INFO: Updating optimization_manager: classifier_version  : 2 -> 8
1 day, 8:15:30.379273 INFO: Updating optimization_manager: score_cutoff        : 33.04757919616699 -> 33.47183542098999
1 day, 8:15:30.379397 INFO: Updating optimization_manager: fwhm_rt             : 2.767432451248169 -> 2.7735908031463623
1 day, 8:15:30.379513 INFO: Updating optimization_manager: fwhm_mobility       : 0.007762253284454346 -> 0.007805380504578352
1 day, 8:15:30.379635 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 16.4649 found after 8 searches.
1 day, 8:15:30.379723 INFO: ==============================================
1 day, 8:15:30.379813 PROGRESS: Optimization finished for rt_error.
1 day, 8:15:30.402141 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:15:30.405409 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:15:30.415734 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:15:30.418596 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:15:30.440501 INFO: Starting optimization step 0.
1 day, 8:15:30.440729 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:15:30.440858 INFO: Using python extraction backend
1 day, 8:15:30.441071 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:15:30.441200 INFO: === Search parameters used ===
1 day, 8:15:30.441296 INFO: rt_error       : 16.46494146117545
1 day, 8:15:30.441383 INFO: mobility_error : 0.1
1 day, 8:15:30.441466 INFO: num_candidates : 3
1 day, 8:15:30.441552 INFO: ms1_error      : 15.0
1 day, 8:15:30.441637 INFO: ms2_error      : 15.0
1 day, 8:15:30.441720 INFO: fwhm_rt        : 2.7735908031463623
1 day, 8:15:30.441894 INFO: quant_window   : 3
1 day, 8:15:30.441997 INFO: ==============================================
1 day, 8:15:30.446909 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:15:30.447013 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:15:30.447077 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 8:15:30.447127 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.62
1 day, 8:15:30.448235 INFO: Starting candidate selection
1 day, 8:15:32.344041 INFO: Starting candidate scoring
1 day, 8:15:34.214692 INFO: Finished candidate processing
1 day, 8:15:34.214898 INFO: Collecting candidate features
1 day, 8:15:34.272619 WARNING: intensity_correlation has 8 NaNs ( 0.02 % out of 44577)
1 day, 8:15:34.277937 INFO: Collecting fragment features
1 day, 8:15:34.304311 INFO: Finished candidate scoring
1 day, 8:15:34.325165 INFO: performing precursor FDR with 47 features
1 day, 8:15:34.325316 INFO: Decoy channel: -1
1 day, 8:15:34.325342 INFO: competitive: True
1 day, 8:15:34.337875 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:15:34.345763 WARNING: dropped 2 target PSMs due to missing features
1 day, 8:15:34.345906 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 8:15:34.352669 INFO: Estimating optimal hyperparameters - samples: 35,655, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:15:34.352920 INFO: Using random state 454222 for train-test-split
1 day, 8:15:37.843941 INFO: Test AUC: 0.826
1 day, 8:15:37.844100 INFO: Train AUC: 0.844
1 day, 8:15:37.844135 INFO: AUC difference: 2.08%
1 day, 8:15:38.121393 INFO: Resetting torch num_threads to 128
1 day, 8:15:38.122804 PROGRESS: === Extracted 44577 precursors and 469634 fragments ===
1 day, 8:15:38.123396 INFO: === FDR correction performed with classifier version 8 ===
1 day, 8:15:38.124803 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:15:38.124911 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:15:38.124979 PROGRESS: Target precursors: 7,871 (98.39%)
1 day, 8:15:38.125049 PROGRESS: Decoy precursors: 129 (1.61%)
1 day, 8:15:38.125107 PROGRESS: 
1 day, 8:15:38.125162 PROGRESS: Precursor Summary:
1 day, 8:15:38.128304 PROGRESS: Channel   0:	 0.050 FDR: 7,871; 0.010 FDR: 7,763; 0.001 FDR: 7,359
1 day, 8:15:38.128423 PROGRESS: 
1 day, 8:15:38.128493 PROGRESS: Protein Summary:
1 day, 8:15:38.133278 PROGRESS: Channel   0:	 0.050 FDR: 4,350; 0.010 FDR: 4,312; 0.001 FDR: 4,136
1 day, 8:15:38.133398 PROGRESS: =========================================================================
1 day, 8:15:38.133618 INFO: Target number of precursors reached.
1 day, 8:15:38.241207 INFO: fragments_df: keeping 5000 of 469634 [sum(precursor_idx_mask)=236969 sum(mass_error_mask)=469634 stop_rank=5000
1 day, 8:15:38.257806 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:15:39.558227 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:15:40.852695 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:15:42.149512 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:15:42.869858 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:15:42.870512 INFO: Using score_cutoff 33.11782507095337 (fac=0.99, q=1)
1 day, 8:15:42.871094 INFO: Updating optimization_manager: fwhm_rt             : 2.7735908031463623 -> 2.7713992595672607
1 day, 8:15:42.871201 INFO: Updating optimization_manager: fwhm_mobility       : 0.007805380504578352 -> 0.007782938424497843
1 day, 8:15:42.871288 INFO: Updating optimization_manager: score_cutoff        : 33.47183542098999 -> 33.11782507095337
1 day, 8:15:42.871380 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:15:42.874314 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:15:42.884109 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:15:42.886678 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:15:42.907830 INFO: === checking if optimization conditions were reached ===
1 day, 8:15:42.908070 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 8:15:42.911268 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07793573136972387
1 day, 8:15:42.911412 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0779.
1 day, 8:15:42.911505 INFO: ==============================================
1 day, 8:15:42.911604 INFO: Starting optimization step 1.
1 day, 8:15:42.911691 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:15:42.911820 INFO: Using python extraction backend
1 day, 8:15:42.912003 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:15:42.912122 INFO: === Search parameters used ===
1 day, 8:15:42.912216 INFO: rt_error       : 16.46494146117545
1 day, 8:15:42.912308 INFO: mobility_error : 0.07793573136972387
1 day, 8:15:42.912400 INFO: num_candidates : 3
1 day, 8:15:42.912489 INFO: ms1_error      : 15.0
1 day, 8:15:42.912574 INFO: ms2_error      : 15.0
1 day, 8:15:42.912659 INFO: fwhm_rt        : 2.7713992595672607
1 day, 8:15:42.912745 INFO: quant_window   : 3
1 day, 8:15:42.912844 INFO: ==============================================
1 day, 8:15:42.918599 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:15:42.918714 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:15:42.918777 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 8:15:42.918825 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.61
1 day, 8:15:42.920252 INFO: Starting candidate selection
1 day, 8:15:44.518618 INFO: Starting candidate scoring
1 day, 8:15:46.315960 INFO: Finished candidate processing
1 day, 8:15:46.316177 INFO: Collecting candidate features
1 day, 8:15:46.376696 WARNING: intensity_correlation has 12 NaNs ( 0.03 % out of 44532)
1 day, 8:15:46.381990 INFO: Collecting fragment features
1 day, 8:15:46.406837 INFO: Finished candidate scoring
1 day, 8:15:46.429275 INFO: performing precursor FDR with 47 features
1 day, 8:15:46.429436 INFO: Decoy channel: -1
1 day, 8:15:46.429465 INFO: competitive: True
1 day, 8:15:46.441245 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:15:46.449170 WARNING: dropped 3 target PSMs due to missing features
1 day, 8:15:46.449317 WARNING: dropped 9 decoy PSMs due to missing features
1 day, 8:15:46.456081 INFO: Estimating optimal hyperparameters - samples: 35,616, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:15:46.456284 INFO: Using random state 454222 for train-test-split
1 day, 8:15:49.897991 INFO: Test AUC: 0.830
1 day, 8:15:49.898144 INFO: Train AUC: 0.843
1 day, 8:15:49.898184 INFO: AUC difference: 1.44%
1 day, 8:15:50.175092 INFO: Resetting torch num_threads to 128
1 day, 8:15:50.176501 PROGRESS: === Extracted 44532 precursors and 467432 fragments ===
1 day, 8:15:50.177093 INFO: === FDR correction performed with classifier version 8 ===
1 day, 8:15:50.178541 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:15:50.178655 PROGRESS: Total precursors accumulated: 7,993
1 day, 8:15:50.178737 PROGRESS: Target precursors: 7,863 (98.37%)
1 day, 8:15:50.178807 PROGRESS: Decoy precursors: 130 (1.63%)
1 day, 8:15:50.178871 PROGRESS: 
1 day, 8:15:50.178933 PROGRESS: Precursor Summary:
1 day, 8:15:50.182110 PROGRESS: Channel   0:	 0.050 FDR: 7,863; 0.010 FDR: 7,750; 0.001 FDR: 7,419
1 day, 8:15:50.182241 PROGRESS: 
1 day, 8:15:50.182321 PROGRESS: Protein Summary:
1 day, 8:15:50.187176 PROGRESS: Channel   0:	 0.050 FDR: 4,349; 0.010 FDR: 4,305; 0.001 FDR: 4,154
1 day, 8:15:50.187296 PROGRESS: =========================================================================
1 day, 8:15:50.187526 INFO: Target number of precursors reached.
1 day, 8:15:50.295533 INFO: fragments_df: keeping 5000 of 467432 [sum(precursor_idx_mask)=235975 sum(mass_error_mask)=467432 stop_rank=5000
1 day, 8:15:50.312270 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:15:51.604374 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:15:52.903813 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:15:54.197378 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:15:54.915426 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:15:54.916034 INFO: Using score_cutoff 32.5972078994751 (fac=0.99, q=1)
1 day, 8:15:54.916625 INFO: Updating optimization_manager: fwhm_rt             : 2.7713992595672607 -> 2.770599842071533
1 day, 8:15:54.916720 INFO: Updating optimization_manager: fwhm_mobility       : 0.007782938424497843 -> 0.007780726067721844
1 day, 8:15:54.916786 INFO: Updating optimization_manager: score_cutoff        : 33.11782507095337 -> 32.5972078994751
1 day, 8:15:54.916873 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:15:54.919736 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:15:54.929402 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:15:54.931926 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:15:54.951431 INFO: === checking if optimization conditions were reached ===
1 day, 8:15:54.951638 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 8:15:54.954964 INFO: Updating optimization_manager: mobility_error      : 0.07793573136972387 -> 0.06752173200613583
1 day, 8:15:54.955133 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0675.
1 day, 8:15:54.955240 INFO: ==============================================
1 day, 8:15:54.955349 INFO: Starting optimization step 2.
1 day, 8:15:54.955447 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:15:54.955546 INFO: Using python extraction backend
1 day, 8:15:54.955714 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:15:54.955824 INFO: === Search parameters used ===
1 day, 8:15:54.955906 INFO: rt_error       : 16.46494146117545
1 day, 8:15:54.956012 INFO: mobility_error : 0.06752173200613583
1 day, 8:15:54.956108 INFO: num_candidates : 3
1 day, 8:15:54.956203 INFO: ms1_error      : 15.0
1 day, 8:15:54.956295 INFO: ms2_error      : 15.0
1 day, 8:15:54.956392 INFO: fwhm_rt        : 2.770599842071533
1 day, 8:15:54.956482 INFO: quant_window   : 3
1 day, 8:15:54.956571 INFO: ==============================================
1 day, 8:15:54.962532 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:15:54.962638 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:15:54.962708 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 8:15:54.962761 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.61
1 day, 8:15:54.963747 INFO: Starting candidate selection
1 day, 8:15:56.554373 INFO: Starting candidate scoring
1 day, 8:15:58.538061 INFO: Finished candidate processing
1 day, 8:15:58.538278 INFO: Collecting candidate features
1 day, 8:15:58.596745 WARNING: intensity_correlation has 9 NaNs ( 0.02 % out of 44467)
1 day, 8:15:58.601996 INFO: Collecting fragment features
1 day, 8:15:58.629652 INFO: Finished candidate scoring
1 day, 8:15:58.646497 INFO: performing precursor FDR with 47 features
1 day, 8:15:58.646650 INFO: Decoy channel: -1
1 day, 8:15:58.646678 INFO: competitive: True
1 day, 8:15:58.658131 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:15:58.666146 WARNING: dropped 2 target PSMs due to missing features
1 day, 8:15:58.666295 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 8:15:58.673037 INFO: Estimating optimal hyperparameters - samples: 35,566, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:15:58.673253 INFO: Using random state 454222 for train-test-split
1 day, 8:16:02.102386 INFO: Test AUC: 0.823
1 day, 8:16:02.102537 INFO: Train AUC: 0.843
1 day, 8:16:02.102570 INFO: AUC difference: 2.35%
1 day, 8:16:02.379613 INFO: Resetting torch num_threads to 128
1 day, 8:16:02.381022 PROGRESS: === Extracted 44467 precursors and 465413 fragments ===
1 day, 8:16:02.381622 INFO: === FDR correction performed with classifier version 8 ===
1 day, 8:16:02.383060 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:16:02.383172 PROGRESS: Total precursors accumulated: 7,988
1 day, 8:16:02.383244 PROGRESS: Target precursors: 7,849 (98.26%)
1 day, 8:16:02.383306 PROGRESS: Decoy precursors: 139 (1.74%)
1 day, 8:16:02.383365 PROGRESS: 
1 day, 8:16:02.383423 PROGRESS: Precursor Summary:
1 day, 8:16:02.386590 PROGRESS: Channel   0:	 0.050 FDR: 7,849; 0.010 FDR: 7,711; 0.001 FDR: 7,329
1 day, 8:16:02.386711 PROGRESS: 
1 day, 8:16:02.386781 PROGRESS: Protein Summary:
1 day, 8:16:02.391667 PROGRESS: Channel   0:	 0.050 FDR: 4,350; 0.010 FDR: 4,298; 0.001 FDR: 4,137
1 day, 8:16:02.391792 PROGRESS: =========================================================================
1 day, 8:16:02.392062 INFO: Target number of precursors reached.
1 day, 8:16:02.501860 INFO: fragments_df: keeping 5000 of 465413 [sum(precursor_idx_mask)=234552 sum(mass_error_mask)=465413 stop_rank=5000
1 day, 8:16:02.518227 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:16:03.802144 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:16:05.087757 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:16:06.372316 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:16:07.089473 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:16:07.090110 INFO: Using score_cutoff 32.60407464981079 (fac=0.99, q=1)
1 day, 8:16:07.090689 INFO: Updating optimization_manager: fwhm_rt             : 2.770599842071533 -> 2.773845672607422
1 day, 8:16:07.090782 INFO: Updating optimization_manager: fwhm_mobility       : 0.007780726067721844 -> 0.007783799432218075
1 day, 8:16:07.090847 INFO: Updating optimization_manager: score_cutoff        : 32.5972078994751 -> 32.60407464981079
1 day, 8:16:07.090917 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:16:07.093786 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:16:07.103463 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:16:07.105893 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:16:07.126761 INFO: === checking if optimization conditions were reached ===
1 day, 8:16:07.126957 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 8:16:07.128123 INFO: Updating optimization_manager: mobility_error      : 0.06752173200613583 -> 0.1
1 day, 8:16:07.128299 INFO: Updating optimization_manager: classifier_version  : 8 -> 11
1 day, 8:16:07.128472 INFO: Updating optimization_manager: score_cutoff        : 32.60407464981079 -> 33.11782507095337
1 day, 8:16:07.128622 INFO: Updating optimization_manager: fwhm_rt             : 2.773845672607422 -> 2.7713992595672607
1 day, 8:16:07.128772 INFO: Updating optimization_manager: fwhm_mobility       : 0.007783799432218075 -> 0.007782938424497843
1 day, 8:16:07.128917 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 8:16:07.129028 INFO: ==============================================
1 day, 8:16:07.129141 PROGRESS: Optimization finished for mobility_error.
1 day, 8:16:07.151495 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:16:07.154802 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:16:07.165156 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:16:07.167985 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:16:07.189419 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 8:16:07.189640 PROGRESS: ==============================================
1 day, 8:16:07.189776 PROGRESS: ms2_error      : 15.0000
1 day, 8:16:07.189895 PROGRESS: ms1_error      : 15.0000
1 day, 8:16:07.189998 PROGRESS: rt_error       : 16.4649
1 day, 8:16:07.190097 PROGRESS: mobility_error : 0.1000
1 day, 8:16:07.190194 PROGRESS: ==============================================
1 day, 8:16:07.191525 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:16:07.215757 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:16:07.322395 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:16:07.344779 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:16:07.640646 INFO: Using python extraction backend
1 day, 8:16:07.641165 PROGRESS: Extracting batch of 182033 precursors
1 day, 8:16:07.641314 INFO: === Search parameters used ===
1 day, 8:16:07.641421 INFO: rt_error       : 16.46494146117545
1 day, 8:16:07.641517 INFO: mobility_error : 0.1
1 day, 8:16:07.641608 INFO: num_candidates : 3
1 day, 8:16:07.641698 INFO: ms1_error      : 15.0
1 day, 8:16:07.641804 INFO: ms2_error      : 15.0
1 day, 8:16:07.641909 INFO: fwhm_rt        : 2.7713992595672607
1 day, 8:16:07.642007 INFO: quant_window   : 3
1 day, 8:16:07.642094 INFO: ==============================================
1 day, 8:16:07.688708 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:16:07.688895 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:16:07.688943 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 8:16:07.688990 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.61
1 day, 8:16:07.689887 INFO: Starting candidate selection
1 day, 8:16:24.007899 INFO: Removed 72762 precursors with score below cutoff 33.11782507095337
1 day, 8:16:24.366061 INFO: Starting candidate scoring
1 day, 8:16:40.845920 INFO: Finished candidate processing
1 day, 8:16:40.846150 INFO: Collecting candidate features
1 day, 8:16:41.695884 INFO: Collecting fragment features
1 day, 8:16:41.967957 INFO: Finished candidate scoring
1 day, 8:16:42.172822 INFO: === Performing FDR correction with classifier version 11 ===
1 day, 8:16:42.173310 INFO: performing precursor FDR with 47 features
1 day, 8:16:42.173348 INFO: Decoy channel: -1
1 day, 8:16:42.173375 INFO: competitive: True
1 day, 8:16:42.266625 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:16:42.311831 WARNING: FDR calculation for 240690 target and 198662 decoy PSMs
1 day, 8:16:42.312017 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 8:16:42.443566 INFO: Estimating optimal hyperparameters - samples: 351,481, batch_size: 1,439, learning_rate: 5.93e-04
1 day, 8:16:42.444334 INFO: Using random state 24941 for train-test-split
1 day, 8:16:52.729712 INFO: Test AUC: 0.839
1 day, 8:16:52.729905 INFO: Train AUC: 0.845
1 day, 8:16:52.731299 INFO: AUC difference: 0.65%
1 day, 8:16:53.127480 INFO: Resetting torch num_threads to 128
1 day, 8:16:53.148229 INFO: Removing fragments below FDR threshold
1 day, 8:16:53.233720 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:16:53.234742 PROGRESS: Total precursors accumulated: 89,492
1 day, 8:16:53.234823 PROGRESS: Target precursors: 88,606 (99.01%)
1 day, 8:16:53.234888 PROGRESS: Decoy precursors: 886 (0.99%)
1 day, 8:16:53.234953 PROGRESS: 
1 day, 8:16:53.235020 PROGRESS: Precursor Summary:
1 day, 8:16:53.274478 PROGRESS: Channel   0:	 0.050 FDR: 88,606; 0.010 FDR: 88,606; 0.001 FDR: 84,658
1 day, 8:16:53.274816 PROGRESS: 
1 day, 8:16:53.274901 PROGRESS: Protein Summary:
1 day, 8:16:53.328654 PROGRESS: Channel   0:	 0.050 FDR: 8,973; 0.010 FDR: 8,973; 0.001 FDR: 8,931
1 day, 8:16:53.328986 PROGRESS: =========================================================================
1 day, 8:16:53.335710 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/psm.parquet
1 day, 8:16:53.683874 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/frag.parquet
1 day, 8:16:53.987103 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 8:16:54.057690 PROGRESS: Loading raw file 2/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500 
1 day, 8:16:54.057900 INFO: Quantification results path: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant
1 day, 8:16:54.057999 INFO: Creating folder /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/figures
1 day, 8:16:54.058216 INFO: Initializing TimingManager
1 day, 8:16:54.058752 INFO: Initializing RawFileManager
1 day, 8:16:54.058926 INFO: Importing data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 8:16:54.058978 INFO: Using .d import for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 8:16:54.059032 INFO: Reading frame metadata for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 8:16:55.925005 INFO: Reading 39,128 frames with 2,860,596,893 detector events for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 8:17:53.790819 INFO: Indexing /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d...
1 day, 8:17:53.793173 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 8:17:53.804394 INFO: Fetching mobility values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 8:17:53.804628 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 8:17:53.804991 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 8:17:53.806226 INFO: Fetching mz values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 8:17:53.857978 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 8:17:53.858355 INFO: Indexing quadrupole dimension
1 day, 8:17:54.285609 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 8:17:54.285780 INFO: Transposing detector events
1 day, 8:18:02.913145 INFO: Finished transposing data
1 day, 8:18:02.995278 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500.d
1 day, 8:18:02.995978 INFO: RT (min)            : 0.0 - 70.0
1 day, 8:18:02.996047 INFO: RT duration (sec)   : 4199.8
1 day, 8:18:02.996073 INFO: RT duration (min)   : 70.0
1 day, 8:18:02.996095 INFO: Cycle len (scans)   : 9
1 day, 8:18:02.996115 INFO: Cycle len (sec)     : 0.97
1 day, 8:18:02.996140 INFO: Number of cycles    : 4347
1 day, 8:18:02.996168 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 8:18:02.996226 INFO: Creating DIA data object took: 68.9373426437378
1 day, 8:18:03.041433 INFO: Initializing CalibrationManager
1 day, 8:18:03.041829 INFO: Setting up calibration estimators ..
1 day, 8:18:03.041922 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 8:18:03.042003 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, 8:18:03.042109 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 8:18:03.042185 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, 8:18:03.042287 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, 8:18:03.042389 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, 8:18:03.042477 INFO: Done setting up calibration estimators.
1 day, 8:18:03.042622 INFO: Initializing OptimizationManager
1 day, 8:18:03.042809 INFO: initial parameter: ms1_error = 30
1 day, 8:18:03.042896 INFO: initial parameter: ms2_error = 30
1 day, 8:18:03.042980 INFO: initial parameter: rt_error = 2099.894844
1 day, 8:18:03.043062 INFO: initial parameter: mobility_error = 0.1
1 day, 8:18:03.043140 INFO: initial parameter: num_candidates = 1
1 day, 8:18:03.043216 INFO: initial parameter: fwhm_rt = 5
1 day, 8:18:03.043291 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 8:18:03.043357 INFO: initial parameter: score_cutoff = 0
1 day, 8:18:03.043434 INFO: initial parameter: classifier_version = -1
1 day, 8:18:03.043547 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 8:18:03.043820 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 8:18:03.043860 INFO: Initializing FDRManager
1 day, 8:18:03.043922 INFO: Loading classifier store from /usr/local/lib/python3.10/site-packages/alphadia/constants/classifier
1 day, 8:18:03.080193 PROGRESS: Initializing spectral library: 91,740 target precursors potentially observable (0 removed)
1 day, 8:18:03.117490 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 8:18:03.118106 INFO: Updating optimization_manager: rt_error            : 2099.894844 -> 2099.894844
1 day, 8:18:03.118230 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 8:18:03.118456 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 8:18:03.118576 PROGRESS: Starting initial search for precursors.
1 day, 8:18:03.118716 INFO: Starting optimization step 0.
1 day, 8:18:03.118814 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:18:03.118911 INFO: Using python extraction backend
1 day, 8:18:03.119086 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:18:03.119182 INFO: === Search parameters used ===
1 day, 8:18:03.119263 INFO: rt_error       : 2099.894844
1 day, 8:18:03.119338 INFO: mobility_error : 0.1
1 day, 8:18:03.119413 INFO: num_candidates : 1
1 day, 8:18:03.119489 INFO: ms1_error      : 30
1 day, 8:18:03.119560 INFO: ms2_error      : 30
1 day, 8:18:03.119633 INFO: fwhm_rt        : 5
1 day, 8:18:03.119689 INFO: quant_window   : 3
1 day, 8:18:03.119757 INFO: ==============================================
1 day, 8:18:03.122532 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:18:03.122592 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:18:03.122627 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 8:18:03.122656 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 8:18:03.124804 INFO: Starting candidate selection
1 day, 8:19:39.103708 INFO: Starting candidate scoring
1 day, 8:19:40.642133 INFO: Finished candidate processing
1 day, 8:19:40.642334 INFO: Collecting candidate features
1 day, 8:19:40.699044 INFO: Collecting fragment features
1 day, 8:19:40.712493 INFO: Finished candidate scoring
1 day, 8:19:40.720723 INFO: performing precursor FDR with 47 features
1 day, 8:19:40.720828 INFO: Decoy channel: -1
1 day, 8:19:40.720857 INFO: competitive: True
1 day, 8:19:40.725438 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:19:40.730613 INFO: Estimating optimal hyperparameters - samples: 12,694, batch_size: 128, learning_rate: 1.77e-04
1 day, 8:19:40.731445 INFO: Using random state 587841 for train-test-split
1 day, 8:19:42.087099 INFO: Test AUC: 0.801
1 day, 8:19:42.087255 INFO: Train AUC: 0.809
1 day, 8:19:42.087288 INFO: AUC difference: 1.01%
1 day, 8:19:42.352423 INFO: Resetting torch num_threads to 128
1 day, 8:19:42.353433 PROGRESS: === Extracted 15868 precursors and 179896 fragments ===
1 day, 8:19:42.354007 INFO: === FDR correction performed with classifier version -1 ===
1 day, 8:19:42.355396 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:19:42.355503 PROGRESS: Total precursors accumulated: 7,995
1 day, 8:19:42.355575 PROGRESS: Target precursors: 7,661 (95.82%)
1 day, 8:19:42.355653 PROGRESS: Decoy precursors: 334 (4.18%)
1 day, 8:19:42.355722 PROGRESS: 
1 day, 8:19:42.355788 PROGRESS: Precursor Summary:
1 day, 8:19:42.358331 PROGRESS: Channel   0:	 0.050 FDR: 7,661; 0.010 FDR: 4,571; 0.001 FDR: 3,708
1 day, 8:19:42.358453 PROGRESS: 
1 day, 8:19:42.358536 PROGRESS: Protein Summary:
1 day, 8:19:42.362317 PROGRESS: Channel   0:	 0.050 FDR: 4,292; 0.010 FDR: 2,831; 0.001 FDR: 2,418
1 day, 8:19:42.362444 PROGRESS: =========================================================================
1 day, 8:19:42.362580 INFO: Target number of precursors reached.
1 day, 8:19:42.391972 INFO: fragments_df: keeping 5000 of 179896 [sum(precursor_idx_mask)=51799 sum(mass_error_mask)=179896 stop_rank=5000
1 day, 8:19:42.408496 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:19:43.000640 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:19:43.611348 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:19:44.208663 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:19:44.856650 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 8:19:44.857262 INFO: Using score_cutoff 48.614491859436036 (fac=0.99, q=1)
1 day, 8:19:44.857854 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.1363837718963623
1 day, 8:19:44.857964 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010348483920097351
1 day, 8:19:44.858044 INFO: Updating optimization_manager: score_cutoff        : 0 -> 48.614491859436036
1 day, 8:19:44.858189 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:19:44.861247 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:19:44.871269 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:19:44.873818 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:19:44.896054 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
1 day, 8:19:44.896305 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 8:19:44.896498 INFO: Starting optimization step 1.
1 day, 8:19:44.896604 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:19:44.896718 INFO: Using python extraction backend
1 day, 8:19:44.896909 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:19:44.897017 INFO: === Search parameters used ===
1 day, 8:19:44.897099 INFO: rt_error       : 2099.894844
1 day, 8:19:44.897177 INFO: mobility_error : 0.1
1 day, 8:19:44.897249 INFO: num_candidates : 3
1 day, 8:19:44.897321 INFO: ms1_error      : 30
1 day, 8:19:44.897394 INFO: ms2_error      : 30
1 day, 8:19:44.897467 INFO: fwhm_rt        : 3.1363837718963623
1 day, 8:19:44.897537 INFO: quant_window   : 3
1 day, 8:19:44.897610 INFO: ==============================================
1 day, 8:19:44.903601 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:19:44.903684 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:19:44.903770 INFO: FWHM in RT is 3.14 seconds, sigma is 0.69
1 day, 8:19:44.903830 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.80
1 day, 8:19:44.904712 INFO: Starting candidate selection
1 day, 8:21:28.890285 INFO: Starting candidate scoring
1 day, 8:21:32.303473 INFO: Finished candidate processing
1 day, 8:21:32.303682 INFO: Collecting candidate features
1 day, 8:21:32.404500 INFO: Collecting fragment features
1 day, 8:21:32.432316 INFO: Finished candidate scoring
1 day, 8:21:32.458241 INFO: performing precursor FDR with 47 features
1 day, 8:21:32.458395 INFO: Decoy channel: -1
1 day, 8:21:32.458428 INFO: competitive: True
1 day, 8:21:32.473431 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:21:32.486377 INFO: Estimating optimal hyperparameters - samples: 36,132, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:21:32.486619 INFO: Using random state 708522 for train-test-split
1 day, 8:21:35.983495 INFO: Test AUC: 0.691
1 day, 8:21:35.983648 INFO: Train AUC: 0.706
1 day, 8:21:35.983683 INFO: AUC difference: 2.17%
1 day, 8:21:36.260740 INFO: Resetting torch num_threads to 128
1 day, 8:21:36.262397 PROGRESS: === Extracted 45166 precursors and 511365 fragments ===
1 day, 8:21:36.263007 INFO: === FDR correction performed with classifier version 0 ===
1 day, 8:21:36.264520 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:21:36.264633 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:21:36.264711 PROGRESS: Target precursors: 7,087 (88.59%)
1 day, 8:21:36.264776 PROGRESS: Decoy precursors: 913 (11.41%)
1 day, 8:21:36.264838 PROGRESS: 
1 day, 8:21:36.264895 PROGRESS: Precursor Summary:
1 day, 8:21:36.267500 PROGRESS: Channel   0:	 0.050 FDR: 6,057; 0.010 FDR: 5,423; 0.001 FDR: 4,385
1 day, 8:21:36.267620 PROGRESS: 
1 day, 8:21:36.267695 PROGRESS: Protein Summary:
1 day, 8:21:36.271562 PROGRESS: Channel   0:	 0.050 FDR: 3,553; 0.010 FDR: 3,251; 0.001 FDR: 2,780
1 day, 8:21:36.271688 PROGRESS: =========================================================================
1 day, 8:21:36.272117 INFO: Target number of precursors reached.
1 day, 8:21:36.374250 INFO: fragments_df: keeping 5000 of 511365 [sum(precursor_idx_mask)=175905 sum(mass_error_mask)=511365 stop_rank=5000
1 day, 8:21:36.400854 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:21:37.202782 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:21:38.012805 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:21:38.813502 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:21:39.533757 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:21:39.534385 INFO: Using score_cutoff 48.475996394348144 (fac=0.99, q=1)
1 day, 8:21:39.534905 INFO: Updating optimization_manager: fwhm_rt             : 3.1363837718963623 -> 3.105316162109375
1 day, 8:21:39.535004 INFO: Updating optimization_manager: fwhm_mobility       : 0.010348483920097351 -> 0.010097661055624485
1 day, 8:21:39.535070 INFO: Updating optimization_manager: score_cutoff        : 48.614491859436036 -> 48.475996394348144
1 day, 8:21:39.535142 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:21:39.538069 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:21:39.547740 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:21:39.550235 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:21:39.575472 INFO: === checking if optimization conditions were reached ===
1 day, 8:21:39.577816 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 8:21:39.577975 INFO: Updating optimization_manager: classifier_version  : 0 -> 1
1 day, 8:21:39.578071 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 8:21:39.580253 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 8:21:39.580386 INFO: Updating optimization_manager: classifier_version  : 1 -> 1
1 day, 8:21:39.580475 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 8:21:39.580556 INFO: ==============================================
1 day, 8:21:39.580657 INFO: Starting optimization step 2.
1 day, 8:21:39.580742 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:21:39.580871 INFO: Using python extraction backend
1 day, 8:21:39.581106 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:21:39.581241 INFO: === Search parameters used ===
1 day, 8:21:39.581338 INFO: rt_error       : 2099.894844
1 day, 8:21:39.581424 INFO: mobility_error : 0.1
1 day, 8:21:39.581505 INFO: num_candidates : 3
1 day, 8:21:39.581589 INFO: ms1_error      : 15.0
1 day, 8:21:39.581669 INFO: ms2_error      : 15.0
1 day, 8:21:39.581764 INFO: fwhm_rt        : 3.105316162109375
1 day, 8:21:39.581860 INFO: quant_window   : 3
1 day, 8:21:39.581950 INFO: ==============================================
1 day, 8:21:39.589835 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:21:39.589941 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:21:39.590011 INFO: FWHM in RT is 3.11 seconds, sigma is 0.68
1 day, 8:21:39.590059 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.68
1 day, 8:21:39.590978 INFO: Starting candidate selection
1 day, 8:23:10.988556 INFO: Starting candidate scoring
1 day, 8:23:13.030561 INFO: Finished candidate processing
1 day, 8:23:13.030705 INFO: Collecting candidate features
1 day, 8:23:13.103297 INFO: Collecting fragment features
1 day, 8:23:13.129083 INFO: Finished candidate scoring
1 day, 8:23:13.149230 INFO: performing precursor FDR with 47 features
1 day, 8:23:13.149387 INFO: Decoy channel: -1
1 day, 8:23:13.149417 INFO: competitive: True
1 day, 8:23:13.164214 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:23:13.177644 INFO: Estimating optimal hyperparameters - samples: 36,093, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:23:13.177931 INFO: Using random state 875986 for train-test-split
1 day, 8:23:16.616716 INFO: Test AUC: 0.736
1 day, 8:23:16.616877 INFO: Train AUC: 0.738
1 day, 8:23:16.616913 INFO: AUC difference: 0.18%
1 day, 8:23:16.896322 INFO: Resetting torch num_threads to 128
1 day, 8:23:16.898001 PROGRESS: === Extracted 45117 precursors and 498507 fragments ===
1 day, 8:23:16.898585 INFO: === FDR correction performed with classifier version 1 ===
1 day, 8:23:16.900165 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:23:16.900276 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:23:16.900355 PROGRESS: Target precursors: 7,459 (93.24%)
1 day, 8:23:16.900421 PROGRESS: Decoy precursors: 541 (6.76%)
1 day, 8:23:16.900483 PROGRESS: 
1 day, 8:23:16.900539 PROGRESS: Precursor Summary:
1 day, 8:23:16.903555 PROGRESS: Channel   0:	 0.050 FDR: 7,155; 0.010 FDR: 6,559; 0.001 FDR: 5,541
1 day, 8:23:16.903679 PROGRESS: 
1 day, 8:23:16.903770 PROGRESS: Protein Summary:
1 day, 8:23:16.908102 PROGRESS: Channel   0:	 0.050 FDR: 4,043; 0.010 FDR: 3,777; 0.001 FDR: 3,343
1 day, 8:23:16.908224 PROGRESS: =========================================================================
1 day, 8:23:16.908572 INFO: Target number of precursors reached.
1 day, 8:23:17.010855 INFO: fragments_df: keeping 5000 of 498507 [sum(precursor_idx_mask)=207727 sum(mass_error_mask)=498507 stop_rank=5000
1 day, 8:23:17.031229 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:23:18.021626 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:23:19.054477 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:23:20.073358 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:23:20.794759 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:23:20.795376 INFO: Using score_cutoff 41.04903576049804 (fac=0.99, q=1)
1 day, 8:23:20.795893 INFO: Updating optimization_manager: fwhm_rt             : 3.105316162109375 -> 2.8164966106414795
1 day, 8:23:20.795990 INFO: Updating optimization_manager: fwhm_mobility       : 0.010097661055624485 -> 0.008316329680383205
1 day, 8:23:20.796058 INFO: Updating optimization_manager: score_cutoff        : 48.475996394348144 -> 41.04903576049804
1 day, 8:23:20.796138 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:23:20.799126 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:23:20.808793 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:23:20.811275 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:23:20.832729 INFO: === checking if optimization conditions were reached ===
1 day, 8:23:20.835073 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 8:23:20.835225 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
1 day, 8:23:20.835332 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 8:23:20.837631 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 8:23:20.837793 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
1 day, 8:23:20.837891 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 8:23:20.837982 INFO: ==============================================
1 day, 8:23:20.838091 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 8:23:20.863183 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:23:20.866565 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:23:20.876654 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:23:20.879444 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:23:20.901771 INFO: Starting optimization step 0.
1 day, 8:23:20.902042 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:23:20.902185 INFO: Using python extraction backend
1 day, 8:23:20.902436 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:23:20.902597 INFO: === Search parameters used ===
1 day, 8:23:20.902700 INFO: rt_error       : 2099.894844
1 day, 8:23:20.902799 INFO: mobility_error : 0.1
1 day, 8:23:20.902888 INFO: num_candidates : 3
1 day, 8:23:20.902977 INFO: ms1_error      : 15.0
1 day, 8:23:20.903066 INFO: ms2_error      : 15.0
1 day, 8:23:20.903153 INFO: fwhm_rt        : 2.8164966106414795
1 day, 8:23:20.903243 INFO: quant_window   : 3
1 day, 8:23:20.903333 INFO: ==============================================
1 day, 8:23:20.909985 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:23:20.910107 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:23:20.910182 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 8:23:20.910227 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.86
1 day, 8:23:20.910994 INFO: Starting candidate selection
1 day, 8:24:54.984972 INFO: Starting candidate scoring
1 day, 8:24:56.965902 INFO: Finished candidate processing
1 day, 8:24:56.966118 INFO: Collecting candidate features
1 day, 8:24:57.068134 INFO: Collecting fragment features
1 day, 8:24:57.094593 INFO: Finished candidate scoring
1 day, 8:24:57.115883 INFO: performing precursor FDR with 47 features
1 day, 8:24:57.116045 INFO: Decoy channel: -1
1 day, 8:24:57.116081 INFO: competitive: True
1 day, 8:24:57.130538 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:24:57.144073 INFO: Estimating optimal hyperparameters - samples: 36,055, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:24:57.144305 INFO: Using random state 988585 for train-test-split
1 day, 8:25:00.605362 INFO: Test AUC: 0.744
1 day, 8:25:00.605518 INFO: Train AUC: 0.752
1 day, 8:25:00.605550 INFO: AUC difference: 1.16%
1 day, 8:25:00.898862 INFO: Resetting torch num_threads to 128
1 day, 8:25:00.900570 PROGRESS: === Extracted 45069 precursors and 497074 fragments ===
1 day, 8:25:00.901136 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:25:00.902771 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:25:00.902898 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:25:00.902997 PROGRESS: Target precursors: 7,463 (93.29%)
1 day, 8:25:00.903087 PROGRESS: Decoy precursors: 537 (6.71%)
1 day, 8:25:00.903166 PROGRESS: 
1 day, 8:25:00.903242 PROGRESS: Precursor Summary:
1 day, 8:25:00.906329 PROGRESS: Channel   0:	 0.050 FDR: 7,191; 0.010 FDR: 6,639; 0.001 FDR: 5,889
1 day, 8:25:00.906466 PROGRESS: 
1 day, 8:25:00.906546 PROGRESS: Protein Summary:
1 day, 8:25:00.911128 PROGRESS: Channel   0:	 0.050 FDR: 4,073; 0.010 FDR: 3,818; 0.001 FDR: 3,484
1 day, 8:25:00.911252 PROGRESS: =========================================================================
1 day, 8:25:00.911512 INFO: Target number of precursors reached.
1 day, 8:25:01.018369 INFO: fragments_df: keeping 5000 of 497074 [sum(precursor_idx_mask)=209700 sum(mass_error_mask)=497074 stop_rank=5000
1 day, 8:25:01.038043 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:25:02.082360 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:25:03.138299 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:25:04.175649 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:25:04.897663 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:25:04.898304 INFO: Using score_cutoff 41.00407592926025 (fac=0.99, q=1)
1 day, 8:25:04.898826 INFO: Updating optimization_manager: fwhm_rt             : 2.8164966106414795 -> 2.7924561500549316
1 day, 8:25:04.898923 INFO: Updating optimization_manager: fwhm_mobility       : 0.008316329680383205 -> 0.008220202289521694
1 day, 8:25:04.898991 INFO: Updating optimization_manager: score_cutoff        : 41.04903576049804 -> 41.00407592926025
1 day, 8:25:04.899072 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:25:04.901887 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:25:04.911530 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:25:04.914006 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:25:04.935471 INFO: === checking if optimization conditions were reached ===
1 day, 8:25:04.935821 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 8:25:04.942201 INFO: Updating optimization_manager: rt_error            : 2099.894844 -> 232.29046314180505
1 day, 8:25:04.942394 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 232.2905.
1 day, 8:25:04.942527 INFO: ==============================================
1 day, 8:25:04.942652 INFO: Starting optimization step 1.
1 day, 8:25:04.942768 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:25:04.942885 INFO: Using python extraction backend
1 day, 8:25:04.943082 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:25:04.943201 INFO: === Search parameters used ===
1 day, 8:25:04.943299 INFO: rt_error       : 232.29046314180505
1 day, 8:25:04.943395 INFO: mobility_error : 0.1
1 day, 8:25:04.943488 INFO: num_candidates : 3
1 day, 8:25:04.943573 INFO: ms1_error      : 15.0
1 day, 8:25:04.943663 INFO: ms2_error      : 15.0
1 day, 8:25:04.943749 INFO: fwhm_rt        : 2.7924561500549316
1 day, 8:25:04.943848 INFO: quant_window   : 3
1 day, 8:25:04.943938 INFO: ==============================================
1 day, 8:25:04.949965 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:25:04.950075 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:25:04.950138 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1 day, 8:25:04.950189 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.81
1 day, 8:25:04.951008 INFO: Starting candidate selection
1 day, 8:25:19.912926 INFO: Starting candidate scoring
1 day, 8:25:22.070891 INFO: Finished candidate processing
1 day, 8:25:22.071118 INFO: Collecting candidate features
1 day, 8:25:22.165004 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 44952)
1 day, 8:25:22.170785 INFO: Collecting fragment features
1 day, 8:25:22.196948 INFO: Finished candidate scoring
1 day, 8:25:22.218706 INFO: performing precursor FDR with 47 features
1 day, 8:25:22.218873 INFO: Decoy channel: -1
1 day, 8:25:22.218901 INFO: competitive: True
1 day, 8:25:22.232169 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:25:22.239388 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 8:25:22.246245 INFO: Estimating optimal hyperparameters - samples: 35,959, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:25:22.246461 INFO: Using random state 988585 for train-test-split
1 day, 8:25:25.627476 INFO: Test AUC: 0.764
1 day, 8:25:25.627645 INFO: Train AUC: 0.770
1 day, 8:25:25.627678 INFO: AUC difference: 0.72%
1 day, 8:25:25.912841 INFO: Resetting torch num_threads to 128
1 day, 8:25:25.914539 PROGRESS: === Extracted 44952 precursors and 487301 fragments ===
1 day, 8:25:25.915122 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:25:25.916598 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:25:25.916710 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:25:25.916784 PROGRESS: Target precursors: 7,667 (95.84%)
1 day, 8:25:25.916851 PROGRESS: Decoy precursors: 333 (4.16%)
1 day, 8:25:25.916919 PROGRESS: 
1 day, 8:25:25.916977 PROGRESS: Precursor Summary:
1 day, 8:25:25.920065 PROGRESS: Channel   0:	 0.050 FDR: 7,667; 0.010 FDR: 7,235; 0.001 FDR: 6,754
1 day, 8:25:25.920188 PROGRESS: 
1 day, 8:25:25.920264 PROGRESS: Protein Summary:
1 day, 8:25:25.925348 PROGRESS: Channel   0:	 0.050 FDR: 4,266; 0.010 FDR: 4,075; 0.001 FDR: 3,869
1 day, 8:25:25.925475 PROGRESS: =========================================================================
1 day, 8:25:25.925766 INFO: Target number of precursors reached.
1 day, 8:25:26.033205 INFO: fragments_df: keeping 5000 of 487301 [sum(precursor_idx_mask)=225648 sum(mass_error_mask)=487301 stop_rank=5000
1 day, 8:25:26.050990 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:25:27.217774 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:25:28.404992 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:25:29.571964 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:25:30.293824 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:25:30.294512 INFO: Using score_cutoff 37.39319164352417 (fac=0.99, q=1)
1 day, 8:25:30.295078 INFO: Updating optimization_manager: fwhm_rt             : 2.7924561500549316 -> 2.7846930027008057
1 day, 8:25:30.295192 INFO: Updating optimization_manager: fwhm_mobility       : 0.008220202289521694 -> 0.008001199923455715
1 day, 8:25:30.295289 INFO: Updating optimization_manager: score_cutoff        : 41.00407592926025 -> 37.39319164352417
1 day, 8:25:30.295388 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:25:30.298310 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:25:30.308001 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:25:30.310501 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:25:30.330652 INFO: === checking if optimization conditions were reached ===
1 day, 8:25:30.330859 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 8:25:30.337555 INFO: Updating optimization_manager: rt_error            : 232.29046314180505 -> 53.775607186337204
1 day, 8:25:30.337727 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 53.7756.
1 day, 8:25:30.337874 INFO: ==============================================
1 day, 8:25:30.338002 INFO: Starting optimization step 2.
1 day, 8:25:30.338113 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:25:30.338222 INFO: Using python extraction backend
1 day, 8:25:30.338408 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:25:30.338535 INFO: === Search parameters used ===
1 day, 8:25:30.338635 INFO: rt_error       : 53.775607186337204
1 day, 8:25:30.338723 INFO: mobility_error : 0.1
1 day, 8:25:30.338806 INFO: num_candidates : 3
1 day, 8:25:30.338893 INFO: ms1_error      : 15.0
1 day, 8:25:30.338981 INFO: ms2_error      : 15.0
1 day, 8:25:30.339064 INFO: fwhm_rt        : 2.7846930027008057
1 day, 8:25:30.339147 INFO: quant_window   : 3
1 day, 8:25:30.339223 INFO: ==============================================
1 day, 8:25:30.345506 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:25:30.345619 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:25:30.345683 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
1 day, 8:25:30.345731 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.71
1 day, 8:25:30.346531 INFO: Starting candidate selection
1 day, 8:25:33.520840 INFO: Starting candidate scoring
1 day, 8:25:35.313205 INFO: Finished candidate processing
1 day, 8:25:35.313402 INFO: Collecting candidate features
1 day, 8:25:35.406664 WARNING: intensity_correlation has 8 NaNs ( 0.02 % out of 44835)
1 day, 8:25:35.411943 INFO: Collecting fragment features
1 day, 8:25:35.437424 INFO: Finished candidate scoring
1 day, 8:25:35.460236 INFO: performing precursor FDR with 47 features
1 day, 8:25:35.460397 INFO: Decoy channel: -1
1 day, 8:25:35.460424 INFO: competitive: True
1 day, 8:25:35.472770 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:25:35.480680 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:25:35.480824 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 8:25:35.487154 INFO: Estimating optimal hyperparameters - samples: 35,861, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:25:35.487348 INFO: Using random state 988585 for train-test-split
1 day, 8:25:38.888244 INFO: Test AUC: 0.796
1 day, 8:25:38.888401 INFO: Train AUC: 0.796
1 day, 8:25:38.888432 INFO: AUC difference: 0.06%
1 day, 8:25:39.163841 INFO: Resetting torch num_threads to 128
1 day, 8:25:39.165476 PROGRESS: === Extracted 44835 precursors and 477507 fragments ===
1 day, 8:25:39.166049 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:25:39.167495 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:25:39.167606 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:25:39.167682 PROGRESS: Target precursors: 7,816 (97.70%)
1 day, 8:25:39.167748 PROGRESS: Decoy precursors: 184 (2.30%)
1 day, 8:25:39.167813 PROGRESS: 
1 day, 8:25:39.167871 PROGRESS: Precursor Summary:
1 day, 8:25:39.171007 PROGRESS: Channel   0:	 0.050 FDR: 7,816; 0.010 FDR: 7,656; 0.001 FDR: 7,282
1 day, 8:25:39.171129 PROGRESS: 
1 day, 8:25:39.171200 PROGRESS: Protein Summary:
1 day, 8:25:39.176206 PROGRESS: Channel   0:	 0.050 FDR: 4,322; 0.010 FDR: 4,265; 0.001 FDR: 4,097
1 day, 8:25:39.176338 PROGRESS: =========================================================================
1 day, 8:25:39.176605 INFO: Target number of precursors reached.
1 day, 8:25:39.288474 INFO: fragments_df: keeping 5000 of 477507 [sum(precursor_idx_mask)=235508 sum(mass_error_mask)=477507 stop_rank=5000
1 day, 8:25:39.306415 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:25:40.566786 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:25:41.849433 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:25:43.112353 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:25:43.833731 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:25:43.834352 INFO: Using score_cutoff 34.29587212371826 (fac=0.99, q=1)
1 day, 8:25:43.834892 INFO: Updating optimization_manager: fwhm_rt             : 2.7846930027008057 -> 2.784613847732544
1 day, 8:25:43.834990 INFO: Updating optimization_manager: fwhm_mobility       : 0.008001199923455715 -> 0.007845641113817692
1 day, 8:25:43.835055 INFO: Updating optimization_manager: score_cutoff        : 37.39319164352417 -> 34.29587212371826
1 day, 8:25:43.835132 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:25:43.838030 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:25:43.847774 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:25:43.850282 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:25:43.871693 INFO: === checking if optimization conditions were reached ===
1 day, 8:25:43.871921 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 8:25:43.879403 INFO: Updating optimization_manager: rt_error            : 53.775607186337204 -> 20.596905685127087
1 day, 8:25:43.879577 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 20.5969.
1 day, 8:25:43.879678 INFO: ==============================================
1 day, 8:25:43.879780 INFO: Starting optimization step 3.
1 day, 8:25:43.879871 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:25:43.879996 INFO: Using python extraction backend
1 day, 8:25:43.880190 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:25:43.880316 INFO: === Search parameters used ===
1 day, 8:25:43.880412 INFO: rt_error       : 20.596905685127087
1 day, 8:25:43.880503 INFO: mobility_error : 0.1
1 day, 8:25:43.880595 INFO: num_candidates : 3
1 day, 8:25:43.880683 INFO: ms1_error      : 15.0
1 day, 8:25:43.880768 INFO: ms2_error      : 15.0
1 day, 8:25:43.880851 INFO: fwhm_rt        : 2.784613847732544
1 day, 8:25:43.880939 INFO: quant_window   : 3
1 day, 8:25:43.881021 INFO: ==============================================
1 day, 8:25:43.887158 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:25:43.887263 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:25:43.887325 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
1 day, 8:25:43.887374 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.64
1 day, 8:25:43.888189 INFO: Starting candidate selection
1 day, 8:25:45.733413 INFO: Starting candidate scoring
1 day, 8:25:47.529142 INFO: Finished candidate processing
1 day, 8:25:47.529366 INFO: Collecting candidate features
1 day, 8:25:47.586954 WARNING: intensity_correlation has 9 NaNs ( 0.02 % out of 44676)
1 day, 8:25:47.587266 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 44676)
1 day, 8:25:47.592265 INFO: Collecting fragment features
1 day, 8:25:47.617484 INFO: Finished candidate scoring
1 day, 8:25:47.639158 INFO: performing precursor FDR with 47 features
1 day, 8:25:47.639331 INFO: Decoy channel: -1
1 day, 8:25:47.639359 INFO: competitive: True
1 day, 8:25:47.652572 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:25:47.661096 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:25:47.661247 WARNING: dropped 9 decoy PSMs due to missing features
1 day, 8:25:47.668013 INFO: Estimating optimal hyperparameters - samples: 35,732, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:25:47.668236 INFO: Using random state 988585 for train-test-split
1 day, 8:25:51.204432 INFO: Test AUC: 0.815
1 day, 8:25:51.204602 INFO: Train AUC: 0.820
1 day, 8:25:51.204635 INFO: AUC difference: 0.59%
1 day, 8:25:51.480948 INFO: Resetting torch num_threads to 128
1 day, 8:25:51.482611 PROGRESS: === Extracted 44676 precursors and 470100 fragments ===
1 day, 8:25:51.483180 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:25:51.484712 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:25:51.484825 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:25:51.484901 PROGRESS: Target precursors: 7,852 (98.15%)
1 day, 8:25:51.484968 PROGRESS: Decoy precursors: 148 (1.85%)
1 day, 8:25:51.485036 PROGRESS: 
1 day, 8:25:51.485096 PROGRESS: Precursor Summary:
1 day, 8:25:51.488311 PROGRESS: Channel   0:	 0.050 FDR: 7,852; 0.010 FDR: 7,752; 0.001 FDR: 7,298
1 day, 8:25:51.488442 PROGRESS: 
1 day, 8:25:51.488514 PROGRESS: Protein Summary:
1 day, 8:25:51.493559 PROGRESS: Channel   0:	 0.050 FDR: 4,345; 0.010 FDR: 4,304; 0.001 FDR: 4,115
1 day, 8:25:51.493692 PROGRESS: =========================================================================
1 day, 8:25:51.493928 INFO: Target number of precursors reached.
1 day, 8:25:51.602417 INFO: fragments_df: keeping 5000 of 470100 [sum(precursor_idx_mask)=236244 sum(mass_error_mask)=470100 stop_rank=5000
1 day, 8:25:51.620069 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:25:54.890180 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:25:56.207764 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:25:57.511693 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:25:58.237526 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:25:58.238164 INFO: Using score_cutoff 33.391488520431515 (fac=0.99, q=1)
1 day, 8:25:58.238789 INFO: Updating optimization_manager: fwhm_rt             : 2.784613847732544 -> 2.7667999267578125
1 day, 8:25:58.238893 INFO: Updating optimization_manager: fwhm_mobility       : 0.007845641113817692 -> 0.007782429456710815
1 day, 8:25:58.238966 INFO: Updating optimization_manager: score_cutoff        : 34.29587212371826 -> 33.391488520431515
1 day, 8:25:58.239086 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:25:58.242411 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:25:58.253889 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:25:58.256474 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:25:58.280737 INFO: === checking if optimization conditions were reached ===
1 day, 8:25:58.280998 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 8:25:58.288604 INFO: Updating optimization_manager: rt_error            : 20.596905685127087 -> 15.206556035019132
1 day, 8:25:58.288777 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 15.2066.
1 day, 8:25:58.288875 INFO: ==============================================
1 day, 8:25:58.288997 INFO: Starting optimization step 4.
1 day, 8:25:58.289089 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:25:58.289188 INFO: Using python extraction backend
1 day, 8:25:58.289375 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:25:58.289477 INFO: === Search parameters used ===
1 day, 8:25:58.289551 INFO: rt_error       : 15.206556035019132
1 day, 8:25:58.289623 INFO: mobility_error : 0.1
1 day, 8:25:58.289692 INFO: num_candidates : 3
1 day, 8:25:58.289806 INFO: ms1_error      : 15.0
1 day, 8:25:58.289911 INFO: ms2_error      : 15.0
1 day, 8:25:58.290006 INFO: fwhm_rt        : 2.7667999267578125
1 day, 8:25:58.290095 INFO: quant_window   : 3
1 day, 8:25:58.290184 INFO: ==============================================
1 day, 8:25:58.298423 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:25:58.298529 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:25:58.298597 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 8:25:58.298646 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.61
1 day, 8:25:58.299470 INFO: Starting candidate selection
1 day, 8:25:59.931308 INFO: Starting candidate scoring
1 day, 8:26:01.816039 INFO: Finished candidate processing
1 day, 8:26:01.816242 INFO: Collecting candidate features
1 day, 8:26:01.897647 WARNING: intensity_correlation has 20 NaNs ( 0.04 % out of 44582)
1 day, 8:26:01.902970 INFO: Collecting fragment features
1 day, 8:26:01.936228 INFO: Finished candidate scoring
1 day, 8:26:01.955220 INFO: performing precursor FDR with 47 features
1 day, 8:26:01.955380 INFO: Decoy channel: -1
1 day, 8:26:01.955408 INFO: competitive: True
1 day, 8:26:01.971024 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:26:01.980581 WARNING: dropped 6 target PSMs due to missing features
1 day, 8:26:01.980740 WARNING: dropped 14 decoy PSMs due to missing features
1 day, 8:26:01.987407 INFO: Estimating optimal hyperparameters - samples: 35,649, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:26:01.987704 INFO: Using random state 988585 for train-test-split
1 day, 8:26:05.373818 INFO: Test AUC: 0.833
1 day, 8:26:05.373977 INFO: Train AUC: 0.838
1 day, 8:26:05.374011 INFO: AUC difference: 0.59%
1 day, 8:26:05.648179 INFO: Resetting torch num_threads to 128
1 day, 8:26:05.649923 PROGRESS: === Extracted 44582 precursors and 465380 fragments ===
1 day, 8:26:05.650541 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:26:05.652053 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:26:05.652173 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:26:05.652253 PROGRESS: Target precursors: 7,876 (98.45%)
1 day, 8:26:05.652323 PROGRESS: Decoy precursors: 124 (1.55%)
1 day, 8:26:05.652389 PROGRESS: 
1 day, 8:26:05.652449 PROGRESS: Precursor Summary:
1 day, 8:26:05.655725 PROGRESS: Channel   0:	 0.050 FDR: 7,876; 0.010 FDR: 7,781; 0.001 FDR: 7,245
1 day, 8:26:05.655862 PROGRESS: 
1 day, 8:26:05.655936 PROGRESS: Protein Summary:
1 day, 8:26:05.661115 PROGRESS: Channel   0:	 0.050 FDR: 4,351; 0.010 FDR: 4,317; 0.001 FDR: 4,100
1 day, 8:26:05.661277 PROGRESS: =========================================================================
1 day, 8:26:05.661838 INFO: Target number of precursors reached.
1 day, 8:26:05.770967 INFO: fragments_df: keeping 5000 of 465380 [sum(precursor_idx_mask)=236512 sum(mass_error_mask)=465380 stop_rank=5000
1 day, 8:26:05.796664 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:26:07.098368 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:26:08.397476 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:26:09.722708 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:26:10.450796 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:26:10.451707 INFO: Using score_cutoff 33.011859375 (fac=0.99, q=1)
1 day, 8:26:10.452450 INFO: Updating optimization_manager: fwhm_rt             : 2.7667999267578125 -> 2.757469654083252
1 day, 8:26:10.452565 INFO: Updating optimization_manager: fwhm_mobility       : 0.007782429456710815 -> 0.007723238319158554
1 day, 8:26:10.452635 INFO: Updating optimization_manager: score_cutoff        : 33.391488520431515 -> 33.011859375
1 day, 8:26:10.452772 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:26:10.456088 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:26:10.466050 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:26:10.468652 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:26:10.490138 INFO: === checking if optimization conditions were reached ===
1 day, 8:26:10.490398 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 8:26:10.498391 INFO: Updating optimization_manager: rt_error            : 15.206556035019132 -> 12.74445080408782
1 day, 8:26:10.498565 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 12.7445.
1 day, 8:26:10.498673 INFO: ==============================================
1 day, 8:26:10.498779 INFO: Starting optimization step 5.
1 day, 8:26:10.498907 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:26:10.499110 INFO: Using python extraction backend
1 day, 8:26:10.499527 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:26:10.499662 INFO: === Search parameters used ===
1 day, 8:26:10.499750 INFO: rt_error       : 12.74445080408782
1 day, 8:26:10.499870 INFO: mobility_error : 0.1
1 day, 8:26:10.499978 INFO: num_candidates : 3
1 day, 8:26:10.500075 INFO: ms1_error      : 15.0
1 day, 8:26:10.500172 INFO: ms2_error      : 15.0
1 day, 8:26:10.500268 INFO: fwhm_rt        : 2.757469654083252
1 day, 8:26:10.500360 INFO: quant_window   : 3
1 day, 8:26:10.500455 INFO: ==============================================
1 day, 8:26:10.578544 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:26:10.578692 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:26:10.578744 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 8:26:10.578771 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.58
1 day, 8:26:10.579545 INFO: Starting candidate selection
1 day, 8:26:12.158100 INFO: Starting candidate scoring
1 day, 8:26:13.982599 INFO: Finished candidate processing
1 day, 8:26:13.982799 INFO: Collecting candidate features
1 day, 8:26:14.085868 WARNING: intensity_correlation has 19 NaNs ( 0.04 % out of 44619)
1 day, 8:26:14.091432 INFO: Collecting fragment features
1 day, 8:26:14.125661 INFO: Finished candidate scoring
1 day, 8:26:14.151330 INFO: performing precursor FDR with 47 features
1 day, 8:26:14.151496 INFO: Decoy channel: -1
1 day, 8:26:14.151533 INFO: competitive: True
1 day, 8:26:14.166369 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:26:14.174603 WARNING: dropped 3 target PSMs due to missing features
1 day, 8:26:14.174757 WARNING: dropped 16 decoy PSMs due to missing features
1 day, 8:26:14.182352 INFO: Estimating optimal hyperparameters - samples: 35,680, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:26:14.182595 INFO: Using random state 988585 for train-test-split
1 day, 8:26:17.631123 INFO: Test AUC: 0.834
1 day, 8:26:17.631278 INFO: Train AUC: 0.838
1 day, 8:26:17.631312 INFO: AUC difference: 0.56%
1 day, 8:26:17.911095 INFO: Resetting torch num_threads to 128
1 day, 8:26:17.912455 PROGRESS: === Extracted 44619 precursors and 465763 fragments ===
1 day, 8:26:17.913010 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:26:17.914442 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:26:17.914569 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:26:17.914660 PROGRESS: Target precursors: 7,842 (98.02%)
1 day, 8:26:17.914741 PROGRESS: Decoy precursors: 158 (1.98%)
1 day, 8:26:17.914815 PROGRESS: 
1 day, 8:26:17.914886 PROGRESS: Precursor Summary:
1 day, 8:26:17.918123 PROGRESS: Channel   0:	 0.050 FDR: 7,842; 0.010 FDR: 7,715; 0.001 FDR: 7,229
1 day, 8:26:17.918278 PROGRESS: 
1 day, 8:26:17.918362 PROGRESS: Protein Summary:
1 day, 8:26:17.923266 PROGRESS: Channel   0:	 0.050 FDR: 4,337; 0.010 FDR: 4,295; 0.001 FDR: 4,087
1 day, 8:26:17.923407 PROGRESS: =========================================================================
1 day, 8:26:17.923725 INFO: Target number of precursors reached.
1 day, 8:26:18.032996 INFO: fragments_df: keeping 5000 of 465763 [sum(precursor_idx_mask)=234609 sum(mass_error_mask)=465763 stop_rank=5000
1 day, 8:26:18.058111 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:26:19.282023 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:26:20.505737 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:26:21.722750 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:26:22.380369 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:26:22.380961 INFO: Using score_cutoff 33.15230958251953 (fac=0.99, q=1)
1 day, 8:26:22.381500 INFO: Updating optimization_manager: fwhm_rt             : 2.757469654083252 -> 2.750913619995117
1 day, 8:26:22.381594 INFO: Updating optimization_manager: fwhm_mobility       : 0.007723238319158554 -> 0.007738209329545498
1 day, 8:26:22.381663 INFO: Updating optimization_manager: score_cutoff        : 33.011859375 -> 33.15230958251953
1 day, 8:26:22.381753 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:26:22.384674 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:26:22.394559 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:26:22.397056 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:26:22.418395 INFO: === checking if optimization conditions were reached ===
1 day, 8:26:22.418603 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 8:26:22.425587 INFO: Updating optimization_manager: rt_error            : 12.74445080408782 -> 12.127592389092014
1 day, 8:26:22.425760 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 12.1276.
1 day, 8:26:22.425869 INFO: ==============================================
1 day, 8:26:22.425972 INFO: Starting optimization step 6.
1 day, 8:26:22.426066 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:26:22.426156 INFO: Using python extraction backend
1 day, 8:26:22.426312 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:26:22.426406 INFO: === Search parameters used ===
1 day, 8:26:22.426476 INFO: rt_error       : 12.127592389092014
1 day, 8:26:22.426540 INFO: mobility_error : 0.1
1 day, 8:26:22.426611 INFO: num_candidates : 3
1 day, 8:26:22.426677 INFO: ms1_error      : 15.0
1 day, 8:26:22.426779 INFO: ms2_error      : 15.0
1 day, 8:26:22.426867 INFO: fwhm_rt        : 2.750913619995117
1 day, 8:26:22.426955 INFO: quant_window   : 3
1 day, 8:26:22.427041 INFO: ==============================================
1 day, 8:26:22.433659 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:26:22.433790 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:26:22.433855 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 8:26:22.433898 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.59
1 day, 8:26:22.434852 INFO: Starting candidate selection
1 day, 8:26:24.128859 INFO: Starting candidate scoring
1 day, 8:26:25.882323 INFO: Finished candidate processing
1 day, 8:26:25.882580 INFO: Collecting candidate features
1 day, 8:26:25.987175 WARNING: intensity_correlation has 20 NaNs ( 0.04 % out of 44618)
1 day, 8:26:25.993056 INFO: Collecting fragment features
1 day, 8:26:26.022287 INFO: Finished candidate scoring
1 day, 8:26:26.052498 INFO: performing precursor FDR with 47 features
1 day, 8:26:26.052663 INFO: Decoy channel: -1
1 day, 8:26:26.052692 INFO: competitive: True
1 day, 8:26:26.068438 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:26:26.078896 WARNING: dropped 4 target PSMs due to missing features
1 day, 8:26:26.079073 WARNING: dropped 16 decoy PSMs due to missing features
1 day, 8:26:26.088132 INFO: Estimating optimal hyperparameters - samples: 35,678, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:26:26.088396 INFO: Using random state 988585 for train-test-split
1 day, 8:26:30.426644 INFO: Test AUC: 0.833
1 day, 8:26:30.426847 INFO: Train AUC: 0.839
1 day, 8:26:30.426893 INFO: AUC difference: 0.69%
1 day, 8:26:30.720831 INFO: Resetting torch num_threads to 128
1 day, 8:26:30.722768 PROGRESS: === Extracted 44618 precursors and 465822 fragments ===
1 day, 8:26:30.723470 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:26:30.725188 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:26:30.725308 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:26:30.725387 PROGRESS: Target precursors: 7,862 (98.28%)
1 day, 8:26:30.725455 PROGRESS: Decoy precursors: 138 (1.73%)
1 day, 8:26:30.725517 PROGRESS: 
1 day, 8:26:30.725575 PROGRESS: Precursor Summary:
1 day, 8:26:30.729063 PROGRESS: Channel   0:	 0.050 FDR: 7,862; 0.010 FDR: 7,755; 0.001 FDR: 7,425
1 day, 8:26:30.729199 PROGRESS: 
1 day, 8:26:30.729284 PROGRESS: Protein Summary:
1 day, 8:26:30.734637 PROGRESS: Channel   0:	 0.050 FDR: 4,347; 0.010 FDR: 4,305; 0.001 FDR: 4,154
1 day, 8:26:30.734778 PROGRESS: =========================================================================
1 day, 8:26:30.735214 INFO: Target number of precursors reached.
1 day, 8:26:30.848639 INFO: fragments_df: keeping 5000 of 465822 [sum(precursor_idx_mask)=235906 sum(mass_error_mask)=465822 stop_rank=5000
1 day, 8:26:30.871147 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:26:32.119616 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:26:33.364948 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:26:34.602765 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:26:35.268755 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:26:35.269455 INFO: Using score_cutoff 32.57710260314941 (fac=0.99, q=1)
1 day, 8:26:35.270113 INFO: Updating optimization_manager: fwhm_rt             : 2.750913619995117 -> 2.7516562938690186
1 day, 8:26:35.270225 INFO: Updating optimization_manager: fwhm_mobility       : 0.007738209329545498 -> 0.007705347612500191
1 day, 8:26:35.270307 INFO: Updating optimization_manager: score_cutoff        : 33.15230958251953 -> 32.57710260314941
1 day, 8:26:35.270400 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:26:35.273607 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:26:35.283675 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:26:35.286374 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:26:35.307678 INFO: === checking if optimization conditions were reached ===
1 day, 8:26:35.307929 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 8:26:35.309561 INFO: Updating optimization_manager: rt_error            : 12.127592389092014 -> 12.127592389092014
1 day, 8:26:35.309731 INFO: Updating optimization_manager: classifier_version  : 2 -> 9
1 day, 8:26:35.309883 INFO: Updating optimization_manager: score_cutoff        : 32.57710260314941 -> 32.57710260314941
1 day, 8:26:35.310012 INFO: Updating optimization_manager: fwhm_rt             : 2.7516562938690186 -> 2.7516562938690186
1 day, 8:26:35.310138 INFO: Updating optimization_manager: fwhm_mobility       : 0.007705347612500191 -> 0.007705347612500191
1 day, 8:26:35.310262 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 12.1276 found after 7 searches.
1 day, 8:26:35.310362 INFO: ==============================================
1 day, 8:26:35.310473 PROGRESS: Optimization finished for rt_error.
1 day, 8:26:35.332814 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:26:35.335922 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:26:35.345791 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:26:35.348288 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:26:35.369599 INFO: Starting optimization step 0.
1 day, 8:26:35.369830 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:26:35.369969 INFO: Using python extraction backend
1 day, 8:26:35.370238 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:26:35.370347 INFO: === Search parameters used ===
1 day, 8:26:35.370423 INFO: rt_error       : 12.127592389092014
1 day, 8:26:35.370489 INFO: mobility_error : 0.1
1 day, 8:26:35.370553 INFO: num_candidates : 3
1 day, 8:26:35.370618 INFO: ms1_error      : 15.0
1 day, 8:26:35.370679 INFO: ms2_error      : 15.0
1 day, 8:26:35.370739 INFO: fwhm_rt        : 2.7516562938690186
1 day, 8:26:35.370797 INFO: quant_window   : 3
1 day, 8:26:35.370854 INFO: ==============================================
1 day, 8:26:35.375910 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:26:35.375987 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:26:35.376033 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 8:26:35.376061 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
1 day, 8:26:35.376868 INFO: Starting candidate selection
1 day, 8:26:36.988221 INFO: Starting candidate scoring
1 day, 8:26:38.808354 INFO: Finished candidate processing
1 day, 8:26:38.808559 INFO: Collecting candidate features
1 day, 8:26:38.865511 WARNING: intensity_correlation has 20 NaNs ( 0.04 % out of 44632)
1 day, 8:26:38.865870 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 44632)
1 day, 8:26:38.870902 INFO: Collecting fragment features
1 day, 8:26:38.895898 INFO: Finished candidate scoring
1 day, 8:26:38.917674 INFO: performing precursor FDR with 47 features
1 day, 8:26:38.917841 INFO: Decoy channel: -1
1 day, 8:26:38.917872 INFO: competitive: True
1 day, 8:26:38.929568 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:26:38.937101 WARNING: dropped 4 target PSMs due to missing features
1 day, 8:26:38.937234 WARNING: dropped 17 decoy PSMs due to missing features
1 day, 8:26:38.943729 INFO: Estimating optimal hyperparameters - samples: 35,688, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:26:38.943927 INFO: Using random state 834833 for train-test-split
1 day, 8:26:42.384692 INFO: Test AUC: 0.846
1 day, 8:26:42.384849 INFO: Train AUC: 0.849
1 day, 8:26:42.384881 INFO: AUC difference: 0.28%
1 day, 8:26:42.667070 INFO: Resetting torch num_threads to 128
1 day, 8:26:42.668502 PROGRESS: === Extracted 44632 precursors and 465918 fragments ===
1 day, 8:26:42.669077 INFO: === FDR correction performed with classifier version 9 ===
1 day, 8:26:42.670527 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:26:42.670655 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:26:42.670741 PROGRESS: Target precursors: 7,867 (98.34%)
1 day, 8:26:42.670820 PROGRESS: Decoy precursors: 133 (1.66%)
1 day, 8:26:42.670892 PROGRESS: 
1 day, 8:26:42.670961 PROGRESS: Precursor Summary:
1 day, 8:26:42.674112 PROGRESS: Channel   0:	 0.050 FDR: 7,867; 0.010 FDR: 7,773; 0.001 FDR: 7,440
1 day, 8:26:42.674250 PROGRESS: 
1 day, 8:26:42.674342 PROGRESS: Protein Summary:
1 day, 8:26:42.679231 PROGRESS: Channel   0:	 0.050 FDR: 4,346; 0.010 FDR: 4,309; 0.001 FDR: 4,168
1 day, 8:26:42.679390 PROGRESS: =========================================================================
1 day, 8:26:42.679631 INFO: Target number of precursors reached.
1 day, 8:26:42.787047 INFO: fragments_df: keeping 5000 of 465918 [sum(precursor_idx_mask)=236528 sum(mass_error_mask)=465918 stop_rank=5000
1 day, 8:26:42.803643 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:26:44.039015 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:26:45.280564 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:26:46.513180 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:26:47.174510 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:26:47.175098 INFO: Using score_cutoff 32.392004054260255 (fac=0.99, q=1)
1 day, 8:26:47.175637 INFO: Updating optimization_manager: fwhm_rt             : 2.7516562938690186 -> 2.7529428005218506
1 day, 8:26:47.175736 INFO: Updating optimization_manager: fwhm_mobility       : 0.007705347612500191 -> 0.00774299306795001
1 day, 8:26:47.175803 INFO: Updating optimization_manager: score_cutoff        : 32.57710260314941 -> 32.392004054260255
1 day, 8:26:47.175875 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:26:47.178696 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:26:47.188522 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:26:47.191035 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:26:47.210379 INFO: === checking if optimization conditions were reached ===
1 day, 8:26:47.210588 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 8:26:47.213734 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07613335635092106
1 day, 8:26:47.213910 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0761.
1 day, 8:26:47.214008 INFO: ==============================================
1 day, 8:26:47.214107 INFO: Starting optimization step 1.
1 day, 8:26:47.214192 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:26:47.214319 INFO: Using python extraction backend
1 day, 8:26:47.214506 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:26:47.214604 INFO: === Search parameters used ===
1 day, 8:26:47.214700 INFO: rt_error       : 12.127592389092014
1 day, 8:26:47.214787 INFO: mobility_error : 0.07613335635092106
1 day, 8:26:47.214873 INFO: num_candidates : 3
1 day, 8:26:47.214957 INFO: ms1_error      : 15.0
1 day, 8:26:47.215040 INFO: ms2_error      : 15.0
1 day, 8:26:47.215107 INFO: fwhm_rt        : 2.7529428005218506
1 day, 8:26:47.215172 INFO: quant_window   : 3
1 day, 8:26:47.215237 INFO: ==============================================
1 day, 8:26:47.221291 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:26:47.221365 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:26:47.221442 INFO: FWHM in RT is 2.75 seconds, sigma is 0.61
1 day, 8:26:47.221474 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.59
1 day, 8:26:47.222482 INFO: Starting candidate selection
1 day, 8:26:48.655447 INFO: Starting candidate scoring
1 day, 8:26:50.394465 INFO: Finished candidate processing
1 day, 8:26:50.394595 INFO: Collecting candidate features
1 day, 8:26:50.451211 WARNING: intensity_correlation has 24 NaNs ( 0.05 % out of 44520)
1 day, 8:26:50.451516 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 44520)
1 day, 8:26:50.456601 INFO: Collecting fragment features
1 day, 8:26:50.482338 INFO: Finished candidate scoring
1 day, 8:26:50.504548 INFO: performing precursor FDR with 47 features
1 day, 8:26:50.504704 INFO: Decoy channel: -1
1 day, 8:26:50.504731 INFO: competitive: True
1 day, 8:26:50.517162 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:26:50.525021 WARNING: dropped 4 target PSMs due to missing features
1 day, 8:26:50.525165 WARNING: dropped 21 decoy PSMs due to missing features
1 day, 8:26:50.531928 INFO: Estimating optimal hyperparameters - samples: 35,596, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:26:50.532146 INFO: Using random state 834833 for train-test-split
1 day, 8:26:53.969908 INFO: Test AUC: 0.841
1 day, 8:26:53.970058 INFO: Train AUC: 0.849
1 day, 8:26:53.970091 INFO: AUC difference: 0.92%
1 day, 8:26:54.252002 INFO: Resetting torch num_threads to 128
1 day, 8:26:54.253356 PROGRESS: === Extracted 44520 precursors and 463091 fragments ===
1 day, 8:26:54.253912 INFO: === FDR correction performed with classifier version 9 ===
1 day, 8:26:54.255310 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:26:54.255430 PROGRESS: Total precursors accumulated: 7,990
1 day, 8:26:54.255507 PROGRESS: Target precursors: 7,842 (98.15%)
1 day, 8:26:54.255582 PROGRESS: Decoy precursors: 148 (1.85%)
1 day, 8:26:54.255643 PROGRESS: 
1 day, 8:26:54.255704 PROGRESS: Precursor Summary:
1 day, 8:26:54.258897 PROGRESS: Channel   0:	 0.050 FDR: 7,842; 0.010 FDR: 7,734; 0.001 FDR: 7,387
1 day, 8:26:54.259026 PROGRESS: 
1 day, 8:26:54.259098 PROGRESS: Protein Summary:
1 day, 8:26:54.264268 PROGRESS: Channel   0:	 0.050 FDR: 4,338; 0.010 FDR: 4,299; 0.001 FDR: 4,142
1 day, 8:26:54.264399 PROGRESS: =========================================================================
1 day, 8:26:54.264661 INFO: Target number of precursors reached.
1 day, 8:26:54.371159 INFO: fragments_df: keeping 5000 of 463091 [sum(precursor_idx_mask)=234640 sum(mass_error_mask)=463087 stop_rank=5000
1 day, 8:26:54.387920 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:26:55.675329 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:26:56.970398 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:26:58.262506 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:26:58.987381 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:26:58.987975 INFO: Using score_cutoff 32.16681863250733 (fac=0.99, q=1)
1 day, 8:26:58.988531 INFO: Updating optimization_manager: fwhm_rt             : 2.7529428005218506 -> 2.760291337966919
1 day, 8:26:58.988631 INFO: Updating optimization_manager: fwhm_mobility       : 0.00774299306795001 -> 0.00775607954710722
1 day, 8:26:58.988699 INFO: Updating optimization_manager: score_cutoff        : 32.392004054260255 -> 32.16681863250733
1 day, 8:26:58.988771 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:26:58.991710 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:26:59.001573 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:26:59.004094 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:26:59.024930 INFO: === checking if optimization conditions were reached ===
1 day, 8:26:59.025178 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 8:26:59.028467 INFO: Updating optimization_manager: mobility_error      : 0.07613335635092106 -> 0.06321494291283064
1 day, 8:26:59.028620 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0632.
1 day, 8:26:59.028716 INFO: ==============================================
1 day, 8:26:59.028824 INFO: Starting optimization step 2.
1 day, 8:26:59.028914 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:26:59.029038 INFO: Using python extraction backend
1 day, 8:26:59.029228 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:26:59.029354 INFO: === Search parameters used ===
1 day, 8:26:59.029451 INFO: rt_error       : 12.127592389092014
1 day, 8:26:59.029538 INFO: mobility_error : 0.06321494291283064
1 day, 8:26:59.029625 INFO: num_candidates : 3
1 day, 8:26:59.029708 INFO: ms1_error      : 15.0
1 day, 8:26:59.029809 INFO: ms2_error      : 15.0
1 day, 8:26:59.029900 INFO: fwhm_rt        : 2.760291337966919
1 day, 8:26:59.029985 INFO: quant_window   : 3
1 day, 8:26:59.030077 INFO: ==============================================
1 day, 8:26:59.036136 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:26:59.036246 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:26:59.036313 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 8:26:59.036358 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.60
1 day, 8:26:59.037353 INFO: Starting candidate selection
1 day, 8:27:00.361127 INFO: Starting candidate scoring
1 day, 8:27:02.163564 INFO: Finished candidate processing
1 day, 8:27:02.163802 INFO: Collecting candidate features
1 day, 8:27:02.232327 WARNING: intensity_correlation has 30 NaNs ( 0.07 % out of 44425)
1 day, 8:27:02.232664 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 44425)
1 day, 8:27:02.237841 INFO: Collecting fragment features
1 day, 8:27:02.264267 INFO: Finished candidate scoring
1 day, 8:27:02.284031 INFO: performing precursor FDR with 47 features
1 day, 8:27:02.284184 INFO: Decoy channel: -1
1 day, 8:27:02.284211 INFO: competitive: True
1 day, 8:27:02.296486 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:27:02.304358 WARNING: dropped 3 target PSMs due to missing features
1 day, 8:27:02.304500 WARNING: dropped 28 decoy PSMs due to missing features
1 day, 8:27:02.311234 INFO: Estimating optimal hyperparameters - samples: 35,515, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:27:02.311453 INFO: Using random state 834833 for train-test-split
1 day, 8:27:05.694555 INFO: Test AUC: 0.842
1 day, 8:27:05.694705 INFO: Train AUC: 0.850
1 day, 8:27:05.694737 INFO: AUC difference: 0.98%
1 day, 8:27:05.972084 INFO: Resetting torch num_threads to 128
1 day, 8:27:05.973408 PROGRESS: === Extracted 44425 precursors and 459747 fragments ===
1 day, 8:27:05.973954 INFO: === FDR correction performed with classifier version 9 ===
1 day, 8:27:05.975406 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:27:05.975523 PROGRESS: Total precursors accumulated: 7,983
1 day, 8:27:05.975614 PROGRESS: Target precursors: 7,830 (98.08%)
1 day, 8:27:05.975694 PROGRESS: Decoy precursors: 153 (1.92%)
1 day, 8:27:05.975765 PROGRESS: 
1 day, 8:27:05.975830 PROGRESS: Precursor Summary:
1 day, 8:27:05.979001 PROGRESS: Channel   0:	 0.050 FDR: 7,830; 0.010 FDR: 7,698; 0.001 FDR: 7,323
1 day, 8:27:05.979140 PROGRESS: 
1 day, 8:27:05.979223 PROGRESS: Protein Summary:
1 day, 8:27:05.984048 PROGRESS: Channel   0:	 0.050 FDR: 4,331; 0.010 FDR: 4,280; 0.001 FDR: 4,129
1 day, 8:27:05.984194 PROGRESS: =========================================================================
1 day, 8:27:05.984435 INFO: Target number of precursors reached.
1 day, 8:27:06.089590 INFO: fragments_df: keeping 5000 of 459747 [sum(precursor_idx_mask)=232645 sum(mass_error_mask)=459747 stop_rank=5000
1 day, 8:27:06.106232 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:27:07.383990 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:27:08.669790 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:27:09.948558 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:27:10.670540 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:27:10.671147 INFO: Using score_cutoff 31.623719449424744 (fac=0.99, q=1)
1 day, 8:27:10.671696 INFO: Updating optimization_manager: fwhm_rt             : 2.760291337966919 -> 2.7608699798583984
1 day, 8:27:10.671794 INFO: Updating optimization_manager: fwhm_mobility       : 0.00775607954710722 -> 0.0077655017375946045
1 day, 8:27:10.671863 INFO: Updating optimization_manager: score_cutoff        : 32.16681863250733 -> 31.623719449424744
1 day, 8:27:10.671938 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:27:10.674821 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:27:10.684615 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:27:10.687097 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:27:10.708102 INFO: === checking if optimization conditions were reached ===
1 day, 8:27:10.708322 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 8:27:10.709490 INFO: Updating optimization_manager: mobility_error      : 0.06321494291283064 -> 0.1
1 day, 8:27:10.709672 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1 day, 8:27:10.709831 INFO: Updating optimization_manager: score_cutoff        : 31.623719449424744 -> 32.392004054260255
1 day, 8:27:10.709975 INFO: Updating optimization_manager: fwhm_rt             : 2.7608699798583984 -> 2.7529428005218506
1 day, 8:27:10.710120 INFO: Updating optimization_manager: fwhm_mobility       : 0.0077655017375946045 -> 0.00774299306795001
1 day, 8:27:10.710253 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 8:27:10.710349 INFO: ==============================================
1 day, 8:27:10.710458 PROGRESS: Optimization finished for mobility_error.
1 day, 8:27:10.733050 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:27:10.736369 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:27:10.746907 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:27:10.749771 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:27:10.772269 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 8:27:10.772553 PROGRESS: ==============================================
1 day, 8:27:10.772681 PROGRESS: ms2_error      : 15.0000
1 day, 8:27:10.772792 PROGRESS: ms1_error      : 15.0000
1 day, 8:27:10.772899 PROGRESS: rt_error       : 12.1276
1 day, 8:27:10.772999 PROGRESS: mobility_error : 0.1000
1 day, 8:27:10.773096 PROGRESS: ==============================================
1 day, 8:27:10.774530 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:27:10.799258 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:27:10.905589 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:27:10.928029 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:27:11.182695 INFO: Using python extraction backend
1 day, 8:27:11.183233 PROGRESS: Extracting batch of 182033 precursors
1 day, 8:27:11.183387 INFO: === Search parameters used ===
1 day, 8:27:11.183497 INFO: rt_error       : 12.127592389092014
1 day, 8:27:11.183608 INFO: mobility_error : 0.1
1 day, 8:27:11.183707 INFO: num_candidates : 3
1 day, 8:27:11.183799 INFO: ms1_error      : 15.0
1 day, 8:27:11.183885 INFO: ms2_error      : 15.0
1 day, 8:27:11.183967 INFO: fwhm_rt        : 2.7529428005218506
1 day, 8:27:11.184049 INFO: quant_window   : 3
1 day, 8:27:11.184129 INFO: ==============================================
1 day, 8:27:11.230999 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:27:11.231168 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:27:11.231216 INFO: FWHM in RT is 2.75 seconds, sigma is 0.61
1 day, 8:27:11.231241 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.59
1 day, 8:27:11.232029 INFO: Starting candidate selection
1 day, 8:27:24.266802 INFO: Removed 83414 precursors with score below cutoff 32.392004054260255
1 day, 8:27:24.623199 INFO: Starting candidate scoring
1 day, 8:27:40.771465 INFO: Finished candidate processing
1 day, 8:27:40.771611 INFO: Collecting candidate features
1 day, 8:27:41.472240 WARNING: intensity_correlation has 3 NaNs ( 0.00 % out of 427958)
1 day, 8:27:41.488622 INFO: Collecting fragment features
1 day, 8:27:41.731803 INFO: Finished candidate scoring
1 day, 8:27:41.931868 INFO: === Performing FDR correction with classifier version 10 ===
1 day, 8:27:41.932493 INFO: performing precursor FDR with 47 features
1 day, 8:27:41.932547 INFO: Decoy channel: -1
1 day, 8:27:41.932578 INFO: competitive: True
1 day, 8:27:42.025970 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:27:42.078716 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 8:27:42.078926 WARNING: FDR calculation for 236972 target and 190983 decoy PSMs
1 day, 8:27:42.078955 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 8:27:42.198647 INFO: Estimating optimal hyperparameters - samples: 342,364, batch_size: 1,402, learning_rate: 5.85e-04
1 day, 8:27:42.199391 INFO: Using random state 367214 for train-test-split
1 day, 8:27:52.152962 INFO: Test AUC: 0.861
1 day, 8:27:52.153159 INFO: Train AUC: 0.865
1 day, 8:27:52.153193 INFO: AUC difference: 0.55%
1 day, 8:27:52.551795 INFO: Resetting torch num_threads to 128
1 day, 8:27:52.574543 INFO: Removing fragments below FDR threshold
1 day, 8:27:52.678099 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:27:52.678430 PROGRESS: Total precursors accumulated: 89,419
1 day, 8:27:52.678508 PROGRESS: Target precursors: 88,534 (99.01%)
1 day, 8:27:52.678572 PROGRESS: Decoy precursors: 885 (0.99%)
1 day, 8:27:52.678648 PROGRESS: 
1 day, 8:27:52.678712 PROGRESS: Precursor Summary:
1 day, 8:27:52.719083 PROGRESS: Channel   0:	 0.050 FDR: 88,534; 0.010 FDR: 88,534; 0.001 FDR: 85,207
1 day, 8:27:52.719435 PROGRESS: 
1 day, 8:27:52.719547 PROGRESS: Protein Summary:
1 day, 8:27:52.777220 PROGRESS: Channel   0:	 0.050 FDR: 8,969; 0.010 FDR: 8,969; 0.001 FDR: 8,945
1 day, 8:27:52.777565 PROGRESS: =========================================================================
1 day, 8:27:52.788362 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/psm.parquet
1 day, 8:27:53.121607 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/frag.parquet
1 day, 8:27:53.415516 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 8:27:53.481059 PROGRESS: Loading raw file 3/6: ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506 
1 day, 8:27:53.481272 INFO: Quantification results path: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant
1 day, 8:27:53.481375 INFO: Creating folder /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/figures
1 day, 8:27:53.481589 INFO: Initializing TimingManager
1 day, 8:27:53.482167 INFO: Initializing RawFileManager
1 day, 8:27:53.482336 INFO: Importing data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 8:27:53.482392 INFO: Using .d import for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 8:27:53.482434 INFO: Reading frame metadata for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 8:27:55.223288 INFO: Reading 39,128 frames with 2,897,842,446 detector events for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 8:28:45.334746 INFO: Indexing /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d...
1 day, 8:28:45.336802 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 8:28:45.338753 INFO: Fetching mobility values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 8:28:45.338978 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 8:28:45.339366 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 8:28:45.340553 INFO: Fetching mz values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 8:28:45.370013 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 8:28:45.370491 INFO: Indexing quadrupole dimension
1 day, 8:28:45.908171 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 8:28:45.908355 INFO: Transposing detector events
1 day, 8:28:54.892394 INFO: Finished transposing data
1 day, 8:28:54.968034 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506.d
1 day, 8:28:54.968969 INFO: RT (min)            : 0.0 - 70.0
1 day, 8:28:54.969041 INFO: RT duration (sec)   : 4199.8
1 day, 8:28:54.969088 INFO: RT duration (min)   : 70.0
1 day, 8:28:54.969123 INFO: Cycle len (scans)   : 9
1 day, 8:28:54.969151 INFO: Cycle len (sec)     : 0.97
1 day, 8:28:54.969171 INFO: Number of cycles    : 4347
1 day, 8:28:54.969190 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 8:28:54.969263 INFO: Creating DIA data object took: 61.48696708679199
1 day, 8:28:55.035892 INFO: Initializing CalibrationManager
1 day, 8:28:55.036288 INFO: Setting up calibration estimators ..
1 day, 8:28:55.036372 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 8:28:55.036490 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, 8:28:55.036633 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 8:28:55.036724 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, 8:28:55.036811 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, 8:28:55.036899 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, 8:28:55.036973 INFO: Done setting up calibration estimators.
1 day, 8:28:55.037124 INFO: Initializing OptimizationManager
1 day, 8:28:55.037300 INFO: initial parameter: ms1_error = 30
1 day, 8:28:55.037376 INFO: initial parameter: ms2_error = 30
1 day, 8:28:55.037448 INFO: initial parameter: rt_error = 2099.8992935
1 day, 8:28:55.037517 INFO: initial parameter: mobility_error = 0.1
1 day, 8:28:55.037583 INFO: initial parameter: num_candidates = 1
1 day, 8:28:55.037649 INFO: initial parameter: fwhm_rt = 5
1 day, 8:28:55.037714 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 8:28:55.037794 INFO: initial parameter: score_cutoff = 0
1 day, 8:28:55.037867 INFO: initial parameter: classifier_version = -1
1 day, 8:28:55.037975 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 8:28:55.038278 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 8:28:55.038321 INFO: Initializing FDRManager
1 day, 8:28:55.038379 INFO: Loading classifier store from /usr/local/lib/python3.10/site-packages/alphadia/constants/classifier
1 day, 8:28:55.068933 PROGRESS: Initializing spectral library: 91,740 target precursors potentially observable (0 removed)
1 day, 8:28:55.110064 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 8:28:55.110727 INFO: Updating optimization_manager: rt_error            : 2099.8992935 -> 2099.8992935
1 day, 8:28:55.110864 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 8:28:55.111101 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 8:28:55.111226 PROGRESS: Starting initial search for precursors.
1 day, 8:28:55.111362 INFO: Starting optimization step 0.
1 day, 8:28:55.111470 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:28:55.111584 INFO: Using python extraction backend
1 day, 8:28:55.111848 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:28:55.111960 INFO: === Search parameters used ===
1 day, 8:28:55.112048 INFO: rt_error       : 2099.8992935
1 day, 8:28:55.112128 INFO: mobility_error : 0.1
1 day, 8:28:55.112205 INFO: num_candidates : 1
1 day, 8:28:55.112278 INFO: ms1_error      : 30
1 day, 8:28:55.112350 INFO: ms2_error      : 30
1 day, 8:28:55.112420 INFO: fwhm_rt        : 5
1 day, 8:28:55.112490 INFO: quant_window   : 3
1 day, 8:28:55.112571 INFO: ==============================================
1 day, 8:28:55.115972 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:28:55.116040 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:28:55.116110 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 8:28:55.116146 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 8:28:55.117504 INFO: Starting candidate selection
1 day, 8:30:30.770097 INFO: Starting candidate scoring
1 day, 8:30:32.417545 INFO: Finished candidate processing
1 day, 8:30:32.417786 INFO: Collecting candidate features
1 day, 8:30:32.482848 INFO: Collecting fragment features
1 day, 8:30:32.495008 INFO: Finished candidate scoring
1 day, 8:30:32.504550 INFO: performing precursor FDR with 47 features
1 day, 8:30:32.504673 INFO: Decoy channel: -1
1 day, 8:30:32.504707 INFO: competitive: True
1 day, 8:30:32.509510 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:30:32.514957 INFO: Estimating optimal hyperparameters - samples: 12,692, batch_size: 128, learning_rate: 1.77e-04
1 day, 8:30:32.515855 INFO: Using random state 320242 for train-test-split
1 day, 8:30:33.926826 INFO: Test AUC: 0.841
1 day, 8:30:33.927018 INFO: Train AUC: 0.843
1 day, 8:30:33.927056 INFO: AUC difference: 0.24%
1 day, 8:30:34.201663 INFO: Resetting torch num_threads to 128
1 day, 8:30:34.203059 PROGRESS: === Extracted 15866 precursors and 179936 fragments ===
1 day, 8:30:34.203728 INFO: === FDR correction performed with classifier version -1 ===
1 day, 8:30:34.205433 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:30:34.205547 PROGRESS: Total precursors accumulated: 7,994
1 day, 8:30:34.205619 PROGRESS: Target precursors: 6,735 (84.25%)
1 day, 8:30:34.205681 PROGRESS: Decoy precursors: 1,259 (15.75%)
1 day, 8:30:34.205739 PROGRESS: 
1 day, 8:30:34.205806 PROGRESS: Precursor Summary:
1 day, 8:30:34.208227 PROGRESS: Channel   0:	 0.050 FDR: 5,102; 0.010 FDR: 4,503; 0.001 FDR: 3,337
1 day, 8:30:34.208346 PROGRESS: 
1 day, 8:30:34.208426 PROGRESS: Protein Summary:
1 day, 8:30:34.211903 PROGRESS: Channel   0:	 0.050 FDR: 3,104; 0.010 FDR: 2,805; 0.001 FDR: 2,198
1 day, 8:30:34.212022 PROGRESS: =========================================================================
1 day, 8:30:34.212189 INFO: Target number of precursors reached.
1 day, 8:30:34.242070 INFO: fragments_df: keeping 5000 of 179936 [sum(precursor_idx_mask)=51034 sum(mass_error_mask)=179936 stop_rank=5000
1 day, 8:30:34.268330 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:30:34.856661 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:30:35.447714 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:30:36.028723 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:30:36.686839 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 8:30:36.687454 INFO: Using score_cutoff 48.98750717010498 (fac=0.99, q=1)
1 day, 8:30:36.687976 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.1158716678619385
1 day, 8:30:36.688073 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.01032501831650734
1 day, 8:30:36.688158 INFO: Updating optimization_manager: score_cutoff        : 0 -> 48.98750717010498
1 day, 8:30:36.688248 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:30:36.691634 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:30:36.701868 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:30:36.704398 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:30:36.726452 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
1 day, 8:30:36.726689 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 8:30:36.726831 INFO: Starting optimization step 1.
1 day, 8:30:36.726935 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:30:36.727047 INFO: Using python extraction backend
1 day, 8:30:36.727252 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:30:36.727359 INFO: === Search parameters used ===
1 day, 8:30:36.727439 INFO: rt_error       : 2099.8992935
1 day, 8:30:36.727513 INFO: mobility_error : 0.1
1 day, 8:30:36.727587 INFO: num_candidates : 3
1 day, 8:30:36.727657 INFO: ms1_error      : 30
1 day, 8:30:36.727727 INFO: ms2_error      : 30
1 day, 8:30:36.727796 INFO: fwhm_rt        : 3.1158716678619385
1 day, 8:30:36.727865 INFO: quant_window   : 3
1 day, 8:30:36.727936 INFO: ==============================================
1 day, 8:30:36.738365 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:30:36.738457 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:30:36.738516 INFO: FWHM in RT is 3.12 seconds, sigma is 0.68
1 day, 8:30:36.738548 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.79
1 day, 8:30:36.739589 INFO: Starting candidate selection
1 day, 8:32:19.831244 INFO: Starting candidate scoring
1 day, 8:32:23.385420 INFO: Finished candidate processing
1 day, 8:32:23.385552 INFO: Collecting candidate features
1 day, 8:32:23.470327 INFO: Collecting fragment features
1 day, 8:32:23.497006 INFO: Finished candidate scoring
1 day, 8:32:23.525538 INFO: performing precursor FDR with 47 features
1 day, 8:32:23.525687 INFO: Decoy channel: -1
1 day, 8:32:23.525720 INFO: competitive: True
1 day, 8:32:23.540096 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:32:23.554271 INFO: Estimating optimal hyperparameters - samples: 36,135, batch_size: 148, learning_rate: 1.90e-04
1 day, 8:32:23.554609 INFO: Using random state 590039 for train-test-split
1 day, 8:32:27.014164 INFO: Test AUC: 0.710
1 day, 8:32:27.014337 INFO: Train AUC: 0.721
1 day, 8:32:27.014371 INFO: AUC difference: 1.55%
1 day, 8:32:27.298538 INFO: Resetting torch num_threads to 128
1 day, 8:32:27.300227 PROGRESS: === Extracted 45169 precursors and 511776 fragments ===
1 day, 8:32:27.300840 INFO: === FDR correction performed with classifier version 0 ===
1 day, 8:32:27.302411 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:32:27.302525 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:32:27.302604 PROGRESS: Target precursors: 7,068 (88.35%)
1 day, 8:32:27.302668 PROGRESS: Decoy precursors: 932 (11.65%)
1 day, 8:32:27.302729 PROGRESS: 
1 day, 8:32:27.302792 PROGRESS: Precursor Summary:
1 day, 8:32:27.305443 PROGRESS: Channel   0:	 0.050 FDR: 5,971; 0.010 FDR: 5,285; 0.001 FDR: 4,541
1 day, 8:32:27.305563 PROGRESS: 
1 day, 8:32:27.305633 PROGRESS: Protein Summary:
1 day, 8:32:27.309595 PROGRESS: Channel   0:	 0.050 FDR: 3,523; 0.010 FDR: 3,192; 0.001 FDR: 2,849
1 day, 8:32:27.309713 PROGRESS: =========================================================================
1 day, 8:32:27.310174 INFO: Target number of precursors reached.
1 day, 8:32:27.401937 INFO: fragments_df: keeping 5000 of 511776 [sum(precursor_idx_mask)=172310 sum(mass_error_mask)=511776 stop_rank=5000
1 day, 8:32:27.425379 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:32:28.205002 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:32:28.995551 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:32:29.770401 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:32:30.486701 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:32:30.487277 INFO: Using score_cutoff 48.831055265808104 (fac=0.99, q=1)
1 day, 8:32:30.487792 INFO: Updating optimization_manager: fwhm_rt             : 3.1158716678619385 -> 3.0837674140930176
1 day, 8:32:30.487888 INFO: Updating optimization_manager: fwhm_mobility       : 0.01032501831650734 -> 0.010046171955764294
1 day, 8:32:30.487957 INFO: Updating optimization_manager: score_cutoff        : 48.98750717010498 -> 48.831055265808104
1 day, 8:32:30.488049 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:32:30.491029 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:32:30.500889 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:32:30.503417 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:32:30.524478 INFO: === checking if optimization conditions were reached ===
1 day, 8:32:30.526776 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 8:32:30.526929 INFO: Updating optimization_manager: classifier_version  : 0 -> 1
1 day, 8:32:30.527025 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 8:32:30.529102 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 8:32:30.529252 INFO: Updating optimization_manager: classifier_version  : 1 -> 1
1 day, 8:32:30.529341 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 8:32:30.529476 INFO: ==============================================
1 day, 8:32:30.529607 INFO: Starting optimization step 2.
1 day, 8:32:30.529719 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:32:30.529886 INFO: Using python extraction backend
1 day, 8:32:30.530123 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:32:30.530252 INFO: === Search parameters used ===
1 day, 8:32:30.530347 INFO: rt_error       : 2099.8992935
1 day, 8:32:30.530435 INFO: mobility_error : 0.1
1 day, 8:32:30.530522 INFO: num_candidates : 3
1 day, 8:32:30.530604 INFO: ms1_error      : 15.0
1 day, 8:32:30.530689 INFO: ms2_error      : 15.0
1 day, 8:32:30.530782 INFO: fwhm_rt        : 3.0837674140930176
1 day, 8:32:30.530876 INFO: quant_window   : 3
1 day, 8:32:30.530963 INFO: ==============================================
1 day, 8:32:30.537130 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:32:30.537245 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:32:30.537311 INFO: FWHM in RT is 3.08 seconds, sigma is 0.68
1 day, 8:32:30.537360 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.66
1 day, 8:32:30.538436 INFO: Starting candidate selection
1 day, 8:34:03.003283 INFO: Starting candidate scoring
1 day, 8:34:04.990721 INFO: Finished candidate processing
1 day, 8:34:04.990851 INFO: Collecting candidate features
1 day, 8:34:05.056232 INFO: Collecting fragment features
1 day, 8:34:05.081738 INFO: Finished candidate scoring
1 day, 8:34:05.102699 INFO: performing precursor FDR with 47 features
1 day, 8:34:05.102863 INFO: Decoy channel: -1
1 day, 8:34:05.102890 INFO: competitive: True
1 day, 8:34:05.117052 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:34:05.129519 INFO: Estimating optimal hyperparameters - samples: 36,129, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:34:05.129782 INFO: Using random state 869843 for train-test-split
1 day, 8:34:08.676072 INFO: Test AUC: 0.737
1 day, 8:34:08.676240 INFO: Train AUC: 0.754
1 day, 8:34:08.676273 INFO: AUC difference: 2.32%
1 day, 8:34:08.957369 INFO: Resetting torch num_threads to 128
1 day, 8:34:08.959048 PROGRESS: === Extracted 45162 precursors and 499837 fragments ===
1 day, 8:34:08.959579 INFO: === FDR correction performed with classifier version 1 ===
1 day, 8:34:08.961082 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:34:08.961193 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:34:08.961279 PROGRESS: Target precursors: 7,442 (93.03%)
1 day, 8:34:08.961372 PROGRESS: Decoy precursors: 558 (6.98%)
1 day, 8:34:08.961448 PROGRESS: 
1 day, 8:34:08.961514 PROGRESS: Precursor Summary:
1 day, 8:34:08.964489 PROGRESS: Channel   0:	 0.050 FDR: 7,091; 0.010 FDR: 6,513; 0.001 FDR: 6,013
1 day, 8:34:08.964616 PROGRESS: 
1 day, 8:34:08.964705 PROGRESS: Protein Summary:
1 day, 8:34:08.969075 PROGRESS: Channel   0:	 0.050 FDR: 4,028; 0.010 FDR: 3,757; 0.001 FDR: 3,527
1 day, 8:34:08.969202 PROGRESS: =========================================================================
1 day, 8:34:08.969473 INFO: Target number of precursors reached.
1 day, 8:34:09.072361 INFO: fragments_df: keeping 5000 of 499837 [sum(precursor_idx_mask)=206639 sum(mass_error_mask)=499837 stop_rank=5000
1 day, 8:34:09.090896 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:34:10.032256 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:34:11.004676 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:34:11.951820 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:34:12.615791 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:34:12.616409 INFO: Using score_cutoff 42.133755720520014 (fac=0.99, q=1)
1 day, 8:34:12.616935 INFO: Updating optimization_manager: fwhm_rt             : 3.0837674140930176 -> 2.7968976497650146
1 day, 8:34:12.617028 INFO: Updating optimization_manager: fwhm_mobility       : 0.010046171955764294 -> 0.00826218817383051
1 day, 8:34:12.617099 INFO: Updating optimization_manager: score_cutoff        : 48.831055265808104 -> 42.133755720520014
1 day, 8:34:12.617181 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:34:12.620068 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:34:12.629808 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:34:12.632240 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:34:12.653242 INFO: === checking if optimization conditions were reached ===
1 day, 8:34:12.655461 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 8:34:12.655622 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
1 day, 8:34:12.655714 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 8:34:12.658033 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 8:34:12.658173 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
1 day, 8:34:12.658263 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 8:34:12.658342 INFO: ==============================================
1 day, 8:34:12.658434 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 8:34:12.683643 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:34:12.686857 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:34:12.696908 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:34:12.699642 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:34:12.721652 INFO: Starting optimization step 0.
1 day, 8:34:12.721964 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:34:12.722110 INFO: Using python extraction backend
1 day, 8:34:12.722311 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:34:12.722444 INFO: === Search parameters used ===
1 day, 8:34:12.722540 INFO: rt_error       : 2099.8992935
1 day, 8:34:12.722630 INFO: mobility_error : 0.1
1 day, 8:34:12.722718 INFO: num_candidates : 3
1 day, 8:34:12.722805 INFO: ms1_error      : 15.0
1 day, 8:34:12.722889 INFO: ms2_error      : 15.0
1 day, 8:34:12.722971 INFO: fwhm_rt        : 2.7968976497650146
1 day, 8:34:12.723053 INFO: quant_window   : 3
1 day, 8:34:12.723136 INFO: ==============================================
1 day, 8:34:12.728830 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:34:12.728937 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:34:12.729001 INFO: FWHM in RT is 2.80 seconds, sigma is 0.61
1 day, 8:34:12.729048 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.83
1 day, 8:34:12.730003 INFO: Starting candidate selection
1 day, 8:35:44.669205 INFO: Starting candidate scoring
1 day, 8:35:46.818906 INFO: Finished candidate processing
1 day, 8:35:46.819132 INFO: Collecting candidate features
1 day, 8:35:46.914667 INFO: Collecting fragment features
1 day, 8:35:46.940653 INFO: Finished candidate scoring
1 day, 8:35:46.960211 INFO: performing precursor FDR with 47 features
1 day, 8:35:46.960371 INFO: Decoy channel: -1
1 day, 8:35:46.960399 INFO: competitive: True
1 day, 8:35:46.972838 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:35:46.984270 INFO: Estimating optimal hyperparameters - samples: 36,092, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:35:46.984501 INFO: Using random state 880283 for train-test-split
1 day, 8:35:50.556408 INFO: Test AUC: 0.753
1 day, 8:35:50.556581 INFO: Train AUC: 0.766
1 day, 8:35:50.556613 INFO: AUC difference: 1.60%
1 day, 8:35:50.838812 INFO: Resetting torch num_threads to 128
1 day, 8:35:50.840470 PROGRESS: === Extracted 45116 precursors and 497758 fragments ===
1 day, 8:35:50.841028 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:35:50.842512 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:35:50.842629 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:35:50.842712 PROGRESS: Target precursors: 7,465 (93.31%)
1 day, 8:35:50.842781 PROGRESS: Decoy precursors: 535 (6.69%)
1 day, 8:35:50.842841 PROGRESS: 
1 day, 8:35:50.842901 PROGRESS: Precursor Summary:
1 day, 8:35:50.845932 PROGRESS: Channel   0:	 0.050 FDR: 7,181; 0.010 FDR: 6,606; 0.001 FDR: 6,085
1 day, 8:35:50.846059 PROGRESS: 
1 day, 8:35:50.846134 PROGRESS: Protein Summary:
1 day, 8:35:50.850749 PROGRESS: Channel   0:	 0.050 FDR: 4,065; 0.010 FDR: 3,792; 0.001 FDR: 3,561
1 day, 8:35:50.850899 PROGRESS: =========================================================================
1 day, 8:35:50.851206 INFO: Target number of precursors reached.
1 day, 8:35:50.956400 INFO: fragments_df: keeping 5000 of 497758 [sum(precursor_idx_mask)=209032 sum(mass_error_mask)=497758 stop_rank=5000
1 day, 8:35:50.974831 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:35:52.000960 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:35:53.053475 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:35:54.086365 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:35:54.805490 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:35:54.806145 INFO: Using score_cutoff 41.700851875305176 (fac=0.99, q=1)
1 day, 8:35:54.806699 INFO: Updating optimization_manager: fwhm_rt             : 2.7968976497650146 -> 2.7917392253875732
1 day, 8:35:54.806799 INFO: Updating optimization_manager: fwhm_mobility       : 0.00826218817383051 -> 0.008175427094101906
1 day, 8:35:54.806868 INFO: Updating optimization_manager: score_cutoff        : 42.133755720520014 -> 41.700851875305176
1 day, 8:35:54.806951 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:35:54.809835 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:35:54.819550 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:35:54.822135 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:35:54.843121 INFO: === checking if optimization conditions were reached ===
1 day, 8:35:54.843396 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 8:35:54.849614 INFO: Updating optimization_manager: rt_error            : 2099.8992935 -> 377.36934369301315
1 day, 8:35:54.849782 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 377.3693.
1 day, 8:35:54.849894 INFO: ==============================================
1 day, 8:35:54.850001 INFO: Starting optimization step 1.
1 day, 8:35:54.850097 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:35:54.850229 INFO: Using python extraction backend
1 day, 8:35:54.850434 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:35:54.850568 INFO: === Search parameters used ===
1 day, 8:35:54.850672 INFO: rt_error       : 377.36934369301315
1 day, 8:35:54.850770 INFO: mobility_error : 0.1
1 day, 8:35:54.850864 INFO: num_candidates : 3
1 day, 8:35:54.850955 INFO: ms1_error      : 15.0
1 day, 8:35:54.851051 INFO: ms2_error      : 15.0
1 day, 8:35:54.851146 INFO: fwhm_rt        : 2.7917392253875732
1 day, 8:35:54.851259 INFO: quant_window   : 3
1 day, 8:35:54.851352 INFO: ==============================================
1 day, 8:35:54.857262 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:35:54.857374 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:35:54.857437 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1 day, 8:35:54.857492 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 8:35:54.858358 INFO: Starting candidate selection
1 day, 8:36:16.944323 INFO: Starting candidate scoring
1 day, 8:36:18.963690 INFO: Finished candidate processing
1 day, 8:36:18.963893 INFO: Collecting candidate features
1 day, 8:36:19.045569 INFO: Collecting fragment features
1 day, 8:36:19.071133 INFO: Finished candidate scoring
1 day, 8:36:19.093060 INFO: performing precursor FDR with 47 features
1 day, 8:36:19.093225 INFO: Decoy channel: -1
1 day, 8:36:19.093252 INFO: competitive: True
1 day, 8:36:19.106850 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:36:19.119400 INFO: Estimating optimal hyperparameters - samples: 35,960, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:36:19.119663 INFO: Using random state 880283 for train-test-split
1 day, 8:36:22.636610 INFO: Test AUC: 0.756
1 day, 8:36:22.636778 INFO: Train AUC: 0.775
1 day, 8:36:22.636811 INFO: AUC difference: 2.46%
1 day, 8:36:22.918249 INFO: Resetting torch num_threads to 128
1 day, 8:36:22.919878 PROGRESS: === Extracted 44950 precursors and 491312 fragments ===
1 day, 8:36:22.920435 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:36:22.921898 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:36:22.922010 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:36:22.922101 PROGRESS: Target precursors: 7,583 (94.79%)
1 day, 8:36:22.922180 PROGRESS: Decoy precursors: 417 (5.21%)
1 day, 8:36:22.922260 PROGRESS: 
1 day, 8:36:22.922344 PROGRESS: Precursor Summary:
1 day, 8:36:22.925480 PROGRESS: Channel   0:	 0.050 FDR: 7,507; 0.010 FDR: 6,998; 0.001 FDR: 6,459
1 day, 8:36:22.925604 PROGRESS: 
1 day, 8:36:22.925680 PROGRESS: Protein Summary:
1 day, 8:36:22.930510 PROGRESS: Channel   0:	 0.050 FDR: 4,197; 0.010 FDR: 3,972; 0.001 FDR: 3,724
1 day, 8:36:22.930637 PROGRESS: =========================================================================
1 day, 8:36:22.930905 INFO: Target number of precursors reached.
1 day, 8:36:23.035840 INFO: fragments_df: keeping 5000 of 491312 [sum(precursor_idx_mask)=219308 sum(mass_error_mask)=491312 stop_rank=5000
1 day, 8:36:23.054534 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:36:24.169991 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:36:25.321681 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:36:26.436072 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:36:27.151826 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:36:27.152459 INFO: Using score_cutoff 39.10772043800354 (fac=0.99, q=1)
1 day, 8:36:27.152989 INFO: Updating optimization_manager: fwhm_rt             : 2.7917392253875732 -> 2.7810699939727783
1 day, 8:36:27.153093 INFO: Updating optimization_manager: fwhm_mobility       : 0.008175427094101906 -> 0.00805016327649355
1 day, 8:36:27.153170 INFO: Updating optimization_manager: score_cutoff        : 41.700851875305176 -> 39.10772043800354
1 day, 8:36:27.153249 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:36:27.156139 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:36:27.165916 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:36:27.168414 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:36:27.189668 INFO: === checking if optimization conditions were reached ===
1 day, 8:36:27.189927 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 8:36:27.196269 INFO: Updating optimization_manager: rt_error            : 377.36934369301315 -> 127.75648855111469
1 day, 8:36:27.196442 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 127.7565.
1 day, 8:36:27.196564 INFO: ==============================================
1 day, 8:36:27.196667 INFO: Starting optimization step 2.
1 day, 8:36:27.196759 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:36:27.196851 INFO: Using python extraction backend
1 day, 8:36:27.197025 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:36:27.197135 INFO: === Search parameters used ===
1 day, 8:36:27.197218 INFO: rt_error       : 127.75648855111469
1 day, 8:36:27.197322 INFO: mobility_error : 0.1
1 day, 8:36:27.197426 INFO: num_candidates : 3
1 day, 8:36:27.197524 INFO: ms1_error      : 15.0
1 day, 8:36:27.197616 INFO: ms2_error      : 15.0
1 day, 8:36:27.197706 INFO: fwhm_rt        : 2.7810699939727783
1 day, 8:36:27.197817 INFO: quant_window   : 3
1 day, 8:36:27.197915 INFO: ==============================================
1 day, 8:36:27.204903 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:36:27.205023 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:36:27.205094 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
1 day, 8:36:27.205145 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.73
1 day, 8:36:27.206147 INFO: Starting candidate selection
1 day, 8:36:34.256456 INFO: Starting candidate scoring
1 day, 8:36:36.104770 INFO: Finished candidate processing
1 day, 8:36:36.104995 INFO: Collecting candidate features
1 day, 8:36:36.196651 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 44910)
1 day, 8:36:36.201977 INFO: Collecting fragment features
1 day, 8:36:36.227345 INFO: Finished candidate scoring
1 day, 8:36:36.248756 INFO: performing precursor FDR with 47 features
1 day, 8:36:36.248919 INFO: Decoy channel: -1
1 day, 8:36:36.248948 INFO: competitive: True
1 day, 8:36:36.261200 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:36:36.267754 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 8:36:36.274511 INFO: Estimating optimal hyperparameters - samples: 35,927, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:36:36.274710 INFO: Using random state 880283 for train-test-split
1 day, 8:36:39.684901 INFO: Test AUC: 0.778
1 day, 8:36:39.685067 INFO: Train AUC: 0.790
1 day, 8:36:39.685100 INFO: AUC difference: 1.52%
1 day, 8:36:39.962857 INFO: Resetting torch num_threads to 128
1 day, 8:36:39.964530 PROGRESS: === Extracted 44910 precursors and 483503 fragments ===
1 day, 8:36:39.965096 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:36:39.966684 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:36:39.966801 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:36:39.966877 PROGRESS: Target precursors: 7,765 (97.06%)
1 day, 8:36:39.966942 PROGRESS: Decoy precursors: 235 (2.94%)
1 day, 8:36:39.967003 PROGRESS: 
1 day, 8:36:39.967062 PROGRESS: Precursor Summary:
1 day, 8:36:39.970174 PROGRESS: Channel   0:	 0.050 FDR: 7,765; 0.010 FDR: 7,465; 0.001 FDR: 6,818
1 day, 8:36:39.970296 PROGRESS: 
1 day, 8:36:39.970369 PROGRESS: Protein Summary:
1 day, 8:36:39.975110 PROGRESS: Channel   0:	 0.050 FDR: 4,294; 0.010 FDR: 4,168; 0.001 FDR: 3,892
1 day, 8:36:39.975266 PROGRESS: =========================================================================
1 day, 8:36:39.975548 INFO: Target number of precursors reached.
1 day, 8:36:40.084663 INFO: fragments_df: keeping 5000 of 483503 [sum(precursor_idx_mask)=230954 sum(mass_error_mask)=483503 stop_rank=5000
1 day, 8:36:40.103056 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:36:41.320109 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:36:42.574941 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:36:43.796364 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:36:44.512729 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:36:44.513341 INFO: Using score_cutoff 36.335408834838866 (fac=0.99, q=1)
1 day, 8:36:44.513910 INFO: Updating optimization_manager: fwhm_rt             : 2.7810699939727783 -> 2.7774388790130615
1 day, 8:36:44.514019 INFO: Updating optimization_manager: fwhm_mobility       : 0.00805016327649355 -> 0.007913242094218731
1 day, 8:36:44.514088 INFO: Updating optimization_manager: score_cutoff        : 39.10772043800354 -> 36.335408834838866
1 day, 8:36:44.514158 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:36:44.516958 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:36:44.526859 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:36:44.529350 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:36:44.551850 INFO: === checking if optimization conditions were reached ===
1 day, 8:36:44.552098 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 8:36:44.558853 INFO: Updating optimization_manager: rt_error            : 127.75648855111469 -> 43.749293610913526
1 day, 8:36:44.559082 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 43.7493.
1 day, 8:36:44.559210 INFO: ==============================================
1 day, 8:36:44.559331 INFO: Starting optimization step 3.
1 day, 8:36:44.559440 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:36:44.559552 INFO: Using python extraction backend
1 day, 8:36:44.559735 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:36:44.559858 INFO: === Search parameters used ===
1 day, 8:36:44.560064 INFO: rt_error       : 43.749293610913526
1 day, 8:36:44.560179 INFO: mobility_error : 0.1
1 day, 8:36:44.560321 INFO: num_candidates : 3
1 day, 8:36:44.560471 INFO: ms1_error      : 15.0
1 day, 8:36:44.560614 INFO: ms2_error      : 15.0
1 day, 8:36:44.560756 INFO: fwhm_rt        : 2.7774388790130615
1 day, 8:36:44.560864 INFO: quant_window   : 3
1 day, 8:36:44.561001 INFO: ==============================================
1 day, 8:36:44.568110 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:36:44.568273 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:36:44.568381 INFO: FWHM in RT is 2.78 seconds, sigma is 0.61
1 day, 8:36:44.568450 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.67
1 day, 8:36:44.569435 INFO: Starting candidate selection
1 day, 8:36:47.510050 INFO: Starting candidate scoring
1 day, 8:36:49.369254 INFO: Finished candidate processing
1 day, 8:36:49.369387 INFO: Collecting candidate features
1 day, 8:36:49.432379 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 44750)
1 day, 8:36:49.437889 INFO: Collecting fragment features
1 day, 8:36:49.466822 INFO: Finished candidate scoring
1 day, 8:36:49.490989 INFO: performing precursor FDR with 47 features
1 day, 8:36:49.491139 INFO: Decoy channel: -1
1 day, 8:36:49.491169 INFO: competitive: True
1 day, 8:36:49.513283 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:36:49.521997 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:36:49.522166 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 8:36:49.528898 INFO: Estimating optimal hyperparameters - samples: 35,798, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:36:49.529195 INFO: Using random state 880283 for train-test-split
1 day, 8:36:52.944032 INFO: Test AUC: 0.795
1 day, 8:36:52.944201 INFO: Train AUC: 0.805
1 day, 8:36:52.944233 INFO: AUC difference: 1.18%
1 day, 8:36:53.221929 INFO: Resetting torch num_threads to 128
1 day, 8:36:53.223571 PROGRESS: === Extracted 44750 precursors and 476313 fragments ===
1 day, 8:36:53.224160 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:36:53.225625 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:36:53.225737 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:36:53.225828 PROGRESS: Target precursors: 7,849 (98.11%)
1 day, 8:36:53.225897 PROGRESS: Decoy precursors: 151 (1.89%)
1 day, 8:36:53.225966 PROGRESS: 
1 day, 8:36:53.226029 PROGRESS: Precursor Summary:
1 day, 8:36:53.229231 PROGRESS: Channel   0:	 0.050 FDR: 7,849; 0.010 FDR: 7,717; 0.001 FDR: 7,270
1 day, 8:36:53.229347 PROGRESS: 
1 day, 8:36:53.229418 PROGRESS: Protein Summary:
1 day, 8:36:53.234481 PROGRESS: Channel   0:	 0.050 FDR: 4,338; 0.010 FDR: 4,287; 0.001 FDR: 4,101
1 day, 8:36:53.234604 PROGRESS: =========================================================================
1 day, 8:36:53.234865 INFO: Target number of precursors reached.
1 day, 8:36:53.343961 INFO: fragments_df: keeping 5000 of 476313 [sum(precursor_idx_mask)=236853 sum(mass_error_mask)=476313 stop_rank=5000
1 day, 8:36:53.362205 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:36:54.639180 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:36:55.938822 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:36:57.216035 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:36:57.934204 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:36:57.934834 INFO: Using score_cutoff 34.944380131530764 (fac=0.99, q=1)
1 day, 8:36:57.935381 INFO: Updating optimization_manager: fwhm_rt             : 2.7774388790130615 -> 2.7651894092559814
1 day, 8:36:57.935477 INFO: Updating optimization_manager: fwhm_mobility       : 0.007913242094218731 -> 0.007836103439331055
1 day, 8:36:57.935550 INFO: Updating optimization_manager: score_cutoff        : 36.335408834838866 -> 34.944380131530764
1 day, 8:36:57.935624 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:36:57.938554 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:36:57.948543 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:36:57.950990 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:36:57.972813 INFO: === checking if optimization conditions were reached ===
1 day, 8:36:57.973047 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 8:36:57.979945 INFO: Updating optimization_manager: rt_error            : 43.749293610913526 -> 18.902328574537677
1 day, 8:36:57.980163 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 18.9023.
1 day, 8:36:57.980293 INFO: ==============================================
1 day, 8:36:57.980420 INFO: Starting optimization step 4.
1 day, 8:36:57.980536 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:36:57.980655 INFO: Using python extraction backend
1 day, 8:36:57.980850 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:36:57.980978 INFO: === Search parameters used ===
1 day, 8:36:57.981082 INFO: rt_error       : 18.902328574537677
1 day, 8:36:57.981184 INFO: mobility_error : 0.1
1 day, 8:36:57.981282 INFO: num_candidates : 3
1 day, 8:36:57.981378 INFO: ms1_error      : 15.0
1 day, 8:36:57.981469 INFO: ms2_error      : 15.0
1 day, 8:36:57.981558 INFO: fwhm_rt        : 2.7651894092559814
1 day, 8:36:57.981647 INFO: quant_window   : 3
1 day, 8:36:57.981739 INFO: ==============================================
1 day, 8:36:57.988506 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:36:57.988613 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:36:57.988678 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 8:36:57.988728 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.63
1 day, 8:36:57.989716 INFO: Starting candidate selection
1 day, 8:36:59.875297 INFO: Starting candidate scoring
1 day, 8:37:02.213170 INFO: Finished candidate processing
1 day, 8:37:02.213379 INFO: Collecting candidate features
1 day, 8:37:02.303811 WARNING: intensity_correlation has 10 NaNs ( 0.02 % out of 44557)
1 day, 8:37:02.309379 INFO: Collecting fragment features
1 day, 8:37:02.338107 INFO: Finished candidate scoring
1 day, 8:37:02.363784 INFO: performing precursor FDR with 47 features
1 day, 8:37:02.363938 INFO: Decoy channel: -1
1 day, 8:37:02.363967 INFO: competitive: True
1 day, 8:37:02.384653 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:37:02.394614 WARNING: dropped 3 target PSMs due to missing features
1 day, 8:37:02.394779 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 8:37:02.401312 INFO: Estimating optimal hyperparameters - samples: 35,637, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:37:02.401518 INFO: Using random state 880283 for train-test-split
1 day, 8:37:05.816138 INFO: Test AUC: 0.821
1 day, 8:37:05.816303 INFO: Train AUC: 0.826
1 day, 8:37:05.816336 INFO: AUC difference: 0.60%
1 day, 8:37:06.091880 INFO: Resetting torch num_threads to 128
1 day, 8:37:06.093480 PROGRESS: === Extracted 44557 precursors and 469505 fragments ===
1 day, 8:37:06.094068 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:37:06.095538 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:37:06.095645 PROGRESS: Total precursors accumulated: 7,999
1 day, 8:37:06.095721 PROGRESS: Target precursors: 7,864 (98.31%)
1 day, 8:37:06.095795 PROGRESS: Decoy precursors: 135 (1.69%)
1 day, 8:37:06.095886 PROGRESS: 
1 day, 8:37:06.095966 PROGRESS: Precursor Summary:
1 day, 8:37:06.099293 PROGRESS: Channel   0:	 0.050 FDR: 7,864; 0.010 FDR: 7,785; 0.001 FDR: 7,502
1 day, 8:37:06.099426 PROGRESS: 
1 day, 8:37:06.099521 PROGRESS: Protein Summary:
1 day, 8:37:06.104625 PROGRESS: Channel   0:	 0.050 FDR: 4,351; 0.010 FDR: 4,321; 0.001 FDR: 4,199
1 day, 8:37:06.104780 PROGRESS: =========================================================================
1 day, 8:37:06.105050 INFO: Target number of precursors reached.
1 day, 8:37:06.216086 INFO: fragments_df: keeping 5000 of 469505 [sum(precursor_idx_mask)=237116 sum(mass_error_mask)=469505 stop_rank=5000
1 day, 8:37:06.235719 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:37:07.532791 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:37:08.833617 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:37:10.128060 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:37:10.847348 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:37:10.847963 INFO: Using score_cutoff 33.72361342163086 (fac=0.99, q=1)
1 day, 8:37:10.848518 INFO: Updating optimization_manager: fwhm_rt             : 2.7651894092559814 -> 2.755542278289795
1 day, 8:37:10.848610 INFO: Updating optimization_manager: fwhm_mobility       : 0.007836103439331055 -> 0.007799066603183746
1 day, 8:37:10.848686 INFO: Updating optimization_manager: score_cutoff        : 34.944380131530764 -> 33.72361342163086
1 day, 8:37:10.848770 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:37:10.851726 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:37:10.861391 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:37:10.863885 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:37:10.883107 INFO: === checking if optimization conditions were reached ===
1 day, 8:37:10.883317 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 8:37:10.890439 INFO: Updating optimization_manager: rt_error            : 18.902328574537677 -> 16.676975934600065
1 day, 8:37:10.890620 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 16.6770.
1 day, 8:37:10.890716 INFO: ==============================================
1 day, 8:37:10.890860 INFO: Starting optimization step 5.
1 day, 8:37:10.890957 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:37:10.891076 INFO: Using python extraction backend
1 day, 8:37:10.891249 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:37:10.891347 INFO: === Search parameters used ===
1 day, 8:37:10.891439 INFO: rt_error       : 16.676975934600065
1 day, 8:37:10.891509 INFO: mobility_error : 0.1
1 day, 8:37:10.891576 INFO: num_candidates : 3
1 day, 8:37:10.891643 INFO: ms1_error      : 15.0
1 day, 8:37:10.891716 INFO: ms2_error      : 15.0
1 day, 8:37:10.891812 INFO: fwhm_rt        : 2.755542278289795
1 day, 8:37:10.891897 INFO: quant_window   : 3
1 day, 8:37:10.891984 INFO: ==============================================
1 day, 8:37:10.899126 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:37:10.899243 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:37:10.899307 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 8:37:10.899355 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.62
1 day, 8:37:10.900226 INFO: Starting candidate selection
1 day, 8:37:12.729522 INFO: Starting candidate scoring
1 day, 8:37:14.587182 INFO: Finished candidate processing
1 day, 8:37:14.587398 INFO: Collecting candidate features
1 day, 8:37:14.664318 WARNING: intensity_correlation has 6 NaNs ( 0.01 % out of 44599)
1 day, 8:37:14.669532 INFO: Collecting fragment features
1 day, 8:37:14.694945 INFO: Finished candidate scoring
1 day, 8:37:14.713631 INFO: performing precursor FDR with 47 features
1 day, 8:37:14.713810 INFO: Decoy channel: -1
1 day, 8:37:14.713838 INFO: competitive: True
1 day, 8:37:14.725964 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:37:14.733885 WARNING: dropped 3 target PSMs due to missing features
1 day, 8:37:14.734038 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 8:37:14.740599 INFO: Estimating optimal hyperparameters - samples: 35,674, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:37:14.740802 INFO: Using random state 880283 for train-test-split
1 day, 8:37:18.190514 INFO: Test AUC: 0.815
1 day, 8:37:18.190679 INFO: Train AUC: 0.829
1 day, 8:37:18.190711 INFO: AUC difference: 1.69%
1 day, 8:37:18.466059 INFO: Resetting torch num_threads to 128
1 day, 8:37:18.467694 PROGRESS: === Extracted 44599 precursors and 469892 fragments ===
1 day, 8:37:18.468238 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:37:18.469647 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:37:18.469767 PROGRESS: Total precursors accumulated: 7,999
1 day, 8:37:18.469847 PROGRESS: Target precursors: 7,871 (98.40%)
1 day, 8:37:18.469918 PROGRESS: Decoy precursors: 128 (1.60%)
1 day, 8:37:18.469999 PROGRESS: 
1 day, 8:37:18.470070 PROGRESS: Precursor Summary:
1 day, 8:37:18.473313 PROGRESS: Channel   0:	 0.050 FDR: 7,871; 0.010 FDR: 7,806; 0.001 FDR: 7,420
1 day, 8:37:18.473441 PROGRESS: 
1 day, 8:37:18.473526 PROGRESS: Protein Summary:
1 day, 8:37:18.478632 PROGRESS: Channel   0:	 0.050 FDR: 4,353; 0.010 FDR: 4,325; 0.001 FDR: 4,163
1 day, 8:37:18.478760 PROGRESS: =========================================================================
1 day, 8:37:18.479002 INFO: Target number of precursors reached.
1 day, 8:37:18.587114 INFO: fragments_df: keeping 5000 of 469892 [sum(precursor_idx_mask)=238012 sum(mass_error_mask)=469892 stop_rank=5000
1 day, 8:37:18.606498 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:37:19.911993 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:37:23.382495 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:37:24.708571 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:37:25.440900 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:37:25.441569 INFO: Using score_cutoff 33.229127712249756 (fac=0.99, q=1)
1 day, 8:37:25.442157 INFO: Updating optimization_manager: fwhm_rt             : 2.755542278289795 -> 2.751432418823242
1 day, 8:37:25.442263 INFO: Updating optimization_manager: fwhm_mobility       : 0.007799066603183746 -> 0.007772074081003666
1 day, 8:37:25.442338 INFO: Updating optimization_manager: score_cutoff        : 33.72361342163086 -> 33.229127712249756
1 day, 8:37:25.442421 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:37:25.446033 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:37:25.456102 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:37:25.458679 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:37:25.480927 INFO: === checking if optimization conditions were reached ===
1 day, 8:37:25.481164 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 8:37:25.488399 INFO: Updating optimization_manager: rt_error            : 16.676975934600065 -> 16.880891800280192
1 day, 8:37:25.488576 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 16.8809.
1 day, 8:37:25.488689 INFO: ==============================================
1 day, 8:37:25.488794 INFO: Starting optimization step 6.
1 day, 8:37:25.488919 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:37:25.489038 INFO: Using python extraction backend
1 day, 8:37:25.489242 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:37:25.489364 INFO: === Search parameters used ===
1 day, 8:37:25.489461 INFO: rt_error       : 16.880891800280192
1 day, 8:37:25.489547 INFO: mobility_error : 0.1
1 day, 8:37:25.489633 INFO: num_candidates : 3
1 day, 8:37:25.489717 INFO: ms1_error      : 15.0
1 day, 8:37:25.489819 INFO: ms2_error      : 15.0
1 day, 8:37:25.489911 INFO: fwhm_rt        : 2.751432418823242
1 day, 8:37:25.489992 INFO: quant_window   : 3
1 day, 8:37:25.490075 INFO: ==============================================
1 day, 8:37:25.498714 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:37:25.498827 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:37:25.498890 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 8:37:25.498938 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.61
1 day, 8:37:25.523158 INFO: Starting candidate selection
1 day, 8:37:27.773224 INFO: Starting candidate scoring
1 day, 8:37:29.632255 INFO: Finished candidate processing
1 day, 8:37:29.632479 INFO: Collecting candidate features
1 day, 8:37:29.733304 WARNING: intensity_correlation has 8 NaNs ( 0.02 % out of 44596)
1 day, 8:37:29.738552 INFO: Collecting fragment features
1 day, 8:37:29.769347 INFO: Finished candidate scoring
1 day, 8:37:29.793576 INFO: performing precursor FDR with 47 features
1 day, 8:37:29.793735 INFO: Decoy channel: -1
1 day, 8:37:29.793770 INFO: competitive: True
1 day, 8:37:29.807571 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:37:29.815696 WARNING: dropped 3 target PSMs due to missing features
1 day, 8:37:29.815842 WARNING: dropped 5 decoy PSMs due to missing features
1 day, 8:37:29.822614 INFO: Estimating optimal hyperparameters - samples: 35,670, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:37:29.822909 INFO: Using random state 880283 for train-test-split
1 day, 8:37:33.234386 INFO: Test AUC: 0.816
1 day, 8:37:33.234548 INFO: Train AUC: 0.829
1 day, 8:37:33.234580 INFO: AUC difference: 1.55%
1 day, 8:37:33.515000 INFO: Resetting torch num_threads to 128
1 day, 8:37:33.516735 PROGRESS: === Extracted 44596 precursors and 469921 fragments ===
1 day, 8:37:33.517299 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:37:33.518951 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:37:33.519072 PROGRESS: Total precursors accumulated: 7,999
1 day, 8:37:33.519148 PROGRESS: Target precursors: 7,871 (98.40%)
1 day, 8:37:33.519212 PROGRESS: Decoy precursors: 128 (1.60%)
1 day, 8:37:33.519276 PROGRESS: 
1 day, 8:37:33.519340 PROGRESS: Precursor Summary:
1 day, 8:37:33.522878 PROGRESS: Channel   0:	 0.050 FDR: 7,871; 0.010 FDR: 7,808; 0.001 FDR: 7,291
1 day, 8:37:33.523012 PROGRESS: 
1 day, 8:37:33.523084 PROGRESS: Protein Summary:
1 day, 8:37:33.528392 PROGRESS: Channel   0:	 0.050 FDR: 4,347; 0.010 FDR: 4,325; 0.001 FDR: 4,104
1 day, 8:37:33.528530 PROGRESS: =========================================================================
1 day, 8:37:33.528799 INFO: Target number of precursors reached.
1 day, 8:37:33.636697 INFO: fragments_df: keeping 5000 of 469921 [sum(precursor_idx_mask)=237922 sum(mass_error_mask)=469921 stop_rank=5000
1 day, 8:37:33.664038 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:37:34.900178 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:37:36.144689 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:37:37.385078 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:37:38.071090 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:37:38.071700 INFO: Using score_cutoff 33.22346186714172 (fac=0.99, q=1)
1 day, 8:37:38.072269 INFO: Updating optimization_manager: fwhm_rt             : 2.751432418823242 -> 2.745615005493164
1 day, 8:37:38.072370 INFO: Updating optimization_manager: fwhm_mobility       : 0.007772074081003666 -> 0.007725386880338192
1 day, 8:37:38.072444 INFO: Updating optimization_manager: score_cutoff        : 33.229127712249756 -> 33.22346186714172
1 day, 8:37:38.072524 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:37:38.075465 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:37:38.085226 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:37:38.087756 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:37:38.108581 INFO: === checking if optimization conditions were reached ===
1 day, 8:37:38.108793 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 8:37:38.110292 INFO: Updating optimization_manager: rt_error            : 16.880891800280192 -> 16.676975934600065
1 day, 8:37:38.110471 INFO: Updating optimization_manager: classifier_version  : 2 -> 8
1 day, 8:37:38.110609 INFO: Updating optimization_manager: score_cutoff        : 33.22346186714172 -> 33.229127712249756
1 day, 8:37:38.110736 INFO: Updating optimization_manager: fwhm_rt             : 2.745615005493164 -> 2.751432418823242
1 day, 8:37:38.110933 INFO: Updating optimization_manager: fwhm_mobility       : 0.007725386880338192 -> 0.007772074081003666
1 day, 8:37:38.111088 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 16.6770 found after 7 searches.
1 day, 8:37:38.111209 INFO: ==============================================
1 day, 8:37:38.111328 PROGRESS: Optimization finished for rt_error.
1 day, 8:37:38.135106 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:37:38.138683 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:37:38.148900 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:37:38.151724 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:37:38.173679 INFO: Starting optimization step 0.
1 day, 8:37:38.173986 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:37:38.174127 INFO: Using python extraction backend
1 day, 8:37:38.174352 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:37:38.174489 INFO: === Search parameters used ===
1 day, 8:37:38.174592 INFO: rt_error       : 16.676975934600065
1 day, 8:37:38.174690 INFO: mobility_error : 0.1
1 day, 8:37:38.174785 INFO: num_candidates : 3
1 day, 8:37:38.174881 INFO: ms1_error      : 15.0
1 day, 8:37:38.174968 INFO: ms2_error      : 15.0
1 day, 8:37:38.175059 INFO: fwhm_rt        : 2.751432418823242
1 day, 8:37:38.175151 INFO: quant_window   : 3
1 day, 8:37:38.175242 INFO: ==============================================
1 day, 8:37:38.181475 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:37:38.181586 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:37:38.181654 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 8:37:38.181704 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.61
1 day, 8:37:38.182570 INFO: Starting candidate selection
1 day, 8:37:40.069886 INFO: Starting candidate scoring
1 day, 8:37:41.917695 INFO: Finished candidate processing
1 day, 8:37:41.917905 INFO: Collecting candidate features
1 day, 8:37:42.004647 WARNING: intensity_correlation has 6 NaNs ( 0.01 % out of 44610)
1 day, 8:37:42.009987 INFO: Collecting fragment features
1 day, 8:37:42.036164 INFO: Finished candidate scoring
1 day, 8:37:42.059472 INFO: performing precursor FDR with 47 features
1 day, 8:37:42.059641 INFO: Decoy channel: -1
1 day, 8:37:42.059667 INFO: competitive: True
1 day, 8:37:42.072834 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:37:42.080853 WARNING: dropped 3 target PSMs due to missing features
1 day, 8:37:42.080995 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 8:37:42.088523 INFO: Estimating optimal hyperparameters - samples: 35,683, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:37:42.088747 INFO: Using random state 875750 for train-test-split
1 day, 8:37:45.522790 INFO: Test AUC: 0.827
1 day, 8:37:45.522967 INFO: Train AUC: 0.840
1 day, 8:37:45.523002 INFO: AUC difference: 1.57%
1 day, 8:37:45.800611 INFO: Resetting torch num_threads to 128
1 day, 8:37:45.802415 PROGRESS: === Extracted 44610 precursors and 470041 fragments ===
1 day, 8:37:45.802986 INFO: === FDR correction performed with classifier version 8 ===
1 day, 8:37:45.804541 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:37:45.804655 PROGRESS: Total precursors accumulated: 7,999
1 day, 8:37:45.804731 PROGRESS: Target precursors: 7,873 (98.42%)
1 day, 8:37:45.804801 PROGRESS: Decoy precursors: 126 (1.58%)
1 day, 8:37:45.804870 PROGRESS: 
1 day, 8:37:45.804935 PROGRESS: Precursor Summary:
1 day, 8:37:45.808267 PROGRESS: Channel   0:	 0.050 FDR: 7,873; 0.010 FDR: 7,815; 0.001 FDR: 7,483
1 day, 8:37:45.808398 PROGRESS: 
1 day, 8:37:45.808474 PROGRESS: Protein Summary:
1 day, 8:37:45.813703 PROGRESS: Channel   0:	 0.050 FDR: 4,351; 0.010 FDR: 4,324; 0.001 FDR: 4,190
1 day, 8:37:45.813852 PROGRESS: =========================================================================
1 day, 8:37:45.814165 INFO: Target number of precursors reached.
1 day, 8:37:45.924191 INFO: fragments_df: keeping 5000 of 470041 [sum(precursor_idx_mask)=238171 sum(mass_error_mask)=470041 stop_rank=5000
1 day, 8:37:45.943202 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:37:47.207019 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:37:48.459013 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:37:49.713470 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:37:50.375238 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:37:50.375878 INFO: Using score_cutoff 33.08539454956054 (fac=0.99, q=1)
1 day, 8:37:50.376480 INFO: Updating optimization_manager: fwhm_rt             : 2.751432418823242 -> 2.751361131668091
1 day, 8:37:50.376581 INFO: Updating optimization_manager: fwhm_mobility       : 0.007772074081003666 -> 0.007769294083118439
1 day, 8:37:50.376669 INFO: Updating optimization_manager: score_cutoff        : 33.229127712249756 -> 33.08539454956054
1 day, 8:37:50.376759 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:37:50.379821 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:37:50.389710 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:37:50.392211 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:37:50.412997 INFO: === checking if optimization conditions were reached ===
1 day, 8:37:50.413249 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 8:37:50.416451 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07906098954695491
1 day, 8:37:50.416594 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0791.
1 day, 8:37:50.416686 INFO: ==============================================
1 day, 8:37:50.416784 INFO: Starting optimization step 1.
1 day, 8:37:50.416868 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:37:50.416956 INFO: Using python extraction backend
1 day, 8:37:50.417132 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:37:50.417233 INFO: === Search parameters used ===
1 day, 8:37:50.417318 INFO: rt_error       : 16.676975934600065
1 day, 8:37:50.417386 INFO: mobility_error : 0.07906098954695491
1 day, 8:37:50.417450 INFO: num_candidates : 3
1 day, 8:37:50.417512 INFO: ms1_error      : 15.0
1 day, 8:37:50.417573 INFO: ms2_error      : 15.0
1 day, 8:37:50.417634 INFO: fwhm_rt        : 2.751361131668091
1 day, 8:37:50.417698 INFO: quant_window   : 3
1 day, 8:37:50.417773 INFO: ==============================================
1 day, 8:37:50.423843 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:37:50.423916 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:37:50.423963 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 8:37:50.423993 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.60
1 day, 8:37:50.424892 INFO: Starting candidate selection
1 day, 8:37:52.169659 INFO: Starting candidate scoring
1 day, 8:37:53.963118 INFO: Finished candidate processing
1 day, 8:37:53.963329 INFO: Collecting candidate features
1 day, 8:37:54.024075 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 44570)
1 day, 8:37:54.029397 INFO: Collecting fragment features
1 day, 8:37:54.054429 INFO: Finished candidate scoring
1 day, 8:37:54.075920 INFO: performing precursor FDR with 47 features
1 day, 8:37:54.076081 INFO: Decoy channel: -1
1 day, 8:37:54.076109 INFO: competitive: True
1 day, 8:37:54.088623 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:37:54.096479 WARNING: dropped 2 target PSMs due to missing features
1 day, 8:37:54.096619 WARNING: dropped 5 decoy PSMs due to missing features
1 day, 8:37:54.103158 INFO: Estimating optimal hyperparameters - samples: 35,650, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:37:54.103371 INFO: Using random state 875750 for train-test-split
1 day, 8:37:57.550454 INFO: Test AUC: 0.826
1 day, 8:37:57.550630 INFO: Train AUC: 0.841
1 day, 8:37:57.550663 INFO: AUC difference: 1.79%
1 day, 8:37:57.829395 INFO: Resetting torch num_threads to 128
1 day, 8:37:57.831067 PROGRESS: === Extracted 44570 precursors and 467932 fragments ===
1 day, 8:37:57.831672 INFO: === FDR correction performed with classifier version 8 ===
1 day, 8:37:57.833221 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:37:57.833333 PROGRESS: Total precursors accumulated: 7,992
1 day, 8:37:57.833411 PROGRESS: Target precursors: 7,855 (98.29%)
1 day, 8:37:57.833486 PROGRESS: Decoy precursors: 137 (1.71%)
1 day, 8:37:57.833547 PROGRESS: 
1 day, 8:37:57.833609 PROGRESS: Precursor Summary:
1 day, 8:37:57.836975 PROGRESS: Channel   0:	 0.050 FDR: 7,855; 0.010 FDR: 7,780; 0.001 FDR: 7,467
1 day, 8:37:57.837112 PROGRESS: 
1 day, 8:37:57.837195 PROGRESS: Protein Summary:
1 day, 8:37:57.842406 PROGRESS: Channel   0:	 0.050 FDR: 4,340; 0.010 FDR: 4,307; 0.001 FDR: 4,185
1 day, 8:37:57.842541 PROGRESS: =========================================================================
1 day, 8:37:57.842792 INFO: Target number of precursors reached.
1 day, 8:37:57.951464 INFO: fragments_df: keeping 5000 of 467932 [sum(precursor_idx_mask)=236761 sum(mass_error_mask)=467932 stop_rank=5000
1 day, 8:37:57.970082 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:37:59.209021 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:38:00.446947 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:38:01.685982 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:38:02.346734 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:38:02.347382 INFO: Using score_cutoff 32.64232170066833 (fac=0.99, q=1)
1 day, 8:38:02.347929 INFO: Updating optimization_manager: fwhm_rt             : 2.751361131668091 -> 2.7484078407287598
1 day, 8:38:02.348029 INFO: Updating optimization_manager: fwhm_mobility       : 0.007769294083118439 -> 0.007786168716847897
1 day, 8:38:02.348098 INFO: Updating optimization_manager: score_cutoff        : 33.08539454956054 -> 32.64232170066833
1 day, 8:38:02.348182 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:38:02.351127 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:38:02.360893 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:38:02.363376 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:38:02.382673 INFO: === checking if optimization conditions were reached ===
1 day, 8:38:02.382886 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 8:38:02.386191 INFO: Updating optimization_manager: mobility_error      : 0.07906098954695491 -> 0.06893049521777025
1 day, 8:38:02.386342 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0689.
1 day, 8:38:02.386472 INFO: ==============================================
1 day, 8:38:02.386569 INFO: Starting optimization step 2.
1 day, 8:38:02.386682 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:38:02.386792 INFO: Using python extraction backend
1 day, 8:38:02.386981 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:38:02.387079 INFO: === Search parameters used ===
1 day, 8:38:02.387194 INFO: rt_error       : 16.676975934600065
1 day, 8:38:02.387282 INFO: mobility_error : 0.06893049521777025
1 day, 8:38:02.387366 INFO: num_candidates : 3
1 day, 8:38:02.387450 INFO: ms1_error      : 15.0
1 day, 8:38:02.387531 INFO: ms2_error      : 15.0
1 day, 8:38:02.387615 INFO: fwhm_rt        : 2.7484078407287598
1 day, 8:38:02.387695 INFO: quant_window   : 3
1 day, 8:38:02.387769 INFO: ==============================================
1 day, 8:38:02.395175 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:38:02.395258 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:38:02.395304 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 8:38:02.395362 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.61
1 day, 8:38:02.396403 INFO: Starting candidate selection
1 day, 8:38:04.062032 INFO: Starting candidate scoring
1 day, 8:38:05.882772 INFO: Finished candidate processing
1 day, 8:38:05.883001 INFO: Collecting candidate features
1 day, 8:38:05.953464 WARNING: intensity_correlation has 9 NaNs ( 0.02 % out of 44533)
1 day, 8:38:05.958840 INFO: Collecting fragment features
1 day, 8:38:05.983711 INFO: Finished candidate scoring
1 day, 8:38:06.002681 INFO: performing precursor FDR with 47 features
1 day, 8:38:06.002842 INFO: Decoy channel: -1
1 day, 8:38:06.002869 INFO: competitive: True
1 day, 8:38:06.015958 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:38:06.023958 WARNING: dropped 3 target PSMs due to missing features
1 day, 8:38:06.024101 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 8:38:06.030747 INFO: Estimating optimal hyperparameters - samples: 35,619, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:38:06.030972 INFO: Using random state 875750 for train-test-split
1 day, 8:38:09.475583 INFO: Test AUC: 0.831
1 day, 8:38:09.475744 INFO: Train AUC: 0.840
1 day, 8:38:09.475777 INFO: AUC difference: 1.06%
1 day, 8:38:09.755981 INFO: Resetting torch num_threads to 128
1 day, 8:38:09.757683 PROGRESS: === Extracted 44533 precursors and 466254 fragments ===
1 day, 8:38:09.758299 INFO: === FDR correction performed with classifier version 8 ===
1 day, 8:38:09.759849 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:38:09.759967 PROGRESS: Total precursors accumulated: 7,988
1 day, 8:38:09.760046 PROGRESS: Target precursors: 7,858 (98.37%)
1 day, 8:38:09.760119 PROGRESS: Decoy precursors: 130 (1.63%)
1 day, 8:38:09.760181 PROGRESS: 
1 day, 8:38:09.760248 PROGRESS: Precursor Summary:
1 day, 8:38:09.763579 PROGRESS: Channel   0:	 0.050 FDR: 7,858; 0.010 FDR: 7,764; 0.001 FDR: 7,479
1 day, 8:38:09.763708 PROGRESS: 
1 day, 8:38:09.763783 PROGRESS: Protein Summary:
1 day, 8:38:09.768966 PROGRESS: Channel   0:	 0.050 FDR: 4,347; 0.010 FDR: 4,311; 0.001 FDR: 4,193
1 day, 8:38:09.769126 PROGRESS: =========================================================================
1 day, 8:38:09.769447 INFO: Target number of precursors reached.
1 day, 8:38:09.876314 INFO: fragments_df: keeping 5000 of 466254 [sum(precursor_idx_mask)=235930 sum(mass_error_mask)=466254 stop_rank=5000
1 day, 8:38:09.894865 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:38:11.122870 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:38:12.366104 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:38:13.590032 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:38:14.249209 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:38:14.249835 INFO: Using score_cutoff 32.188596865081784 (fac=0.99, q=1)
1 day, 8:38:14.250390 INFO: Updating optimization_manager: fwhm_rt             : 2.7484078407287598 -> 2.751432418823242
1 day, 8:38:14.250486 INFO: Updating optimization_manager: fwhm_mobility       : 0.007786168716847897 -> 0.007800833322107792
1 day, 8:38:14.250554 INFO: Updating optimization_manager: score_cutoff        : 32.64232170066833 -> 32.188596865081784
1 day, 8:38:14.250624 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:38:14.253547 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:38:14.263420 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:38:14.265919 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:38:14.286522 INFO: === checking if optimization conditions were reached ===
1 day, 8:38:14.286742 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 8:38:14.287838 INFO: Updating optimization_manager: mobility_error      : 0.06893049521777025 -> 0.1
1 day, 8:38:14.288002 INFO: Updating optimization_manager: classifier_version  : 8 -> 10
1 day, 8:38:14.288135 INFO: Updating optimization_manager: score_cutoff        : 32.188596865081784 -> 33.08539454956054
1 day, 8:38:14.288257 INFO: Updating optimization_manager: fwhm_rt             : 2.751432418823242 -> 2.751361131668091
1 day, 8:38:14.288377 INFO: Updating optimization_manager: fwhm_mobility       : 0.007800833322107792 -> 0.007769294083118439
1 day, 8:38:14.288496 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 8:38:14.288582 INFO: ==============================================
1 day, 8:38:14.288688 PROGRESS: Optimization finished for mobility_error.
1 day, 8:38:14.312357 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:38:14.315879 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:38:14.326060 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:38:14.328807 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:38:14.350321 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 8:38:14.350514 PROGRESS: ==============================================
1 day, 8:38:14.350618 PROGRESS: ms2_error      : 15.0000
1 day, 8:38:14.350701 PROGRESS: ms1_error      : 15.0000
1 day, 8:38:14.350775 PROGRESS: rt_error       : 16.6770
1 day, 8:38:14.350843 PROGRESS: mobility_error : 0.1000
1 day, 8:38:14.350909 PROGRESS: ==============================================
1 day, 8:38:14.352339 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:38:14.376521 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:38:14.481449 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:38:14.505450 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:38:14.753064 INFO: Using python extraction backend
1 day, 8:38:14.753569 PROGRESS: Extracting batch of 182033 precursors
1 day, 8:38:14.753696 INFO: === Search parameters used ===
1 day, 8:38:14.753792 INFO: rt_error       : 16.676975934600065
1 day, 8:38:14.753926 INFO: mobility_error : 0.1
1 day, 8:38:14.754009 INFO: num_candidates : 3
1 day, 8:38:14.754076 INFO: ms1_error      : 15.0
1 day, 8:38:14.754164 INFO: ms2_error      : 15.0
1 day, 8:38:14.754228 INFO: fwhm_rt        : 2.751361131668091
1 day, 8:38:14.754291 INFO: quant_window   : 3
1 day, 8:38:14.754352 INFO: ==============================================
1 day, 8:38:14.812786 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:38:14.812963 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:38:14.813009 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 8:38:14.813034 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.60
1 day, 8:38:14.813811 INFO: Starting candidate selection
1 day, 8:38:31.324667 INFO: Removed 73406 precursors with score below cutoff 33.08539454956054
1 day, 8:38:31.683788 INFO: Starting candidate scoring
1 day, 8:38:48.070752 INFO: Finished candidate processing
1 day, 8:38:48.070963 INFO: Collecting candidate features
1 day, 8:38:48.825278 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 438872)
1 day, 8:38:48.841992 INFO: Collecting fragment features
1 day, 8:38:49.094791 INFO: Finished candidate scoring
1 day, 8:38:49.293643 INFO: === Performing FDR correction with classifier version 10 ===
1 day, 8:38:49.294475 INFO: performing precursor FDR with 47 features
1 day, 8:38:49.294535 INFO: Decoy channel: -1
1 day, 8:38:49.294563 INFO: competitive: True
1 day, 8:38:49.414407 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:38:49.479804 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:38:49.480027 WARNING: FDR calculation for 240190 target and 198681 decoy PSMs
1 day, 8:38:49.480059 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 8:38:49.611320 INFO: Estimating optimal hyperparameters - samples: 351,096, batch_size: 1,438, learning_rate: 5.93e-04
1 day, 8:38:49.612087 INFO: Using random state 793213 for train-test-split
1 day, 8:38:59.900112 INFO: Test AUC: 0.841
1 day, 8:38:59.900297 INFO: Train AUC: 0.844
1 day, 8:38:59.900331 INFO: AUC difference: 0.32%
1 day, 8:39:00.308258 INFO: Resetting torch num_threads to 128
1 day, 8:39:00.334202 INFO: Removing fragments below FDR threshold
1 day, 8:39:00.421143 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:39:00.421498 PROGRESS: Total precursors accumulated: 89,771
1 day, 8:39:00.421581 PROGRESS: Target precursors: 88,883 (99.01%)
1 day, 8:39:00.421650 PROGRESS: Decoy precursors: 888 (0.99%)
1 day, 8:39:00.421715 PROGRESS: 
1 day, 8:39:00.421789 PROGRESS: Precursor Summary:
1 day, 8:39:00.470263 PROGRESS: Channel   0:	 0.050 FDR: 88,883; 0.010 FDR: 88,883; 0.001 FDR: 85,159
1 day, 8:39:00.470608 PROGRESS: 
1 day, 8:39:00.470729 PROGRESS: Protein Summary:
1 day, 8:39:00.544271 PROGRESS: Channel   0:	 0.050 FDR: 8,971; 0.010 FDR: 8,971; 0.001 FDR: 8,935
1 day, 8:39:00.544636 PROGRESS: =========================================================================
1 day, 8:39:00.553090 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/psm.parquet
1 day, 8:39:00.933481 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/frag.parquet
1 day, 8:39:01.239535 INFO: Finished workflow for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 8:39:01.309694 PROGRESS: Loading raw file 4/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496 
1 day, 8:39:01.309919 INFO: Quantification results path: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant
1 day, 8:39:01.310019 INFO: Creating folder /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/figures
1 day, 8:39:01.310271 INFO: Initializing TimingManager
1 day, 8:39:01.310877 INFO: Initializing RawFileManager
1 day, 8:39:01.311036 INFO: Importing data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 8:39:01.311084 INFO: Using .d import for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 8:39:01.311122 INFO: Reading frame metadata for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 8:39:02.464732 INFO: Reading 39,128 frames with 2,751,035,867 detector events for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 8:40:10.090768 INFO: Indexing /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d...
1 day, 8:40:10.092292 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 8:40:10.097410 INFO: Fetching mobility values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 8:40:10.097659 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 8:40:10.098136 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 8:40:10.099525 INFO: Fetching mz values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 8:40:10.137934 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 8:40:10.138340 INFO: Indexing quadrupole dimension
1 day, 8:40:10.568855 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 8:40:10.569028 INFO: Transposing detector events
1 day, 8:40:19.282606 INFO: Finished transposing data
1 day, 8:40:19.372098 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496.d
1 day, 8:40:19.372990 INFO: RT (min)            : 0.0 - 70.0
1 day, 8:40:19.373071 INFO: RT duration (sec)   : 4199.8
1 day, 8:40:19.373130 INFO: RT duration (min)   : 70.0
1 day, 8:40:19.373179 INFO: Cycle len (scans)   : 9
1 day, 8:40:19.373225 INFO: Cycle len (sec)     : 0.97
1 day, 8:40:19.373267 INFO: Number of cycles    : 4347
1 day, 8:40:19.373312 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 8:40:19.373374 INFO: Creating DIA data object took: 78.06235027313232
1 day, 8:40:19.416703 INFO: Initializing CalibrationManager
1 day, 8:40:19.417098 INFO: Setting up calibration estimators ..
1 day, 8:40:19.417207 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 8:40:19.417315 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, 8:40:19.417418 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 8:40:19.417507 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, 8:40:19.417593 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, 8:40:19.417679 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, 8:40:19.417764 INFO: Done setting up calibration estimators.
1 day, 8:40:19.417906 INFO: Initializing OptimizationManager
1 day, 8:40:19.418033 INFO: initial parameter: ms1_error = 30
1 day, 8:40:19.418111 INFO: initial parameter: ms2_error = 30
1 day, 8:40:19.418184 INFO: initial parameter: rt_error = 2099.891532
1 day, 8:40:19.418248 INFO: initial parameter: mobility_error = 0.1
1 day, 8:40:19.418313 INFO: initial parameter: num_candidates = 1
1 day, 8:40:19.418376 INFO: initial parameter: fwhm_rt = 5
1 day, 8:40:19.418448 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 8:40:19.418514 INFO: initial parameter: score_cutoff = 0
1 day, 8:40:19.418582 INFO: initial parameter: classifier_version = -1
1 day, 8:40:19.418685 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 8:40:19.418910 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 8:40:19.418949 INFO: Initializing FDRManager
1 day, 8:40:19.418985 INFO: Loading classifier store from /usr/local/lib/python3.10/site-packages/alphadia/constants/classifier
1 day, 8:40:19.455747 PROGRESS: Initializing spectral library: 91,740 target precursors potentially observable (0 removed)
1 day, 8:40:19.495267 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 8:40:19.495894 INFO: Updating optimization_manager: rt_error            : 2099.891532 -> 2099.891532
1 day, 8:40:19.496018 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 8:40:19.496237 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 8:40:19.496339 PROGRESS: Starting initial search for precursors.
1 day, 8:40:19.496442 INFO: Starting optimization step 0.
1 day, 8:40:19.496524 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:40:19.496603 INFO: Using python extraction backend
1 day, 8:40:19.496768 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:40:19.496859 INFO: === Search parameters used ===
1 day, 8:40:19.496934 INFO: rt_error       : 2099.891532
1 day, 8:40:19.497003 INFO: mobility_error : 0.1
1 day, 8:40:19.497072 INFO: num_candidates : 1
1 day, 8:40:19.497136 INFO: ms1_error      : 30
1 day, 8:40:19.497208 INFO: ms2_error      : 30
1 day, 8:40:19.497277 INFO: fwhm_rt        : 5
1 day, 8:40:19.497338 INFO: quant_window   : 3
1 day, 8:40:19.497407 INFO: ==============================================
1 day, 8:40:19.500275 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:40:19.500331 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:40:19.500361 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 8:40:19.500390 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 8:40:19.501413 INFO: Starting candidate selection
1 day, 8:41:54.941885 INFO: Starting candidate scoring
1 day, 8:41:56.494355 INFO: Finished candidate processing
1 day, 8:41:56.494553 INFO: Collecting candidate features
1 day, 8:41:56.560589 INFO: Collecting fragment features
1 day, 8:41:56.573856 INFO: Finished candidate scoring
1 day, 8:41:56.583481 INFO: performing precursor FDR with 47 features
1 day, 8:41:56.583609 INFO: Decoy channel: -1
1 day, 8:41:56.583643 INFO: competitive: True
1 day, 8:41:56.589390 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:41:56.594943 INFO: Estimating optimal hyperparameters - samples: 12,693, batch_size: 128, learning_rate: 1.77e-04
1 day, 8:41:56.595819 INFO: Using random state 97121 for train-test-split
1 day, 8:41:58.031170 INFO: Test AUC: 0.819
1 day, 8:41:58.031330 INFO: Train AUC: 0.840
1 day, 8:41:58.031363 INFO: AUC difference: 2.58%
1 day, 8:41:58.299514 INFO: Resetting torch num_threads to 128
1 day, 8:41:58.300855 PROGRESS: === Extracted 15867 precursors and 179722 fragments ===
1 day, 8:41:58.301497 INFO: === FDR correction performed with classifier version -1 ===
1 day, 8:41:58.303137 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:41:58.303277 PROGRESS: Total precursors accumulated: 7,995
1 day, 8:41:58.303377 PROGRESS: Target precursors: 6,704 (83.85%)
1 day, 8:41:58.303464 PROGRESS: Decoy precursors: 1,291 (16.15%)
1 day, 8:41:58.303547 PROGRESS: 
1 day, 8:41:58.303620 PROGRESS: Precursor Summary:
1 day, 8:41:58.306262 PROGRESS: Channel   0:	 0.050 FDR: 5,153; 0.010 FDR: 4,551; 0.001 FDR: 3,357
1 day, 8:41:58.306403 PROGRESS: 
1 day, 8:41:58.306497 PROGRESS: Protein Summary:
1 day, 8:41:58.310170 PROGRESS: Channel   0:	 0.050 FDR: 3,100; 0.010 FDR: 2,796; 0.001 FDR: 2,199
1 day, 8:41:58.310304 PROGRESS: =========================================================================
1 day, 8:41:58.310469 INFO: Target number of precursors reached.
1 day, 8:41:58.341044 INFO: fragments_df: keeping 5000 of 179722 [sum(precursor_idx_mask)=51569 sum(mass_error_mask)=179722 stop_rank=5000
1 day, 8:41:58.370340 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:41:58.961113 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:41:59.575678 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:42:00.173323 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:42:00.824442 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 8:42:00.825090 INFO: Using score_cutoff 49.21660388946533 (fac=0.99, q=1)
1 day, 8:42:00.825567 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.115100622177124
1 day, 8:42:00.825664 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010344716720283031
1 day, 8:42:00.825731 INFO: Updating optimization_manager: score_cutoff        : 0 -> 49.21660388946533
1 day, 8:42:00.825821 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:42:00.828906 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:42:00.838606 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:42:00.841133 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:42:00.862695 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
1 day, 8:42:00.862919 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 8:42:00.863042 INFO: Starting optimization step 1.
1 day, 8:42:00.863137 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:42:00.863233 INFO: Using python extraction backend
1 day, 8:42:00.863426 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:42:00.863532 INFO: === Search parameters used ===
1 day, 8:42:00.863611 INFO: rt_error       : 2099.891532
1 day, 8:42:00.863683 INFO: mobility_error : 0.1
1 day, 8:42:00.863754 INFO: num_candidates : 3
1 day, 8:42:00.863822 INFO: ms1_error      : 30
1 day, 8:42:00.863889 INFO: ms2_error      : 30
1 day, 8:42:00.863957 INFO: fwhm_rt        : 3.115100622177124
1 day, 8:42:00.864025 INFO: quant_window   : 3
1 day, 8:42:00.864091 INFO: ==============================================
1 day, 8:42:00.871773 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:42:00.871870 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:42:00.871921 INFO: FWHM in RT is 3.12 seconds, sigma is 0.68
1 day, 8:42:00.871954 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.80
1 day, 8:42:00.872916 INFO: Starting candidate selection
1 day, 8:43:45.749510 INFO: Starting candidate scoring
1 day, 8:43:49.135589 INFO: Finished candidate processing
1 day, 8:43:49.135807 INFO: Collecting candidate features
1 day, 8:43:49.243797 INFO: Collecting fragment features
1 day, 8:43:49.271569 INFO: Finished candidate scoring
1 day, 8:43:49.298946 INFO: performing precursor FDR with 47 features
1 day, 8:43:49.299101 INFO: Decoy channel: -1
1 day, 8:43:49.299138 INFO: competitive: True
1 day, 8:43:49.313670 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:43:49.325364 INFO: Estimating optimal hyperparameters - samples: 36,042, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:43:49.325624 INFO: Using random state 407820 for train-test-split
1 day, 8:43:52.989653 INFO: Test AUC: 0.708
1 day, 8:43:52.989869 INFO: Train AUC: 0.718
1 day, 8:43:52.989903 INFO: AUC difference: 1.38%
1 day, 8:43:53.281205 INFO: Resetting torch num_threads to 128
1 day, 8:43:53.282953 PROGRESS: === Extracted 45053 precursors and 509678 fragments ===
1 day, 8:43:53.283616 INFO: === FDR correction performed with classifier version 0 ===
1 day, 8:43:53.285189 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:43:53.285308 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:43:53.285384 PROGRESS: Target precursors: 7,115 (88.94%)
1 day, 8:43:53.285453 PROGRESS: Decoy precursors: 885 (11.06%)
1 day, 8:43:53.285516 PROGRESS: 
1 day, 8:43:53.285573 PROGRESS: Precursor Summary:
1 day, 8:43:53.288273 PROGRESS: Channel   0:	 0.050 FDR: 6,359; 0.010 FDR: 5,230; 0.001 FDR: 4,005
1 day, 8:43:53.288403 PROGRESS: 
1 day, 8:43:53.288473 PROGRESS: Protein Summary:
1 day, 8:43:53.292455 PROGRESS: Channel   0:	 0.050 FDR: 3,684; 0.010 FDR: 3,120; 0.001 FDR: 2,557
1 day, 8:43:53.292588 PROGRESS: =========================================================================
1 day, 8:43:53.292968 INFO: Target number of precursors reached.
1 day, 8:43:53.383645 INFO: fragments_df: keeping 5000 of 509678 [sum(precursor_idx_mask)=168829 sum(mass_error_mask)=509678 stop_rank=5000
1 day, 8:43:53.412953 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:43:54.114231 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:43:54.835380 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:43:55.535501 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:43:56.190776 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:43:56.191414 INFO: Using score_cutoff 48.902281268692015 (fac=0.99, q=1)
1 day, 8:43:56.191960 INFO: Updating optimization_manager: fwhm_rt             : 3.115100622177124 -> 3.0861833095550537
1 day, 8:43:56.192069 INFO: Updating optimization_manager: fwhm_mobility       : 0.010344716720283031 -> 0.009979696944355965
1 day, 8:43:56.192154 INFO: Updating optimization_manager: score_cutoff        : 49.21660388946533 -> 48.902281268692015
1 day, 8:43:56.192250 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:43:56.195358 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:43:56.205106 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:43:56.207705 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:43:56.230116 INFO: === checking if optimization conditions were reached ===
1 day, 8:43:56.232472 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 8:43:56.232621 INFO: Updating optimization_manager: classifier_version  : 0 -> 1
1 day, 8:43:56.232719 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 8:43:56.234841 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 8:43:56.234998 INFO: Updating optimization_manager: classifier_version  : 1 -> 1
1 day, 8:43:56.235087 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 8:43:56.235169 INFO: ==============================================
1 day, 8:43:56.235262 INFO: Starting optimization step 2.
1 day, 8:43:56.235349 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:43:56.235434 INFO: Using python extraction backend
1 day, 8:43:56.235612 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:43:56.235710 INFO: === Search parameters used ===
1 day, 8:43:56.235785 INFO: rt_error       : 2099.891532
1 day, 8:43:56.235852 INFO: mobility_error : 0.1
1 day, 8:43:56.235917 INFO: num_candidates : 3
1 day, 8:43:56.235981 INFO: ms1_error      : 15.0
1 day, 8:43:56.236044 INFO: ms2_error      : 15.0
1 day, 8:43:56.236108 INFO: fwhm_rt        : 3.0861833095550537
1 day, 8:43:56.236186 INFO: quant_window   : 3
1 day, 8:43:56.236254 INFO: ==============================================
1 day, 8:43:56.244164 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:43:56.244245 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:43:56.244293 INFO: FWHM in RT is 3.09 seconds, sigma is 0.68
1 day, 8:43:56.244334 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.63
1 day, 8:43:56.245295 INFO: Starting candidate selection
1 day, 8:45:28.052884 INFO: Starting candidate scoring
1 day, 8:45:30.061505 INFO: Finished candidate processing
1 day, 8:45:30.061693 INFO: Collecting candidate features
1 day, 8:45:30.160136 INFO: Collecting fragment features
1 day, 8:45:30.185656 INFO: Finished candidate scoring
1 day, 8:45:30.207622 INFO: performing precursor FDR with 47 features
1 day, 8:45:30.207780 INFO: Decoy channel: -1
1 day, 8:45:30.207808 INFO: competitive: True
1 day, 8:45:30.220592 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:45:30.233020 INFO: Estimating optimal hyperparameters - samples: 36,066, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:45:30.233302 INFO: Using random state 538522 for train-test-split
1 day, 8:45:33.902720 INFO: Test AUC: 0.732
1 day, 8:45:33.902884 INFO: Train AUC: 0.746
1 day, 8:45:33.902917 INFO: AUC difference: 1.90%
1 day, 8:45:34.186116 INFO: Resetting torch num_threads to 128
1 day, 8:45:34.187879 PROGRESS: === Extracted 45083 precursors and 496373 fragments ===
1 day, 8:45:34.188509 INFO: === FDR correction performed with classifier version 1 ===
1 day, 8:45:34.190138 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:45:34.190259 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:45:34.190344 PROGRESS: Target precursors: 7,458 (93.23%)
1 day, 8:45:34.190419 PROGRESS: Decoy precursors: 542 (6.78%)
1 day, 8:45:34.190489 PROGRESS: 
1 day, 8:45:34.190570 PROGRESS: Precursor Summary:
1 day, 8:45:34.193551 PROGRESS: Channel   0:	 0.050 FDR: 7,150; 0.010 FDR: 6,581; 0.001 FDR: 5,715
1 day, 8:45:34.193689 PROGRESS: 
1 day, 8:45:34.193792 PROGRESS: Protein Summary:
1 day, 8:45:34.198365 PROGRESS: Channel   0:	 0.050 FDR: 4,033; 0.010 FDR: 3,755; 0.001 FDR: 3,371
1 day, 8:45:34.198488 PROGRESS: =========================================================================
1 day, 8:45:34.198941 INFO: Target number of precursors reached.
1 day, 8:45:34.299780 INFO: fragments_df: keeping 5000 of 496373 [sum(precursor_idx_mask)=207570 sum(mass_error_mask)=496373 stop_rank=5000
1 day, 8:45:34.328442 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:45:35.284514 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:45:36.263143 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:45:37.229867 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:45:37.883178 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:45:37.883829 INFO: Using score_cutoff 40.90902710723877 (fac=0.99, q=1)
1 day, 8:45:37.884404 INFO: Updating optimization_manager: fwhm_rt             : 3.0861833095550537 -> 2.823873996734619
1 day, 8:45:37.884517 INFO: Updating optimization_manager: fwhm_mobility       : 0.009979696944355965 -> 0.008210577070713043
1 day, 8:45:37.884604 INFO: Updating optimization_manager: score_cutoff        : 48.902281268692015 -> 40.90902710723877
1 day, 8:45:37.884703 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:45:37.887762 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:45:37.897994 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:45:37.900570 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:45:37.923006 INFO: === checking if optimization conditions were reached ===
1 day, 8:45:37.925329 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 8:45:37.925478 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
1 day, 8:45:37.925587 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 8:45:37.927894 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 8:45:37.928042 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
1 day, 8:45:37.928146 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 8:45:37.928239 INFO: ==============================================
1 day, 8:45:37.928371 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 8:45:37.951748 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:45:37.955254 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:45:37.965341 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:45:37.968093 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:45:37.991018 INFO: Starting optimization step 0.
1 day, 8:45:37.991273 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:45:37.991389 INFO: Using python extraction backend
1 day, 8:45:37.991609 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:45:37.991748 INFO: === Search parameters used ===
1 day, 8:45:37.991847 INFO: rt_error       : 2099.891532
1 day, 8:45:37.991934 INFO: mobility_error : 0.1
1 day, 8:45:37.992027 INFO: num_candidates : 3
1 day, 8:45:37.992119 INFO: ms1_error      : 15.0
1 day, 8:45:37.992200 INFO: ms2_error      : 15.0
1 day, 8:45:37.992286 INFO: fwhm_rt        : 2.823873996734619
1 day, 8:45:37.992376 INFO: quant_window   : 3
1 day, 8:45:37.992463 INFO: ==============================================
1 day, 8:45:37.998048 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:45:37.998214 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:45:37.998279 INFO: FWHM in RT is 2.82 seconds, sigma is 0.62
1 day, 8:45:37.998322 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.81
1 day, 8:45:37.999454 INFO: Starting candidate selection
1 day, 8:47:10.850846 INFO: Starting candidate scoring
1 day, 8:47:12.750125 INFO: Finished candidate processing
1 day, 8:47:12.750263 INFO: Collecting candidate features
1 day, 8:47:12.816607 INFO: Collecting fragment features
1 day, 8:47:12.842327 INFO: Finished candidate scoring
1 day, 8:47:12.862966 INFO: performing precursor FDR with 47 features
1 day, 8:47:12.863128 INFO: Decoy channel: -1
1 day, 8:47:12.863156 INFO: competitive: True
1 day, 8:47:12.875811 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:47:12.888367 INFO: Estimating optimal hyperparameters - samples: 35,992, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:47:12.888632 INFO: Using random state 33920 for train-test-split
1 day, 8:47:16.415454 INFO: Test AUC: 0.749
1 day, 8:47:16.415610 INFO: Train AUC: 0.757
1 day, 8:47:16.415642 INFO: AUC difference: 1.10%
1 day, 8:47:16.702322 INFO: Resetting torch num_threads to 128
1 day, 8:47:16.704056 PROGRESS: === Extracted 44990 precursors and 495824 fragments ===
1 day, 8:47:16.704680 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:47:16.706190 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:47:16.706308 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:47:16.706393 PROGRESS: Target precursors: 7,480 (93.50%)
1 day, 8:47:16.706464 PROGRESS: Decoy precursors: 520 (6.50%)
1 day, 8:47:16.706523 PROGRESS: 
1 day, 8:47:16.706582 PROGRESS: Precursor Summary:
1 day, 8:47:16.709555 PROGRESS: Channel   0:	 0.050 FDR: 7,219; 0.010 FDR: 6,632; 0.001 FDR: 5,794
1 day, 8:47:16.709679 PROGRESS: 
1 day, 8:47:16.709760 PROGRESS: Protein Summary:
1 day, 8:47:16.714302 PROGRESS: Channel   0:	 0.050 FDR: 4,060; 0.010 FDR: 3,774; 0.001 FDR: 3,396
1 day, 8:47:16.714446 PROGRESS: =========================================================================
1 day, 8:47:16.714770 INFO: Target number of precursors reached.
1 day, 8:47:16.815569 INFO: fragments_df: keeping 5000 of 495824 [sum(precursor_idx_mask)=208617 sum(mass_error_mask)=495824 stop_rank=5000
1 day, 8:47:16.845307 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:47:17.832506 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:47:18.829674 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:47:19.799230 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:47:20.449014 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:47:20.449649 INFO: Using score_cutoff 40.7087239025116 (fac=0.99, q=1)
1 day, 8:47:20.450186 INFO: Updating optimization_manager: fwhm_rt             : 2.823873996734619 -> 2.8052616119384766
1 day, 8:47:20.450289 INFO: Updating optimization_manager: fwhm_mobility       : 0.008210577070713043 -> 0.008122963830828667
1 day, 8:47:20.450360 INFO: Updating optimization_manager: score_cutoff        : 40.90902710723877 -> 40.7087239025116
1 day, 8:47:20.450441 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:47:20.453375 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:47:20.463141 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:47:20.465590 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:47:20.486916 INFO: === checking if optimization conditions were reached ===
1 day, 8:47:20.487154 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 8:47:20.493268 INFO: Updating optimization_manager: rt_error            : 2099.891532 -> 268.84023677758563
1 day, 8:47:20.493438 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 268.8402.
1 day, 8:47:20.493536 INFO: ==============================================
1 day, 8:47:20.493636 INFO: Starting optimization step 1.
1 day, 8:47:20.493727 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:47:20.493840 INFO: Using python extraction backend
1 day, 8:47:20.494016 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:47:20.494116 INFO: === Search parameters used ===
1 day, 8:47:20.494191 INFO: rt_error       : 268.84023677758563
1 day, 8:47:20.494260 INFO: mobility_error : 0.1
1 day, 8:47:20.494327 INFO: num_candidates : 3
1 day, 8:47:20.494452 INFO: ms1_error      : 15.0
1 day, 8:47:20.494546 INFO: ms2_error      : 15.0
1 day, 8:47:20.494634 INFO: fwhm_rt        : 2.8052616119384766
1 day, 8:47:20.494736 INFO: quant_window   : 3
1 day, 8:47:20.494826 INFO: ==============================================
1 day, 8:47:20.501153 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:47:20.501291 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:47:20.501358 INFO: FWHM in RT is 2.81 seconds, sigma is 0.62
1 day, 8:47:20.501403 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.77
1 day, 8:47:20.502420 INFO: Starting candidate selection
1 day, 8:47:37.420337 INFO: Starting candidate scoring
1 day, 8:47:39.353246 INFO: Finished candidate processing
1 day, 8:47:39.353449 INFO: Collecting candidate features
1 day, 8:47:39.440653 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 44893)
1 day, 8:47:39.445970 INFO: Collecting fragment features
1 day, 8:47:39.471795 INFO: Finished candidate scoring
1 day, 8:47:39.493509 INFO: performing precursor FDR with 47 features
1 day, 8:47:39.493664 INFO: Decoy channel: -1
1 day, 8:47:39.493691 INFO: competitive: True
1 day, 8:47:39.505846 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:47:39.512552 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 8:47:39.519256 INFO: Estimating optimal hyperparameters - samples: 35,913, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:47:39.519474 INFO: Using random state 33920 for train-test-split
1 day, 8:47:42.891077 INFO: Test AUC: 0.760
1 day, 8:47:42.891236 INFO: Train AUC: 0.776
1 day, 8:47:42.891269 INFO: AUC difference: 2.00%
1 day, 8:47:43.176607 INFO: Resetting torch num_threads to 128
1 day, 8:47:43.178286 PROGRESS: === Extracted 44893 precursors and 487101 fragments ===
1 day, 8:47:43.178897 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:47:43.180411 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:47:43.180521 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:47:43.180598 PROGRESS: Target precursors: 7,662 (95.78%)
1 day, 8:47:43.180665 PROGRESS: Decoy precursors: 338 (4.23%)
1 day, 8:47:43.180737 PROGRESS: 
1 day, 8:47:43.180798 PROGRESS: Precursor Summary:
1 day, 8:47:43.183862 PROGRESS: Channel   0:	 0.050 FDR: 7,662; 0.010 FDR: 7,275; 0.001 FDR: 6,230
1 day, 8:47:43.183982 PROGRESS: 
1 day, 8:47:43.184054 PROGRESS: Protein Summary:
1 day, 8:47:43.188780 PROGRESS: Channel   0:	 0.050 FDR: 4,245; 0.010 FDR: 4,073; 0.001 FDR: 3,613
1 day, 8:47:43.188902 PROGRESS: =========================================================================
1 day, 8:47:43.189167 INFO: Target number of precursors reached.
1 day, 8:47:43.295664 INFO: fragments_df: keeping 5000 of 487101 [sum(precursor_idx_mask)=226108 sum(mass_error_mask)=487101 stop_rank=5000
1 day, 8:47:43.313577 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:47:44.438212 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:47:45.582056 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:47:46.686427 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:47:47.335077 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:47:47.335757 INFO: Using score_cutoff 36.17400859222412 (fac=0.99, q=1)
1 day, 8:47:47.336321 INFO: Updating optimization_manager: fwhm_rt             : 2.8052616119384766 -> 2.795508623123169
1 day, 8:47:47.336428 INFO: Updating optimization_manager: fwhm_mobility       : 0.008122963830828667 -> 0.007928338833153248
1 day, 8:47:47.336512 INFO: Updating optimization_manager: score_cutoff        : 40.7087239025116 -> 36.17400859222412
1 day, 8:47:47.336608 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:47:47.339560 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:47:47.349316 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:47:47.351955 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:47:47.372599 INFO: === checking if optimization conditions were reached ===
1 day, 8:47:47.372818 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 8:47:47.379454 INFO: Updating optimization_manager: rt_error            : 268.84023677758563 -> 134.71198168262373
1 day, 8:47:47.379613 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 134.7120.
1 day, 8:47:47.379710 INFO: ==============================================
1 day, 8:47:47.379804 INFO: Starting optimization step 2.
1 day, 8:47:47.379890 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:47:47.379983 INFO: Using python extraction backend
1 day, 8:47:47.380155 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:47:47.380263 INFO: === Search parameters used ===
1 day, 8:47:47.380344 INFO: rt_error       : 134.71198168262373
1 day, 8:47:47.380411 INFO: mobility_error : 0.1
1 day, 8:47:47.380476 INFO: num_candidates : 3
1 day, 8:47:47.380541 INFO: ms1_error      : 15.0
1 day, 8:47:47.380606 INFO: ms2_error      : 15.0
1 day, 8:47:47.380671 INFO: fwhm_rt        : 2.795508623123169
1 day, 8:47:47.380735 INFO: quant_window   : 3
1 day, 8:47:47.380795 INFO: ==============================================
1 day, 8:47:47.387182 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:47:47.387295 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:47:47.387363 INFO: FWHM in RT is 2.80 seconds, sigma is 0.61
1 day, 8:47:47.387412 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.68
1 day, 8:47:47.388422 INFO: Starting candidate selection
1 day, 8:47:54.534670 INFO: Starting candidate scoring
1 day, 8:47:56.358779 INFO: Finished candidate processing
1 day, 8:47:56.358983 INFO: Collecting candidate features
1 day, 8:47:56.431633 WARNING: intensity_correlation has 3 NaNs ( 0.01 % out of 44836)
1 day, 8:47:56.436864 INFO: Collecting fragment features
1 day, 8:47:56.462470 INFO: Finished candidate scoring
1 day, 8:47:56.482031 INFO: performing precursor FDR with 47 features
1 day, 8:47:56.482187 INFO: Decoy channel: -1
1 day, 8:47:56.482214 INFO: competitive: True
1 day, 8:47:56.494637 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:47:56.501506 WARNING: dropped 3 decoy PSMs due to missing features
1 day, 8:47:56.509619 INFO: Estimating optimal hyperparameters - samples: 35,866, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:47:56.509862 INFO: Using random state 33920 for train-test-split
1 day, 8:47:59.930135 INFO: Test AUC: 0.783
1 day, 8:47:59.930301 INFO: Train AUC: 0.784
1 day, 8:47:59.930333 INFO: AUC difference: 0.12%
1 day, 8:48:00.212304 INFO: Resetting torch num_threads to 128
1 day, 8:48:00.214028 PROGRESS: === Extracted 44836 precursors and 481219 fragments ===
1 day, 8:48:00.214631 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:48:00.216102 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:48:00.216215 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:48:00.216289 PROGRESS: Target precursors: 7,764 (97.05%)
1 day, 8:48:00.216357 PROGRESS: Decoy precursors: 236 (2.95%)
1 day, 8:48:00.216417 PROGRESS: 
1 day, 8:48:00.216475 PROGRESS: Precursor Summary:
1 day, 8:48:00.219558 PROGRESS: Channel   0:	 0.050 FDR: 7,764; 0.010 FDR: 7,465; 0.001 FDR: 6,740
1 day, 8:48:00.219681 PROGRESS: 
1 day, 8:48:00.219756 PROGRESS: Protein Summary:
1 day, 8:48:00.224587 PROGRESS: Channel   0:	 0.050 FDR: 4,292; 0.010 FDR: 4,166; 0.001 FDR: 3,842
1 day, 8:48:00.224712 PROGRESS: =========================================================================
1 day, 8:48:00.224955 INFO: Target number of precursors reached.
1 day, 8:48:00.330965 INFO: fragments_df: keeping 5000 of 481219 [sum(precursor_idx_mask)=230237 sum(mass_error_mask)=481219 stop_rank=5000
1 day, 8:48:00.348959 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:48:01.504843 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:48:02.681288 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:48:03.831513 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:48:04.484593 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:48:04.485252 INFO: Using score_cutoff 35.17628267669678 (fac=0.99, q=1)
1 day, 8:48:04.485821 INFO: Updating optimization_manager: fwhm_rt             : 2.795508623123169 -> 2.785567283630371
1 day, 8:48:04.485924 INFO: Updating optimization_manager: fwhm_mobility       : 0.007928338833153248 -> 0.007841610349714756
1 day, 8:48:04.485993 INFO: Updating optimization_manager: score_cutoff        : 36.17400859222412 -> 35.17628267669678
1 day, 8:48:04.486070 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:48:04.488980 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:48:04.498831 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:48:04.501289 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:48:04.522277 INFO: === checking if optimization conditions were reached ===
1 day, 8:48:04.522491 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 8:48:04.529311 INFO: Updating optimization_manager: rt_error            : 134.71198168262373 -> 33.33072201783018
1 day, 8:48:04.529497 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 33.3307.
1 day, 8:48:04.529594 INFO: ==============================================
1 day, 8:48:04.529694 INFO: Starting optimization step 3.
1 day, 8:48:04.529796 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:48:04.529894 INFO: Using python extraction backend
1 day, 8:48:04.530062 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:48:04.530236 INFO: === Search parameters used ===
1 day, 8:48:04.530344 INFO: rt_error       : 33.33072201783018
1 day, 8:48:04.530440 INFO: mobility_error : 0.1
1 day, 8:48:04.530538 INFO: num_candidates : 3
1 day, 8:48:04.530628 INFO: ms1_error      : 15.0
1 day, 8:48:04.530715 INFO: ms2_error      : 15.0
1 day, 8:48:04.530819 INFO: fwhm_rt        : 2.785567283630371
1 day, 8:48:04.530904 INFO: quant_window   : 3
1 day, 8:48:04.530989 INFO: ==============================================
1 day, 8:48:04.538082 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:48:04.538206 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:48:04.538272 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1 day, 8:48:04.538318 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.64
1 day, 8:48:04.539356 INFO: Starting candidate selection
1 day, 8:48:07.037010 INFO: Starting candidate scoring
1 day, 8:48:08.782966 INFO: Finished candidate processing
1 day, 8:48:08.783168 INFO: Collecting candidate features
1 day, 8:48:08.874201 WARNING: intensity_correlation has 7 NaNs ( 0.02 % out of 44573)
1 day, 8:48:08.874535 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 44573)
1 day, 8:48:08.879896 INFO: Collecting fragment features
1 day, 8:48:08.908622 INFO: Finished candidate scoring
1 day, 8:48:08.931621 INFO: performing precursor FDR with 47 features
1 day, 8:48:08.931777 INFO: Decoy channel: -1
1 day, 8:48:08.931810 INFO: competitive: True
1 day, 8:48:08.945872 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:48:08.954665 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:48:08.954818 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 8:48:08.963415 INFO: Estimating optimal hyperparameters - samples: 35,652, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:48:08.963684 INFO: Using random state 33920 for train-test-split
1 day, 8:48:12.388104 INFO: Test AUC: 0.808
1 day, 8:48:12.388270 INFO: Train AUC: 0.814
1 day, 8:48:12.388303 INFO: AUC difference: 0.79%
1 day, 8:48:12.663561 INFO: Resetting torch num_threads to 128
1 day, 8:48:12.665224 PROGRESS: === Extracted 44573 precursors and 471169 fragments ===
1 day, 8:48:12.665830 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:48:12.667333 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:48:12.667456 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:48:12.667533 PROGRESS: Target precursors: 7,869 (98.36%)
1 day, 8:48:12.667601 PROGRESS: Decoy precursors: 131 (1.64%)
1 day, 8:48:12.667673 PROGRESS: 
1 day, 8:48:12.667735 PROGRESS: Precursor Summary:
1 day, 8:48:12.670911 PROGRESS: Channel   0:	 0.050 FDR: 7,869; 0.010 FDR: 7,766; 0.001 FDR: 7,017
1 day, 8:48:12.671043 PROGRESS: 
1 day, 8:48:12.671137 PROGRESS: Protein Summary:
1 day, 8:48:12.676187 PROGRESS: Channel   0:	 0.050 FDR: 4,335; 0.010 FDR: 4,294; 0.001 FDR: 3,965
1 day, 8:48:12.676338 PROGRESS: =========================================================================
1 day, 8:48:12.676633 INFO: Target number of precursors reached.
1 day, 8:48:12.784339 INFO: fragments_df: keeping 5000 of 471169 [sum(precursor_idx_mask)=236310 sum(mass_error_mask)=471169 stop_rank=5000
1 day, 8:48:12.802212 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:48:14.025518 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:48:15.271141 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:48:16.501828 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:48:17.153644 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:48:17.154342 INFO: Using score_cutoff 32.672274805068966 (fac=0.99, q=1)
1 day, 8:48:17.154910 INFO: Updating optimization_manager: fwhm_rt             : 2.785567283630371 -> 2.774378538131714
1 day, 8:48:17.155015 INFO: Updating optimization_manager: fwhm_mobility       : 0.007841610349714756 -> 0.007746440824121237
1 day, 8:48:17.155096 INFO: Updating optimization_manager: score_cutoff        : 35.17628267669678 -> 32.672274805068966
1 day, 8:48:17.155179 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:48:17.158185 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:48:17.168070 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:48:17.170669 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:48:17.191968 INFO: === checking if optimization conditions were reached ===
1 day, 8:48:17.192182 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 8:48:17.199232 INFO: Updating optimization_manager: rt_error            : 33.33072201783018 -> 18.096974880686215
1 day, 8:48:17.199411 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 18.0970.
1 day, 8:48:17.199505 INFO: ==============================================
1 day, 8:48:17.199602 INFO: Starting optimization step 4.
1 day, 8:48:17.199687 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:48:17.199777 INFO: Using python extraction backend
1 day, 8:48:17.199942 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:48:17.200037 INFO: === Search parameters used ===
1 day, 8:48:17.200107 INFO: rt_error       : 18.096974880686215
1 day, 8:48:17.200170 INFO: mobility_error : 0.1
1 day, 8:48:17.200234 INFO: num_candidates : 3
1 day, 8:48:17.200296 INFO: ms1_error      : 15.0
1 day, 8:48:17.200361 INFO: ms2_error      : 15.0
1 day, 8:48:17.200420 INFO: fwhm_rt        : 2.774378538131714
1 day, 8:48:17.200485 INFO: quant_window   : 3
1 day, 8:48:17.200544 INFO: ==============================================
1 day, 8:48:17.207683 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:48:17.207776 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:48:17.207822 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 8:48:17.207850 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.59
1 day, 8:48:17.209054 INFO: Starting candidate selection
1 day, 8:48:19.078771 INFO: Starting candidate scoring
1 day, 8:48:20.758343 INFO: Finished candidate processing
1 day, 8:48:20.758553 INFO: Collecting candidate features
1 day, 8:48:20.847784 WARNING: intensity_correlation has 10 NaNs ( 0.02 % out of 44523)
1 day, 8:48:20.848140 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 44523)
1 day, 8:48:20.853454 INFO: Collecting fragment features
1 day, 8:48:20.880891 INFO: Finished candidate scoring
1 day, 8:48:20.907991 INFO: performing precursor FDR with 47 features
1 day, 8:48:20.908143 INFO: Decoy channel: -1
1 day, 8:48:20.908170 INFO: competitive: True
1 day, 8:48:20.929316 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:48:20.938019 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:48:20.938178 WARNING: dropped 10 decoy PSMs due to missing features
1 day, 8:48:20.946325 INFO: Estimating optimal hyperparameters - samples: 35,609, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:48:20.946686 INFO: Using random state 33920 for train-test-split
1 day, 8:48:24.235004 INFO: Test AUC: 0.824
1 day, 8:48:24.235168 INFO: Train AUC: 0.834
1 day, 8:48:24.235200 INFO: AUC difference: 1.17%
1 day, 8:48:24.508994 INFO: Resetting torch num_threads to 128
1 day, 8:48:24.510701 PROGRESS: === Extracted 44523 precursors and 467177 fragments ===
1 day, 8:48:24.511305 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:48:24.512813 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:48:24.512929 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:48:24.513005 PROGRESS: Target precursors: 7,897 (98.71%)
1 day, 8:48:24.513071 PROGRESS: Decoy precursors: 103 (1.29%)
1 day, 8:48:24.513136 PROGRESS: 
1 day, 8:48:24.513197 PROGRESS: Precursor Summary:
1 day, 8:48:24.516421 PROGRESS: Channel   0:	 0.050 FDR: 7,897; 0.010 FDR: 7,873; 0.001 FDR: 7,175
1 day, 8:48:24.516542 PROGRESS: 
1 day, 8:48:24.516618 PROGRESS: Protein Summary:
1 day, 8:48:24.521687 PROGRESS: Channel   0:	 0.050 FDR: 4,354; 0.010 FDR: 4,343; 0.001 FDR: 4,043
1 day, 8:48:24.521838 PROGRESS: =========================================================================
1 day, 8:48:24.522156 INFO: Target number of precursors reached.
1 day, 8:48:24.628458 INFO: fragments_df: keeping 5000 of 467177 [sum(precursor_idx_mask)=238511 sum(mass_error_mask)=467177 stop_rank=5000
1 day, 8:48:24.646200 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:48:25.961134 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:48:27.277000 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:48:28.590262 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:48:29.305065 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:48:29.305764 INFO: Using score_cutoff 32.053494026184076 (fac=0.99, q=1)
1 day, 8:48:29.306342 INFO: Updating optimization_manager: fwhm_rt             : 2.774378538131714 -> 2.7561964988708496
1 day, 8:48:29.306443 INFO: Updating optimization_manager: fwhm_mobility       : 0.007746440824121237 -> 0.007653582841157913
1 day, 8:48:29.306515 INFO: Updating optimization_manager: score_cutoff        : 32.672274805068966 -> 32.053494026184076
1 day, 8:48:29.306583 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:48:29.309507 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:48:29.319321 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:48:29.321831 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:48:29.343036 INFO: === checking if optimization conditions were reached ===
1 day, 8:48:29.343247 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 8:48:29.350275 INFO: Updating optimization_manager: rt_error            : 18.096974880686215 -> 17.60783994645608
1 day, 8:48:29.350435 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 17.6078.
1 day, 8:48:29.350531 INFO: ==============================================
1 day, 8:48:29.350630 INFO: Starting optimization step 5.
1 day, 8:48:29.350718 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:48:29.350806 INFO: Using python extraction backend
1 day, 8:48:29.350971 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:48:29.351069 INFO: === Search parameters used ===
1 day, 8:48:29.351141 INFO: rt_error       : 17.60783994645608
1 day, 8:48:29.351219 INFO: mobility_error : 0.1
1 day, 8:48:29.351331 INFO: num_candidates : 3
1 day, 8:48:29.351423 INFO: ms1_error      : 15.0
1 day, 8:48:29.351511 INFO: ms2_error      : 15.0
1 day, 8:48:29.351596 INFO: fwhm_rt        : 2.7561964988708496
1 day, 8:48:29.351679 INFO: quant_window   : 3
1 day, 8:48:29.351763 INFO: ==============================================
1 day, 8:48:29.357824 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:48:29.357936 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:48:29.358002 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 8:48:29.358048 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.55
1 day, 8:48:29.359440 INFO: Starting candidate selection
1 day, 8:48:31.301140 INFO: Starting candidate scoring
1 day, 8:48:32.978034 INFO: Finished candidate processing
1 day, 8:48:32.978173 INFO: Collecting candidate features
1 day, 8:48:33.066337 WARNING: intensity_correlation has 8 NaNs ( 0.02 % out of 44540)
1 day, 8:48:33.066676 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 44540)
1 day, 8:48:33.071882 INFO: Collecting fragment features
1 day, 8:48:33.100408 INFO: Finished candidate scoring
1 day, 8:48:33.128453 INFO: performing precursor FDR with 47 features
1 day, 8:48:33.128610 INFO: Decoy channel: -1
1 day, 8:48:33.128641 INFO: competitive: True
1 day, 8:48:33.151256 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:48:33.158780 WARNING: dropped 9 decoy PSMs due to missing features
1 day, 8:48:33.167655 INFO: Estimating optimal hyperparameters - samples: 35,624, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:48:33.168024 INFO: Using random state 33920 for train-test-split
1 day, 8:48:36.530780 INFO: Test AUC: 0.827
1 day, 8:48:36.530940 INFO: Train AUC: 0.833
1 day, 8:48:36.530995 INFO: AUC difference: 0.71%
1 day, 8:48:36.806389 INFO: Resetting torch num_threads to 128
1 day, 8:48:36.808074 PROGRESS: === Extracted 44540 precursors and 467344 fragments ===
1 day, 8:48:36.808696 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:48:36.810199 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:48:36.810310 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:48:36.810387 PROGRESS: Target precursors: 7,893 (98.66%)
1 day, 8:48:36.810452 PROGRESS: Decoy precursors: 107 (1.34%)
1 day, 8:48:36.810513 PROGRESS: 
1 day, 8:48:36.810570 PROGRESS: Precursor Summary:
1 day, 8:48:36.813686 PROGRESS: Channel   0:	 0.050 FDR: 7,893; 0.010 FDR: 7,844; 0.001 FDR: 6,898
1 day, 8:48:36.813814 PROGRESS: 
1 day, 8:48:36.813894 PROGRESS: Protein Summary:
1 day, 8:48:36.818913 PROGRESS: Channel   0:	 0.050 FDR: 4,354; 0.010 FDR: 4,328; 0.001 FDR: 3,912
1 day, 8:48:36.819054 PROGRESS: =========================================================================
1 day, 8:48:36.819356 INFO: Target number of precursors reached.
1 day, 8:48:36.926581 INFO: fragments_df: keeping 5000 of 467344 [sum(precursor_idx_mask)=237677 sum(mass_error_mask)=467344 stop_rank=5000
1 day, 8:48:36.944309 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:48:38.186610 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:48:39.430797 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:48:40.677119 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:48:41.327338 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:48:41.327965 INFO: Using score_cutoff 32.66424706764221 (fac=0.99, q=1)
1 day, 8:48:41.328516 INFO: Updating optimization_manager: fwhm_rt             : 2.7561964988708496 -> 2.75748872756958
1 day, 8:48:41.328612 INFO: Updating optimization_manager: fwhm_mobility       : 0.007653582841157913 -> 0.007697969675064087
1 day, 8:48:41.328681 INFO: Updating optimization_manager: score_cutoff        : 32.053494026184076 -> 32.66424706764221
1 day, 8:48:41.328767 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:48:41.331657 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:48:41.341380 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:48:41.343871 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:48:41.365093 INFO: === checking if optimization conditions were reached ===
1 day, 8:48:41.365327 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 8:48:41.366892 INFO: Updating optimization_manager: rt_error            : 17.60783994645608 -> 17.60783994645608
1 day, 8:48:41.367084 INFO: Updating optimization_manager: classifier_version  : 2 -> 8
1 day, 8:48:41.367240 INFO: Updating optimization_manager: score_cutoff        : 32.66424706764221 -> 32.66424706764221
1 day, 8:48:41.367411 INFO: Updating optimization_manager: fwhm_rt             : 2.75748872756958 -> 2.75748872756958
1 day, 8:48:41.367564 INFO: Updating optimization_manager: fwhm_mobility       : 0.007697969675064087 -> 0.007697969675064087
1 day, 8:48:41.367712 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 17.6078 found after 6 searches.
1 day, 8:48:41.367832 INFO: ==============================================
1 day, 8:48:41.367948 PROGRESS: Optimization finished for rt_error.
1 day, 8:48:41.392708 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:48:41.395971 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:48:41.406186 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:48:41.408930 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:48:41.431319 INFO: Starting optimization step 0.
1 day, 8:48:41.431559 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:48:41.431694 INFO: Using python extraction backend
1 day, 8:48:41.431913 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:48:41.432050 INFO: === Search parameters used ===
1 day, 8:48:41.432150 INFO: rt_error       : 17.60783994645608
1 day, 8:48:41.432243 INFO: mobility_error : 0.1
1 day, 8:48:41.432330 INFO: num_candidates : 3
1 day, 8:48:41.432414 INFO: ms1_error      : 15.0
1 day, 8:48:41.432494 INFO: ms2_error      : 15.0
1 day, 8:48:41.432578 INFO: fwhm_rt        : 2.75748872756958
1 day, 8:48:41.432667 INFO: quant_window   : 3
1 day, 8:48:41.432756 INFO: ==============================================
1 day, 8:48:41.438919 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:48:41.439039 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:48:41.439106 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 8:48:41.439150 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
1 day, 8:48:41.440326 INFO: Starting candidate selection
1 day, 8:48:43.361853 INFO: Starting candidate scoring
1 day, 8:48:45.108798 INFO: Finished candidate processing
1 day, 8:48:45.109016 INFO: Collecting candidate features
1 day, 8:48:45.200225 WARNING: intensity_correlation has 8 NaNs ( 0.02 % out of 44535)
1 day, 8:48:45.200560 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 44535)
1 day, 8:48:45.206044 INFO: Collecting fragment features
1 day, 8:48:45.234438 INFO: Finished candidate scoring
1 day, 8:48:45.260614 INFO: performing precursor FDR with 47 features
1 day, 8:48:45.260766 INFO: Decoy channel: -1
1 day, 8:48:45.260802 INFO: competitive: True
1 day, 8:48:45.274757 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:48:45.281576 WARNING: dropped 9 decoy PSMs due to missing features
1 day, 8:48:45.290442 INFO: Estimating optimal hyperparameters - samples: 35,620, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:48:45.290702 INFO: Using random state 903296 for train-test-split
1 day, 8:48:48.852077 INFO: Test AUC: 0.834
1 day, 8:48:48.852250 INFO: Train AUC: 0.844
1 day, 8:48:48.852284 INFO: AUC difference: 1.13%
1 day, 8:48:49.127798 INFO: Resetting torch num_threads to 128
1 day, 8:48:49.129484 PROGRESS: === Extracted 44535 precursors and 467325 fragments ===
1 day, 8:48:49.130081 INFO: === FDR correction performed with classifier version 8 ===
1 day, 8:48:49.131580 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:48:49.131691 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:48:49.131768 PROGRESS: Target precursors: 7,903 (98.79%)
1 day, 8:48:49.131834 PROGRESS: Decoy precursors: 97 (1.21%)
1 day, 8:48:49.131899 PROGRESS: 
1 day, 8:48:49.131966 PROGRESS: Precursor Summary:
1 day, 8:48:49.135235 PROGRESS: Channel   0:	 0.050 FDR: 7,903; 0.010 FDR: 7,860; 0.001 FDR: 7,501
1 day, 8:48:49.135368 PROGRESS: 
1 day, 8:48:49.135444 PROGRESS: Protein Summary:
1 day, 8:48:49.140514 PROGRESS: Channel   0:	 0.050 FDR: 4,358; 0.010 FDR: 4,336; 0.001 FDR: 4,185
1 day, 8:48:49.140637 PROGRESS: =========================================================================
1 day, 8:48:49.140881 INFO: Target number of precursors reached.
1 day, 8:48:49.249835 INFO: fragments_df: keeping 5000 of 467325 [sum(precursor_idx_mask)=238195 sum(mass_error_mask)=467325 stop_rank=5000
1 day, 8:48:49.267640 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:48:50.516689 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:48:51.768824 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:48:53.013633 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:48:53.661428 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:48:53.662089 INFO: Using score_cutoff 32.33242111816406 (fac=0.99, q=1)
1 day, 8:48:53.662617 INFO: Updating optimization_manager: fwhm_rt             : 2.75748872756958 -> 2.7609519958496094
1 day, 8:48:53.662716 INFO: Updating optimization_manager: fwhm_mobility       : 0.007697969675064087 -> 0.00767882727086544
1 day, 8:48:53.662805 INFO: Updating optimization_manager: score_cutoff        : 32.66424706764221 -> 32.33242111816406
1 day, 8:48:53.662893 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:48:53.665921 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:48:53.675593 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:48:53.678154 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:48:53.699133 INFO: === checking if optimization conditions were reached ===
1 day, 8:48:53.699372 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 8:48:53.702541 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07716735265626533
1 day, 8:48:53.702687 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0772.
1 day, 8:48:53.702785 INFO: ==============================================
1 day, 8:48:53.702887 INFO: Starting optimization step 1.
1 day, 8:48:53.702979 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:48:53.703071 INFO: Using python extraction backend
1 day, 8:48:53.703244 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:48:53.703357 INFO: === Search parameters used ===
1 day, 8:48:53.703436 INFO: rt_error       : 17.60783994645608
1 day, 8:48:53.703507 INFO: mobility_error : 0.07716735265626533
1 day, 8:48:53.703575 INFO: num_candidates : 3
1 day, 8:48:53.703640 INFO: ms1_error      : 15.0
1 day, 8:48:53.703710 INFO: ms2_error      : 15.0
1 day, 8:48:53.703778 INFO: fwhm_rt        : 2.7609519958496094
1 day, 8:48:53.703842 INFO: quant_window   : 3
1 day, 8:48:53.703911 INFO: ==============================================
1 day, 8:48:53.710116 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:48:53.710196 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:48:53.710269 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 8:48:53.710316 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.56
1 day, 8:48:53.711411 INFO: Starting candidate selection
1 day, 8:48:55.338478 INFO: Starting candidate scoring
1 day, 8:48:57.042048 INFO: Finished candidate processing
1 day, 8:48:57.042258 INFO: Collecting candidate features
1 day, 8:48:57.134920 WARNING: intensity_correlation has 9 NaNs ( 0.02 % out of 44472)
1 day, 8:48:57.135278 WARNING: height_correlation has 1 NaNs ( 0.00 % out of 44472)
1 day, 8:48:57.141314 INFO: Collecting fragment features
1 day, 8:48:57.172204 INFO: Finished candidate scoring
1 day, 8:48:57.199943 INFO: performing precursor FDR with 47 features
1 day, 8:48:57.200108 INFO: Decoy channel: -1
1 day, 8:48:57.200150 INFO: competitive: True
1 day, 8:48:57.213872 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:48:57.222559 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:48:57.222733 WARNING: dropped 9 decoy PSMs due to missing features
1 day, 8:48:57.230787 INFO: Estimating optimal hyperparameters - samples: 35,569, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:48:57.231025 INFO: Using random state 903296 for train-test-split
1 day, 8:49:00.744030 INFO: Test AUC: 0.830
1 day, 8:49:00.744203 INFO: Train AUC: 0.845
1 day, 8:49:00.744236 INFO: AUC difference: 1.68%
1 day, 8:49:01.018402 INFO: Resetting torch num_threads to 128
1 day, 8:49:01.020088 PROGRESS: === Extracted 44472 precursors and 464873 fragments ===
1 day, 8:49:01.020700 INFO: === FDR correction performed with classifier version 8 ===
1 day, 8:49:01.022187 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:49:01.022303 PROGRESS: Total precursors accumulated: 7,991
1 day, 8:49:01.022380 PROGRESS: Target precursors: 7,883 (98.65%)
1 day, 8:49:01.022447 PROGRESS: Decoy precursors: 108 (1.35%)
1 day, 8:49:01.022515 PROGRESS: 
1 day, 8:49:01.022575 PROGRESS: Precursor Summary:
1 day, 8:49:01.025767 PROGRESS: Channel   0:	 0.050 FDR: 7,883; 0.010 FDR: 7,825; 0.001 FDR: 7,318
1 day, 8:49:01.025890 PROGRESS: 
1 day, 8:49:01.025975 PROGRESS: Protein Summary:
1 day, 8:49:01.031007 PROGRESS: Channel   0:	 0.050 FDR: 4,351; 0.010 FDR: 4,329; 0.001 FDR: 4,101
1 day, 8:49:01.031154 PROGRESS: =========================================================================
1 day, 8:49:01.031444 INFO: Target number of precursors reached.
1 day, 8:49:01.138482 INFO: fragments_df: keeping 5000 of 464873 [sum(precursor_idx_mask)=236732 sum(mass_error_mask)=464873 stop_rank=5000
1 day, 8:49:01.155894 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:49:02.406037 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:49:03.646831 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:49:04.885726 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:49:05.538347 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:49:05.539008 INFO: Using score_cutoff 31.596388233947753 (fac=0.99, q=1)
1 day, 8:49:05.539575 INFO: Updating optimization_manager: fwhm_rt             : 2.7609519958496094 -> 2.76041316986084
1 day, 8:49:05.539671 INFO: Updating optimization_manager: fwhm_mobility       : 0.00767882727086544 -> 0.007699367590248585
1 day, 8:49:05.539737 INFO: Updating optimization_manager: score_cutoff        : 32.33242111816406 -> 31.596388233947753
1 day, 8:49:05.539810 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:49:05.542829 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:49:05.552523 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:49:05.555041 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:49:05.575512 INFO: === checking if optimization conditions were reached ===
1 day, 8:49:05.575706 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 8:49:05.578956 INFO: Updating optimization_manager: mobility_error      : 0.07716735265626533 -> 0.06638076154962222
1 day, 8:49:05.579120 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0664.
1 day, 8:49:05.579214 INFO: ==============================================
1 day, 8:49:05.579308 INFO: Starting optimization step 2.
1 day, 8:49:05.579392 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:49:05.579479 INFO: Using python extraction backend
1 day, 8:49:05.579643 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:49:05.579736 INFO: === Search parameters used ===
1 day, 8:49:05.579812 INFO: rt_error       : 17.60783994645608
1 day, 8:49:05.579879 INFO: mobility_error : 0.06638076154962222
1 day, 8:49:05.579944 INFO: num_candidates : 3
1 day, 8:49:05.580008 INFO: ms1_error      : 15.0
1 day, 8:49:05.580075 INFO: ms2_error      : 15.0
1 day, 8:49:05.580137 INFO: fwhm_rt        : 2.76041316986084
1 day, 8:49:05.580212 INFO: quant_window   : 3
1 day, 8:49:05.580275 INFO: ==============================================
1 day, 8:49:05.587684 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:49:05.587761 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:49:05.587810 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 8:49:05.587843 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
1 day, 8:49:05.588734 INFO: Starting candidate selection
1 day, 8:49:07.126928 INFO: Starting candidate scoring
1 day, 8:49:08.807795 INFO: Finished candidate processing
1 day, 8:49:08.808018 INFO: Collecting candidate features
1 day, 8:49:08.898184 WARNING: intensity_correlation has 12 NaNs ( 0.03 % out of 44439)
1 day, 8:49:08.898479 WARNING: height_correlation has 2 NaNs ( 0.00 % out of 44439)
1 day, 8:49:08.903611 INFO: Collecting fragment features
1 day, 8:49:08.931782 INFO: Finished candidate scoring
1 day, 8:49:08.957431 INFO: performing precursor FDR with 47 features
1 day, 8:49:08.957583 INFO: Decoy channel: -1
1 day, 8:49:08.957611 INFO: competitive: True
1 day, 8:49:08.979368 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:49:08.988133 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:49:08.988294 WARNING: dropped 12 decoy PSMs due to missing features
1 day, 8:49:08.995093 INFO: Estimating optimal hyperparameters - samples: 35,540, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:49:08.995438 INFO: Using random state 903296 for train-test-split
1 day, 8:49:12.410740 INFO: Test AUC: 0.836
1 day, 8:49:12.410905 INFO: Train AUC: 0.841
1 day, 8:49:12.410938 INFO: AUC difference: 0.64%
1 day, 8:49:12.684184 INFO: Resetting torch num_threads to 128
1 day, 8:49:12.685920 PROGRESS: === Extracted 44439 precursors and 463068 fragments ===
1 day, 8:49:12.686514 INFO: === FDR correction performed with classifier version 8 ===
1 day, 8:49:12.688000 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:49:12.688110 PROGRESS: Total precursors accumulated: 7,987
1 day, 8:49:12.688185 PROGRESS: Target precursors: 7,860 (98.41%)
1 day, 8:49:12.688257 PROGRESS: Decoy precursors: 127 (1.59%)
1 day, 8:49:12.688323 PROGRESS: 
1 day, 8:49:12.688386 PROGRESS: Precursor Summary:
1 day, 8:49:12.691566 PROGRESS: Channel   0:	 0.050 FDR: 7,860; 0.010 FDR: 7,780; 0.001 FDR: 7,303
1 day, 8:49:12.691690 PROGRESS: 
1 day, 8:49:12.691779 PROGRESS: Protein Summary:
1 day, 8:49:12.696836 PROGRESS: Channel   0:	 0.050 FDR: 4,351; 0.010 FDR: 4,316; 0.001 FDR: 4,097
1 day, 8:49:12.696998 PROGRESS: =========================================================================
1 day, 8:49:12.697294 INFO: Target number of precursors reached.
1 day, 8:49:12.802628 INFO: fragments_df: keeping 5000 of 463068 [sum(precursor_idx_mask)=235114 sum(mass_error_mask)=463068 stop_rank=5000
1 day, 8:49:12.820426 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:49:14.067267 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:49:15.298580 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:49:16.530941 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:49:19.508515 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:49:19.509214 INFO: Using score_cutoff 31.63019219226837 (fac=0.99, q=1)
1 day, 8:49:19.509796 INFO: Updating optimization_manager: fwhm_rt             : 2.76041316986084 -> 2.7612664699554443
1 day, 8:49:19.509900 INFO: Updating optimization_manager: fwhm_mobility       : 0.007699367590248585 -> 0.0077141039073467255
1 day, 8:49:19.509970 INFO: Updating optimization_manager: score_cutoff        : 31.596388233947753 -> 31.63019219226837
1 day, 8:49:19.510046 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:49:19.513261 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:49:19.523132 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:49:19.525756 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:49:19.547762 INFO: === checking if optimization conditions were reached ===
1 day, 8:49:19.548025 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 8:49:19.549205 INFO: Updating optimization_manager: mobility_error      : 0.06638076154962222 -> 0.1
1 day, 8:49:19.549379 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1 day, 8:49:19.549512 INFO: Updating optimization_manager: score_cutoff        : 31.63019219226837 -> 32.33242111816406
1 day, 8:49:19.549637 INFO: Updating optimization_manager: fwhm_rt             : 2.7612664699554443 -> 2.7609519958496094
1 day, 8:49:19.549803 INFO: Updating optimization_manager: fwhm_mobility       : 0.0077141039073467255 -> 0.00767882727086544
1 day, 8:49:19.549971 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 8:49:19.550090 INFO: ==============================================
1 day, 8:49:19.550208 PROGRESS: Optimization finished for mobility_error.
1 day, 8:49:19.574209 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:49:19.577882 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:49:19.588137 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:49:19.590982 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:49:19.613950 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 8:49:19.614224 PROGRESS: ==============================================
1 day, 8:49:19.614355 PROGRESS: ms2_error      : 15.0000
1 day, 8:49:19.614464 PROGRESS: ms1_error      : 15.0000
1 day, 8:49:19.614562 PROGRESS: rt_error       : 17.6078
1 day, 8:49:19.614655 PROGRESS: mobility_error : 0.1000
1 day, 8:49:19.614743 PROGRESS: ==============================================
1 day, 8:49:19.616196 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:49:19.638919 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:49:19.745019 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:49:19.769300 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:49:20.038114 INFO: Using python extraction backend
1 day, 8:49:20.038708 PROGRESS: Extracting batch of 182033 precursors
1 day, 8:49:20.038860 INFO: === Search parameters used ===
1 day, 8:49:20.038965 INFO: rt_error       : 17.60783994645608
1 day, 8:49:20.039063 INFO: mobility_error : 0.1
1 day, 8:49:20.039158 INFO: num_candidates : 3
1 day, 8:49:20.039248 INFO: ms1_error      : 15.0
1 day, 8:49:20.039335 INFO: ms2_error      : 15.0
1 day, 8:49:20.039430 INFO: fwhm_rt        : 2.7609519958496094
1 day, 8:49:20.039514 INFO: quant_window   : 3
1 day, 8:49:20.039602 INFO: ==============================================
1 day, 8:49:20.092257 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:49:20.092440 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:49:20.092492 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 8:49:20.092517 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.56
1 day, 8:49:20.093307 INFO: Starting candidate selection
1 day, 8:49:36.575089 INFO: Removed 70492 precursors with score below cutoff 32.33242111816406
1 day, 8:49:36.992354 INFO: Starting candidate scoring
1 day, 8:49:52.859866 INFO: Finished candidate processing
1 day, 8:49:52.860096 INFO: Collecting candidate features
1 day, 8:49:53.886360 INFO: Collecting fragment features
1 day, 8:49:54.321379 INFO: Finished candidate scoring
1 day, 8:49:54.591337 INFO: === Performing FDR correction with classifier version 9 ===
1 day, 8:49:54.594404 INFO: performing precursor FDR with 47 features
1 day, 8:49:54.594464 INFO: Decoy channel: -1
1 day, 8:49:54.594514 INFO: competitive: True
1 day, 8:49:54.710511 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:49:54.759458 WARNING: FDR calculation for 241357 target and 200177 decoy PSMs
1 day, 8:49:54.759636 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 8:49:54.972416 INFO: Estimating optimal hyperparameters - samples: 353,227, batch_size: 1,446, learning_rate: 5.94e-04
1 day, 8:49:54.973330 INFO: Using random state 950788 for train-test-split
1 day, 8:50:08.444225 INFO: Test AUC: 0.844
1 day, 8:50:08.444407 INFO: Train AUC: 0.848
1 day, 8:50:08.444439 INFO: AUC difference: 0.49%
1 day, 8:50:08.860536 INFO: Resetting torch num_threads to 128
1 day, 8:50:08.882699 INFO: Removing fragments below FDR threshold
1 day, 8:50:09.014361 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:50:09.014710 PROGRESS: Total precursors accumulated: 90,482
1 day, 8:50:09.014795 PROGRESS: Target precursors: 89,587 (99.01%)
1 day, 8:50:09.014883 PROGRESS: Decoy precursors: 895 (0.99%)
1 day, 8:50:09.014973 PROGRESS: 
1 day, 8:50:09.015055 PROGRESS: Precursor Summary:
1 day, 8:50:09.059843 PROGRESS: Channel   0:	 0.050 FDR: 89,587; 0.010 FDR: 89,587; 0.001 FDR: 85,443
1 day, 8:50:09.060224 PROGRESS: 
1 day, 8:50:09.060356 PROGRESS: Protein Summary:
1 day, 8:50:09.118191 PROGRESS: Channel   0:	 0.050 FDR: 8,979; 0.010 FDR: 8,979; 0.001 FDR: 8,962
1 day, 8:50:09.118553 PROGRESS: =========================================================================
1 day, 8:50:09.128425 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/psm.parquet
1 day, 8:50:09.499752 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/frag.parquet
1 day, 8:50:09.818679 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 8:50:09.883944 PROGRESS: Loading raw file 5/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502 
1 day, 8:50:09.884141 INFO: Quantification results path: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant
1 day, 8:50:09.884237 INFO: Creating folder /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/figures
1 day, 8:50:09.884430 INFO: Initializing TimingManager
1 day, 8:50:09.885280 INFO: Initializing RawFileManager
1 day, 8:50:09.885412 INFO: Importing data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 8:50:09.885453 INFO: Using .d import for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 8:50:09.885484 INFO: Reading frame metadata for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 8:50:10.212928 INFO: Reading 39,128 frames with 2,766,418,119 detector events for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 8:50:19.790464 INFO: Indexing /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d...
1 day, 8:50:19.792046 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 8:50:19.794538 INFO: Fetching mobility values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 8:50:19.794778 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 8:50:19.795224 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 8:50:19.797291 INFO: Fetching mz values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 8:50:19.830014 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 8:50:19.830324 INFO: Indexing quadrupole dimension
1 day, 8:50:20.368228 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 8:50:20.368393 INFO: Transposing detector events
1 day, 8:50:29.232900 INFO: Finished transposing data
1 day, 8:50:29.315574 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502.d
1 day, 8:50:29.316344 INFO: RT (min)            : 0.0 - 70.0
1 day, 8:50:29.316395 INFO: RT duration (sec)   : 4199.9
1 day, 8:50:29.316427 INFO: RT duration (min)   : 70.0
1 day, 8:50:29.316453 INFO: Cycle len (scans)   : 9
1 day, 8:50:29.316477 INFO: Cycle len (sec)     : 0.97
1 day, 8:50:29.316505 INFO: Number of cycles    : 4347
1 day, 8:50:29.316531 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 8:50:29.316567 INFO: Creating DIA data object took: 19.431167364120483
1 day, 8:50:29.367847 INFO: Initializing CalibrationManager
1 day, 8:50:29.368247 INFO: Setting up calibration estimators ..
1 day, 8:50:29.368331 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 8:50:29.368428 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, 8:50:29.368546 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 8:50:29.368628 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, 8:50:29.368706 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, 8:50:29.368788 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, 8:50:29.368860 INFO: Done setting up calibration estimators.
1 day, 8:50:29.368999 INFO: Initializing OptimizationManager
1 day, 8:50:29.369126 INFO: initial parameter: ms1_error = 30
1 day, 8:50:29.369194 INFO: initial parameter: ms2_error = 30
1 day, 8:50:29.369256 INFO: initial parameter: rt_error = 2099.9331315
1 day, 8:50:29.369318 INFO: initial parameter: mobility_error = 0.1
1 day, 8:50:29.369378 INFO: initial parameter: num_candidates = 1
1 day, 8:50:29.369436 INFO: initial parameter: fwhm_rt = 5
1 day, 8:50:29.369496 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 8:50:29.369554 INFO: initial parameter: score_cutoff = 0
1 day, 8:50:29.369612 INFO: initial parameter: classifier_version = -1
1 day, 8:50:29.369710 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 8:50:29.369974 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 8:50:29.370019 INFO: Initializing FDRManager
1 day, 8:50:29.370063 INFO: Loading classifier store from /usr/local/lib/python3.10/site-packages/alphadia/constants/classifier
1 day, 8:50:29.403042 PROGRESS: Initializing spectral library: 91,740 target precursors potentially observable (0 removed)
1 day, 8:50:29.440745 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 8:50:29.441384 INFO: Updating optimization_manager: rt_error            : 2099.9331315 -> 2099.9331315
1 day, 8:50:29.441510 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 8:50:29.441732 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 8:50:29.441857 PROGRESS: Starting initial search for precursors.
1 day, 8:50:29.441972 INFO: Starting optimization step 0.
1 day, 8:50:29.442058 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:50:29.442145 INFO: Using python extraction backend
1 day, 8:50:29.442308 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:50:29.442395 INFO: === Search parameters used ===
1 day, 8:50:29.442465 INFO: rt_error       : 2099.9331315
1 day, 8:50:29.442532 INFO: mobility_error : 0.1
1 day, 8:50:29.442594 INFO: num_candidates : 1
1 day, 8:50:29.442657 INFO: ms1_error      : 30
1 day, 8:50:29.442720 INFO: ms2_error      : 30
1 day, 8:50:29.442781 INFO: fwhm_rt        : 5
1 day, 8:50:29.442842 INFO: quant_window   : 3
1 day, 8:50:29.442904 INFO: ==============================================
1 day, 8:50:29.445952 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:50:29.446017 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:50:29.446051 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 8:50:29.446077 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 8:50:29.450113 INFO: Starting candidate selection
1 day, 8:52:01.443604 INFO: Starting candidate scoring
1 day, 8:52:02.667826 INFO: Finished candidate processing
1 day, 8:52:02.668030 INFO: Collecting candidate features
1 day, 8:52:02.732167 INFO: Collecting fragment features
1 day, 8:52:02.747126 INFO: Finished candidate scoring
1 day, 8:52:02.761779 INFO: performing precursor FDR with 47 features
1 day, 8:52:02.761915 INFO: Decoy channel: -1
1 day, 8:52:02.761940 INFO: competitive: True
1 day, 8:52:02.767901 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:52:02.773908 INFO: Estimating optimal hyperparameters - samples: 12,695, batch_size: 128, learning_rate: 1.77e-04
1 day, 8:52:02.774976 INFO: Using random state 783304 for train-test-split
1 day, 8:52:04.398384 INFO: Test AUC: 0.830
1 day, 8:52:04.398532 INFO: Train AUC: 0.845
1 day, 8:52:04.398563 INFO: AUC difference: 1.77%
1 day, 8:52:04.677393 INFO: Resetting torch num_threads to 128
1 day, 8:52:04.678548 PROGRESS: === Extracted 15869 precursors and 179808 fragments ===
1 day, 8:52:04.679128 INFO: === FDR correction performed with classifier version -1 ===
1 day, 8:52:04.680742 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:52:04.680859 PROGRESS: Total precursors accumulated: 7,995
1 day, 8:52:04.680930 PROGRESS: Target precursors: 6,743 (84.34%)
1 day, 8:52:04.681011 PROGRESS: Decoy precursors: 1,252 (15.66%)
1 day, 8:52:04.681085 PROGRESS: 
1 day, 8:52:04.681154 PROGRESS: Precursor Summary:
1 day, 8:52:04.684238 PROGRESS: Channel   0:	 0.050 FDR: 5,261; 0.010 FDR: 4,642; 0.001 FDR: 3,765
1 day, 8:52:04.684373 PROGRESS: 
1 day, 8:52:04.684464 PROGRESS: Protein Summary:
1 day, 8:52:04.688222 PROGRESS: Channel   0:	 0.050 FDR: 3,137; 0.010 FDR: 2,826; 0.001 FDR: 2,410
1 day, 8:52:04.688346 PROGRESS: =========================================================================
1 day, 8:52:04.688495 INFO: Target number of precursors reached.
1 day, 8:52:04.719683 INFO: fragments_df: keeping 5000 of 179808 [sum(precursor_idx_mask)=52699 sum(mass_error_mask)=179808 stop_rank=5000
1 day, 8:52:04.755306 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:52:05.429731 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:52:06.119807 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:52:06.798673 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:52:07.534549 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 8:52:07.535196 INFO: Using score_cutoff 48.80401010513306 (fac=0.99, q=1)
1 day, 8:52:07.535721 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.1077070236206055
1 day, 8:52:07.535827 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010354103520512581
1 day, 8:52:07.535907 INFO: Updating optimization_manager: score_cutoff        : 0 -> 48.80401010513306
1 day, 8:52:07.535996 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:52:07.539275 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:52:07.548742 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:52:07.551303 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:52:07.571595 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
1 day, 8:52:07.571814 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 8:52:07.571927 INFO: Starting optimization step 1.
1 day, 8:52:07.572017 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:52:07.572108 INFO: Using python extraction backend
1 day, 8:52:07.572259 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:52:07.572352 INFO: === Search parameters used ===
1 day, 8:52:07.572428 INFO: rt_error       : 2099.9331315
1 day, 8:52:07.572492 INFO: mobility_error : 0.1
1 day, 8:52:07.572559 INFO: num_candidates : 3
1 day, 8:52:07.572634 INFO: ms1_error      : 30
1 day, 8:52:07.572700 INFO: ms2_error      : 30
1 day, 8:52:07.572773 INFO: fwhm_rt        : 3.1077070236206055
1 day, 8:52:07.572843 INFO: quant_window   : 3
1 day, 8:52:07.572911 INFO: ==============================================
1 day, 8:52:07.577125 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:52:07.577199 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:52:07.577243 INFO: FWHM in RT is 3.11 seconds, sigma is 0.68
1 day, 8:52:07.577276 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.80
1 day, 8:52:07.578158 INFO: Starting candidate selection
1 day, 8:53:50.163827 INFO: Starting candidate scoring
1 day, 8:53:53.596591 INFO: Finished candidate processing
1 day, 8:53:53.596790 INFO: Collecting candidate features
1 day, 8:53:53.692075 INFO: Collecting fragment features
1 day, 8:53:53.721117 INFO: Finished candidate scoring
1 day, 8:53:53.747160 INFO: performing precursor FDR with 47 features
1 day, 8:53:53.747321 INFO: Decoy channel: -1
1 day, 8:53:53.747349 INFO: competitive: True
1 day, 8:53:53.762479 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:53:53.776691 INFO: Estimating optimal hyperparameters - samples: 36,076, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:53:53.777083 INFO: Using random state 676172 for train-test-split
1 day, 8:53:57.974329 INFO: Test AUC: 0.711
1 day, 8:53:57.974581 INFO: Train AUC: 0.717
1 day, 8:53:57.974617 INFO: AUC difference: 0.90%
1 day, 8:53:58.273555 INFO: Resetting torch num_threads to 128
1 day, 8:53:58.275054 PROGRESS: === Extracted 45095 precursors and 510387 fragments ===
1 day, 8:53:58.275751 INFO: === FDR correction performed with classifier version 0 ===
1 day, 8:53:58.277357 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:53:58.277480 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:53:58.277564 PROGRESS: Target precursors: 7,088 (88.60%)
1 day, 8:53:58.277636 PROGRESS: Decoy precursors: 912 (11.40%)
1 day, 8:53:58.277700 PROGRESS: 
1 day, 8:53:58.277772 PROGRESS: Precursor Summary:
1 day, 8:53:58.280786 PROGRESS: Channel   0:	 0.050 FDR: 6,138; 0.010 FDR: 5,473; 0.001 FDR: 4,236
1 day, 8:53:58.280920 PROGRESS: 
1 day, 8:53:58.280993 PROGRESS: Protein Summary:
1 day, 8:53:58.284959 PROGRESS: Channel   0:	 0.050 FDR: 3,567; 0.010 FDR: 3,232; 0.001 FDR: 2,663
1 day, 8:53:58.285094 PROGRESS: =========================================================================
1 day, 8:53:58.285633 INFO: Target number of precursors reached.
1 day, 8:53:58.383719 INFO: fragments_df: keeping 5000 of 510387 [sum(precursor_idx_mask)=176709 sum(mass_error_mask)=510387 stop_rank=5000
1 day, 8:53:58.410910 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:53:59.234239 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:54:00.064710 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:54:00.886428 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:54:01.609714 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:54:01.610351 INFO: Using score_cutoff 48.389767781066894 (fac=0.99, q=1)
1 day, 8:54:01.610929 INFO: Updating optimization_manager: fwhm_rt             : 3.1077070236206055 -> 3.066870927810669
1 day, 8:54:01.611032 INFO: Updating optimization_manager: fwhm_mobility       : 0.010354103520512581 -> 0.010009457357227802
1 day, 8:54:01.611104 INFO: Updating optimization_manager: score_cutoff        : 48.80401010513306 -> 48.389767781066894
1 day, 8:54:01.611184 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:54:01.614293 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:54:01.623873 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:54:01.626392 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:54:01.646817 INFO: === checking if optimization conditions were reached ===
1 day, 8:54:01.648908 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 8:54:01.649035 INFO: Updating optimization_manager: classifier_version  : 0 -> 1
1 day, 8:54:01.649118 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 8:54:01.651026 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 8:54:01.651167 INFO: Updating optimization_manager: classifier_version  : 1 -> 1
1 day, 8:54:01.651245 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 8:54:01.651316 INFO: ==============================================
1 day, 8:54:01.651399 INFO: Starting optimization step 2.
1 day, 8:54:01.651474 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:54:01.651551 INFO: Using python extraction backend
1 day, 8:54:01.651730 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:54:01.651815 INFO: === Search parameters used ===
1 day, 8:54:01.651880 INFO: rt_error       : 2099.9331315
1 day, 8:54:01.651934 INFO: mobility_error : 0.1
1 day, 8:54:01.651985 INFO: num_candidates : 3
1 day, 8:54:01.652039 INFO: ms1_error      : 15.0
1 day, 8:54:01.652091 INFO: ms2_error      : 15.0
1 day, 8:54:01.652145 INFO: fwhm_rt        : 3.066870927810669
1 day, 8:54:01.652211 INFO: quant_window   : 3
1 day, 8:54:01.652261 INFO: ==============================================
1 day, 8:54:01.656388 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:54:01.656459 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:54:01.656515 INFO: FWHM in RT is 3.07 seconds, sigma is 0.67
1 day, 8:54:01.656541 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 8:54:01.657461 INFO: Starting candidate selection
1 day, 8:55:33.308480 INFO: Starting candidate scoring
1 day, 8:55:35.388381 INFO: Finished candidate processing
1 day, 8:55:35.388601 INFO: Collecting candidate features
1 day, 8:55:35.489506 INFO: Collecting fragment features
1 day, 8:55:35.517586 INFO: Finished candidate scoring
1 day, 8:55:35.540859 INFO: performing precursor FDR with 47 features
1 day, 8:55:35.541017 INFO: Decoy channel: -1
1 day, 8:55:35.541045 INFO: competitive: True
1 day, 8:55:35.555616 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:55:35.569998 INFO: Estimating optimal hyperparameters - samples: 36,127, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:55:35.570245 INFO: Using random state 12471 for train-test-split
1 day, 8:55:39.187374 INFO: Test AUC: 0.734
1 day, 8:55:39.187537 INFO: Train AUC: 0.745
1 day, 8:55:39.187572 INFO: AUC difference: 1.41%
1 day, 8:55:39.478588 INFO: Resetting torch num_threads to 128
1 day, 8:55:39.480381 PROGRESS: === Extracted 45159 precursors and 498587 fragments ===
1 day, 8:55:39.481044 INFO: === FDR correction performed with classifier version 1 ===
1 day, 8:55:39.482615 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:55:39.482739 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:55:39.482814 PROGRESS: Target precursors: 7,460 (93.25%)
1 day, 8:55:39.482881 PROGRESS: Decoy precursors: 540 (6.75%)
1 day, 8:55:39.482944 PROGRESS: 
1 day, 8:55:39.483002 PROGRESS: Precursor Summary:
1 day, 8:55:39.486135 PROGRESS: Channel   0:	 0.050 FDR: 7,209; 0.010 FDR: 6,688; 0.001 FDR: 6,052
1 day, 8:55:39.486268 PROGRESS: 
1 day, 8:55:39.486343 PROGRESS: Protein Summary:
1 day, 8:55:39.491032 PROGRESS: Channel   0:	 0.050 FDR: 4,046; 0.010 FDR: 3,787; 0.001 FDR: 3,496
1 day, 8:55:39.491163 PROGRESS: =========================================================================
1 day, 8:55:39.491574 INFO: Target number of precursors reached.
1 day, 8:55:39.596859 INFO: fragments_df: keeping 5000 of 498587 [sum(precursor_idx_mask)=211302 sum(mass_error_mask)=498587 stop_rank=5000
1 day, 8:55:39.627981 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:55:40.683252 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:55:41.758212 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:55:42.812255 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:55:43.528789 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:55:43.529416 INFO: Using score_cutoff 40.7173902168274 (fac=0.99, q=1)
1 day, 8:55:43.529999 INFO: Updating optimization_manager: fwhm_rt             : 3.066870927810669 -> 2.7917656898498535
1 day, 8:55:43.530113 INFO: Updating optimization_manager: fwhm_mobility       : 0.010009457357227802 -> 0.008226835168898106
1 day, 8:55:43.530183 INFO: Updating optimization_manager: score_cutoff        : 48.389767781066894 -> 40.7173902168274
1 day, 8:55:43.530255 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:55:43.533232 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:55:43.542639 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:55:43.545114 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:55:43.566998 INFO: === checking if optimization conditions were reached ===
1 day, 8:55:43.569376 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 8:55:43.569528 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
1 day, 8:55:43.569626 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 8:55:43.572003 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 8:55:43.572151 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
1 day, 8:55:43.572247 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 8:55:43.572332 INFO: ==============================================
1 day, 8:55:43.572430 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 8:55:43.596849 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:55:43.600550 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:55:43.610543 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:55:43.613467 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:55:43.635646 INFO: Starting optimization step 0.
1 day, 8:55:43.635898 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:55:43.636032 INFO: Using python extraction backend
1 day, 8:55:43.636275 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:55:43.636411 INFO: === Search parameters used ===
1 day, 8:55:43.636508 INFO: rt_error       : 2099.9331315
1 day, 8:55:43.636598 INFO: mobility_error : 0.1
1 day, 8:55:43.636685 INFO: num_candidates : 3
1 day, 8:55:43.636770 INFO: ms1_error      : 15.0
1 day, 8:55:43.636856 INFO: ms2_error      : 15.0
1 day, 8:55:43.636938 INFO: fwhm_rt        : 2.7917656898498535
1 day, 8:55:43.637018 INFO: quant_window   : 3
1 day, 8:55:43.637103 INFO: ==============================================
1 day, 8:55:43.642999 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:55:43.643121 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:55:43.643186 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1 day, 8:55:43.643240 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 8:55:43.644434 INFO: Starting candidate selection
1 day, 8:57:17.428000 INFO: Starting candidate scoring
1 day, 8:57:19.301724 INFO: Finished candidate processing
1 day, 8:57:19.301947 INFO: Collecting candidate features
1 day, 8:57:19.369385 INFO: Collecting fragment features
1 day, 8:57:19.397702 INFO: Finished candidate scoring
1 day, 8:57:19.423446 INFO: performing precursor FDR with 47 features
1 day, 8:57:19.423597 INFO: Decoy channel: -1
1 day, 8:57:19.423624 INFO: competitive: True
1 day, 8:57:19.437812 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:57:19.452409 INFO: Estimating optimal hyperparameters - samples: 36,081, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:57:19.452702 INFO: Using random state 463569 for train-test-split
1 day, 8:57:23.735719 INFO: Test AUC: 0.745
1 day, 8:57:23.735893 INFO: Train AUC: 0.756
1 day, 8:57:23.735927 INFO: AUC difference: 1.44%
1 day, 8:57:24.030761 INFO: Resetting torch num_threads to 128
1 day, 8:57:24.032279 PROGRESS: === Extracted 45102 precursors and 496382 fragments ===
1 day, 8:57:24.032900 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:57:24.034466 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:57:24.034604 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:57:24.034686 PROGRESS: Target precursors: 7,476 (93.45%)
1 day, 8:57:24.034752 PROGRESS: Decoy precursors: 524 (6.55%)
1 day, 8:57:24.034816 PROGRESS: 
1 day, 8:57:24.034868 PROGRESS: Precursor Summary:
1 day, 8:57:24.038048 PROGRESS: Channel   0:	 0.050 FDR: 7,231; 0.010 FDR: 6,725; 0.001 FDR: 6,148
1 day, 8:57:24.038184 PROGRESS: 
1 day, 8:57:24.038285 PROGRESS: Protein Summary:
1 day, 8:57:24.042913 PROGRESS: Channel   0:	 0.050 FDR: 4,056; 0.010 FDR: 3,809; 0.001 FDR: 3,531
1 day, 8:57:24.043076 PROGRESS: =========================================================================
1 day, 8:57:24.043396 INFO: Target number of precursors reached.
1 day, 8:57:24.150439 INFO: fragments_df: keeping 5000 of 496382 [sum(precursor_idx_mask)=211419 sum(mass_error_mask)=496382 stop_rank=5000
1 day, 8:57:24.169964 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:57:25.239283 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:57:26.323348 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:57:27.390626 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:57:28.118182 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:57:28.118835 INFO: Using score_cutoff 40.575404539489746 (fac=0.99, q=1)
1 day, 8:57:28.119407 INFO: Updating optimization_manager: fwhm_rt             : 2.7917656898498535 -> 2.7895047664642334
1 day, 8:57:28.119503 INFO: Updating optimization_manager: fwhm_mobility       : 0.008226835168898106 -> 0.008195990696549416
1 day, 8:57:28.119571 INFO: Updating optimization_manager: score_cutoff        : 40.7173902168274 -> 40.575404539489746
1 day, 8:57:28.119660 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:57:28.122758 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:57:28.132255 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:57:28.134744 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:57:28.158084 INFO: === checking if optimization conditions were reached ===
1 day, 8:57:28.158338 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 8:57:28.164732 INFO: Updating optimization_manager: rt_error            : 2099.9331315 -> 388.8882512424043
1 day, 8:57:28.164900 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 388.8883.
1 day, 8:57:28.164997 INFO: ==============================================
1 day, 8:57:28.165095 INFO: Starting optimization step 1.
1 day, 8:57:28.165182 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:57:28.165270 INFO: Using python extraction backend
1 day, 8:57:28.165435 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:57:28.165528 INFO: === Search parameters used ===
1 day, 8:57:28.165597 INFO: rt_error       : 388.8882512424043
1 day, 8:57:28.165662 INFO: mobility_error : 0.1
1 day, 8:57:28.165727 INFO: num_candidates : 3
1 day, 8:57:28.165808 INFO: ms1_error      : 15.0
1 day, 8:57:28.165874 INFO: ms2_error      : 15.0
1 day, 8:57:28.165934 INFO: fwhm_rt        : 2.7895047664642334
1 day, 8:57:28.166007 INFO: quant_window   : 3
1 day, 8:57:28.166070 INFO: ==============================================
1 day, 8:57:28.171566 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:57:28.171640 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:57:28.171689 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1 day, 8:57:28.171719 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.80
1 day, 8:57:28.172684 INFO: Starting candidate selection
1 day, 8:57:45.888566 INFO: Starting candidate scoring
1 day, 8:57:47.674290 INFO: Finished candidate processing
1 day, 8:57:47.674484 INFO: Collecting candidate features
1 day, 8:57:47.736626 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 44916)
1 day, 8:57:47.742221 INFO: Collecting fragment features
1 day, 8:57:47.770487 INFO: Finished candidate scoring
1 day, 8:57:47.796527 INFO: performing precursor FDR with 47 features
1 day, 8:57:47.796680 INFO: Decoy channel: -1
1 day, 8:57:47.796707 INFO: competitive: True
1 day, 8:57:47.811459 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:57:47.818446 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 8:57:47.826023 INFO: Estimating optimal hyperparameters - samples: 35,932, batch_size: 147, learning_rate: 1.89e-04
1 day, 8:57:47.826260 INFO: Using random state 463569 for train-test-split
1 day, 8:57:52.080293 INFO: Test AUC: 0.756
1 day, 8:57:52.080448 INFO: Train AUC: 0.767
1 day, 8:57:52.080480 INFO: AUC difference: 1.46%
1 day, 8:57:52.383419 INFO: Resetting torch num_threads to 128
1 day, 8:57:52.384907 PROGRESS: === Extracted 44916 precursors and 489544 fragments ===
1 day, 8:57:52.385515 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:57:52.387174 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:57:52.387292 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:57:52.387374 PROGRESS: Target precursors: 7,604 (95.05%)
1 day, 8:57:52.387444 PROGRESS: Decoy precursors: 396 (4.95%)
1 day, 8:57:52.387505 PROGRESS: 
1 day, 8:57:52.387577 PROGRESS: Precursor Summary:
1 day, 8:57:52.390950 PROGRESS: Channel   0:	 0.050 FDR: 7,579; 0.010 FDR: 7,092; 0.001 FDR: 6,635
1 day, 8:57:52.391106 PROGRESS: 
1 day, 8:57:52.391198 PROGRESS: Protein Summary:
1 day, 8:57:52.396068 PROGRESS: Channel   0:	 0.050 FDR: 4,209; 0.010 FDR: 3,969; 0.001 FDR: 3,754
1 day, 8:57:52.396212 PROGRESS: =========================================================================
1 day, 8:57:52.396526 INFO: Target number of precursors reached.
1 day, 8:57:52.509017 INFO: fragments_df: keeping 5000 of 489544 [sum(precursor_idx_mask)=221324 sum(mass_error_mask)=489544 stop_rank=5000
1 day, 8:57:52.528679 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:57:53.620151 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:57:54.742655 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:57:55.835538 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:57:56.507100 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:57:56.507757 INFO: Using score_cutoff 37.95862302246094 (fac=0.99, q=1)
1 day, 8:57:56.508353 INFO: Updating optimization_manager: fwhm_rt             : 2.7895047664642334 -> 2.7587156295776367
1 day, 8:57:56.508457 INFO: Updating optimization_manager: fwhm_mobility       : 0.008195990696549416 -> 0.007960494607686996
1 day, 8:57:56.508530 INFO: Updating optimization_manager: score_cutoff        : 40.575404539489746 -> 37.95862302246094
1 day, 8:57:56.508612 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:57:56.511661 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:57:56.521190 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:57:56.523654 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:57:56.543598 INFO: === checking if optimization conditions were reached ===
1 day, 8:57:56.543821 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 8:57:56.549920 INFO: Updating optimization_manager: rt_error            : 388.8882512424043 -> 136.92567591911433
1 day, 8:57:56.550073 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 136.9257.
1 day, 8:57:56.550160 INFO: ==============================================
1 day, 8:57:56.550249 INFO: Starting optimization step 2.
1 day, 8:57:56.550331 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:57:56.550416 INFO: Using python extraction backend
1 day, 8:57:56.550573 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:57:56.550670 INFO: === Search parameters used ===
1 day, 8:57:56.550745 INFO: rt_error       : 136.92567591911433
1 day, 8:57:56.550830 INFO: mobility_error : 0.1
1 day, 8:57:56.550910 INFO: num_candidates : 3
1 day, 8:57:56.550974 INFO: ms1_error      : 15.0
1 day, 8:57:56.551045 INFO: ms2_error      : 15.0
1 day, 8:57:56.551114 INFO: fwhm_rt        : 2.7587156295776367
1 day, 8:57:56.551181 INFO: quant_window   : 3
1 day, 8:57:56.551247 INFO: ==============================================
1 day, 8:57:56.555642 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:57:56.555712 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:57:56.555754 INFO: FWHM in RT is 2.76 seconds, sigma is 0.61
1 day, 8:57:56.555786 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.69
1 day, 8:57:56.556753 INFO: Starting candidate selection
1 day, 8:58:04.090584 INFO: Starting candidate scoring
1 day, 8:58:05.881289 INFO: Finished candidate processing
1 day, 8:58:05.881487 INFO: Collecting candidate features
1 day, 8:58:05.961581 WARNING: intensity_correlation has 2 NaNs ( 0.00 % out of 44860)
1 day, 8:58:05.967083 INFO: Collecting fragment features
1 day, 8:58:05.994335 INFO: Finished candidate scoring
1 day, 8:58:06.017884 INFO: performing precursor FDR with 47 features
1 day, 8:58:06.018039 INFO: Decoy channel: -1
1 day, 8:58:06.018066 INFO: competitive: True
1 day, 8:58:06.032594 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:58:06.041028 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:58:06.041174 WARNING: dropped 1 decoy PSMs due to missing features
1 day, 8:58:06.048874 INFO: Estimating optimal hyperparameters - samples: 35,886, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:58:06.049098 INFO: Using random state 463569 for train-test-split
1 day, 8:58:10.265757 INFO: Test AUC: 0.776
1 day, 8:58:10.265914 INFO: Train AUC: 0.784
1 day, 8:58:10.265946 INFO: AUC difference: 1.06%
1 day, 8:58:10.566262 INFO: Resetting torch num_threads to 128
1 day, 8:58:10.567766 PROGRESS: === Extracted 44860 precursors and 480533 fragments ===
1 day, 8:58:10.568390 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:58:10.570051 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:58:10.570190 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:58:10.570293 PROGRESS: Target precursors: 7,743 (96.79%)
1 day, 8:58:10.570389 PROGRESS: Decoy precursors: 257 (3.21%)
1 day, 8:58:10.570480 PROGRESS: 
1 day, 8:58:10.570566 PROGRESS: Precursor Summary:
1 day, 8:58:10.573878 PROGRESS: Channel   0:	 0.050 FDR: 7,743; 0.010 FDR: 7,472; 0.001 FDR: 6,864
1 day, 8:58:10.574026 PROGRESS: 
1 day, 8:58:10.574127 PROGRESS: Protein Summary:
1 day, 8:58:10.579120 PROGRESS: Channel   0:	 0.050 FDR: 4,279; 0.010 FDR: 4,149; 0.001 FDR: 3,879
1 day, 8:58:10.579271 PROGRESS: =========================================================================
1 day, 8:58:10.579571 INFO: Target number of precursors reached.
1 day, 8:58:10.692582 INFO: fragments_df: keeping 5000 of 480533 [sum(precursor_idx_mask)=230469 sum(mass_error_mask)=480533 stop_rank=5000
1 day, 8:58:10.711871 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:58:11.881841 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:58:13.078428 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:58:14.242257 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:58:14.907975 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:58:14.908603 INFO: Using score_cutoff 35.26663350791931 (fac=0.99, q=1)
1 day, 8:58:14.909162 INFO: Updating optimization_manager: fwhm_rt             : 2.7587156295776367 -> 2.7508740425109863
1 day, 8:58:14.909263 INFO: Updating optimization_manager: fwhm_mobility       : 0.007960494607686996 -> 0.00779014453291893
1 day, 8:58:14.909333 INFO: Updating optimization_manager: score_cutoff        : 37.95862302246094 -> 35.26663350791931
1 day, 8:58:14.909410 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:58:14.912435 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:58:14.921979 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:58:14.924526 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:58:14.944815 INFO: === checking if optimization conditions were reached ===
1 day, 8:58:14.945011 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 8:58:14.951534 INFO: Updating optimization_manager: rt_error            : 136.92567591911433 -> 28.368751692712618
1 day, 8:58:14.951694 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 28.3688.
1 day, 8:58:14.951798 INFO: ==============================================
1 day, 8:58:14.951898 INFO: Starting optimization step 3.
1 day, 8:58:14.951989 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:58:14.952086 INFO: Using python extraction backend
1 day, 8:58:14.952252 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:58:14.952345 INFO: === Search parameters used ===
1 day, 8:58:14.952415 INFO: rt_error       : 28.368751692712618
1 day, 8:58:14.952482 INFO: mobility_error : 0.1
1 day, 8:58:14.952567 INFO: num_candidates : 3
1 day, 8:58:14.952643 INFO: ms1_error      : 15.0
1 day, 8:58:14.952721 INFO: ms2_error      : 15.0
1 day, 8:58:14.952793 INFO: fwhm_rt        : 2.7508740425109863
1 day, 8:58:14.952864 INFO: quant_window   : 3
1 day, 8:58:14.952933 INFO: ==============================================
1 day, 8:58:14.957281 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:58:14.957355 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:58:14.957409 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 8:58:14.957436 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.61
1 day, 8:58:14.958326 INFO: Starting candidate selection
1 day, 8:58:17.207967 INFO: Starting candidate scoring
1 day, 8:58:18.958345 INFO: Finished candidate processing
1 day, 8:58:18.958550 INFO: Collecting candidate features
1 day, 8:58:19.051054 WARNING: intensity_correlation has 19 NaNs ( 0.04 % out of 44649)
1 day, 8:58:19.056507 INFO: Collecting fragment features
1 day, 8:58:19.084284 INFO: Finished candidate scoring
1 day, 8:58:19.109342 INFO: performing precursor FDR with 47 features
1 day, 8:58:19.109493 INFO: Decoy channel: -1
1 day, 8:58:19.109521 INFO: competitive: True
1 day, 8:58:19.123645 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:58:19.132026 WARNING: dropped 3 target PSMs due to missing features
1 day, 8:58:19.132173 WARNING: dropped 16 decoy PSMs due to missing features
1 day, 8:58:19.140479 INFO: Estimating optimal hyperparameters - samples: 35,704, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:58:19.140730 INFO: Using random state 463569 for train-test-split
1 day, 8:58:23.323013 INFO: Test AUC: 0.812
1 day, 8:58:23.323169 INFO: Train AUC: 0.813
1 day, 8:58:23.323201 INFO: AUC difference: 0.16%
1 day, 8:58:23.608984 INFO: Resetting torch num_threads to 128
1 day, 8:58:23.610422 PROGRESS: === Extracted 44649 precursors and 470175 fragments ===
1 day, 8:58:23.610995 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:58:23.612444 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:58:23.612555 PROGRESS: Total precursors accumulated: 8,000
1 day, 8:58:23.612627 PROGRESS: Target precursors: 7,877 (98.46%)
1 day, 8:58:23.612695 PROGRESS: Decoy precursors: 123 (1.54%)
1 day, 8:58:23.612754 PROGRESS: 
1 day, 8:58:23.612808 PROGRESS: Precursor Summary:
1 day, 8:58:23.616087 PROGRESS: Channel   0:	 0.050 FDR: 7,877; 0.010 FDR: 7,812; 0.001 FDR: 7,522
1 day, 8:58:23.616236 PROGRESS: 
1 day, 8:58:23.616325 PROGRESS: Protein Summary:
1 day, 8:58:23.621330 PROGRESS: Channel   0:	 0.050 FDR: 4,338; 0.010 FDR: 4,306; 0.001 FDR: 4,179
1 day, 8:58:23.621465 PROGRESS: =========================================================================
1 day, 8:58:23.621777 INFO: Target number of precursors reached.
1 day, 8:58:23.736049 INFO: fragments_df: keeping 5000 of 470175 [sum(precursor_idx_mask)=238208 sum(mass_error_mask)=470175 stop_rank=5000
1 day, 8:58:23.755357 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:58:25.066917 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:58:26.396399 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:58:27.711341 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:58:28.436502 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:58:28.437175 INFO: Using score_cutoff 32.99507177810669 (fac=0.99, q=1)
1 day, 8:58:28.437728 INFO: Updating optimization_manager: fwhm_rt             : 2.7508740425109863 -> 2.7169179916381836
1 day, 8:58:28.437834 INFO: Updating optimization_manager: fwhm_mobility       : 0.00779014453291893 -> 0.0076495879329741
1 day, 8:58:28.437901 INFO: Updating optimization_manager: score_cutoff        : 35.26663350791931 -> 32.99507177810669
1 day, 8:58:28.437984 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:58:28.441020 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:58:28.450571 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:58:28.453054 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:58:28.472790 INFO: === checking if optimization conditions were reached ===
1 day, 8:58:28.473009 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 8:58:28.480208 INFO: Updating optimization_manager: rt_error            : 28.368751692712618 -> 16.272318214756513
1 day, 8:58:28.480377 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 16.2723.
1 day, 8:58:28.480469 INFO: ==============================================
1 day, 8:58:28.480573 INFO: Starting optimization step 4.
1 day, 8:58:28.480657 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:58:28.480741 INFO: Using python extraction backend
1 day, 8:58:28.480903 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:58:28.480996 INFO: === Search parameters used ===
1 day, 8:58:28.481065 INFO: rt_error       : 16.272318214756513
1 day, 8:58:28.481129 INFO: mobility_error : 0.1
1 day, 8:58:28.481191 INFO: num_candidates : 3
1 day, 8:58:28.481253 INFO: ms1_error      : 15.0
1 day, 8:58:28.481313 INFO: ms2_error      : 15.0
1 day, 8:58:28.481372 INFO: fwhm_rt        : 2.7169179916381836
1 day, 8:58:28.481437 INFO: quant_window   : 3
1 day, 8:58:28.481513 INFO: ==============================================
1 day, 8:58:28.487232 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:58:28.487319 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:58:28.487401 INFO: FWHM in RT is 2.72 seconds, sigma is 0.60
1 day, 8:58:28.487446 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.55
1 day, 8:58:28.488456 INFO: Starting candidate selection
1 day, 8:58:30.407524 INFO: Starting candidate scoring
1 day, 8:58:32.101913 INFO: Finished candidate processing
1 day, 8:58:32.102115 INFO: Collecting candidate features
1 day, 8:58:32.169433 WARNING: intensity_correlation has 16 NaNs ( 0.04 % out of 44629)
1 day, 8:58:32.175673 INFO: Collecting fragment features
1 day, 8:58:32.203422 INFO: Finished candidate scoring
1 day, 8:58:32.228877 INFO: performing precursor FDR with 47 features
1 day, 8:58:32.229040 INFO: Decoy channel: -1
1 day, 8:58:32.229073 INFO: competitive: True
1 day, 8:58:32.243657 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:58:32.252130 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:58:32.252281 WARNING: dropped 15 decoy PSMs due to missing features
1 day, 8:58:32.260112 INFO: Estimating optimal hyperparameters - samples: 35,690, batch_size: 146, learning_rate: 1.89e-04
1 day, 8:58:32.260347 INFO: Using random state 463569 for train-test-split
1 day, 8:58:36.535451 INFO: Test AUC: 0.821
1 day, 8:58:36.535622 INFO: Train AUC: 0.829
1 day, 8:58:36.535656 INFO: AUC difference: 0.88%
1 day, 8:58:36.818557 INFO: Resetting torch num_threads to 128
1 day, 8:58:36.820001 PROGRESS: === Extracted 44629 precursors and 467302 fragments ===
1 day, 8:58:36.820612 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:58:36.822185 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:58:36.822298 PROGRESS: Total precursors accumulated: 7,999
1 day, 8:58:36.822369 PROGRESS: Target precursors: 7,898 (98.74%)
1 day, 8:58:36.822430 PROGRESS: Decoy precursors: 101 (1.26%)
1 day, 8:58:36.822487 PROGRESS: 
1 day, 8:58:36.822541 PROGRESS: Precursor Summary:
1 day, 8:58:36.825765 PROGRESS: Channel   0:	 0.050 FDR: 7,898; 0.010 FDR: 7,837; 0.001 FDR: 7,374
1 day, 8:58:36.825894 PROGRESS: 
1 day, 8:58:36.825963 PROGRESS: Protein Summary:
1 day, 8:58:36.830949 PROGRESS: Channel   0:	 0.050 FDR: 4,352; 0.010 FDR: 4,328; 0.001 FDR: 4,106
1 day, 8:58:36.831077 PROGRESS: =========================================================================
1 day, 8:58:36.831334 INFO: Target number of precursors reached.
1 day, 8:58:36.944337 INFO: fragments_df: keeping 5000 of 467302 [sum(precursor_idx_mask)=238185 sum(mass_error_mask)=467302 stop_rank=5000
1 day, 8:58:36.962919 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:58:38.235126 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:58:39.498293 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:58:40.743143 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:58:41.400608 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:58:41.401247 INFO: Using score_cutoff 32.588730450439456 (fac=0.99, q=1)
1 day, 8:58:41.401816 INFO: Updating optimization_manager: fwhm_rt             : 2.7169179916381836 -> 2.7142014503479004
1 day, 8:58:41.401914 INFO: Updating optimization_manager: fwhm_mobility       : 0.0076495879329741 -> 0.007643282879143953
1 day, 8:58:41.401980 INFO: Updating optimization_manager: score_cutoff        : 32.99507177810669 -> 32.588730450439456
1 day, 8:58:41.402050 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:58:41.405021 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:58:41.414518 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:58:41.416967 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:58:41.436924 INFO: === checking if optimization conditions were reached ===
1 day, 8:58:41.437130 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 8:58:41.443624 INFO: Updating optimization_manager: rt_error            : 16.272318214756513 -> 14.816188937344869
1 day, 8:58:41.443767 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 14.8162.
1 day, 8:58:41.443860 INFO: ==============================================
1 day, 8:58:41.443951 INFO: Starting optimization step 5.
1 day, 8:58:41.444037 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:58:41.444117 INFO: Using python extraction backend
1 day, 8:58:41.444260 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:58:41.444346 INFO: === Search parameters used ===
1 day, 8:58:41.444417 INFO: rt_error       : 14.816188937344869
1 day, 8:58:41.444478 INFO: mobility_error : 0.1
1 day, 8:58:41.444540 INFO: num_candidates : 3
1 day, 8:58:41.444600 INFO: ms1_error      : 15.0
1 day, 8:58:41.444656 INFO: ms2_error      : 15.0
1 day, 8:58:41.444715 INFO: fwhm_rt        : 2.7142014503479004
1 day, 8:58:41.444787 INFO: quant_window   : 3
1 day, 8:58:41.444853 INFO: ==============================================
1 day, 8:58:41.448686 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:58:41.448756 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:58:41.448802 INFO: FWHM in RT is 2.71 seconds, sigma is 0.60
1 day, 8:58:41.448842 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.55
1 day, 8:58:41.449799 INFO: Starting candidate selection
1 day, 8:58:43.075887 INFO: Starting candidate scoring
1 day, 8:58:44.845188 INFO: Finished candidate processing
1 day, 8:58:44.845393 INFO: Collecting candidate features
1 day, 8:58:44.914109 WARNING: intensity_correlation has 19 NaNs ( 0.04 % out of 44506)
1 day, 8:58:44.919472 INFO: Collecting fragment features
1 day, 8:58:44.947134 INFO: Finished candidate scoring
1 day, 8:58:44.973545 INFO: performing precursor FDR with 47 features
1 day, 8:58:44.973717 INFO: Decoy channel: -1
1 day, 8:58:44.973753 INFO: competitive: True
1 day, 8:58:44.987684 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:58:44.995989 WARNING: dropped 4 target PSMs due to missing features
1 day, 8:58:44.996141 WARNING: dropped 15 decoy PSMs due to missing features
1 day, 8:58:45.003213 INFO: Estimating optimal hyperparameters - samples: 35,589, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:58:45.003435 INFO: Using random state 463569 for train-test-split
1 day, 8:58:49.183432 INFO: Test AUC: 0.836
1 day, 8:58:49.183598 INFO: Train AUC: 0.849
1 day, 8:58:49.183632 INFO: AUC difference: 1.49%
1 day, 8:58:49.471453 INFO: Resetting torch num_threads to 128
1 day, 8:58:49.472847 PROGRESS: === Extracted 44506 precursors and 462267 fragments ===
1 day, 8:58:49.473443 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:58:49.474963 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:58:49.475086 PROGRESS: Total precursors accumulated: 7,999
1 day, 8:58:49.475165 PROGRESS: Target precursors: 7,894 (98.69%)
1 day, 8:58:49.475243 PROGRESS: Decoy precursors: 105 (1.31%)
1 day, 8:58:49.475305 PROGRESS: 
1 day, 8:58:49.475363 PROGRESS: Precursor Summary:
1 day, 8:58:49.478605 PROGRESS: Channel   0:	 0.050 FDR: 7,894; 0.010 FDR: 7,839; 0.001 FDR: 7,406
1 day, 8:58:49.478734 PROGRESS: 
1 day, 8:58:49.478807 PROGRESS: Protein Summary:
1 day, 8:58:49.483697 PROGRESS: Channel   0:	 0.050 FDR: 4,346; 0.010 FDR: 4,327; 0.001 FDR: 4,129
1 day, 8:58:49.483832 PROGRESS: =========================================================================
1 day, 8:58:49.484140 INFO: Target number of precursors reached.
1 day, 8:58:49.598513 INFO: fragments_df: keeping 5000 of 462267 [sum(precursor_idx_mask)=236798 sum(mass_error_mask)=462267 stop_rank=5000
1 day, 8:58:49.617604 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:58:50.876748 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:58:52.130352 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:58:53.377704 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:58:54.038672 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:58:54.039349 INFO: Using score_cutoff 31.918524726104735 (fac=0.99, q=1)
1 day, 8:58:54.039916 INFO: Updating optimization_manager: fwhm_rt             : 2.7142014503479004 -> 2.700911045074463
1 day, 8:58:54.040012 INFO: Updating optimization_manager: fwhm_mobility       : 0.007643282879143953 -> 0.007611413486301899
1 day, 8:58:54.040079 INFO: Updating optimization_manager: score_cutoff        : 32.588730450439456 -> 31.918524726104735
1 day, 8:58:54.040151 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:58:54.043161 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:58:54.052710 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:58:54.055226 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:58:54.076547 INFO: === checking if optimization conditions were reached ===
1 day, 8:58:54.076734 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 8:58:54.083349 INFO: Updating optimization_manager: rt_error            : 14.816188937344869 -> 12.408446749493763
1 day, 8:58:54.083485 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 12.4084.
1 day, 8:58:54.083593 INFO: ==============================================
1 day, 8:58:54.083708 INFO: Starting optimization step 6.
1 day, 8:58:54.083789 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:58:54.083881 INFO: Using python extraction backend
1 day, 8:58:54.084045 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:58:54.084133 INFO: === Search parameters used ===
1 day, 8:58:54.084199 INFO: rt_error       : 12.408446749493763
1 day, 8:58:54.084259 INFO: mobility_error : 0.1
1 day, 8:58:54.084325 INFO: num_candidates : 3
1 day, 8:58:54.084389 INFO: ms1_error      : 15.0
1 day, 8:58:54.084450 INFO: ms2_error      : 15.0
1 day, 8:58:54.084512 INFO: fwhm_rt        : 2.700911045074463
1 day, 8:58:54.084574 INFO: quant_window   : 3
1 day, 8:58:54.084636 INFO: ==============================================
1 day, 8:58:54.088806 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:58:54.088882 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:58:54.088931 INFO: FWHM in RT is 2.70 seconds, sigma is 0.59
1 day, 8:58:54.088960 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.53
1 day, 8:58:54.089829 INFO: Starting candidate selection
1 day, 8:58:55.689777 INFO: Starting candidate scoring
1 day, 8:58:57.462656 INFO: Finished candidate processing
1 day, 8:58:57.462849 INFO: Collecting candidate features
1 day, 8:58:57.548245 WARNING: intensity_correlation has 31 NaNs ( 0.07 % out of 44488)
1 day, 8:58:57.554490 INFO: Collecting fragment features
1 day, 8:58:57.582465 INFO: Finished candidate scoring
1 day, 8:58:57.609739 INFO: performing precursor FDR with 47 features
1 day, 8:58:57.609912 INFO: Decoy channel: -1
1 day, 8:58:57.609939 INFO: competitive: True
1 day, 8:58:57.624437 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:58:57.632756 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:58:57.632905 WARNING: dropped 30 decoy PSMs due to missing features
1 day, 8:58:57.640082 INFO: Estimating optimal hyperparameters - samples: 35,565, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:58:57.640306 INFO: Using random state 463569 for train-test-split
1 day, 8:59:01.884632 INFO: Test AUC: 0.842
1 day, 8:59:01.884792 INFO: Train AUC: 0.845
1 day, 8:59:01.884825 INFO: AUC difference: 0.38%
1 day, 8:59:02.167470 INFO: Resetting torch num_threads to 128
1 day, 8:59:02.168899 PROGRESS: === Extracted 44488 precursors and 462505 fragments ===
1 day, 8:59:02.169487 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:59:02.170990 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:59:02.171102 PROGRESS: Total precursors accumulated: 7,999
1 day, 8:59:02.171173 PROGRESS: Target precursors: 7,881 (98.52%)
1 day, 8:59:02.171234 PROGRESS: Decoy precursors: 118 (1.48%)
1 day, 8:59:02.171295 PROGRESS: 
1 day, 8:59:02.171354 PROGRESS: Precursor Summary:
1 day, 8:59:02.174616 PROGRESS: Channel   0:	 0.050 FDR: 7,881; 0.010 FDR: 7,810; 0.001 FDR: 7,326
1 day, 8:59:02.174735 PROGRESS: 
1 day, 8:59:02.174807 PROGRESS: Protein Summary:
1 day, 8:59:02.179835 PROGRESS: Channel   0:	 0.050 FDR: 4,340; 0.010 FDR: 4,313; 0.001 FDR: 4,088
1 day, 8:59:02.179962 PROGRESS: =========================================================================
1 day, 8:59:02.180254 INFO: Target number of precursors reached.
1 day, 8:59:02.292437 INFO: fragments_df: keeping 5000 of 462505 [sum(precursor_idx_mask)=235995 sum(mass_error_mask)=462505 stop_rank=5000
1 day, 8:59:02.311049 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:59:03.547138 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:59:04.798727 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:59:06.036128 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:59:06.688462 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:59:06.689107 INFO: Using score_cutoff 31.84230019454956 (fac=0.99, q=1)
1 day, 8:59:06.689688 INFO: Updating optimization_manager: fwhm_rt             : 2.700911045074463 -> 2.7027931213378906
1 day, 8:59:06.689798 INFO: Updating optimization_manager: fwhm_mobility       : 0.007611413486301899 -> 0.00761058833450079
1 day, 8:59:06.689870 INFO: Updating optimization_manager: score_cutoff        : 31.918524726104735 -> 31.84230019454956
1 day, 8:59:06.689943 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:59:06.692898 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:59:06.702458 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:59:06.704884 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:59:06.725073 INFO: === checking if optimization conditions were reached ===
1 day, 8:59:06.725273 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 8:59:06.731813 INFO: Updating optimization_manager: rt_error            : 12.408446749493763 -> 11.713930634865465
1 day, 8:59:06.731956 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 11.7139.
1 day, 8:59:06.732060 INFO: ==============================================
1 day, 8:59:06.732172 INFO: Starting optimization step 7.
1 day, 8:59:06.732265 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:59:06.732356 INFO: Using python extraction backend
1 day, 8:59:06.732513 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:59:06.732605 INFO: === Search parameters used ===
1 day, 8:59:06.732676 INFO: rt_error       : 11.713930634865465
1 day, 8:59:06.732742 INFO: mobility_error : 0.1
1 day, 8:59:06.732811 INFO: num_candidates : 3
1 day, 8:59:06.732876 INFO: ms1_error      : 15.0
1 day, 8:59:06.732943 INFO: ms2_error      : 15.0
1 day, 8:59:06.733019 INFO: fwhm_rt        : 2.7027931213378906
1 day, 8:59:06.733102 INFO: quant_window   : 3
1 day, 8:59:06.733176 INFO: ==============================================
1 day, 8:59:06.737028 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:59:06.737104 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:59:06.737159 INFO: FWHM in RT is 2.70 seconds, sigma is 0.59
1 day, 8:59:06.737194 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.53
1 day, 8:59:06.738178 INFO: Starting candidate selection
1 day, 8:59:08.384969 INFO: Starting candidate scoring
1 day, 8:59:10.053792 INFO: Finished candidate processing
1 day, 8:59:10.054014 INFO: Collecting candidate features
1 day, 8:59:10.142024 WARNING: intensity_correlation has 25 NaNs ( 0.06 % out of 44475)
1 day, 8:59:10.147557 INFO: Collecting fragment features
1 day, 8:59:10.172947 INFO: Finished candidate scoring
1 day, 8:59:10.195415 INFO: performing precursor FDR with 47 features
1 day, 8:59:10.195577 INFO: Decoy channel: -1
1 day, 8:59:10.195606 INFO: competitive: True
1 day, 8:59:10.214070 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:59:10.223174 WARNING: dropped 2 target PSMs due to missing features
1 day, 8:59:10.223336 WARNING: dropped 23 decoy PSMs due to missing features
1 day, 8:59:10.231763 INFO: Estimating optimal hyperparameters - samples: 35,560, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:59:10.232153 INFO: Using random state 463569 for train-test-split
1 day, 8:59:14.415023 INFO: Test AUC: 0.839
1 day, 8:59:14.415183 INFO: Train AUC: 0.847
1 day, 8:59:14.415215 INFO: AUC difference: 0.93%
1 day, 8:59:14.696755 INFO: Resetting torch num_threads to 128
1 day, 8:59:14.698168 PROGRESS: === Extracted 44475 precursors and 462310 fragments ===
1 day, 8:59:14.698778 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:59:14.700202 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:59:14.700310 PROGRESS: Total precursors accumulated: 7,999
1 day, 8:59:14.700384 PROGRESS: Target precursors: 7,886 (98.59%)
1 day, 8:59:14.700445 PROGRESS: Decoy precursors: 113 (1.41%)
1 day, 8:59:14.700514 PROGRESS: 
1 day, 8:59:14.700568 PROGRESS: Precursor Summary:
1 day, 8:59:14.703736 PROGRESS: Channel   0:	 0.050 FDR: 7,886; 0.010 FDR: 7,825; 0.001 FDR: 7,353
1 day, 8:59:14.703865 PROGRESS: 
1 day, 8:59:14.703932 PROGRESS: Protein Summary:
1 day, 8:59:14.708746 PROGRESS: Channel   0:	 0.050 FDR: 4,343; 0.010 FDR: 4,319; 0.001 FDR: 4,102
1 day, 8:59:14.708869 PROGRESS: =========================================================================
1 day, 8:59:14.709127 INFO: Target number of precursors reached.
1 day, 8:59:14.819887 INFO: fragments_df: keeping 5000 of 462310 [sum(precursor_idx_mask)=236411 sum(mass_error_mask)=462310 stop_rank=5000
1 day, 8:59:14.838428 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:59:16.146853 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:59:17.460281 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:59:18.766372 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:59:19.486213 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:59:19.486848 INFO: Using score_cutoff 32.0016791519165 (fac=0.99, q=1)
1 day, 8:59:19.487394 INFO: Updating optimization_manager: fwhm_rt             : 2.7027931213378906 -> 2.7027854919433594
1 day, 8:59:19.487487 INFO: Updating optimization_manager: fwhm_mobility       : 0.00761058833450079 -> 0.007617454510182142
1 day, 8:59:19.487550 INFO: Updating optimization_manager: score_cutoff        : 31.84230019454956 -> 32.0016791519165
1 day, 8:59:19.487620 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:59:19.490575 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:59:19.499991 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:59:19.502441 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:59:19.520929 INFO: === checking if optimization conditions were reached ===
1 day, 8:59:19.521119 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 2 ===
1 day, 8:59:19.527499 INFO: Updating optimization_manager: rt_error            : 11.713930634865465 -> 11.977481731915267
1 day, 8:59:19.527642 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 11.9775.
1 day, 8:59:19.527721 INFO: ==============================================
1 day, 8:59:19.527802 INFO: Starting optimization step 8.
1 day, 8:59:19.527875 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:59:19.527950 INFO: Using python extraction backend
1 day, 8:59:19.528102 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:59:19.528193 INFO: === Search parameters used ===
1 day, 8:59:19.528264 INFO: rt_error       : 11.977481731915267
1 day, 8:59:19.528330 INFO: mobility_error : 0.1
1 day, 8:59:19.528400 INFO: num_candidates : 3
1 day, 8:59:19.528466 INFO: ms1_error      : 15.0
1 day, 8:59:19.528529 INFO: ms2_error      : 15.0
1 day, 8:59:19.528588 INFO: fwhm_rt        : 2.7027854919433594
1 day, 8:59:19.528643 INFO: quant_window   : 3
1 day, 8:59:19.528705 INFO: ==============================================
1 day, 8:59:19.533031 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:59:19.533096 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:59:19.533143 INFO: FWHM in RT is 2.70 seconds, sigma is 0.59
1 day, 8:59:19.533166 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.53
1 day, 8:59:19.534110 INFO: Starting candidate selection
1 day, 8:59:21.136923 INFO: Starting candidate scoring
1 day, 8:59:22.826774 INFO: Finished candidate processing
1 day, 8:59:22.826961 INFO: Collecting candidate features
1 day, 8:59:22.917098 WARNING: intensity_correlation has 25 NaNs ( 0.06 % out of 44502)
1 day, 8:59:22.922616 INFO: Collecting fragment features
1 day, 8:59:22.949530 INFO: Finished candidate scoring
1 day, 8:59:22.971654 INFO: performing precursor FDR with 47 features
1 day, 8:59:22.971816 INFO: Decoy channel: -1
1 day, 8:59:22.971862 INFO: competitive: True
1 day, 8:59:22.993389 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:59:23.004982 WARNING: dropped 1 target PSMs due to missing features
1 day, 8:59:23.005169 WARNING: dropped 24 decoy PSMs due to missing features
1 day, 8:59:23.016458 INFO: Estimating optimal hyperparameters - samples: 35,581, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:59:23.016825 INFO: Using random state 463569 for train-test-split
1 day, 8:59:27.232032 INFO: Test AUC: 0.840
1 day, 8:59:27.232187 INFO: Train AUC: 0.847
1 day, 8:59:27.232224 INFO: AUC difference: 0.78%
1 day, 8:59:27.514183 INFO: Resetting torch num_threads to 128
1 day, 8:59:27.515701 PROGRESS: === Extracted 44502 precursors and 462638 fragments ===
1 day, 8:59:27.516281 INFO: === FDR correction performed with classifier version 2 ===
1 day, 8:59:27.517783 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:59:27.517902 PROGRESS: Total precursors accumulated: 7,999
1 day, 8:59:27.517995 PROGRESS: Target precursors: 7,878 (98.49%)
1 day, 8:59:27.518070 PROGRESS: Decoy precursors: 121 (1.51%)
1 day, 8:59:27.518143 PROGRESS: 
1 day, 8:59:27.518202 PROGRESS: Precursor Summary:
1 day, 8:59:27.521395 PROGRESS: Channel   0:	 0.050 FDR: 7,878; 0.010 FDR: 7,780; 0.001 FDR: 7,342
1 day, 8:59:27.521515 PROGRESS: 
1 day, 8:59:27.521620 PROGRESS: Protein Summary:
1 day, 8:59:27.526558 PROGRESS: Channel   0:	 0.050 FDR: 4,337; 0.010 FDR: 4,296; 0.001 FDR: 4,096
1 day, 8:59:27.526682 PROGRESS: =========================================================================
1 day, 8:59:27.526960 INFO: Target number of precursors reached.
1 day, 8:59:27.640054 INFO: fragments_df: keeping 5000 of 462638 [sum(precursor_idx_mask)=235249 sum(mass_error_mask)=462638 stop_rank=5000
1 day, 8:59:27.658678 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:59:28.894436 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:59:30.138520 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:59:31.381927 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:59:32.103752 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:59:32.104380 INFO: Using score_cutoff 32.23198791732788 (fac=0.99, q=1)
1 day, 8:59:32.104959 INFO: Updating optimization_manager: fwhm_rt             : 2.7027854919433594 -> 2.700965166091919
1 day, 8:59:32.105054 INFO: Updating optimization_manager: fwhm_mobility       : 0.007617454510182142 -> 0.007626709062606096
1 day, 8:59:32.105123 INFO: Updating optimization_manager: score_cutoff        : 32.0016791519165 -> 32.23198791732788
1 day, 8:59:32.105208 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:59:32.108213 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:59:32.117765 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:59:32.120227 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:59:32.142223 INFO: === checking if optimization conditions were reached ===
1 day, 8:59:32.142431 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 2 ===
1 day, 8:59:32.143916 INFO: Updating optimization_manager: rt_error            : 11.977481731915267 -> 11.713930634865465
1 day, 8:59:32.144091 INFO: Updating optimization_manager: classifier_version  : 2 -> 10
1 day, 8:59:32.144238 INFO: Updating optimization_manager: score_cutoff        : 32.23198791732788 -> 32.0016791519165
1 day, 8:59:32.144376 INFO: Updating optimization_manager: fwhm_rt             : 2.700965166091919 -> 2.7027854919433594
1 day, 8:59:32.144515 INFO: Updating optimization_manager: fwhm_mobility       : 0.007626709062606096 -> 0.007617454510182142
1 day, 8:59:32.144665 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 11.7139 found after 9 searches.
1 day, 8:59:32.144757 INFO: ==============================================
1 day, 8:59:32.144861 PROGRESS: Optimization finished for rt_error.
1 day, 8:59:32.162834 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:59:32.166015 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:59:32.175455 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:59:32.177939 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:59:32.200146 INFO: Starting optimization step 0.
1 day, 8:59:32.200354 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:59:32.200455 INFO: Using python extraction backend
1 day, 8:59:32.200630 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:59:32.200745 INFO: === Search parameters used ===
1 day, 8:59:32.200829 INFO: rt_error       : 11.713930634865465
1 day, 8:59:32.200910 INFO: mobility_error : 0.1
1 day, 8:59:32.200986 INFO: num_candidates : 3
1 day, 8:59:32.201064 INFO: ms1_error      : 15.0
1 day, 8:59:32.201123 INFO: ms2_error      : 15.0
1 day, 8:59:32.201223 INFO: fwhm_rt        : 2.7027854919433594
1 day, 8:59:32.201306 INFO: quant_window   : 3
1 day, 8:59:32.201372 INFO: ==============================================
1 day, 8:59:32.205099 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:59:32.205166 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:59:32.205218 INFO: FWHM in RT is 2.70 seconds, sigma is 0.59
1 day, 8:59:32.205254 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.53
1 day, 8:59:32.206236 INFO: Starting candidate selection
1 day, 8:59:33.818772 INFO: Starting candidate scoring
1 day, 8:59:35.540545 INFO: Finished candidate processing
1 day, 8:59:35.540715 INFO: Collecting candidate features
1 day, 8:59:35.630569 WARNING: intensity_correlation has 21 NaNs ( 0.05 % out of 44496)
1 day, 8:59:35.636191 INFO: Collecting fragment features
1 day, 8:59:35.664541 INFO: Finished candidate scoring
1 day, 8:59:35.685513 INFO: performing precursor FDR with 47 features
1 day, 8:59:35.685660 INFO: Decoy channel: -1
1 day, 8:59:35.685687 INFO: competitive: True
1 day, 8:59:35.699602 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:59:35.707475 WARNING: dropped 2 target PSMs due to missing features
1 day, 8:59:35.707608 WARNING: dropped 19 decoy PSMs due to missing features
1 day, 8:59:35.715477 INFO: Estimating optimal hyperparameters - samples: 35,580, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:59:35.715727 INFO: Using random state 98558 for train-test-split
1 day, 8:59:39.935192 INFO: Test AUC: 0.853
1 day, 8:59:39.935347 INFO: Train AUC: 0.856
1 day, 8:59:39.935379 INFO: AUC difference: 0.32%
1 day, 8:59:40.216563 INFO: Resetting torch num_threads to 128
1 day, 8:59:40.217916 PROGRESS: === Extracted 44496 precursors and 462617 fragments ===
1 day, 8:59:40.218519 INFO: === FDR correction performed with classifier version 10 ===
1 day, 8:59:40.219954 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:59:40.220068 PROGRESS: Total precursors accumulated: 7,999
1 day, 8:59:40.220148 PROGRESS: Target precursors: 7,896 (98.71%)
1 day, 8:59:40.220219 PROGRESS: Decoy precursors: 103 (1.29%)
1 day, 8:59:40.220282 PROGRESS: 
1 day, 8:59:40.220341 PROGRESS: Precursor Summary:
1 day, 8:59:40.223504 PROGRESS: Channel   0:	 0.050 FDR: 7,896; 0.010 FDR: 7,843; 0.001 FDR: 7,555
1 day, 8:59:40.223628 PROGRESS: 
1 day, 8:59:40.223704 PROGRESS: Protein Summary:
1 day, 8:59:40.228747 PROGRESS: Channel   0:	 0.050 FDR: 4,348; 0.010 FDR: 4,328; 0.001 FDR: 4,201
1 day, 8:59:40.228901 PROGRESS: =========================================================================
1 day, 8:59:40.229153 INFO: Target number of precursors reached.
1 day, 8:59:40.340617 INFO: fragments_df: keeping 5000 of 462617 [sum(precursor_idx_mask)=236954 sum(mass_error_mask)=462617 stop_rank=5000
1 day, 8:59:40.359141 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:59:41.604770 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:59:42.858511 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:59:44.108433 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:59:44.765553 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:59:44.766166 INFO: Using score_cutoff 31.7590878364563 (fac=0.99, q=1)
1 day, 8:59:44.766732 INFO: Updating optimization_manager: fwhm_rt             : 2.7027854919433594 -> 2.701375722885132
1 day, 8:59:44.766825 INFO: Updating optimization_manager: fwhm_mobility       : 0.007617454510182142 -> 0.0076416837982833385
1 day, 8:59:44.766908 INFO: Updating optimization_manager: score_cutoff        : 32.0016791519165 -> 31.7590878364563
1 day, 8:59:44.766999 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:59:44.769894 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:59:44.779408 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:59:44.781849 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:59:44.803802 INFO: === checking if optimization conditions were reached ===
1 day, 8:59:44.803999 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 8:59:44.806695 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07840320731914449
1 day, 8:59:44.806834 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0784.
1 day, 8:59:44.806931 INFO: ==============================================
1 day, 8:59:44.807029 INFO: Starting optimization step 1.
1 day, 8:59:44.807118 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:59:44.807220 INFO: Using python extraction backend
1 day, 8:59:44.807388 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:59:44.807498 INFO: === Search parameters used ===
1 day, 8:59:44.807580 INFO: rt_error       : 11.713930634865465
1 day, 8:59:44.807654 INFO: mobility_error : 0.07840320731914449
1 day, 8:59:44.807723 INFO: num_candidates : 3
1 day, 8:59:44.807793 INFO: ms1_error      : 15.0
1 day, 8:59:44.807868 INFO: ms2_error      : 15.0
1 day, 8:59:44.807946 INFO: fwhm_rt        : 2.701375722885132
1 day, 8:59:44.808026 INFO: quant_window   : 3
1 day, 8:59:44.808102 INFO: ==============================================
1 day, 8:59:44.813560 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:59:44.813631 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:59:44.813681 INFO: FWHM in RT is 2.70 seconds, sigma is 0.59
1 day, 8:59:44.813711 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.54
1 day, 8:59:44.814721 INFO: Starting candidate selection
1 day, 8:59:46.260953 INFO: Starting candidate scoring
1 day, 8:59:47.928650 INFO: Finished candidate processing
1 day, 8:59:47.928911 INFO: Collecting candidate features
1 day, 8:59:48.031693 WARNING: intensity_correlation has 16 NaNs ( 0.04 % out of 44424)
1 day, 8:59:48.036956 INFO: Collecting fragment features
1 day, 8:59:48.069055 INFO: Finished candidate scoring
1 day, 8:59:48.095606 INFO: performing precursor FDR with 47 features
1 day, 8:59:48.095747 INFO: Decoy channel: -1
1 day, 8:59:48.095774 INFO: competitive: True
1 day, 8:59:48.109161 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 8:59:48.116211 WARNING: dropped 16 decoy PSMs due to missing features
1 day, 8:59:48.124061 INFO: Estimating optimal hyperparameters - samples: 35,526, batch_size: 145, learning_rate: 1.88e-04
1 day, 8:59:48.124294 INFO: Using random state 98558 for train-test-split
1 day, 8:59:52.369908 INFO: Test AUC: 0.839
1 day, 8:59:52.370059 INFO: Train AUC: 0.856
1 day, 8:59:52.370092 INFO: AUC difference: 1.99%
1 day, 8:59:52.655976 INFO: Resetting torch num_threads to 128
1 day, 8:59:52.657368 PROGRESS: === Extracted 44424 precursors and 460146 fragments ===
1 day, 8:59:52.657996 INFO: === FDR correction performed with classifier version 10 ===
1 day, 8:59:52.659465 PROGRESS: ============================= Precursor FDR =============================
1 day, 8:59:52.659587 PROGRESS: Total precursors accumulated: 7,991
1 day, 8:59:52.659663 PROGRESS: Target precursors: 7,856 (98.31%)
1 day, 8:59:52.659728 PROGRESS: Decoy precursors: 135 (1.69%)
1 day, 8:59:52.659789 PROGRESS: 
1 day, 8:59:52.659845 PROGRESS: Precursor Summary:
1 day, 8:59:52.663035 PROGRESS: Channel   0:	 0.050 FDR: 7,856; 0.010 FDR: 7,766; 0.001 FDR: 7,390
1 day, 8:59:52.663163 PROGRESS: 
1 day, 8:59:52.663237 PROGRESS: Protein Summary:
1 day, 8:59:52.668120 PROGRESS: Channel   0:	 0.050 FDR: 4,332; 0.010 FDR: 4,301; 0.001 FDR: 4,123
1 day, 8:59:52.668247 PROGRESS: =========================================================================
1 day, 8:59:52.668547 INFO: Target number of precursors reached.
1 day, 8:59:52.782982 INFO: fragments_df: keeping 5000 of 460146 [sum(precursor_idx_mask)=234306 sum(mass_error_mask)=460146 stop_rank=5000
1 day, 8:59:52.809518 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:59:54.114838 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:59:55.350237 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:59:56.608247 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:59:57.262546 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 8:59:57.263153 INFO: Using score_cutoff 31.790574560165403 (fac=0.99, q=1)
1 day, 8:59:57.263698 INFO: Updating optimization_manager: fwhm_rt             : 2.701375722885132 -> 2.7005248069763184
1 day, 8:59:57.263795 INFO: Updating optimization_manager: fwhm_mobility       : 0.0076416837982833385 -> 0.007644710596650839
1 day, 8:59:57.263861 INFO: Updating optimization_manager: score_cutoff        : 31.7590878364563 -> 31.790574560165403
1 day, 8:59:57.263934 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 8:59:57.266876 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 8:59:57.276318 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 8:59:57.278813 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 8:59:57.298854 INFO: === checking if optimization conditions were reached ===
1 day, 8:59:57.299040 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 8:59:57.301891 INFO: Updating optimization_manager: mobility_error      : 0.07840320731914449 -> 0.06638698672101627
1 day, 8:59:57.302037 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0664.
1 day, 8:59:57.302134 INFO: ==============================================
1 day, 8:59:57.302238 INFO: Starting optimization step 2.
1 day, 8:59:57.302325 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 8:59:57.302421 INFO: Using python extraction backend
1 day, 8:59:57.302585 PROGRESS: Extracting batch of 15888 precursors
1 day, 8:59:57.302680 INFO: === Search parameters used ===
1 day, 8:59:57.302762 INFO: rt_error       : 11.713930634865465
1 day, 8:59:57.302836 INFO: mobility_error : 0.06638698672101627
1 day, 8:59:57.302909 INFO: num_candidates : 3
1 day, 8:59:57.302981 INFO: ms1_error      : 15.0
1 day, 8:59:57.303050 INFO: ms2_error      : 15.0
1 day, 8:59:57.303117 INFO: fwhm_rt        : 2.7005248069763184
1 day, 8:59:57.303185 INFO: quant_window   : 3
1 day, 8:59:57.303251 INFO: ==============================================
1 day, 8:59:57.307561 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 8:59:57.307622 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 8:59:57.307677 INFO: FWHM in RT is 2.70 seconds, sigma is 0.59
1 day, 8:59:57.307706 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.55
1 day, 8:59:57.308717 INFO: Starting candidate selection
1 day, 8:59:58.704124 INFO: Starting candidate scoring
1 day, 9:00:00.453432 INFO: Finished candidate processing
1 day, 9:00:00.453641 INFO: Collecting candidate features
1 day, 9:00:00.516579 WARNING: intensity_correlation has 18 NaNs ( 0.04 % out of 44342)
1 day, 9:00:00.522026 INFO: Collecting fragment features
1 day, 9:00:00.549196 INFO: Finished candidate scoring
1 day, 9:00:00.572810 INFO: performing precursor FDR with 47 features
1 day, 9:00:00.572961 INFO: Decoy channel: -1
1 day, 9:00:00.572987 INFO: competitive: True
1 day, 9:00:00.585768 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:00:00.592546 WARNING: dropped 18 decoy PSMs due to missing features
1 day, 9:00:00.601198 INFO: Estimating optimal hyperparameters - samples: 35,459, batch_size: 145, learning_rate: 1.88e-04
1 day, 9:00:00.601426 INFO: Using random state 98558 for train-test-split
1 day, 9:00:04.799815 INFO: Test AUC: 0.845
1 day, 9:00:04.799970 INFO: Train AUC: 0.857
1 day, 9:00:04.800003 INFO: AUC difference: 1.37%
1 day, 9:00:05.080034 INFO: Resetting torch num_threads to 128
1 day, 9:00:05.081390 PROGRESS: === Extracted 44342 precursors and 457841 fragments ===
1 day, 9:00:05.081960 INFO: === FDR correction performed with classifier version 10 ===
1 day, 9:00:05.083413 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:00:05.083527 PROGRESS: Total precursors accumulated: 7,985
1 day, 9:00:05.083606 PROGRESS: Target precursors: 7,857 (98.40%)
1 day, 9:00:05.083675 PROGRESS: Decoy precursors: 128 (1.60%)
1 day, 9:00:05.083750 PROGRESS: 
1 day, 9:00:05.083812 PROGRESS: Precursor Summary:
1 day, 9:00:05.087047 PROGRESS: Channel   0:	 0.050 FDR: 7,857; 0.010 FDR: 7,768; 0.001 FDR: 7,489
1 day, 9:00:05.087174 PROGRESS: 
1 day, 9:00:05.087247 PROGRESS: Protein Summary:
1 day, 9:00:05.092243 PROGRESS: Channel   0:	 0.050 FDR: 4,332; 0.010 FDR: 4,304; 0.001 FDR: 4,191
1 day, 9:00:05.092392 PROGRESS: =========================================================================
1 day, 9:00:05.092657 INFO: Target number of precursors reached.
1 day, 9:00:05.204947 INFO: fragments_df: keeping 5000 of 457841 [sum(precursor_idx_mask)=233992 sum(mass_error_mask)=457841 stop_rank=5000
1 day, 9:00:05.223294 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:00:06.517961 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:00:07.823479 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:00:09.126623 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:00:09.851201 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:00:09.851896 INFO: Using score_cutoff 31.429694155311584 (fac=0.99, q=1)
1 day, 9:00:09.852522 INFO: Updating optimization_manager: fwhm_rt             : 2.7005248069763184 -> 2.7058067321777344
1 day, 9:00:09.852623 INFO: Updating optimization_manager: fwhm_mobility       : 0.007644710596650839 -> 0.0076427822932600975
1 day, 9:00:09.852687 INFO: Updating optimization_manager: score_cutoff        : 31.790574560165403 -> 31.429694155311584
1 day, 9:00:09.852787 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:00:09.855777 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:00:09.865147 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:00:09.867604 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:00:09.887362 INFO: === checking if optimization conditions were reached ===
1 day, 9:00:09.887571 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 9:00:09.888731 INFO: Updating optimization_manager: mobility_error      : 0.06638698672101627 -> 0.1
1 day, 9:00:09.888902 INFO: Updating optimization_manager: classifier_version  : 10 -> 12
1 day, 9:00:09.889043 INFO: Updating optimization_manager: score_cutoff        : 31.429694155311584 -> 31.7590878364563
1 day, 9:00:09.889179 INFO: Updating optimization_manager: fwhm_rt             : 2.7058067321777344 -> 2.701375722885132
1 day, 9:00:09.889307 INFO: Updating optimization_manager: fwhm_mobility       : 0.0076427822932600975 -> 0.0076416837982833385
1 day, 9:00:09.889434 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.1000 found after 3 searches.
1 day, 9:00:09.889526 INFO: ==============================================
1 day, 9:00:09.889615 PROGRESS: Optimization finished for mobility_error.
1 day, 9:00:09.915099 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:00:09.918256 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:00:09.927772 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:00:09.930187 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:00:09.951440 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 9:00:09.951645 PROGRESS: ==============================================
1 day, 9:00:09.951749 PROGRESS: ms2_error      : 15.0000
1 day, 9:00:09.951859 PROGRESS: ms1_error      : 15.0000
1 day, 9:00:09.951957 PROGRESS: rt_error       : 11.7139
1 day, 9:00:09.952043 PROGRESS: mobility_error : 0.1000
1 day, 9:00:09.952118 PROGRESS: ==============================================
1 day, 9:00:09.953481 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:00:09.975021 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:00:10.077278 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:00:10.103401 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:00:10.358061 INFO: Using python extraction backend
1 day, 9:00:10.358461 PROGRESS: Extracting batch of 182033 precursors
1 day, 9:00:10.358567 INFO: === Search parameters used ===
1 day, 9:00:10.358644 INFO: rt_error       : 11.713930634865465
1 day, 9:00:10.358718 INFO: mobility_error : 0.1
1 day, 9:00:10.358778 INFO: num_candidates : 3
1 day, 9:00:10.358851 INFO: ms1_error      : 15.0
1 day, 9:00:10.358923 INFO: ms2_error      : 15.0
1 day, 9:00:10.358993 INFO: fwhm_rt        : 2.701375722885132
1 day, 9:00:10.359064 INFO: quant_window   : 3
1 day, 9:00:10.359130 INFO: ==============================================
1 day, 9:00:10.405340 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 9:00:10.405504 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 9:00:10.405557 INFO: FWHM in RT is 2.70 seconds, sigma is 0.59
1 day, 9:00:10.405581 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.54
1 day, 9:00:10.406365 INFO: Starting candidate selection
1 day, 9:00:23.551939 INFO: Removed 82730 precursors with score below cutoff 31.7590878364563
1 day, 9:00:23.912941 INFO: Starting candidate scoring
1 day, 9:00:38.647743 INFO: Finished candidate processing
1 day, 9:00:38.647954 INFO: Collecting candidate features
1 day, 9:00:39.391849 WARNING: intensity_correlation has 4 NaNs ( 0.00 % out of 428784)
1 day, 9:00:39.409779 INFO: Collecting fragment features
1 day, 9:00:39.710494 INFO: Finished candidate scoring
1 day, 9:00:39.962956 INFO: === Performing FDR correction with classifier version 12 ===
1 day, 9:00:39.963505 INFO: performing precursor FDR with 47 features
1 day, 9:00:39.963567 INFO: Decoy channel: -1
1 day, 9:00:39.963593 INFO: competitive: True
1 day, 9:00:40.065259 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:00:40.122631 WARNING: dropped 4 decoy PSMs due to missing features
1 day, 9:00:40.122824 WARNING: FDR calculation for 237373 target and 191407 decoy PSMs
1 day, 9:00:40.122856 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 9:00:40.332850 INFO: Estimating optimal hyperparameters - samples: 343,024, batch_size: 1,405, learning_rate: 5.86e-04
1 day, 9:00:40.333707 INFO: Using random state 770110 for train-test-split
1 day, 9:00:53.019702 INFO: Test AUC: 0.862
1 day, 9:00:53.019869 INFO: Train AUC: 0.869
1 day, 9:00:53.019902 INFO: AUC difference: 0.85%
1 day, 9:00:53.422466 INFO: Resetting torch num_threads to 128
1 day, 9:00:53.444069 INFO: Removing fragments below FDR threshold
1 day, 9:00:53.530871 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:00:53.531200 PROGRESS: Total precursors accumulated: 90,040
1 day, 9:00:53.531311 PROGRESS: Target precursors: 89,149 (99.01%)
1 day, 9:00:53.531387 PROGRESS: Decoy precursors: 891 (0.99%)
1 day, 9:00:53.531470 PROGRESS: 
1 day, 9:00:53.531551 PROGRESS: Precursor Summary:
1 day, 9:00:53.573097 PROGRESS: Channel   0:	 0.050 FDR: 89,149; 0.010 FDR: 89,149; 0.001 FDR: 85,121
1 day, 9:00:53.573429 PROGRESS: 
1 day, 9:00:53.573543 PROGRESS: Protein Summary:
1 day, 9:00:53.631767 PROGRESS: Channel   0:	 0.050 FDR: 8,975; 0.010 FDR: 8,975; 0.001 FDR: 8,966
1 day, 9:00:53.632107 PROGRESS: =========================================================================
1 day, 9:00:53.633173 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/psm.parquet
1 day, 9:00:53.983600 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/frag.parquet
1 day, 9:00:54.287453 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 9:00:54.357080 PROGRESS: Loading raw file 6/6: ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508 
1 day, 9:00:54.357276 INFO: Quantification results path: /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant
1 day, 9:00:54.357377 INFO: Creating folder /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/figures
1 day, 9:00:54.357592 INFO: Initializing TimingManager
1 day, 9:00:54.358150 INFO: Initializing RawFileManager
1 day, 9:00:54.358322 INFO: Importing data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 9:00:54.358378 INFO: Using .d import for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 9:00:54.358423 INFO: Reading frame metadata for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 9:00:54.870052 INFO: Reading 39,129 frames with 2,804,178,635 detector events for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 9:01:04.254206 INFO: Indexing /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d...
1 day, 9:01:04.256357 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 9:01:04.259287 INFO: Fetching mobility values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 9:01:04.259607 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 9:01:04.260070 INFO: Opening handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 9:01:04.262522 INFO: Fetching mz values from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 9:01:04.278089 INFO: Closing handle for /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 9:01:04.278345 INFO: Indexing quadrupole dimension
1 day, 9:01:04.817763 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 9:01:04.817936 INFO: Transposing detector events
1 day, 9:01:13.697299 INFO: Finished transposing data
1 day, 9:01:13.777064 INFO: Successfully imported data from /public/local/ProteoBench/HYE_diaPASEF/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508.d
1 day, 9:01:13.777923 INFO: RT (min)            : 0.0 - 70.0
1 day, 9:01:13.777983 INFO: RT duration (sec)   : 4199.8
1 day, 9:01:13.778018 INFO: RT duration (min)   : 70.0
1 day, 9:01:13.778052 INFO: Cycle len (scans)   : 9
1 day, 9:01:13.778076 INFO: Cycle len (sec)     : 0.97
1 day, 9:01:13.778095 INFO: Number of cycles    : 4347
1 day, 9:01:13.778123 INFO: MS2 range (m/z)     : 400.0 - 1000.0
1 day, 9:01:13.778181 INFO: Creating DIA data object took: 19.4198899269104
1 day, 9:01:13.838293 INFO: Initializing CalibrationManager
1 day, 9:01:13.838675 INFO: Setting up calibration estimators ..
1 day, 9:01:13.838768 INFO: Found 1 estimator(s) in calibration group 'fragment'
1 day, 9:01:13.838868 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, 9:01:13.838992 INFO: Found 3 estimator(s) in calibration group 'precursor'
1 day, 9:01:13.839076 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, 9:01:13.839163 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, 9:01:13.839265 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, 9:01:13.839337 INFO: Done setting up calibration estimators.
1 day, 9:01:13.839482 INFO: Initializing OptimizationManager
1 day, 9:01:13.839605 INFO: initial parameter: ms1_error = 30
1 day, 9:01:13.839674 INFO: initial parameter: ms2_error = 30
1 day, 9:01:13.839749 INFO: initial parameter: rt_error = 2099.9231665
1 day, 9:01:13.839818 INFO: initial parameter: mobility_error = 0.1
1 day, 9:01:13.839883 INFO: initial parameter: num_candidates = 1
1 day, 9:01:13.839951 INFO: initial parameter: fwhm_rt = 5
1 day, 9:01:13.840017 INFO: initial parameter: fwhm_mobility = 0.01
1 day, 9:01:13.840080 INFO: initial parameter: score_cutoff = 0
1 day, 9:01:13.840146 INFO: initial parameter: classifier_version = -1
1 day, 9:01:13.840255 PROGRESS: Initializing workflow ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 9:01:13.840531 INFO: FDRManager: loading saved state not requested, will be initialized.
1 day, 9:01:13.840577 INFO: Initializing FDRManager
1 day, 9:01:13.840640 INFO: Loading classifier store from /usr/local/lib/python3.10/site-packages/alphadia/constants/classifier
1 day, 9:01:13.876305 PROGRESS: Initializing spectral library: 91,740 target precursors potentially observable (0 removed)
1 day, 9:01:13.923702 INFO: Updating optimization_manager: ms2_error           : 30 -> 30
1 day, 9:01:13.924339 INFO: Updating optimization_manager: rt_error            : 2099.9231665 -> 2099.9231665
1 day, 9:01:13.924477 INFO: Updating optimization_manager: ms1_error           : 30 -> 30
1 day, 9:01:13.924717 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.1
1 day, 9:01:13.924837 PROGRESS: Starting initial search for precursors.
1 day, 9:01:13.924953 INFO: Starting optimization step 0.
1 day, 9:01:13.925049 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 9:01:13.925142 INFO: Using python extraction backend
1 day, 9:01:13.925337 PROGRESS: Extracting batch of 15888 precursors
1 day, 9:01:13.925445 INFO: === Search parameters used ===
1 day, 9:01:13.925523 INFO: rt_error       : 2099.9231665
1 day, 9:01:13.925589 INFO: mobility_error : 0.1
1 day, 9:01:13.925654 INFO: num_candidates : 1
1 day, 9:01:13.925720 INFO: ms1_error      : 30
1 day, 9:01:13.925799 INFO: ms2_error      : 30
1 day, 9:01:13.925877 INFO: fwhm_rt        : 5
1 day, 9:01:13.925947 INFO: quant_window   : 3
1 day, 9:01:13.926017 INFO: ==============================================
1 day, 9:01:13.928935 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 9:01:13.928995 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 9:01:13.929036 INFO: FWHM in RT is 5.00 seconds, sigma is 1.10
1 day, 9:01:13.929067 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.64
1 day, 9:01:13.930202 INFO: Starting candidate selection
1 day, 9:02:50.781665 INFO: Starting candidate scoring
1 day, 9:02:52.261657 INFO: Finished candidate processing
1 day, 9:02:52.261902 INFO: Collecting candidate features
1 day, 9:02:52.325717 INFO: Collecting fragment features
1 day, 9:02:52.339385 INFO: Finished candidate scoring
1 day, 9:02:52.348889 INFO: performing precursor FDR with 47 features
1 day, 9:02:52.349009 INFO: Decoy channel: -1
1 day, 9:02:52.349036 INFO: competitive: True
1 day, 9:02:52.353976 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:02:52.359684 INFO: Estimating optimal hyperparameters - samples: 12,692, batch_size: 128, learning_rate: 1.77e-04
1 day, 9:02:52.360698 INFO: Using random state 860258 for train-test-split
1 day, 9:02:53.979959 INFO: Test AUC: 0.827
1 day, 9:02:53.980103 INFO: Train AUC: 0.847
1 day, 9:02:53.980136 INFO: AUC difference: 2.35%
1 day, 9:02:54.256060 INFO: Resetting torch num_threads to 128
1 day, 9:02:54.257105 PROGRESS: === Extracted 15866 precursors and 179859 fragments ===
1 day, 9:02:54.257700 INFO: === FDR correction performed with classifier version -1 ===
1 day, 9:02:54.259238 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:02:54.259354 PROGRESS: Total precursors accumulated: 7,994
1 day, 9:02:54.259436 PROGRESS: Target precursors: 6,747 (84.40%)
1 day, 9:02:54.259508 PROGRESS: Decoy precursors: 1,247 (15.60%)
1 day, 9:02:54.259589 PROGRESS: 
1 day, 9:02:54.259660 PROGRESS: Precursor Summary:
1 day, 9:02:54.262147 PROGRESS: Channel   0:	 0.050 FDR: 5,162; 0.010 FDR: 4,504; 0.001 FDR: 3,307
1 day, 9:02:54.262272 PROGRESS: 
1 day, 9:02:54.262362 PROGRESS: Protein Summary:
1 day, 9:02:54.265779 PROGRESS: Channel   0:	 0.050 FDR: 3,109; 0.010 FDR: 2,766; 0.001 FDR: 2,209
1 day, 9:02:54.265905 PROGRESS: =========================================================================
1 day, 9:02:54.266066 INFO: Target number of precursors reached.
1 day, 9:02:54.298757 INFO: fragments_df: keeping 5000 of 179859 [sum(precursor_idx_mask)=51034 sum(mass_error_mask)=179859 stop_rank=5000
1 day, 9:02:54.320539 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:02:54.981070 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:02:55.644292 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:02:56.298722 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:02:57.021237 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1 day, 9:02:57.021854 INFO: Using score_cutoff 48.78639019432068 (fac=0.99, q=1)
1 day, 9:02:57.022441 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0899109840393066
1 day, 9:02:57.022549 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> 0.010372316464781761
1 day, 9:02:57.022619 INFO: Updating optimization_manager: score_cutoff        : 0 -> 48.78639019432068
1 day, 9:02:57.022700 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:02:57.025703 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:02:57.035183 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:02:57.037645 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:02:57.058783 INFO: Updating optimization_manager: classifier_version  : -1 -> 0
1 day, 9:02:57.059003 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1 day, 9:02:57.059113 INFO: Starting optimization step 1.
1 day, 9:02:57.059192 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 9:02:57.059270 INFO: Using python extraction backend
1 day, 9:02:57.059431 PROGRESS: Extracting batch of 15888 precursors
1 day, 9:02:57.059521 INFO: === Search parameters used ===
1 day, 9:02:57.059582 INFO: rt_error       : 2099.9231665
1 day, 9:02:57.059647 INFO: mobility_error : 0.1
1 day, 9:02:57.059703 INFO: num_candidates : 3
1 day, 9:02:57.059754 INFO: ms1_error      : 30
1 day, 9:02:57.059803 INFO: ms2_error      : 30
1 day, 9:02:57.059860 INFO: fwhm_rt        : 3.0899109840393066
1 day, 9:02:57.059912 INFO: quant_window   : 3
1 day, 9:02:57.059959 INFO: ==============================================
1 day, 9:02:57.064534 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 9:02:57.064606 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 9:02:57.064653 INFO: FWHM in RT is 3.09 seconds, sigma is 0.68
1 day, 9:02:57.064685 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.81
1 day, 9:02:57.065787 INFO: Starting candidate selection
1 day, 9:04:39.236125 INFO: Starting candidate scoring
1 day, 9:04:42.557119 INFO: Finished candidate processing
1 day, 9:04:42.557323 INFO: Collecting candidate features
1 day, 9:04:42.650286 INFO: Collecting fragment features
1 day, 9:04:42.677773 INFO: Finished candidate scoring
1 day, 9:04:42.696925 INFO: performing precursor FDR with 47 features
1 day, 9:04:42.697088 INFO: Decoy channel: -1
1 day, 9:04:42.697118 INFO: competitive: True
1 day, 9:04:42.710391 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:04:42.722281 INFO: Estimating optimal hyperparameters - samples: 36,128, batch_size: 147, learning_rate: 1.89e-04
1 day, 9:04:42.722543 INFO: Using random state 39177 for train-test-split
1 day, 9:04:46.426790 INFO: Test AUC: 0.705
1 day, 9:04:46.426965 INFO: Train AUC: 0.718
1 day, 9:04:46.426997 INFO: AUC difference: 1.76%
1 day, 9:04:49.282906 INFO: Resetting torch num_threads to 128
1 day, 9:04:49.284592 PROGRESS: === Extracted 45161 precursors and 511327 fragments ===
1 day, 9:04:49.285233 INFO: === FDR correction performed with classifier version 0 ===
1 day, 9:04:49.286997 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:04:49.287134 PROGRESS: Total precursors accumulated: 8,000
1 day, 9:04:49.287230 PROGRESS: Target precursors: 7,161 (89.51%)
1 day, 9:04:49.287311 PROGRESS: Decoy precursors: 839 (10.49%)
1 day, 9:04:49.287387 PROGRESS: 
1 day, 9:04:49.287462 PROGRESS: Precursor Summary:
1 day, 9:04:49.290513 PROGRESS: Channel   0:	 0.050 FDR: 6,104; 0.010 FDR: 5,308; 0.001 FDR: 4,306
1 day, 9:04:49.290666 PROGRESS: 
1 day, 9:04:49.290755 PROGRESS: Protein Summary:
1 day, 9:04:49.294982 PROGRESS: Channel   0:	 0.050 FDR: 3,540; 0.010 FDR: 3,154; 0.001 FDR: 2,710
1 day, 9:04:49.295127 PROGRESS: =========================================================================
1 day, 9:04:49.295445 INFO: Target number of precursors reached.
1 day, 9:04:49.395545 INFO: fragments_df: keeping 5000 of 511327 [sum(precursor_idx_mask)=171952 sum(mass_error_mask)=511327 stop_rank=5000
1 day, 9:04:49.422115 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:04:50.156574 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:04:50.910071 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:04:51.630969 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:04:52.291571 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:04:52.292243 INFO: Using score_cutoff 48.48658051643372 (fac=0.99, q=1)
1 day, 9:04:52.292775 INFO: Updating optimization_manager: fwhm_rt             : 3.0899109840393066 -> 3.0823655128479004
1 day, 9:04:52.292875 INFO: Updating optimization_manager: fwhm_mobility       : 0.010372316464781761 -> 0.010055182501673698
1 day, 9:04:52.292946 INFO: Updating optimization_manager: score_cutoff        : 48.78639019432068 -> 48.48658051643372
1 day, 9:04:52.293022 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:04:52.296028 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:04:52.305426 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:04:52.308076 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:04:52.328072 INFO: === checking if optimization conditions were reached ===
1 day, 9:04:52.330298 INFO: Updating optimization_manager: ms2_error           : 30 -> 15.0
1 day, 9:04:52.330455 INFO: Updating optimization_manager: classifier_version  : 0 -> 1
1 day, 9:04:52.330581 PROGRESS: ❌ ms2_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 9:04:52.332740 INFO: Updating optimization_manager: ms1_error           : 30 -> 15.0
1 day, 9:04:52.332886 INFO: Updating optimization_manager: classifier_version  : 1 -> 1
1 day, 9:04:52.333028 PROGRESS: ❌ ms1_error      : 15.0000 > 15.0000 or insufficient steps taken.
1 day, 9:04:52.333133 INFO: ==============================================
1 day, 9:04:52.333279 INFO: Starting optimization step 2.
1 day, 9:04:52.333388 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 9:04:52.333528 INFO: Using python extraction backend
1 day, 9:04:52.333720 PROGRESS: Extracting batch of 15888 precursors
1 day, 9:04:52.333855 INFO: === Search parameters used ===
1 day, 9:04:52.333978 INFO: rt_error       : 2099.9231665
1 day, 9:04:52.334073 INFO: mobility_error : 0.1
1 day, 9:04:52.334182 INFO: num_candidates : 3
1 day, 9:04:52.334274 INFO: ms1_error      : 15.0
1 day, 9:04:52.334383 INFO: ms2_error      : 15.0
1 day, 9:04:52.334471 INFO: fwhm_rt        : 3.0823655128479004
1 day, 9:04:52.334590 INFO: quant_window   : 3
1 day, 9:04:52.334700 INFO: ==============================================
1 day, 9:04:52.340187 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 9:04:52.340261 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 9:04:52.340318 INFO: FWHM in RT is 3.08 seconds, sigma is 0.68
1 day, 9:04:52.340377 INFO: FWHM in mobility is 0.010 1/K_0, sigma is 4.66
1 day, 9:04:52.341407 INFO: Starting candidate selection
1 day, 9:06:25.183003 INFO: Starting candidate scoring
1 day, 9:06:27.116457 INFO: Finished candidate processing
1 day, 9:06:27.116604 INFO: Collecting candidate features
1 day, 9:06:27.205637 INFO: Collecting fragment features
1 day, 9:06:27.240009 INFO: Finished candidate scoring
1 day, 9:06:27.266497 INFO: performing precursor FDR with 47 features
1 day, 9:06:27.266662 INFO: Decoy channel: -1
1 day, 9:06:27.266689 INFO: competitive: True
1 day, 9:06:27.284596 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:06:27.298051 INFO: Estimating optimal hyperparameters - samples: 36,156, batch_size: 148, learning_rate: 1.90e-04
1 day, 9:06:27.298322 INFO: Using random state 284232 for train-test-split
1 day, 9:06:31.050637 INFO: Test AUC: 0.732
1 day, 9:06:31.050812 INFO: Train AUC: 0.750
1 day, 9:06:31.050843 INFO: AUC difference: 2.30%
1 day, 9:06:31.342104 INFO: Resetting torch num_threads to 128
1 day, 9:06:31.343846 PROGRESS: === Extracted 45195 precursors and 497757 fragments ===
1 day, 9:06:31.344516 INFO: === FDR correction performed with classifier version 1 ===
1 day, 9:06:31.346288 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:06:31.346420 PROGRESS: Total precursors accumulated: 8,000
1 day, 9:06:31.346502 PROGRESS: Target precursors: 7,531 (94.14%)
1 day, 9:06:31.346572 PROGRESS: Decoy precursors: 469 (5.86%)
1 day, 9:06:31.346635 PROGRESS: 
1 day, 9:06:31.346696 PROGRESS: Precursor Summary:
1 day, 9:06:31.349981 PROGRESS: Channel   0:	 0.050 FDR: 7,365; 0.010 FDR: 6,670; 0.001 FDR: 5,174
1 day, 9:06:31.350124 PROGRESS: 
1 day, 9:06:31.350197 PROGRESS: Protein Summary:
1 day, 9:06:31.354818 PROGRESS: Channel   0:	 0.050 FDR: 4,110; 0.010 FDR: 3,783; 0.001 FDR: 3,119
1 day, 9:06:31.354977 PROGRESS: =========================================================================
1 day, 9:06:31.355678 INFO: Target number of precursors reached.
1 day, 9:06:31.462296 INFO: fragments_df: keeping 5000 of 497757 [sum(precursor_idx_mask)=210614 sum(mass_error_mask)=497757 stop_rank=5000
1 day, 9:06:31.520597 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:06:32.506495 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:06:33.518041 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:06:34.502839 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:06:35.160406 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:06:35.161043 INFO: Using score_cutoff 41.18814831390381 (fac=0.99, q=1)
1 day, 9:06:35.161589 INFO: Updating optimization_manager: fwhm_rt             : 3.0823655128479004 -> 2.796727418899536
1 day, 9:06:35.161686 INFO: Updating optimization_manager: fwhm_mobility       : 0.010055182501673698 -> 0.008226241916418076
1 day, 9:06:35.161768 INFO: Updating optimization_manager: score_cutoff        : 48.48658051643372 -> 41.18814831390381
1 day, 9:06:35.161855 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:06:35.164979 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:06:35.174390 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:06:35.176876 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:06:35.197195 INFO: === checking if optimization conditions were reached ===
1 day, 9:06:35.199596 INFO: Updating optimization_manager: ms2_error           : 15.0 -> 15.0
1 day, 9:06:35.199739 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
1 day, 9:06:35.199865 PROGRESS: ✅ ms2_error      : 15.0000 <= 15.0000
1 day, 9:06:35.202350 INFO: Updating optimization_manager: ms1_error           : 15.0 -> 15.0
1 day, 9:06:35.202491 INFO: Updating optimization_manager: classifier_version  : 2 -> 2
1 day, 9:06:35.202581 PROGRESS: ✅ ms1_error      : 15.0000 <= 15.0000
1 day, 9:06:35.202665 INFO: ==============================================
1 day, 9:06:35.202756 PROGRESS: Optimization finished for ms2_error, ms1_error.
1 day, 9:06:35.227598 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:06:35.231180 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:06:35.241159 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:06:35.243974 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:06:35.265478 INFO: Starting optimization step 0.
1 day, 9:06:35.265696 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 9:06:35.265819 INFO: Using python extraction backend
1 day, 9:06:35.266013 PROGRESS: Extracting batch of 15888 precursors
1 day, 9:06:35.266122 INFO: === Search parameters used ===
1 day, 9:06:35.266196 INFO: rt_error       : 2099.9231665
1 day, 9:06:35.266265 INFO: mobility_error : 0.1
1 day, 9:06:35.266329 INFO: num_candidates : 3
1 day, 9:06:35.266393 INFO: ms1_error      : 15.0
1 day, 9:06:35.266458 INFO: ms2_error      : 15.0
1 day, 9:06:35.266523 INFO: fwhm_rt        : 2.796727418899536
1 day, 9:06:35.266587 INFO: quant_window   : 3
1 day, 9:06:35.266690 INFO: ==============================================
1 day, 9:06:35.273257 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 9:06:35.273337 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 9:06:35.273385 INFO: FWHM in RT is 2.80 seconds, sigma is 0.61
1 day, 9:06:35.273441 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.82
1 day, 9:06:35.274503 INFO: Starting candidate selection
1 day, 9:08:12.395687 INFO: Starting candidate scoring
1 day, 9:08:14.384762 INFO: Finished candidate processing
1 day, 9:08:14.384965 INFO: Collecting candidate features
1 day, 9:08:14.481176 INFO: Collecting fragment features
1 day, 9:08:14.509286 INFO: Finished candidate scoring
1 day, 9:08:14.533172 INFO: performing precursor FDR with 47 features
1 day, 9:08:14.533326 INFO: Decoy channel: -1
1 day, 9:08:14.533353 INFO: competitive: True
1 day, 9:08:14.547978 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:08:14.561596 INFO: Estimating optimal hyperparameters - samples: 36,096, batch_size: 147, learning_rate: 1.89e-04
1 day, 9:08:14.561881 INFO: Using random state 775072 for train-test-split
1 day, 9:08:18.354939 INFO: Test AUC: 0.745
1 day, 9:08:18.355101 INFO: Train AUC: 0.764
1 day, 9:08:18.355134 INFO: AUC difference: 2.38%
1 day, 9:08:18.653183 INFO: Resetting torch num_threads to 128
1 day, 9:08:18.655022 PROGRESS: === Extracted 45120 precursors and 497223 fragments ===
1 day, 9:08:18.655713 INFO: === FDR correction performed with classifier version 2 ===
1 day, 9:08:18.657291 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:08:18.657414 PROGRESS: Total precursors accumulated: 8,000
1 day, 9:08:18.657497 PROGRESS: Target precursors: 7,530 (94.12%)
1 day, 9:08:18.657565 PROGRESS: Decoy precursors: 470 (5.88%)
1 day, 9:08:18.657625 PROGRESS: 
1 day, 9:08:18.657682 PROGRESS: Precursor Summary:
1 day, 9:08:18.660774 PROGRESS: Channel   0:	 0.050 FDR: 7,341; 0.010 FDR: 6,787; 0.001 FDR: 5,684
1 day, 9:08:18.660914 PROGRESS: 
1 day, 9:08:18.660988 PROGRESS: Protein Summary:
1 day, 9:08:18.665722 PROGRESS: Channel   0:	 0.050 FDR: 4,105; 0.010 FDR: 3,834; 0.001 FDR: 3,349
1 day, 9:08:18.665883 PROGRESS: =========================================================================
1 day, 9:08:18.666378 INFO: Target number of precursors reached.
1 day, 9:08:18.770406 INFO: fragments_df: keeping 5000 of 497223 [sum(precursor_idx_mask)=213610 sum(mass_error_mask)=497223 stop_rank=5000
1 day, 9:08:18.791725 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:08:19.864783 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:08:20.958639 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:08:22.030174 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:08:22.754020 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:08:22.754719 INFO: Using score_cutoff 40.93837286682129 (fac=0.99, q=1)
1 day, 9:08:22.755329 INFO: Updating optimization_manager: fwhm_rt             : 2.796727418899536 -> 2.7907164096832275
1 day, 9:08:22.755443 INFO: Updating optimization_manager: fwhm_mobility       : 0.008226241916418076 -> 0.00818057730793953
1 day, 9:08:22.755531 INFO: Updating optimization_manager: score_cutoff        : 41.18814831390381 -> 40.93837286682129
1 day, 9:08:22.755634 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:08:22.758734 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:08:22.768220 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:08:22.770754 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:08:22.790482 INFO: === checking if optimization conditions were reached ===
1 day, 9:08:22.790756 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 2 ===
1 day, 9:08:22.797021 INFO: Updating optimization_manager: rt_error            : 2099.9231665 -> 279.25593080910124
1 day, 9:08:22.797184 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 279.2559.
1 day, 9:08:22.797323 INFO: ==============================================
1 day, 9:08:22.797451 INFO: Starting optimization step 1.
1 day, 9:08:22.797565 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 9:08:22.797675 INFO: Using python extraction backend
1 day, 9:08:22.797897 PROGRESS: Extracting batch of 15888 precursors
1 day, 9:08:22.798029 INFO: === Search parameters used ===
1 day, 9:08:22.798131 INFO: rt_error       : 279.25593080910124
1 day, 9:08:22.798222 INFO: mobility_error : 0.1
1 day, 9:08:22.798311 INFO: num_candidates : 3
1 day, 9:08:22.798398 INFO: ms1_error      : 15.0
1 day, 9:08:22.798483 INFO: ms2_error      : 15.0
1 day, 9:08:22.798561 INFO: fwhm_rt        : 2.7907164096832275
1 day, 9:08:22.798654 INFO: quant_window   : 3
1 day, 9:08:22.798744 INFO: ==============================================
1 day, 9:08:22.806290 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 9:08:22.806401 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 9:08:22.806462 INFO: FWHM in RT is 2.79 seconds, sigma is 0.61
1 day, 9:08:22.806517 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.79
1 day, 9:08:22.807467 INFO: Starting candidate selection
1 day, 9:08:36.598364 INFO: Starting candidate scoring
1 day, 9:08:38.482525 INFO: Finished candidate processing
1 day, 9:08:38.482785 INFO: Collecting candidate features
1 day, 9:08:38.552513 INFO: Collecting fragment features
1 day, 9:08:38.580958 INFO: Finished candidate scoring
1 day, 9:08:38.606077 INFO: performing precursor FDR with 47 features
1 day, 9:08:38.606218 INFO: Decoy channel: -1
1 day, 9:08:38.606245 INFO: competitive: True
1 day, 9:08:38.620139 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:08:38.633259 INFO: Estimating optimal hyperparameters - samples: 35,884, batch_size: 146, learning_rate: 1.89e-04
1 day, 9:08:38.633505 INFO: Using random state 775072 for train-test-split
1 day, 9:08:42.577148 INFO: Test AUC: 0.767
1 day, 9:08:42.577317 INFO: Train AUC: 0.776
1 day, 9:08:42.577348 INFO: AUC difference: 1.20%
1 day, 9:08:42.866093 INFO: Resetting torch num_threads to 128
1 day, 9:08:42.867850 PROGRESS: === Extracted 44856 precursors and 486737 fragments ===
1 day, 9:08:42.868456 INFO: === FDR correction performed with classifier version 2 ===
1 day, 9:08:42.870082 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:08:42.870205 PROGRESS: Total precursors accumulated: 8,000
1 day, 9:08:42.870283 PROGRESS: Target precursors: 7,669 (95.86%)
1 day, 9:08:42.870349 PROGRESS: Decoy precursors: 331 (4.14%)
1 day, 9:08:42.870412 PROGRESS: 
1 day, 9:08:42.870475 PROGRESS: Precursor Summary:
1 day, 9:08:42.873678 PROGRESS: Channel   0:	 0.050 FDR: 7,669; 0.010 FDR: 7,281; 0.001 FDR: 6,600
1 day, 9:08:42.873822 PROGRESS: 
1 day, 9:08:42.873900 PROGRESS: Protein Summary:
1 day, 9:08:42.878810 PROGRESS: Channel   0:	 0.050 FDR: 4,248; 0.010 FDR: 4,066; 0.001 FDR: 3,765
1 day, 9:08:42.878938 PROGRESS: =========================================================================
1 day, 9:08:42.879212 INFO: Target number of precursors reached.
1 day, 9:08:42.987347 INFO: fragments_df: keeping 5000 of 486737 [sum(precursor_idx_mask)=225935 sum(mass_error_mask)=486737 stop_rank=5000
1 day, 9:08:43.007119 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:08:44.130782 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:08:45.273242 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:08:46.390362 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:08:47.046690 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:08:47.047341 INFO: Using score_cutoff 36.56611058807373 (fac=0.99, q=1)
1 day, 9:08:47.047894 INFO: Updating optimization_manager: fwhm_rt             : 2.7907164096832275 -> 2.774855613708496
1 day, 9:08:47.047993 INFO: Updating optimization_manager: fwhm_mobility       : 0.00818057730793953 -> 0.007964636199176311
1 day, 9:08:47.048062 INFO: Updating optimization_manager: score_cutoff        : 40.93837286682129 -> 36.56611058807373
1 day, 9:08:47.048142 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:08:47.051166 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:08:47.060806 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:08:47.063344 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:08:47.083680 INFO: === checking if optimization conditions were reached ===
1 day, 9:08:47.083894 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 2 ===
1 day, 9:08:47.090664 INFO: Updating optimization_manager: rt_error            : 279.25593080910124 -> 95.26002610531765
1 day, 9:08:47.090832 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 95.2600.
1 day, 9:08:47.090968 INFO: ==============================================
1 day, 9:08:47.091096 INFO: Starting optimization step 2.
1 day, 9:08:47.091225 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 9:08:47.091340 INFO: Using python extraction backend
1 day, 9:08:47.091534 PROGRESS: Extracting batch of 15888 precursors
1 day, 9:08:47.091662 INFO: === Search parameters used ===
1 day, 9:08:47.091762 INFO: rt_error       : 95.26002610531765
1 day, 9:08:47.091850 INFO: mobility_error : 0.1
1 day, 9:08:47.091937 INFO: num_candidates : 3
1 day, 9:08:47.092018 INFO: ms1_error      : 15.0
1 day, 9:08:47.092105 INFO: ms2_error      : 15.0
1 day, 9:08:47.092190 INFO: fwhm_rt        : 2.774855613708496
1 day, 9:08:47.092271 INFO: quant_window   : 3
1 day, 9:08:47.092355 INFO: ==============================================
1 day, 9:08:47.099581 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 9:08:47.099706 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 9:08:47.099771 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 9:08:47.099822 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.69
1 day, 9:08:47.100928 INFO: Starting candidate selection
1 day, 9:08:52.406378 INFO: Starting candidate scoring
1 day, 9:08:54.293915 INFO: Finished candidate processing
1 day, 9:08:54.294112 INFO: Collecting candidate features
1 day, 9:08:54.354516 WARNING: intensity_correlation has 8 NaNs ( 0.02 % out of 44731)
1 day, 9:08:54.360603 INFO: Collecting fragment features
1 day, 9:08:54.387332 INFO: Finished candidate scoring
1 day, 9:08:54.409095 INFO: performing precursor FDR with 47 features
1 day, 9:08:54.409259 INFO: Decoy channel: -1
1 day, 9:08:54.409286 INFO: competitive: True
1 day, 9:08:54.423137 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:08:54.431427 WARNING: dropped 2 target PSMs due to missing features
1 day, 9:08:54.431577 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 9:08:54.438385 INFO: Estimating optimal hyperparameters - samples: 35,778, batch_size: 146, learning_rate: 1.89e-04
1 day, 9:08:54.438601 INFO: Using random state 775072 for train-test-split
1 day, 9:08:58.235249 INFO: Test AUC: 0.779
1 day, 9:08:58.235426 INFO: Train AUC: 0.792
1 day, 9:08:58.235461 INFO: AUC difference: 1.55%
1 day, 9:08:58.514070 INFO: Resetting torch num_threads to 128
1 day, 9:08:58.515797 PROGRESS: === Extracted 44731 precursors and 478165 fragments ===
1 day, 9:08:58.516388 INFO: === FDR correction performed with classifier version 2 ===
1 day, 9:08:58.517915 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:08:58.518036 PROGRESS: Total precursors accumulated: 8,000
1 day, 9:08:58.518109 PROGRESS: Target precursors: 7,800 (97.50%)
1 day, 9:08:58.518172 PROGRESS: Decoy precursors: 200 (2.50%)
1 day, 9:08:58.518230 PROGRESS: 
1 day, 9:08:58.518283 PROGRESS: Precursor Summary:
1 day, 9:08:58.521626 PROGRESS: Channel   0:	 0.050 FDR: 7,800; 0.010 FDR: 7,610; 0.001 FDR: 7,190
1 day, 9:08:58.521775 PROGRESS: 
1 day, 9:08:58.521857 PROGRESS: Protein Summary:
1 day, 9:08:58.527084 PROGRESS: Channel   0:	 0.050 FDR: 4,310; 0.010 FDR: 4,230; 0.001 FDR: 4,021
1 day, 9:08:58.527244 PROGRESS: =========================================================================
1 day, 9:08:58.527504 INFO: Target number of precursors reached.
1 day, 9:08:58.639662 INFO: fragments_df: keeping 5000 of 478165 [sum(precursor_idx_mask)=233784 sum(mass_error_mask)=478165 stop_rank=5000
1 day, 9:08:58.659167 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:08:59.868795 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:09:01.107029 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:09:02.306206 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:09:02.966062 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:09:02.966750 INFO: Using score_cutoff 34.99279565734863 (fac=0.99, q=1)
1 day, 9:09:02.967322 INFO: Updating optimization_manager: fwhm_rt             : 2.774855613708496 -> 2.766038417816162
1 day, 9:09:02.967430 INFO: Updating optimization_manager: fwhm_mobility       : 0.007964636199176311 -> 0.007837386801838875
1 day, 9:09:02.967527 INFO: Updating optimization_manager: score_cutoff        : 36.56611058807373 -> 34.99279565734863
1 day, 9:09:02.967621 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:09:02.970695 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:09:02.980309 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:09:02.982872 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:09:03.002633 INFO: === checking if optimization conditions were reached ===
1 day, 9:09:03.002853 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 2 ===
1 day, 9:09:03.009953 INFO: Updating optimization_manager: rt_error            : 95.26002610531765 -> 31.225720294283605
1 day, 9:09:03.010130 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 31.2257.
1 day, 9:09:03.010242 INFO: ==============================================
1 day, 9:09:03.010356 INFO: Starting optimization step 3.
1 day, 9:09:03.010464 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 9:09:03.010571 INFO: Using python extraction backend
1 day, 9:09:03.010761 PROGRESS: Extracting batch of 15888 precursors
1 day, 9:09:03.010876 INFO: === Search parameters used ===
1 day, 9:09:03.011000 INFO: rt_error       : 31.225720294283605
1 day, 9:09:03.011106 INFO: mobility_error : 0.1
1 day, 9:09:03.011205 INFO: num_candidates : 3
1 day, 9:09:03.011299 INFO: ms1_error      : 15.0
1 day, 9:09:03.011394 INFO: ms2_error      : 15.0
1 day, 9:09:03.011483 INFO: fwhm_rt        : 2.766038417816162
1 day, 9:09:03.011566 INFO: quant_window   : 3
1 day, 9:09:03.011655 INFO: ==============================================
1 day, 9:09:03.018791 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 9:09:03.018915 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 9:09:03.018982 INFO: FWHM in RT is 2.77 seconds, sigma is 0.61
1 day, 9:09:03.019028 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.64
1 day, 9:09:03.020276 INFO: Starting candidate selection
1 day, 9:09:05.439770 INFO: Starting candidate scoring
1 day, 9:09:07.196849 INFO: Finished candidate processing
1 day, 9:09:07.197068 INFO: Collecting candidate features
1 day, 9:09:07.277900 WARNING: intensity_correlation has 10 NaNs ( 0.02 % out of 44531)
1 day, 9:09:07.283427 INFO: Collecting fragment features
1 day, 9:09:07.311707 INFO: Finished candidate scoring
1 day, 9:09:07.332925 INFO: performing precursor FDR with 47 features
1 day, 9:09:07.333090 INFO: Decoy channel: -1
1 day, 9:09:07.333118 INFO: competitive: True
1 day, 9:09:07.346611 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:09:07.355353 WARNING: dropped 1 target PSMs due to missing features
1 day, 9:09:07.355501 WARNING: dropped 9 decoy PSMs due to missing features
1 day, 9:09:07.361660 INFO: Estimating optimal hyperparameters - samples: 35,616, batch_size: 145, learning_rate: 1.88e-04
1 day, 9:09:07.361884 INFO: Using random state 775072 for train-test-split
1 day, 9:09:11.118536 INFO: Test AUC: 0.806
1 day, 9:09:11.118710 INFO: Train AUC: 0.811
1 day, 9:09:11.118744 INFO: AUC difference: 0.60%
1 day, 9:09:11.400712 INFO: Resetting torch num_threads to 128
1 day, 9:09:11.402440 PROGRESS: === Extracted 44531 precursors and 470075 fragments ===
1 day, 9:09:11.403041 INFO: === FDR correction performed with classifier version 2 ===
1 day, 9:09:11.404591 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:09:11.404712 PROGRESS: Total precursors accumulated: 8,000
1 day, 9:09:11.404789 PROGRESS: Target precursors: 7,873 (98.41%)
1 day, 9:09:11.404871 PROGRESS: Decoy precursors: 127 (1.59%)
1 day, 9:09:11.404937 PROGRESS: 
1 day, 9:09:11.404994 PROGRESS: Precursor Summary:
1 day, 9:09:11.408310 PROGRESS: Channel   0:	 0.050 FDR: 7,873; 0.010 FDR: 7,805; 0.001 FDR: 7,515
1 day, 9:09:11.408443 PROGRESS: 
1 day, 9:09:11.408526 PROGRESS: Protein Summary:
1 day, 9:09:11.413688 PROGRESS: Channel   0:	 0.050 FDR: 4,345; 0.010 FDR: 4,322; 0.001 FDR: 4,176
1 day, 9:09:11.413824 PROGRESS: =========================================================================
1 day, 9:09:11.414089 INFO: Target number of precursors reached.
1 day, 9:09:11.523499 INFO: fragments_df: keeping 5000 of 470075 [sum(precursor_idx_mask)=237382 sum(mass_error_mask)=470075 stop_rank=5000
1 day, 9:09:11.543013 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:09:12.843634 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:09:14.168205 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:09:15.471178 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:09:16.196236 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:09:16.196937 INFO: Using score_cutoff 33.584563407897946 (fac=0.99, q=1)
1 day, 9:09:16.197505 INFO: Updating optimization_manager: fwhm_rt             : 2.766038417816162 -> 2.7469635009765625
1 day, 9:09:16.197607 INFO: Updating optimization_manager: fwhm_mobility       : 0.007837386801838875 -> 0.007757585495710373
1 day, 9:09:16.197688 INFO: Updating optimization_manager: score_cutoff        : 34.99279565734863 -> 33.584563407897946
1 day, 9:09:16.197774 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:09:16.200753 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:09:16.210310 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:09:16.212859 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:09:16.232504 INFO: === checking if optimization conditions were reached ===
1 day, 9:09:16.232736 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 2 ===
1 day, 9:09:16.239865 INFO: Updating optimization_manager: rt_error            : 31.225720294283605 -> 21.193807401037322
1 day, 9:09:16.240034 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 21.1938.
1 day, 9:09:16.240171 INFO: ==============================================
1 day, 9:09:16.240308 INFO: Starting optimization step 4.
1 day, 9:09:16.240428 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 9:09:16.240548 INFO: Using python extraction backend
1 day, 9:09:16.240750 PROGRESS: Extracting batch of 15888 precursors
1 day, 9:09:16.240873 INFO: === Search parameters used ===
1 day, 9:09:16.240975 INFO: rt_error       : 21.193807401037322
1 day, 9:09:16.241072 INFO: mobility_error : 0.1
1 day, 9:09:16.241167 INFO: num_candidates : 3
1 day, 9:09:16.241257 INFO: ms1_error      : 15.0
1 day, 9:09:16.241344 INFO: ms2_error      : 15.0
1 day, 9:09:16.241433 INFO: fwhm_rt        : 2.7469635009765625
1 day, 9:09:16.241516 INFO: quant_window   : 3
1 day, 9:09:16.241616 INFO: ==============================================
1 day, 9:09:16.248774 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 9:09:16.248889 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 9:09:16.248954 INFO: FWHM in RT is 2.75 seconds, sigma is 0.60
1 day, 9:09:16.249006 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.60
1 day, 9:09:16.250360 INFO: Starting candidate selection
1 day, 9:09:18.171729 INFO: Starting candidate scoring
1 day, 9:09:19.984138 INFO: Finished candidate processing
1 day, 9:09:19.984360 INFO: Collecting candidate features
1 day, 9:09:20.061182 WARNING: intensity_correlation has 16 NaNs ( 0.04 % out of 44498)
1 day, 9:09:20.067339 INFO: Collecting fragment features
1 day, 9:09:20.094457 INFO: Finished candidate scoring
1 day, 9:09:20.117199 INFO: performing precursor FDR with 47 features
1 day, 9:09:20.117362 INFO: Decoy channel: -1
1 day, 9:09:20.117390 INFO: competitive: True
1 day, 9:09:20.130552 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:09:20.138487 WARNING: dropped 1 target PSMs due to missing features
1 day, 9:09:20.138666 WARNING: dropped 15 decoy PSMs due to missing features
1 day, 9:09:20.145942 INFO: Estimating optimal hyperparameters - samples: 35,585, batch_size: 145, learning_rate: 1.88e-04
1 day, 9:09:20.146139 INFO: Using random state 775072 for train-test-split
1 day, 9:09:23.894524 INFO: Test AUC: 0.819
1 day, 9:09:23.894692 INFO: Train AUC: 0.828
1 day, 9:09:23.894726 INFO: AUC difference: 1.09%
1 day, 9:09:24.174341 INFO: Resetting torch num_threads to 128
1 day, 9:09:24.175992 PROGRESS: === Extracted 44498 precursors and 466316 fragments ===
1 day, 9:09:24.176592 INFO: === FDR correction performed with classifier version 2 ===
1 day, 9:09:24.178111 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:09:24.178222 PROGRESS: Total precursors accumulated: 8,000
1 day, 9:09:24.178294 PROGRESS: Target precursors: 7,899 (98.74%)
1 day, 9:09:24.178356 PROGRESS: Decoy precursors: 101 (1.26%)
1 day, 9:09:24.178413 PROGRESS: 
1 day, 9:09:24.178468 PROGRESS: Precursor Summary:
1 day, 9:09:24.181684 PROGRESS: Channel   0:	 0.050 FDR: 7,899; 0.010 FDR: 7,853; 0.001 FDR: 7,421
1 day, 9:09:24.181837 PROGRESS: 
1 day, 9:09:24.181908 PROGRESS: Protein Summary:
1 day, 9:09:24.187106 PROGRESS: Channel   0:	 0.050 FDR: 4,359; 0.010 FDR: 4,344; 0.001 FDR: 4,134
1 day, 9:09:24.187244 PROGRESS: =========================================================================
1 day, 9:09:24.187512 INFO: Target number of precursors reached.
1 day, 9:09:24.297153 INFO: fragments_df: keeping 5000 of 466316 [sum(precursor_idx_mask)=238048 sum(mass_error_mask)=466316 stop_rank=5000
1 day, 9:09:24.316508 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:09:25.568282 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:09:26.823509 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:09:28.073832 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:09:28.738222 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:09:28.738900 INFO: Using score_cutoff 32.773954531860355 (fac=0.99, q=1)
1 day, 9:09:28.739475 INFO: Updating optimization_manager: fwhm_rt             : 2.7469635009765625 -> 2.7378852367401123
1 day, 9:09:28.739575 INFO: Updating optimization_manager: fwhm_mobility       : 0.007757585495710373 -> 0.0077102091163396835
1 day, 9:09:28.739645 INFO: Updating optimization_manager: score_cutoff        : 33.584563407897946 -> 32.773954531860355
1 day, 9:09:28.739722 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:09:28.742709 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:09:28.752251 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:09:28.754735 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:09:28.775839 INFO: === checking if optimization conditions were reached ===
1 day, 9:09:28.776049 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 2 ===
1 day, 9:09:28.783220 INFO: Updating optimization_manager: rt_error            : 21.193807401037322 -> 16.66215152917215
1 day, 9:09:28.783386 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 16.6622.
1 day, 9:09:28.783491 INFO: ==============================================
1 day, 9:09:28.783627 INFO: Starting optimization step 5.
1 day, 9:09:28.783746 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 9:09:28.783867 INFO: Using python extraction backend
1 day, 9:09:28.784068 PROGRESS: Extracting batch of 15888 precursors
1 day, 9:09:28.784189 INFO: === Search parameters used ===
1 day, 9:09:28.784301 INFO: rt_error       : 16.66215152917215
1 day, 9:09:28.784400 INFO: mobility_error : 0.1
1 day, 9:09:28.784490 INFO: num_candidates : 3
1 day, 9:09:28.784579 INFO: ms1_error      : 15.0
1 day, 9:09:28.784665 INFO: ms2_error      : 15.0
1 day, 9:09:28.784751 INFO: fwhm_rt        : 2.7378852367401123
1 day, 9:09:28.784837 INFO: quant_window   : 3
1 day, 9:09:28.784930 INFO: ==============================================
1 day, 9:09:28.792159 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 9:09:28.792277 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 9:09:28.792341 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
1 day, 9:09:28.792386 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.58
1 day, 9:09:28.793541 INFO: Starting candidate selection
1 day, 9:09:30.772859 INFO: Starting candidate scoring
1 day, 9:09:32.505901 INFO: Finished candidate processing
1 day, 9:09:32.506111 INFO: Collecting candidate features
1 day, 9:09:32.568054 WARNING: intensity_correlation has 8 NaNs ( 0.02 % out of 44486)
1 day, 9:09:32.573620 INFO: Collecting fragment features
1 day, 9:09:32.605965 INFO: Finished candidate scoring
1 day, 9:09:32.628470 INFO: performing precursor FDR with 47 features
1 day, 9:09:32.628639 INFO: Decoy channel: -1
1 day, 9:09:32.628666 INFO: competitive: True
1 day, 9:09:32.642202 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:09:32.650362 WARNING: dropped 3 target PSMs due to missing features
1 day, 9:09:32.650517 WARNING: dropped 5 decoy PSMs due to missing features
1 day, 9:09:32.657205 INFO: Estimating optimal hyperparameters - samples: 35,582, batch_size: 145, learning_rate: 1.88e-04
1 day, 9:09:32.657410 INFO: Using random state 775072 for train-test-split
1 day, 9:09:36.411980 INFO: Test AUC: 0.819
1 day, 9:09:36.412153 INFO: Train AUC: 0.827
1 day, 9:09:36.412186 INFO: AUC difference: 1.02%
1 day, 9:09:36.688627 INFO: Resetting torch num_threads to 128
1 day, 9:09:36.690327 PROGRESS: === Extracted 44486 precursors and 466121 fragments ===
1 day, 9:09:36.690952 INFO: === FDR correction performed with classifier version 2 ===
1 day, 9:09:36.692513 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:09:36.692630 PROGRESS: Total precursors accumulated: 8,000
1 day, 9:09:36.692706 PROGRESS: Target precursors: 7,890 (98.62%)
1 day, 9:09:36.692774 PROGRESS: Decoy precursors: 110 (1.38%)
1 day, 9:09:36.692836 PROGRESS: 
1 day, 9:09:36.692898 PROGRESS: Precursor Summary:
1 day, 9:09:36.696304 PROGRESS: Channel   0:	 0.050 FDR: 7,890; 0.010 FDR: 7,823; 0.001 FDR: 7,479
1 day, 9:09:36.696442 PROGRESS: 
1 day, 9:09:36.696517 PROGRESS: Protein Summary:
1 day, 9:09:36.701702 PROGRESS: Channel   0:	 0.050 FDR: 4,359; 0.010 FDR: 4,336; 0.001 FDR: 4,165
1 day, 9:09:36.701845 PROGRESS: =========================================================================
1 day, 9:09:36.702136 INFO: Target number of precursors reached.
1 day, 9:09:36.813622 INFO: fragments_df: keeping 5000 of 466121 [sum(precursor_idx_mask)=236996 sum(mass_error_mask)=466121 stop_rank=5000
1 day, 9:09:36.832872 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:09:38.071213 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:09:39.313256 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:09:40.559047 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:09:41.213369 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:09:41.214042 INFO: Using score_cutoff 32.481058131408695 (fac=0.99, q=1)
1 day, 9:09:41.214602 INFO: Updating optimization_manager: fwhm_rt             : 2.7378852367401123 -> 2.7373533248901367
1 day, 9:09:41.214701 INFO: Updating optimization_manager: fwhm_mobility       : 0.0077102091163396835 -> 0.0076895165257155895
1 day, 9:09:41.214773 INFO: Updating optimization_manager: score_cutoff        : 32.773954531860355 -> 32.481058131408695
1 day, 9:09:41.214848 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:09:41.217691 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:09:41.227124 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:09:41.229594 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:09:41.248286 INFO: === checking if optimization conditions were reached ===
1 day, 9:09:41.248534 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 2 ===
1 day, 9:09:41.255851 INFO: Updating optimization_manager: rt_error            : 16.66215152917215 -> 16.73717853213458
1 day, 9:09:41.256018 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 16.7372.
1 day, 9:09:41.256129 INFO: ==============================================
1 day, 9:09:41.256236 INFO: Starting optimization step 6.
1 day, 9:09:41.256333 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 9:09:41.256429 INFO: Using python extraction backend
1 day, 9:09:41.256615 PROGRESS: Extracting batch of 15888 precursors
1 day, 9:09:41.256715 INFO: === Search parameters used ===
1 day, 9:09:41.256795 INFO: rt_error       : 16.73717853213458
1 day, 9:09:41.256867 INFO: mobility_error : 0.1
1 day, 9:09:41.256940 INFO: num_candidates : 3
1 day, 9:09:41.257007 INFO: ms1_error      : 15.0
1 day, 9:09:41.257076 INFO: ms2_error      : 15.0
1 day, 9:09:41.257142 INFO: fwhm_rt        : 2.7373533248901367
1 day, 9:09:41.257209 INFO: quant_window   : 3
1 day, 9:09:41.257275 INFO: ==============================================
1 day, 9:09:41.264148 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 9:09:41.264233 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 9:09:41.264284 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
1 day, 9:09:41.264320 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
1 day, 9:09:41.265358 INFO: Starting candidate selection
1 day, 9:09:43.215951 INFO: Starting candidate scoring
1 day, 9:09:44.956124 INFO: Finished candidate processing
1 day, 9:09:44.956341 INFO: Collecting candidate features
1 day, 9:09:45.045491 WARNING: intensity_correlation has 9 NaNs ( 0.02 % out of 44494)
1 day, 9:09:45.051636 INFO: Collecting fragment features
1 day, 9:09:45.076706 INFO: Finished candidate scoring
1 day, 9:09:45.102643 INFO: performing precursor FDR with 47 features
1 day, 9:09:45.102789 INFO: Decoy channel: -1
1 day, 9:09:45.102823 INFO: competitive: True
1 day, 9:09:45.116473 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:09:45.124809 WARNING: dropped 3 target PSMs due to missing features
1 day, 9:09:45.124957 WARNING: dropped 6 decoy PSMs due to missing features
1 day, 9:09:45.132421 INFO: Estimating optimal hyperparameters - samples: 35,588, batch_size: 145, learning_rate: 1.88e-04
1 day, 9:09:45.132666 INFO: Using random state 775072 for train-test-split
1 day, 9:09:49.456927 INFO: Test AUC: 0.819
1 day, 9:09:49.457085 INFO: Train AUC: 0.828
1 day, 9:09:49.457125 INFO: AUC difference: 0.99%
1 day, 9:09:49.746846 INFO: Resetting torch num_threads to 128
1 day, 9:09:49.748292 PROGRESS: === Extracted 44494 precursors and 466190 fragments ===
1 day, 9:09:49.748894 INFO: === FDR correction performed with classifier version 2 ===
1 day, 9:09:49.750417 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:09:49.750529 PROGRESS: Total precursors accumulated: 8,000
1 day, 9:09:49.750603 PROGRESS: Target precursors: 7,871 (98.39%)
1 day, 9:09:49.750668 PROGRESS: Decoy precursors: 129 (1.61%)
1 day, 9:09:49.750727 PROGRESS: 
1 day, 9:09:49.750791 PROGRESS: Precursor Summary:
1 day, 9:09:49.754061 PROGRESS: Channel   0:	 0.050 FDR: 7,871; 0.010 FDR: 7,775; 0.001 FDR: 7,345
1 day, 9:09:49.754185 PROGRESS: 
1 day, 9:09:49.754254 PROGRESS: Protein Summary:
1 day, 9:09:49.759193 PROGRESS: Channel   0:	 0.050 FDR: 4,350; 0.010 FDR: 4,311; 0.001 FDR: 4,107
1 day, 9:09:49.759319 PROGRESS: =========================================================================
1 day, 9:09:49.759596 INFO: Target number of precursors reached.
1 day, 9:09:49.871737 INFO: fragments_df: keeping 5000 of 466190 [sum(precursor_idx_mask)=235646 sum(mass_error_mask)=466190 stop_rank=5000
1 day, 9:09:49.892755 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:09:51.125809 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:09:52.392008 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:09:53.640762 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:09:54.316875 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:09:54.317547 INFO: Using score_cutoff 32.76525351104736 (fac=0.99, q=1)
1 day, 9:09:54.318145 INFO: Updating optimization_manager: fwhm_rt             : 2.7373533248901367 -> 2.73665189743042
1 day, 9:09:54.318243 INFO: Updating optimization_manager: fwhm_mobility       : 0.0076895165257155895 -> 0.007712163962423801
1 day, 9:09:54.318307 INFO: Updating optimization_manager: score_cutoff        : 32.481058131408695 -> 32.76525351104736
1 day, 9:09:54.318377 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:09:54.321386 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:09:54.331062 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:09:54.333484 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:09:54.355820 INFO: === checking if optimization conditions were reached ===
1 day, 9:09:54.356025 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 2 ===
1 day, 9:09:54.357578 INFO: Updating optimization_manager: rt_error            : 16.73717853213458 -> 16.66215152917215
1 day, 9:09:54.357761 INFO: Updating optimization_manager: classifier_version  : 2 -> 8
1 day, 9:09:54.357904 INFO: Updating optimization_manager: score_cutoff        : 32.76525351104736 -> 32.481058131408695
1 day, 9:09:54.358023 INFO: Updating optimization_manager: fwhm_rt             : 2.73665189743042 -> 2.7373533248901367
1 day, 9:09:54.358137 INFO: Updating optimization_manager: fwhm_mobility       : 0.007712163962423801 -> 0.0076895165257155895
1 day, 9:09:54.358251 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 16.6622 found after 7 searches.
1 day, 9:09:54.358332 INFO: ==============================================
1 day, 9:09:54.358424 PROGRESS: Optimization finished for rt_error.
1 day, 9:09:54.383775 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:09:54.387103 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:09:54.396787 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:09:54.399229 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:09:54.422127 INFO: Starting optimization step 0.
1 day, 9:09:54.422357 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 9:09:54.422472 INFO: Using python extraction backend
1 day, 9:09:54.422662 PROGRESS: Extracting batch of 15888 precursors
1 day, 9:09:54.422770 INFO: === Search parameters used ===
1 day, 9:09:54.422845 INFO: rt_error       : 16.66215152917215
1 day, 9:09:54.422918 INFO: mobility_error : 0.1
1 day, 9:09:54.422992 INFO: num_candidates : 3
1 day, 9:09:54.423061 INFO: ms1_error      : 15.0
1 day, 9:09:54.423123 INFO: ms2_error      : 15.0
1 day, 9:09:54.423189 INFO: fwhm_rt        : 2.7373533248901367
1 day, 9:09:54.423264 INFO: quant_window   : 3
1 day, 9:09:54.423326 INFO: ==============================================
1 day, 9:09:54.427834 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 9:09:54.427900 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 9:09:54.427958 INFO: FWHM in RT is 2.74 seconds, sigma is 0.60
1 day, 9:09:54.427994 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
1 day, 9:09:54.428890 INFO: Starting candidate selection
1 day, 9:09:56.264494 INFO: Starting candidate scoring
1 day, 9:09:58.053221 INFO: Finished candidate processing
1 day, 9:09:58.053367 INFO: Collecting candidate features
1 day, 9:09:58.113222 WARNING: intensity_correlation has 9 NaNs ( 0.02 % out of 44497)
1 day, 9:09:58.118679 INFO: Collecting fragment features
1 day, 9:09:58.145761 INFO: Finished candidate scoring
1 day, 9:09:58.168009 INFO: performing precursor FDR with 47 features
1 day, 9:09:58.168190 INFO: Decoy channel: -1
1 day, 9:09:58.168223 INFO: competitive: True
1 day, 9:09:58.181052 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:09:58.189024 WARNING: dropped 2 target PSMs due to missing features
1 day, 9:09:58.189160 WARNING: dropped 7 decoy PSMs due to missing features
1 day, 9:09:58.196740 INFO: Estimating optimal hyperparameters - samples: 35,590, batch_size: 145, learning_rate: 1.88e-04
1 day, 9:09:58.196959 INFO: Using random state 871614 for train-test-split
1 day, 9:10:01.831494 INFO: Test AUC: 0.827
1 day, 9:10:01.831661 INFO: Train AUC: 0.840
1 day, 9:10:01.831695 INFO: AUC difference: 1.54%
1 day, 9:10:02.108207 INFO: Resetting torch num_threads to 128
1 day, 9:10:02.109841 PROGRESS: === Extracted 44497 precursors and 465945 fragments ===
1 day, 9:10:02.110435 INFO: === FDR correction performed with classifier version 8 ===
1 day, 9:10:02.112060 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:10:02.112174 PROGRESS: Total precursors accumulated: 8,000
1 day, 9:10:02.112269 PROGRESS: Target precursors: 7,881 (98.51%)
1 day, 9:10:02.112353 PROGRESS: Decoy precursors: 119 (1.49%)
1 day, 9:10:02.112428 PROGRESS: 
1 day, 9:10:02.112500 PROGRESS: Precursor Summary:
1 day, 9:10:02.115825 PROGRESS: Channel   0:	 0.050 FDR: 7,881; 0.010 FDR: 7,823; 0.001 FDR: 7,439
1 day, 9:10:02.115967 PROGRESS: 
1 day, 9:10:02.116052 PROGRESS: Protein Summary:
1 day, 9:10:02.121208 PROGRESS: Channel   0:	 0.050 FDR: 4,348; 0.010 FDR: 4,325; 0.001 FDR: 4,143
1 day, 9:10:02.121348 PROGRESS: =========================================================================
1 day, 9:10:02.121600 INFO: Target number of precursors reached.
1 day, 9:10:02.229396 INFO: fragments_df: keeping 5000 of 465945 [sum(precursor_idx_mask)=236918 sum(mass_error_mask)=465945 stop_rank=5000
1 day, 9:10:02.248743 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:10:03.491915 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:10:04.739698 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:10:05.979647 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:10:06.667376 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:10:06.668048 INFO: Using score_cutoff 32.50520320358277 (fac=0.99, q=1)
1 day, 9:10:06.668614 INFO: Updating optimization_manager: fwhm_rt             : 2.7373533248901367 -> 2.7339468002319336
1 day, 9:10:06.668729 INFO: Updating optimization_manager: fwhm_mobility       : 0.0076895165257155895 -> 0.007695091888308525
1 day, 9:10:06.668811 INFO: Updating optimization_manager: score_cutoff        : 32.481058131408695 -> 32.50520320358277
1 day, 9:10:06.668917 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:10:06.671977 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:10:06.681562 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:10:06.684036 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:10:06.704805 INFO: === checking if optimization conditions were reached ===
1 day, 9:10:06.705029 PROGRESS: === Optimization of mobility_error has been performed 1 time(s); minimum number is 2 ===
1 day, 9:10:06.708227 INFO: Updating optimization_manager: mobility_error      : 0.1 -> 0.07782482515418258
1 day, 9:10:06.708390 PROGRESS: ❌ mobility_error : optimization incomplete after 1 search(es). Will search with parameter 0.0778.
1 day, 9:10:06.708503 INFO: ==============================================
1 day, 9:10:06.708623 INFO: Starting optimization step 1.
1 day, 9:10:06.708733 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 9:10:06.708847 INFO: Using python extraction backend
1 day, 9:10:06.709041 PROGRESS: Extracting batch of 15888 precursors
1 day, 9:10:06.709163 INFO: === Search parameters used ===
1 day, 9:10:06.709261 INFO: rt_error       : 16.66215152917215
1 day, 9:10:06.709351 INFO: mobility_error : 0.07782482515418258
1 day, 9:10:06.709451 INFO: num_candidates : 3
1 day, 9:10:06.709540 INFO: ms1_error      : 15.0
1 day, 9:10:06.709625 INFO: ms2_error      : 15.0
1 day, 9:10:06.709734 INFO: fwhm_rt        : 2.7339468002319336
1 day, 9:10:06.709856 INFO: quant_window   : 3
1 day, 9:10:06.709959 INFO: ==============================================
1 day, 9:10:06.717384 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 9:10:06.717496 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 9:10:06.717562 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
1 day, 9:10:06.717614 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
1 day, 9:10:06.718579 INFO: Starting candidate selection
1 day, 9:10:08.358829 INFO: Starting candidate scoring
1 day, 9:10:10.065242 INFO: Finished candidate processing
1 day, 9:10:10.065447 INFO: Collecting candidate features
1 day, 9:10:10.152137 WARNING: intensity_correlation has 12 NaNs ( 0.03 % out of 44453)
1 day, 9:10:10.158023 INFO: Collecting fragment features
1 day, 9:10:10.183470 INFO: Finished candidate scoring
1 day, 9:10:10.208824 INFO: performing precursor FDR with 47 features
1 day, 9:10:10.209278 INFO: Decoy channel: -1
1 day, 9:10:10.209415 INFO: competitive: True
1 day, 9:10:10.226731 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:10:10.235163 WARNING: dropped 3 target PSMs due to missing features
1 day, 9:10:10.235336 WARNING: dropped 9 decoy PSMs due to missing features
1 day, 9:10:10.243739 INFO: Estimating optimal hyperparameters - samples: 35,552, batch_size: 145, learning_rate: 1.88e-04
1 day, 9:10:10.244001 INFO: Using random state 871614 for train-test-split
1 day, 9:10:13.834013 INFO: Test AUC: 0.830
1 day, 9:10:13.834177 INFO: Train AUC: 0.837
1 day, 9:10:13.834209 INFO: AUC difference: 0.85%
1 day, 9:10:14.109949 INFO: Resetting torch num_threads to 128
1 day, 9:10:14.111592 PROGRESS: === Extracted 44453 precursors and 463488 fragments ===
1 day, 9:10:14.112189 INFO: === FDR correction performed with classifier version 8 ===
1 day, 9:10:14.113776 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:10:14.113890 PROGRESS: Total precursors accumulated: 7,991
1 day, 9:10:14.113975 PROGRESS: Target precursors: 7,870 (98.49%)
1 day, 9:10:14.114041 PROGRESS: Decoy precursors: 121 (1.51%)
1 day, 9:10:14.114099 PROGRESS: 
1 day, 9:10:14.114155 PROGRESS: Precursor Summary:
1 day, 9:10:14.117446 PROGRESS: Channel   0:	 0.050 FDR: 7,870; 0.010 FDR: 7,810; 0.001 FDR: 7,506
1 day, 9:10:14.117571 PROGRESS: 
1 day, 9:10:14.117640 PROGRESS: Protein Summary:
1 day, 9:10:14.122821 PROGRESS: Channel   0:	 0.050 FDR: 4,342; 0.010 FDR: 4,322; 0.001 FDR: 4,188
1 day, 9:10:14.122951 PROGRESS: =========================================================================
1 day, 9:10:14.123246 INFO: Target number of precursors reached.
1 day, 9:10:14.231526 INFO: fragments_df: keeping 5000 of 463488 [sum(precursor_idx_mask)=236102 sum(mass_error_mask)=463488 stop_rank=5000
1 day, 9:10:14.250256 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:10:15.487899 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:10:16.732036 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:10:17.969110 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:10:18.623483 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:10:18.624136 INFO: Using score_cutoff 31.752832887268067 (fac=0.99, q=1)
1 day, 9:10:18.624708 INFO: Updating optimization_manager: fwhm_rt             : 2.7339468002319336 -> 2.7319984436035156
1 day, 9:10:18.624810 INFO: Updating optimization_manager: fwhm_mobility       : 0.007695091888308525 -> 0.007696033455431461
1 day, 9:10:18.624879 INFO: Updating optimization_manager: score_cutoff        : 32.50520320358277 -> 31.752832887268067
1 day, 9:10:18.624964 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:10:18.627868 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:10:18.637596 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:10:18.640115 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:10:18.661732 INFO: === checking if optimization conditions were reached ===
1 day, 9:10:18.661966 PROGRESS: === Optimization of mobility_error has been performed 2 time(s); minimum number is 2 ===
1 day, 9:10:18.665407 INFO: Updating optimization_manager: mobility_error      : 0.07782482515418258 -> 0.06720262519444163
1 day, 9:10:18.665551 PROGRESS: ❌ mobility_error : optimization incomplete after 2 search(es). Will search with parameter 0.0672.
1 day, 9:10:18.665687 INFO: ==============================================
1 day, 9:10:18.665831 INFO: Starting optimization step 2.
1 day, 9:10:18.665960 PROGRESS: === Extracting elution groups 0 to 8000 ===
1 day, 9:10:18.666077 INFO: Using python extraction backend
1 day, 9:10:18.666276 PROGRESS: Extracting batch of 15888 precursors
1 day, 9:10:18.666401 INFO: === Search parameters used ===
1 day, 9:10:18.666498 INFO: rt_error       : 16.66215152917215
1 day, 9:10:18.666593 INFO: mobility_error : 0.06720262519444163
1 day, 9:10:18.666686 INFO: num_candidates : 3
1 day, 9:10:18.666776 INFO: ms1_error      : 15.0
1 day, 9:10:18.666866 INFO: ms2_error      : 15.0
1 day, 9:10:18.666952 INFO: fwhm_rt        : 2.7319984436035156
1 day, 9:10:18.667048 INFO: quant_window   : 3
1 day, 9:10:18.667140 INFO: ==============================================
1 day, 9:10:18.673393 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 9:10:18.673505 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 9:10:18.673568 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
1 day, 9:10:18.673615 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
1 day, 9:10:18.674734 INFO: Starting candidate selection
1 day, 9:10:20.295215 INFO: Starting candidate scoring
1 day, 9:10:22.028223 INFO: Finished candidate processing
1 day, 9:10:22.028393 INFO: Collecting candidate features
1 day, 9:10:22.115959 WARNING: intensity_correlation has 13 NaNs ( 0.03 % out of 44393)
1 day, 9:10:22.121297 INFO: Collecting fragment features
1 day, 9:10:22.147867 INFO: Finished candidate scoring
1 day, 9:10:22.173989 INFO: performing precursor FDR with 47 features
1 day, 9:10:22.174139 INFO: Decoy channel: -1
1 day, 9:10:22.174167 INFO: competitive: True
1 day, 9:10:22.193610 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:10:22.202221 WARNING: dropped 3 target PSMs due to missing features
1 day, 9:10:22.202380 WARNING: dropped 10 decoy PSMs due to missing features
1 day, 9:10:22.210810 INFO: Estimating optimal hyperparameters - samples: 35,504, batch_size: 145, learning_rate: 1.88e-04
1 day, 9:10:22.211181 INFO: Using random state 871614 for train-test-split
1 day, 9:10:25.775473 INFO: Test AUC: 0.828
1 day, 9:10:25.775634 INFO: Train AUC: 0.837
1 day, 9:10:25.775666 INFO: AUC difference: 1.07%
1 day, 9:10:26.049502 INFO: Resetting torch num_threads to 128
1 day, 9:10:26.051164 PROGRESS: === Extracted 44393 precursors and 461789 fragments ===
1 day, 9:10:26.051793 INFO: === FDR correction performed with classifier version 8 ===
1 day, 9:10:26.053289 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:10:26.053402 PROGRESS: Total precursors accumulated: 7,987
1 day, 9:10:26.053479 PROGRESS: Target precursors: 7,879 (98.65%)
1 day, 9:10:26.053546 PROGRESS: Decoy precursors: 108 (1.35%)
1 day, 9:10:26.053608 PROGRESS: 
1 day, 9:10:26.053675 PROGRESS: Precursor Summary:
1 day, 9:10:26.056893 PROGRESS: Channel   0:	 0.050 FDR: 7,879; 0.010 FDR: 7,825; 0.001 FDR: 7,368
1 day, 9:10:26.057017 PROGRESS: 
1 day, 9:10:26.057094 PROGRESS: Protein Summary:
1 day, 9:10:26.062174 PROGRESS: Channel   0:	 0.050 FDR: 4,356; 0.010 FDR: 4,339; 0.001 FDR: 4,131
1 day, 9:10:26.062301 PROGRESS: =========================================================================
1 day, 9:10:26.062608 INFO: Target number of precursors reached.
1 day, 9:10:26.170973 INFO: fragments_df: keeping 5000 of 461789 [sum(precursor_idx_mask)=236115 sum(mass_error_mask)=461789 stop_rank=5000
1 day, 9:10:26.190132 INFO: Fitting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:10:27.498473 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:10:28.780478 INFO: Fitting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:10:30.012911 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:10:30.667183 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1 day, 9:10:30.667863 INFO: Using score_cutoff 31.42029592666626 (fac=0.99, q=1)
1 day, 9:10:30.668439 INFO: Updating optimization_manager: fwhm_rt             : 2.7319984436035156 -> 2.730442762374878
1 day, 9:10:30.668532 INFO: Updating optimization_manager: fwhm_mobility       : 0.007696033455431461 -> 0.00769834453240037
1 day, 9:10:30.668599 INFO: Updating optimization_manager: score_cutoff        : 31.752832887268067 -> 31.42029592666626
1 day, 9:10:30.668671 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:10:30.671602 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:10:30.681088 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:10:30.683548 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:10:30.705629 INFO: === checking if optimization conditions were reached ===
1 day, 9:10:30.705883 PROGRESS: === Optimization of mobility_error has been performed 3 time(s); minimum number is 2 ===
1 day, 9:10:30.707034 INFO: Updating optimization_manager: mobility_error      : 0.06720262519444163 -> 0.06720262519444163
1 day, 9:10:30.707202 INFO: Updating optimization_manager: classifier_version  : 8 -> 12
1 day, 9:10:30.707339 INFO: Updating optimization_manager: score_cutoff        : 31.42029592666626 -> 31.42029592666626
1 day, 9:10:30.707462 INFO: Updating optimization_manager: fwhm_rt             : 2.730442762374878 -> 2.730442762374878
1 day, 9:10:30.707581 INFO: Updating optimization_manager: fwhm_mobility       : 0.00769834453240037 -> 0.00769834453240037
1 day, 9:10:30.707700 PROGRESS: ✅ mobility_error : optimization just completed. Optimal parameter 0.0672 found after 3 searches.
1 day, 9:10:30.707796 INFO: ==============================================
1 day, 9:10:30.707891 PROGRESS: Optimization finished for mobility_error.
1 day, 9:10:30.732309 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:10:30.735775 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:10:30.745789 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:10:30.748566 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:10:30.772954 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1 day, 9:10:30.773189 PROGRESS: ==============================================
1 day, 9:10:30.773315 PROGRESS: ms2_error      : 15.0000
1 day, 9:10:30.773420 PROGRESS: ms1_error      : 15.0000
1 day, 9:10:30.773516 PROGRESS: rt_error       : 16.6622
1 day, 9:10:30.773611 PROGRESS: mobility_error : 0.0672
1 day, 9:10:30.773698 PROGRESS: ==============================================
1 day, 9:10:30.775276 INFO: Predicting estimator 'mz' in calibration group 'precursor' ..
1 day, 9:10:30.799317 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1 day, 9:10:30.905056 INFO: Predicting estimator 'mobility' in calibration group 'precursor' ..
1 day, 9:10:30.929259 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1 day, 9:10:31.198434 INFO: Using python extraction backend
1 day, 9:10:31.199018 PROGRESS: Extracting batch of 182033 precursors
1 day, 9:10:31.199175 INFO: === Search parameters used ===
1 day, 9:10:31.199311 INFO: rt_error       : 16.66215152917215
1 day, 9:10:31.199415 INFO: mobility_error : 0.06720262519444163
1 day, 9:10:31.199513 INFO: num_candidates : 3
1 day, 9:10:31.199604 INFO: ms1_error      : 15.0
1 day, 9:10:31.199692 INFO: ms2_error      : 15.0
1 day, 9:10:31.199786 INFO: fwhm_rt        : 2.730442762374878
1 day, 9:10:31.199871 INFO: quant_window   : 3
1 day, 9:10:31.199953 INFO: ==============================================
1 day, 9:10:31.251240 INFO: Duty cycle consists of 9 frames, 0.97 seconds cycle time
1 day, 9:10:31.251425 INFO: Duty cycle consists of 919 scans, 0.00092 1/K_0 resolution
1 day, 9:10:31.251473 INFO: FWHM in RT is 2.73 seconds, sigma is 0.60
1 day, 9:10:31.251497 INFO: FWHM in mobility is 0.008 1/K_0, sigma is 3.57
1 day, 9:10:31.252308 INFO: Starting candidate selection
1 day, 9:10:44.077045 INFO: Removed 72508 precursors with score below cutoff 31.42029592666626
1 day, 9:10:44.435879 INFO: Starting candidate scoring
1 day, 9:10:59.995285 INFO: Finished candidate processing
1 day, 9:10:59.995509 INFO: Collecting candidate features
1 day, 9:11:00.681725 WARNING: intensity_correlation has 1 NaNs ( 0.00 % out of 438594)
1 day, 9:11:00.699374 INFO: Collecting fragment features
1 day, 9:11:00.935062 INFO: Finished candidate scoring
1 day, 9:11:01.184917 INFO: === Performing FDR correction with classifier version 12 ===
1 day, 9:11:01.185463 INFO: performing precursor FDR with 47 features
1 day, 9:11:01.185531 INFO: Decoy channel: -1
1 day, 9:11:01.185559 INFO: competitive: True
1 day, 9:11:01.299896 INFO: Setting torch num_threads to 2 for FDR classification task
1 day, 9:11:01.366310 WARNING: dropped 1 target PSMs due to missing features
1 day, 9:11:01.366542 WARNING: FDR calculation for 239968 target and 198625 decoy PSMs
1 day, 9:11:01.366574 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
1 day, 9:11:01.547369 INFO: Estimating optimal hyperparameters - samples: 350,874, batch_size: 1,437, learning_rate: 5.92e-04
1 day, 9:11:01.548235 INFO: Using random state 52898 for train-test-split
1 day, 9:11:12.712223 INFO: Test AUC: 0.846
1 day, 9:11:12.712408 INFO: Train AUC: 0.849
1 day, 9:11:12.712441 INFO: AUC difference: 0.40%
1 day, 9:11:13.100050 INFO: Resetting torch num_threads to 128
1 day, 9:11:13.126311 INFO: Removing fragments below FDR threshold
1 day, 9:11:13.221109 PROGRESS: ============================= Precursor FDR =============================
1 day, 9:11:13.221465 PROGRESS: Total precursors accumulated: 89,833
1 day, 9:11:13.221551 PROGRESS: Target precursors: 88,944 (99.01%)
1 day, 9:11:13.221622 PROGRESS: Decoy precursors: 889 (0.99%)
1 day, 9:11:13.221687 PROGRESS: 
1 day, 9:11:13.221759 PROGRESS: Precursor Summary:
1 day, 9:11:13.269072 PROGRESS: Channel   0:	 0.050 FDR: 88,944; 0.010 FDR: 88,944; 0.001 FDR: 85,293
1 day, 9:11:13.269448 PROGRESS: 
1 day, 9:11:13.269541 PROGRESS: Protein Summary:
1 day, 9:11:13.337386 PROGRESS: Channel   0:	 0.050 FDR: 8,977; 0.010 FDR: 8,977; 0.001 FDR: 8,969
1 day, 9:11:13.337765 PROGRESS: =========================================================================
1 day, 9:11:13.345676 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/psm.parquet
1 day, 9:11:13.710237 INFO: Saving results to /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/frag.parquet
1 day, 9:11:14.021933 INFO: Finished workflow for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 9:11:14.522835 PROGRESS: Processing search outputs
1 day, 9:11:14.522975 PROGRESS: === Performing protein grouping and FDR ===
1 day, 9:11:14.523021 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 9:11:14.582041 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 9:11:14.653480 INFO: Building output for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 9:11:14.724646 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 9:11:14.797234 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 9:11:14.870233 INFO: Building output for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 9:11:14.985164 INFO: Performing protein inference
1 day, 9:11:15.599451 INFO: Inference strategy: library. Using library grouping for protein inference
1 day, 9:11:15.603875 INFO: Performing protein FDR
1 day, 9:11:18.991518 INFO: Normalizing q-values using 8,980 targets and 2,700 decoys
1 day, 9:11:18.994195 INFO: Test AUC: 1.000
1 day, 9:11:18.994260 INFO: Train AUC: 1.000
1 day, 9:11:18.994324 INFO: AUC difference: 0.01%
1 day, 9:11:19.960865 INFO: ================ Protein FDR =================
1 day, 9:11:19.961088 INFO: Unique protein groups in output
1 day, 9:11:19.961130 INFO:   1% protein FDR: 8,979
1 day, 9:11:19.961157 INFO: 
1 day, 9:11:19.961181 INFO: Unique precursor in output
1 day, 9:11:19.961205 INFO:   1% protein FDR: 91,560
1 day, 9:11:19.961229 INFO: ================================================
1 day, 9:11:20.039318 PROGRESS: Building search statistics
1 day, 9:11:20.175873 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/optimization_manager.pkl
1 day, 9:11:20.176159 INFO: Initializing OptimizationManager
1 day, 9:11:20.176522 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/calibration_manager.pkl
1 day, 9:11:20.176623 INFO: Initializing CalibrationManager
1 day, 9:11:20.176892 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/raw_file_manager.pkl
1 day, 9:11:20.176997 INFO: Initializing RawFileManager
1 day, 9:11:20.215090 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/optimization_manager.pkl
1 day, 9:11:20.215365 INFO: Initializing OptimizationManager
1 day, 9:11:20.215660 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/calibration_manager.pkl
1 day, 9:11:20.215760 INFO: Initializing CalibrationManager
1 day, 9:11:20.216038 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/raw_file_manager.pkl
1 day, 9:11:20.216141 INFO: Initializing RawFileManager
1 day, 9:11:20.253973 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/optimization_manager.pkl
1 day, 9:11:20.254250 INFO: Initializing OptimizationManager
1 day, 9:11:20.254553 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/calibration_manager.pkl
1 day, 9:11:20.254651 INFO: Initializing CalibrationManager
1 day, 9:11:20.254903 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/raw_file_manager.pkl
1 day, 9:11:20.255003 INFO: Initializing RawFileManager
1 day, 9:11:20.293254 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/optimization_manager.pkl
1 day, 9:11:20.293541 INFO: Initializing OptimizationManager
1 day, 9:11:20.293832 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/calibration_manager.pkl
1 day, 9:11:20.293933 INFO: Initializing CalibrationManager
1 day, 9:11:20.294184 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/raw_file_manager.pkl
1 day, 9:11:20.294288 INFO: Initializing RawFileManager
1 day, 9:11:20.331479 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/optimization_manager.pkl
1 day, 9:11:20.331743 INFO: Initializing OptimizationManager
1 day, 9:11:20.332053 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/calibration_manager.pkl
1 day, 9:11:20.332150 INFO: Initializing CalibrationManager
1 day, 9:11:20.332394 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/raw_file_manager.pkl
1 day, 9:11:20.332490 INFO: Initializing RawFileManager
1 day, 9:11:20.369912 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/optimization_manager.pkl
1 day, 9:11:20.370178 INFO: Initializing OptimizationManager
1 day, 9:11:20.370477 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/calibration_manager.pkl
1 day, 9:11:20.370576 INFO: Initializing CalibrationManager
1 day, 9:11:20.370828 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/raw_file_manager.pkl
1 day, 9:11:20.370929 INFO: Initializing RawFileManager
1 day, 9:11:20.374077 INFO: Writing stat output to disk
1 day, 9:11:20.374159 INFO: Saving /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/stat.tsv to disk
1 day, 9:11:20.384596 PROGRESS: Building internal statistics
1 day, 9:11:20.385041 INFO: Loaded TimingManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494/timing_manager.pkl
1 day, 9:11:20.385100 INFO: Initializing TimingManager
1 day, 9:11:20.385561 INFO: Loaded TimingManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500/timing_manager.pkl
1 day, 9:11:20.385616 INFO: Initializing TimingManager
1 day, 9:11:20.385883 INFO: Loaded TimingManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506/timing_manager.pkl
1 day, 9:11:20.385934 INFO: Initializing TimingManager
1 day, 9:11:20.386177 INFO: Loaded TimingManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496/timing_manager.pkl
1 day, 9:11:20.386226 INFO: Initializing TimingManager
1 day, 9:11:20.386462 INFO: Loaded TimingManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502/timing_manager.pkl
1 day, 9:11:20.386510 INFO: Initializing TimingManager
1 day, 9:11:20.386737 INFO: Loaded TimingManager from /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/quant/ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508/timing_manager.pkl
1 day, 9:11:20.386784 INFO: Initializing TimingManager
1 day, 9:11:20.387367 INFO: Writing internal output to disk
1 day, 9:11:20.387422 INFO: Saving /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/internal.tsv to disk
1 day, 9:11:20.486969 INFO: Performing label free quantification
1 day, 9:11:20.487187 INFO: Accumulating fragment data
1 day, 9:11:20.487275 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_01_11494
1 day, 9:11:20.555758 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_02_11500
1 day, 9:11:22.017929 INFO: reading frag file for ttSCP_diaPASEF_Condition_A_Sample_Alpha_03_11506
1 day, 9:11:23.455315 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_01_11496
1 day, 9:11:24.883019 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_02_11502
1 day, 9:11:26.296824 INFO: reading frag file for ttSCP_diaPASEF_Condition_B_Sample_Alpha_03_11508
1 day, 9:11:27.860776 INFO: Performing label free quantification on the precursor level
1 day, 9:11:27.860991 INFO: Filtering fragments by quality
1 day, 9:11:28.162214 INFO: Performing label-free quantification with directlfq normalization
1 day, 9:11:28.664759 INFO: Applying directLFQ normalization
1 day, 9:11:29.364296 INFO: 91560 lfq-groups total
1 day, 9:14:06.183962 INFO: using 100 processes
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1 day, 9:19:05.900629 INFO: lfq-object 82400
1 day, 9:19:05.904941 INFO: lfq-object 82300
1 day, 9:19:06.006155 INFO: lfq-object 82600
1 day, 9:19:06.035002 INFO: lfq-object 82500
1 day, 9:19:06.099834 INFO: lfq-object 82800
1 day, 9:19:06.140583 INFO: lfq-object 82700
1 day, 9:19:06.187270 INFO: lfq-object 83000
1 day, 9:19:06.231379 INFO: lfq-object 82900
1 day, 9:19:06.243370 INFO: lfq-object 83200
1 day, 9:19:06.322077 INFO: lfq-object 83600
1 day, 9:19:06.324422 INFO: lfq-object 83400
1 day, 9:19:06.333599 INFO: lfq-object 83100
1 day, 9:19:06.378330 INFO: lfq-object 83300
1 day, 9:19:06.458917 INFO: lfq-object 83500
1 day, 9:19:14.582703 INFO: Performing label free quantification on the pg level
1 day, 9:19:14.583133 INFO: Filtering fragments by quality
1 day, 9:19:14.942546 INFO: Performing label-free quantification with directlfq normalization
1 day, 9:19:15.151484 INFO: Applying directLFQ normalization
1 day, 9:19:15.393583 INFO: 8979 lfq-groups total
1 day, 9:21:33.031199 INFO: using 100 processes
1 day, 9:21:33.063570 INFO: lfq-object 0
1 day, 9:21:33.150662 INFO: lfq-object 100
1 day, 9:21:33.225284 INFO: lfq-object 300
1 day, 9:21:33.384368 INFO: lfq-object 600
1 day, 9:21:33.409148 INFO: lfq-object 200
1 day, 9:21:33.670884 INFO: lfq-object 700
1 day, 9:21:33.692542 INFO: lfq-object 400
1 day, 9:21:33.740099 INFO: lfq-object 900
1 day, 9:21:33.770282 INFO: lfq-object 500
1 day, 9:21:33.940781 INFO: lfq-object 1000
1 day, 9:21:33.964627 INFO: lfq-object 1200
1 day, 9:21:34.058117 INFO: lfq-object 800
1 day, 9:21:34.080881 INFO: lfq-object 1500
1 day, 9:21:34.109085 INFO: lfq-object 1300
1 day, 9:21:34.190333 INFO: lfq-object 1100
1 day, 9:21:34.217340 INFO: lfq-object 1800
1 day, 9:21:34.354517 INFO: lfq-object 1400
1 day, 9:21:34.380067 INFO: lfq-object 1600
1 day, 9:21:34.388473 INFO: lfq-object 1700
1 day, 9:21:34.473954 INFO: lfq-object 1900
1 day, 9:21:34.588702 INFO: lfq-object 2300
1 day, 9:21:34.742852 INFO: lfq-object 2000
1 day, 9:21:34.776714 INFO: lfq-object 2400
1 day, 9:21:34.794232 INFO: lfq-object 2600
1 day, 9:21:34.816837 INFO: lfq-object 2100
1 day, 9:21:34.834136 INFO: lfq-object 2500
1 day, 9:21:34.850708 INFO: lfq-object 2700
1 day, 9:21:34.965858 INFO: lfq-object 2200
1 day, 9:21:34.967521 INFO: lfq-object 2800
1 day, 9:21:35.056524 INFO: lfq-object 2900
1 day, 9:21:35.190023 INFO: lfq-object 3100
1 day, 9:21:35.210299 INFO: lfq-object 3200
1 day, 9:21:35.250722 INFO: lfq-object 3000
1 day, 9:21:35.319969 INFO: lfq-object 3300
1 day, 9:21:35.366515 INFO: lfq-object 3500
1 day, 9:21:35.453526 INFO: lfq-object 3400
1 day, 9:21:35.538996 INFO: lfq-object 3700
1 day, 9:21:35.583723 INFO: lfq-object 3600
1 day, 9:21:35.614934 INFO: lfq-object 3800
1 day, 9:21:35.717108 INFO: lfq-object 4000
1 day, 9:21:35.791196 INFO: lfq-object 4100
1 day, 9:21:35.819420 INFO: lfq-object 3900
1 day, 9:21:35.846469 INFO: lfq-object 4400
1 day, 9:21:35.923118 INFO: lfq-object 4200
1 day, 9:21:35.981807 INFO: lfq-object 4600
1 day, 9:21:36.057163 INFO: lfq-object 4500
1 day, 9:21:36.067335 INFO: lfq-object 4300
1 day, 9:21:36.164418 INFO: lfq-object 4700
1 day, 9:21:36.168839 INFO: lfq-object 4900
1 day, 9:21:36.172543 INFO: lfq-object 4800
1 day, 9:21:36.226387 INFO: lfq-object 5000
1 day, 9:21:36.407757 INFO: lfq-object 5200
1 day, 9:21:36.439537 INFO: lfq-object 5100
1 day, 9:21:36.522847 INFO: lfq-object 5400
1 day, 9:21:36.586356 INFO: lfq-object 5300
1 day, 9:21:36.605214 INFO: lfq-object 5500
1 day, 9:21:36.666062 INFO: lfq-object 5600
1 day, 9:21:36.778632 INFO: lfq-object 5800
1 day, 9:21:36.819300 INFO: lfq-object 5700
1 day, 9:21:36.895967 INFO: lfq-object 6100
1 day, 9:21:36.901578 INFO: lfq-object 5900
1 day, 9:21:36.908688 INFO: lfq-object 6000
1 day, 9:21:36.976660 INFO: lfq-object 6200
1 day, 9:21:37.071504 INFO: lfq-object 6300
1 day, 9:21:37.202683 INFO: lfq-object 6400
1 day, 9:21:37.212922 INFO: lfq-object 6500
1 day, 9:21:37.356212 INFO: lfq-object 6600
1 day, 9:21:37.375947 INFO: lfq-object 6700
1 day, 9:21:37.434642 INFO: lfq-object 6800
1 day, 9:21:37.487508 INFO: lfq-object 6900
1 day, 9:21:37.564999 INFO: lfq-object 7000
1 day, 9:21:37.645119 INFO: lfq-object 7200
1 day, 9:21:37.749562 INFO: lfq-object 7300
1 day, 9:21:37.811187 INFO: lfq-object 7100
1 day, 9:21:37.871148 INFO: lfq-object 7500
1 day, 9:21:37.874841 INFO: lfq-object 7400
1 day, 9:21:37.933478 INFO: lfq-object 7600
1 day, 9:21:38.040144 INFO: lfq-object 7800
1 day, 9:21:38.111725 INFO: lfq-object 7700
1 day, 9:21:38.127506 INFO: lfq-object 7900
1 day, 9:21:38.227363 INFO: lfq-object 8100
1 day, 9:21:38.281117 INFO: lfq-object 8000
1 day, 9:21:38.325972 INFO: lfq-object 8200
1 day, 9:21:38.396460 INFO: lfq-object 8400
1 day, 9:21:38.451230 INFO: lfq-object 8300
1 day, 9:21:38.618926 INFO: lfq-object 8500
1 day, 9:21:38.628104 INFO: lfq-object 8700
1 day, 9:21:38.668192 INFO: lfq-object 8600
1 day, 9:21:38.695597 INFO: lfq-object 8800
1 day, 9:21:38.821795 INFO: lfq-object 8900
1 day, 9:21:45.394977 INFO: Writing psm output to disk
1 day, 9:21:45.494604 INFO: Saving /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/precursors.parquet to disk
1 day, 9:21:46.335079 INFO: Writing precursor output to disk
1 day, 9:21:46.339210 INFO: Saving /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/precursor.matrix.parquet to disk
1 day, 9:21:46.442229 INFO: Writing peptide output to disk
1 day, 9:21:46.446653 INFO: Saving /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/peptide.matrix.parquet to disk
1 day, 9:21:46.518497 INFO: Writing pg output to disk
1 day, 9:21:46.521679 INFO: Saving /home/robbe/PB_output/results/diaPASEFManuscriptMBR/HYE_diaPASEF/alphadia_vlatest/pg.matrix.parquet to disk
1 day, 9:21:46.609806 PROGRESS: Building MBR spectral library
1 day, 9:21:46.610046 INFO: Running MbrLibraryBuilder
1 day, 9:21:47.105468 INFO: MBR spectral library contains 91,560 precursors, 8,979 proteins
1 day, 9:21:47.105653 INFO: Writing MBR spectral library to disk
1 day, 9:21:47.814322 PROGRESS: =================== Search step 'mbr' finished ===================
1 day, 9:21:47.860496 INFO: =================== Search Finished ===================
