0:00:00.000055 INFO: Output directory: /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1, cwd: /home/robbe/PB_output.
0:00:00.000160 INFO: User provided config file: /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/alphadia_config.yaml.
0:00:00.014537 PROGRESS:           _      _         ___ ___   _   
0:00:00.014642 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.014683 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.014713 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.014737 PROGRESS:            |_|                           
0:00:00.014763 PROGRESS: 
0:00:00.014793 PROGRESS: version: 2.1.0
0:00:00.014817 PROGRESS: Please cite: Wallmann, et al., Nature Biotechnology (2025), https://doi.org/10.1038/s41587-025-02791-w
0:00:00.014846 INFO: hostname: thestral
0:00:00.014875 PROGRESS: os: Linux 6.12.48+deb13-amd64 (x86_64)
0:00:00.014902 PROGRESS: python: 3.11.11 (CPython)
0:00:00.014962 INFO: date: 2026-04-26 20:05:33
0:00:00.014987 INFO: ================ AlphaX Environment ===============
0:00:00.015010 INFO: alphabase       : 1.7.4
0:00:00.015031 INFO: alpharaw        : 0.4.8
0:00:00.015052 INFO: alphatims       : 1.0.9
0:00:00.015076 INFO: alphapeptdeep   : 1.4.1
0:00:00.015103 INFO: directlfq       : 0.3.3
0:00:00.015131 INFO: ===================================================
0:00:00.015156 INFO: ================= Pip Environment =================
0:00:00.099412 INFO: pytz==2025.2 et_xmlfile==2.0.0 scikit-learn==1.7.2 networkx==3.6 rdkit==2025.9.1 pyparsing==3.2.5 nvidia-nvjitlink-cu12==12.4.127 alpharaw==0.4.8 matplotlib==3.10.7 plotly==6.6.0 clr_loader==0.2.8 tqdm==4.67.1 MarkupSafe==3.0.3 regex==2025.11.3 pip==24.0 numpy==1.26.4 nvidia-nvshmem-cu12==3.3.20 dill==0.4.0 peptdeep==1.4.1 contextlib2==21.6.0 directlfq==0.3.3 argparse==1.4.0 nvidia-cuda-cupti-cu12==12.4.127 pandas==2.3.3 lightning-utilities==0.15.2 idna==3.11 tokenizers==0.22.1 safetensors==0.7.0 lxml==6.0.2 nvidia-cuda-nvrtc-cu12==12.4.127 pyteomics==4.7.5 PyYAML==6.0.3 mpmath==1.3.0 fonttools==4.60.1 six==1.17.0 narwhals==2.19.0 h5py==3.15.1 cycler==0.12.1 threadpoolctl==3.6.0 pythonnet==3.0.5 triton==3.2.0 pycparser==2.23 alphatims==1.0.9 typing_extensions==4.15.0 pyzstd==0.18.0 kiwisolver==1.4.9 multiprocess==0.70.18 alphabase==1.7.4 click==8.3.1 python-dateutil==2.9.0.post0 fsspec==2025.10.0 torch==2.6.0 openpyxl==3.1.5 huggingface-hub==0.36.0 nvidia-cusparse-cu12==12.3.1.170 contourpy==1.3.3 rocket-fft==0.2.5 numba==0.62.1 nvidia-cufile-cu12==1.13.1.3 certifi==2025.11.12 quantselect==0.1.3 joblib==1.5.2 pyahocorasick==2.2.0 seaborn==0.13.2 alphadia-search-rs==1.1.1 biopython==1.86 scipy==1.12.0 tzdata==2025.2 requests==2.32.5 urllib3==2.5.0 torchmetrics==1.8.2 Jinja2==3.1.6 nvidia-nvtx-cu12==12.4.127 nvidia-cusolver-cu12==11.6.1.9 pyarrow==22.0.0 filelock==3.20.0 llvmlite==0.45.1 nvidia-cufft-cu12==11.2.1.3 alphadia==2.1.0 pillow==12.0.0 charset-normalizer==3.4.4 transformers==4.57.3 sympy==1.13.1 nvidia-cublas-cu12==12.4.5.8 nvidia-cudnn-cu12==9.1.0.70 packaging==25.0 nvidia-curand-cu12==10.3.5.147 cffi==2.0.0 setuptools==65.5.0 nvidia-cuda-runtime-cu12==12.4.127 nvidia-nccl-cu12==2.21.5 hf-xet==1.2.0 xxhash==3.6.0 nvidia-cusparselt-cu12==0.6.2 psutil==7.1.3
0:00:00.099508 INFO: ===================================================
0:00:00.099539 INFO: =================== Running step 'library' ===================
0:00:00.099610 INFO: loading default config from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.112607 INFO: loading additional config provided via CLI
0:00:00.112719 INFO: loading additional config provided via CLI parameters
0:00:00.113077 INFO: Updating config with 'user defined'
0:00:00.113149 INFO: Updating config with 'user defined (cli)'
0:00:00.113210 INFO: updating config with user defined values: [{'raw_paths': ['/public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw', '/public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw', '/public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw', '/public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw', '/public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw', '/public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw'], 'fasta_paths': ['/public/local/ProteoBench/fastas/ProteoBenchFASTA_DDAQuantification_noecoli.fasta'], 'output_directory': '/home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1', 'general': {'thread_count': 32, 'mbr_step_enabled': False}, 'library_prediction': {'enabled': True, 'enzyme': 'trypsin', 'missed_cleavages': 2, 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M', 'max_var_mod_num': 3, 'precursor_len': [7, 30], 'precursor_charge': [2, 4], 'precursor_mz': [400.0, 1200.0], 'fragment_mz': [200.0, 2000.0]}, 'search_initial': {'ms1_tolerance': 20, 'ms2_tolerance': 20}, 'fdr': {'fdr': 0.01}, 'search': {'extraction_backend': 'rust'}}, {'raw_paths': ['/public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw', '/public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw', '/public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw', '/public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw', '/public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw', '/public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw']}]
0:00:00.113436 INFO: Updating config with 'user defined'
0:00:00.113484 INFO: Updating config with 'user defined (cli)'
0:00:00.113519 INFO: ├──version: None
0:00:00.113548 INFO: ├──workflow_name: None
0:00:00.113572 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1 [user defined, default: None][0m
0:00:00.113594 INFO: ├──library_path: None
0:00:00.113615 INFO: ├──raw_paths:
0:00:00.113637 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw [user defined (cli), default: None][0m
0:00:00.113660 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw [user defined (cli), default: None][0m
0:00:00.113682 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw [user defined (cli), default: None][0m
0:00:00.113706 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw [user defined (cli), default: None][0m
0:00:00.113726 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw [user defined (cli), default: None][0m
0:00:00.113746 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral_Single_Cell/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw [user defined (cli), default: None][0m
0:00:00.113768 INFO: ├──fasta_paths:
0:00:00.113788 INFO: │   [32;20m- /public/local/ProteoBench/fastas/ProteoBenchFASTA_DDAQuantification_noecoli.fasta [user defined, default: None][0m
0:00:00.113811 INFO: ├──quant_directory: None
0:00:00.113832 INFO: ├──general
0:00:00.113854 INFO: │   [32;20m├──thread_count: 32 [user defined, default: 10][0m
0:00:00.113881 INFO: │   ├──transfer_step_enabled: False
0:00:00.113903 INFO: │   ├──mbr_step_enabled: False
0:00:00.113930 INFO: │   ├──reuse_calibration: False
0:00:00.113952 INFO: │   ├──reuse_quant: False
0:00:00.113973 INFO: │   ├──log_level: INFO
0:00:00.113995 INFO: │   ├──use_gpu: True
0:00:00.114015 INFO: │   ├──save_figures: True
0:00:00.114035 INFO: │   ├──save_library: True
0:00:00.114058 INFO: │   ├──save_flat_library: False
0:00:00.114079 INFO: │   ├──input_library_type: base
0:00:00.114100 INFO: │   ├──save_mbr_library: True
0:00:00.114121 INFO: │   └──random_state: None
0:00:00.114142 INFO: ├──library_loading
0:00:00.114164 INFO: │   └──drop_decoys: False
0:00:00.114184 INFO: ├──library_prediction
0:00:00.114207 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.114230 INFO: │   ├──enzyme: trypsin
0:00:00.114250 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.114271 INFO: │   [32;20m├──variable_modifications: Oxidation@M [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
0:00:00.114293 INFO: │   [32;20m├──max_var_mod_num: 3 [user defined, default: 2][0m
0:00:00.114313 INFO: │   [32;20m├──missed_cleavages: 2 [user defined, default: 1][0m
0:00:00.114338 INFO: │   ├──precursor_len:
0:00:00.114387 INFO: │   │   - 7
0:00:00.114411 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.114434 INFO: │   ├──precursor_charge:
0:00:00.114460 INFO: │   │   - 2
0:00:00.114480 INFO: │   │   - 4
0:00:00.114499 INFO: │   ├──precursor_mz:
0:00:00.114520 INFO: │   │   - 400.0
0:00:00.114541 INFO: │   │   - 1200.0
0:00:00.114560 INFO: │   ├──fragment_mz:
0:00:00.114579 INFO: │   │   - 200.0
0:00:00.114604 INFO: │   │   - 2000.0
0:00:00.114625 INFO: │   ├──nce: 25.0
0:00:00.114644 INFO: │   ├──fragment_types:
0:00:00.114666 INFO: │   │   - b
0:00:00.114685 INFO: │   │   - y
0:00:00.114705 INFO: │   ├──max_fragment_charge: 2
0:00:00.114726 INFO: │   ├──instrument: Lumos
0:00:00.114747 INFO: │   ├──peptdeep_model_path: None
0:00:00.114768 INFO: │   ├──peptdeep_model_type: generic
0:00:00.114789 INFO: │   ├──predict_charge: False
0:00:00.114811 INFO: │   └──min_charge_probability: 0.1
0:00:00.114831 INFO: ├──custom_modifications:
0:00:00.114854 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.114874 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.114898 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.114918 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.114939 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.114959 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.114979 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.115000 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.115020 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.115043 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.115064 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.115087 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.115107 INFO: │   ├──name: Label:13C(12)@K
0:00:00.115130 INFO: │   └──composition: C(12)
0:00:00.115150 INFO: ├──search
0:00:00.115170 INFO: │   ├──extraction_backend: rust
0:00:00.115192 INFO: │   ├──target_ms1_tolerance: 5
0:00:00.115212 INFO: │   ├──target_ms2_tolerance: 10
0:00:00.115233 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.115253 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.115276 INFO: │   ├──quant_window: 3
0:00:00.115296 INFO: │   ├──target_num_candidates: 3
0:00:00.115317 INFO: │   ├──channel_filter: 
0:00:00.115338 INFO: │   ├──compete_for_fragments: True
0:00:00.115361 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.115391 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.115411 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.115436 INFO: │   ├──optimized_peak_group_score: False
0:00:00.115458 INFO: │   ├──exclude_shared_ions: True
0:00:00.115479 INFO: │   ├──quant_all: True
0:00:00.115498 INFO: │   └──experimental_xic: True
0:00:00.115518 INFO: ├──calibration
0:00:00.115540 INFO: │   ├──batch_size: 1000
0:00:00.115562 INFO: │   ├──optimization_lock_target: 1000
0:00:00.115583 INFO: │   ├──max_steps: 20
0:00:00.115605 INFO: │   ├──min_steps: 5
0:00:00.115625 INFO: │   ├──max_skips: 1
0:00:00.115649 INFO: │   ├──max_fragments: 5000
0:00:00.115670 INFO: │   └──min_correlation: 0.7
0:00:00.115693 INFO: ├──search_initial
0:00:00.115714 INFO: │   ├──num_candidates: 1
0:00:00.115741 INFO: │   [32;20m├──ms1_tolerance: 20 [user defined, default: 30][0m
0:00:00.115762 INFO: │   [32;20m├──ms2_tolerance: 20 [user defined, default: 30][0m
0:00:00.115782 INFO: │   ├──mobility_tolerance: 0.1
0:00:00.115804 INFO: │   └──rt_tolerance: 0.5
0:00:00.115824 INFO: ├──library_multiplexing
0:00:00.115846 INFO: │   ├──enabled: False
0:00:00.115867 INFO: │   ├──input_channel: 0
0:00:00.115889 INFO: │   └──multiplex_mapping:
0:00:00.115909 INFO: ├──multiplexing
0:00:00.115932 INFO: │   ├──enabled: False
0:00:00.115952 INFO: │   ├──target_channels: 4,8
0:00:00.115973 INFO: │   ├──decoy_channel: 12
0:00:00.115993 INFO: │   ├──reference_channel: 0
0:00:00.116014 INFO: │   └──competitive_scoring: True
0:00:00.116034 INFO: ├──fdr
0:00:00.116054 INFO: │   ├──fdr: 0.01
0:00:00.116074 INFO: │   ├──group_level: proteins
0:00:00.116094 INFO: │   ├──inference_strategy: heuristic
0:00:00.116115 INFO: │   ├──competitive_scoring: True
0:00:00.116135 INFO: │   ├──keep_decoys: False
0:00:00.116155 INFO: │   ├──keep_decoys_in_mbr_library: False
0:00:00.116176 INFO: │   ├──channel_wise_fdr: False
0:00:00.116196 INFO: │   └──enable_nn_hyperparameter_tuning: True
0:00:00.116216 INFO: ├──search_output
0:00:00.116237 INFO: │   ├──file_format: parquet
0:00:00.116259 INFO: │   ├──precursor_level_lfq: True
0:00:00.116279 INFO: │   ├──peptide_level_lfq: True
0:00:00.116300 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.116320 INFO: │   ├──min_k_fragments: 12
0:00:00.116341 INFO: │   ├──min_correlation: 0.9
0:00:00.116361 INFO: │   ├──num_samples_quadratic: 50
0:00:00.116381 INFO: │   ├──min_nonnan: 3
0:00:00.116401 INFO: │   ├──normalization_method: directlfq
0:00:00.116423 INFO: │   └──normalize_directlfq: True
0:00:00.116442 INFO: ├──optimization
0:00:00.116464 INFO: │   ├──order_of_optimization: None
0:00:00.116484 INFO: │   ├──ms2_error
0:00:00.116507 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.116528 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.116550 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.116570 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.116591 INFO: │   │   ├──try_narrower_values: True
0:00:00.116612 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.116633 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.116653 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.116674 INFO: │   ├──ms1_error
0:00:00.116694 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.116715 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.116735 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.116756 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.116776 INFO: │   │   ├──try_narrower_values: False
0:00:00.116801 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.116821 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.116846 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.116866 INFO: │   ├──mobility_error
0:00:00.116887 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.116907 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.116928 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.116948 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.116968 INFO: │   │   ├──try_narrower_values: False
0:00:00.116990 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.117011 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.117033 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.117052 INFO: │   └──rt_error
0:00:00.117074 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.117094 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.117115 INFO: │       ├──automatic_update_percentile_range: 0.999
0:00:00.117136 INFO: │       ├──automatic_update_factor: 1.5
0:00:00.117158 INFO: │       ├──try_narrower_values: True
0:00:00.117178 INFO: │       ├──maximal_decrease: 0.1
0:00:00.117200 INFO: │       ├──favour_narrower_optimum: False
0:00:00.117220 INFO: │       └──maximum_decrease_from_maximum: 0.5
0:00:00.117241 INFO: ├──optimization_manager
0:00:00.117263 INFO: │   ├──fwhm_rt: 5
0:00:00.117284 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.117305 INFO: │   └──score_cutoff: 0
0:00:00.117326 INFO: ├──transfer_library
0:00:00.117347 INFO: │   ├──enabled: False
0:00:00.117368 INFO: │   ├──fragment_types:
0:00:00.117387 INFO: │   │   - b
0:00:00.117407 INFO: │   │   - y
0:00:00.117428 INFO: │   ├──max_charge: 2
0:00:00.117451 INFO: │   ├──top_k_samples: 3
0:00:00.117471 INFO: │   ├──norm_delta_max: True
0:00:00.117493 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.117514 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.117535 INFO: └──transfer_learning
0:00:00.117555 INFO:     ├──enabled: False
0:00:00.117576 INFO:     ├──batch_size: 2000
0:00:00.117596 INFO:     ├──max_lr: 0.0001
0:00:00.117618 INFO:     ├──train_fraction: 0.7
0:00:00.117638 INFO:     ├──validation_fraction: 0.2
0:00:00.117659 INFO:     ├──test_fraction: 0.1
0:00:00.117679 INFO:     ├──test_interval: 1
0:00:00.117699 INFO:     ├──lr_patience: 3
0:00:00.117719 INFO:     ├──epochs: 51
0:00:00.117740 INFO:     ├──warmup_epochs: 5
0:00:00.117760 INFO:     ├──nce: 25
0:00:00.117781 INFO:     └──instrument: Lumos
0:00:00.123166 INFO: Registering 7 custom modifications
0:00:00.158724 INFO: Searching 6 files:
0:00:00.158823 INFO:   20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1.raw
0:00:00.158850 INFO:   20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2.raw
0:00:00.158871 INFO:   20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3.raw
0:00:00.158890 INFO:   20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1.raw
0:00:00.158909 INFO:   20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2.raw
0:00:00.158928 INFO:   20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3.raw
0:00:00.158947 INFO: Using 1 fasta files:
0:00:00.158967 INFO:   /public/local/ProteoBench/fastas/ProteoBenchFASTA_DDAQuantification_noecoli.fasta
0:00:00.158988 INFO: Using library: None
0:00:00.159007 INFO: Saving output to: /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1
0:00:00.159042 PROGRESS: Loading spectral library
0:00:00.159068 PROGRESS: No library provided. Building library from fasta files.
0:00:00.159104 INFO: Running FastaDigest
0:00:00.160266 INFO: Digesting fasta file
0:00:09.470235 INFO: Adding modifications
0:02:27.883873 INFO: Removing non-canonical amino acids
0:02:36.938414 INFO: Fasta library contains 8,010,756 precursors
0:02:36.938623 PROGRESS: Predicting library properties.
0:02:36.938711 INFO: Running PeptDeepPrediction
0:02:36.940120 INFO: Device set to cpu
0:02:38.161655 INFO: Loading PeptDeep models of type generic
0:02:39.200591 INFO: Predicting RT, MS2 and mobility
0:02:39.200784 INFO: Using multiprocessing with 32 processes ...
0:02:39.597337 INFO: Predicting rt,ms2,mobility ...
0:16:10.370220 INFO: Adding fragment mz information
0:16:10.825979 INFO: Adding fragment intensity information
0:16:11.286817 INFO: Adding precursor information
0:16:11.941475 INFO: Running PrecursorInitializer
0:16:11.972953 INFO: Running AnnotateFasta
0:16:45.581918 INFO: Running IsotopeGenerator
0:16:45.583291 WARNING: Multiprocessing not compatible with custom modifications yet, falling back to single process.
0:22:46.558914 INFO: Running RTNormalization
0:22:46.559238 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:22:46.559357 INFO: Saving library to /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/speclib.hdf
0:23:32.658598 INFO: Running DecoyGenerator
0:26:20.342848 INFO: Running FlattenLibrary
0:26:58.256834 INFO: Running InitFlatColumns
0:26:58.564532 INFO: Running LogFlatLibraryStats
0:26:58.564666 INFO: ============ Library Stats ============
0:26:58.564703 INFO: Number of precursors: 16,019,568
0:27:00.669725 INFO: 	thereof targets:8,010,756
0:27:00.669886 INFO: 	thereof decoys: 8,008,812
0:27:00.808633 INFO: Number of elution groups: 8,010,756
0:27:00.808768 INFO: 	average size: 2.00
0:27:01.187804 INFO: Number of proteins: 47,331
0:27:01.233080 INFO: Number of channels: 1 ([0])
0:27:01.233267 INFO: Isotopes Distribution for 4 isotopes
0:27:01.233307 INFO: =======================================
0:27:01.233352 PROGRESS: =================== Starting Search Workflows for step library ===================
0:27:01.233436 PROGRESS: Loading raw file 1/6: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1 
0:27:01.233493 INFO: Quantification results path: /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant
0:27:01.233569 INFO: Creating folder /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1/figures
0:27:01.233776 INFO: Initializing TimingManager
0:27:01.234215 INFO: Initializing RawFileManager
0:27:07.819051 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:27:07.820078 INFO: Determining DIA cycle
0:27:08.578465 INFO: Found cycle with start 0.00 min and length 20.
0:27:08.636209 INFO: RT (min)            : 0.0 - 23.9
0:27:08.636305 INFO: RT duration (sec)   : 1433.8
0:27:08.636338 INFO: RT duration (min)   : 23.9
0:27:08.636363 INFO: Cycle len (scans)   : 20
0:27:08.636386 INFO: Cycle len (sec)     : 1.03
0:27:08.636408 INFO: Number of cycles    : 1389
0:27:08.636432 INFO: MS2 range (m/z)     : 400.4 - 800.6
0:27:08.636462 INFO: Creating DIA data object took: 7.402137994766235
0:27:09.355317 INFO: Creating DIA data NG object took: 0.7187314033508301
0:27:11.031300 INFO: Initializing CalibrationManager
0:27:11.031562 INFO: Setting up calibration estimators ..
0:27:11.031633 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:27:11.031711 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'}' ..
0:27:11.031791 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:27:11.031853 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:27:11.031913 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}}' ..
0:27:11.031984 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:27:11.032035 INFO: Done setting up calibration estimators.
0:27:11.032138 INFO: Initializing OptimizationManager
0:27:11.032262 INFO: initial parameter: ms1_error = 20
0:27:11.032321 INFO: initial parameter: ms2_error = 20
0:27:11.032373 INFO: initial parameter: rt_error = 716.952392578125
0:27:11.032422 INFO: initial parameter: mobility_error = 0.1
0:27:11.032469 INFO: initial parameter: num_candidates = 1
0:27:11.032515 INFO: initial parameter: fwhm_rt = 5
0:27:11.032560 INFO: initial parameter: fwhm_mobility = 0.01
0:27:11.032607 INFO: initial parameter: score_cutoff = 0
0:27:11.032660 INFO: initial parameter: classifier_version = -1
0:27:11.032732 PROGRESS: Initializing workflow 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1
0:27:11.032949 INFO: FDRManager: loading saved state not requested, will be initialized.
0:27:11.032984 INFO: Initializing FDRManager
0:27:11.033020 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
0:27:12.517363 PROGRESS: Initializing spectral library: 5,415,345 target precursors potentially observable (2,595,411 removed)
0:27:13.961911 INFO: Updating optimization_manager: ms2_error           : 20 -> 20
0:27:13.962388 INFO: Updating optimization_manager: rt_error            : 716.952392578125 -> 716.952392578125
0:27:13.962511 PROGRESS: Starting initial search for precursors.
0:27:13.962600 INFO: Starting optimization step 0.
0:27:13.962667 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:27:13.962729 INFO: Using rust extraction backend
0:27:13.962797 PROGRESS: Extracting batch of 1960 precursors
0:27:13.967634 INFO: === Search parameters used ===
0:27:13.967740 INFO: rt_error       : 716.952392578125
0:27:13.967793 INFO: mobility_error : 0.1
0:27:13.967840 INFO: num_candidates : 1
0:27:13.967885 INFO: ms1_error      : 20
0:27:13.967929 INFO: ms2_error      : 20
0:27:13.967972 INFO: fwhm_rt        : 5
0:27:13.968016 INFO: quant_window   : 3
0:27:13.968060 INFO: ==============================================
0:27:14.006285 INFO: performing precursor FDR with 40 features
0:27:14.006391 INFO: Decoy channel: -1
0:27:14.006420 INFO: competitive: True
0:27:14.007661 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:14.009682 INFO: Estimating optimal hyperparameters - samples: 1,565, batch_size: 128, learning_rate: 1.77e-04
0:27:14.010544 INFO: Using random state 533135 for train-test-split
0:27:14.192844 INFO: Test AUC: 0.522
0:27:14.192921 INFO: Train AUC: 0.564
0:27:14.192952 INFO: AUC difference: 7.49%
0:27:14.192974 WARNING: AUC difference > 5%. This may indicate overfitting.
0:27:14.506435 INFO: Resetting torch num_threads to 32
0:27:14.507921 PROGRESS: === Extracted 1957 precursors and 10959 fragments ===
0:27:14.508282 INFO: === FDR correction performed with classifier version -1 ===
0:27:14.508753 PROGRESS: ============================= Precursor FDR =============================
0:27:14.508839 PROGRESS: Total precursors accumulated: 0
0:27:14.508902 PROGRESS: Target precursors: 0 (0.00%)
0:27:14.508957 PROGRESS: Decoy precursors: 0 (0.00%)
0:27:14.509006 PROGRESS: 
0:27:14.509053 PROGRESS: Precursor Summary:
0:27:14.509167 PROGRESS: 
0:27:14.509230 PROGRESS: Protein Summary:
0:27:14.509306 PROGRESS: =========================================================================
0:27:14.509487 INFO: Target number of precursors not reached yet.
0:27:14.587330 INFO: Starting optimization step 1.
0:27:14.587547 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:27:14.587641 INFO: Using rust extraction backend
0:27:14.587711 PROGRESS: Extracting batch of 3921 precursors
0:27:14.595954 INFO: === Search parameters used ===
0:27:14.596078 INFO: rt_error       : 716.952392578125
0:27:14.596134 INFO: mobility_error : 0.1
0:27:14.596182 INFO: num_candidates : 1
0:27:14.596236 INFO: ms1_error      : 20
0:27:14.596282 INFO: ms2_error      : 20
0:27:14.596333 INFO: fwhm_rt        : 5
0:27:14.596378 INFO: quant_window   : 3
0:27:14.596421 INFO: ==============================================
0:27:14.667362 INFO: performing precursor FDR with 40 features
0:27:14.667461 INFO: Decoy channel: -1
0:27:14.667488 INFO: competitive: True
0:27:14.671689 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:14.674033 INFO: Estimating optimal hyperparameters - samples: 4,700, batch_size: 128, learning_rate: 1.77e-04
0:27:14.674119 INFO: Using random state 825081 for train-test-split
0:27:15.249055 INFO: Test AUC: 0.534
0:27:15.249140 INFO: Train AUC: 0.573
0:27:15.249171 INFO: AUC difference: 6.80%
0:27:15.249194 WARNING: AUC difference > 5%. This may indicate overfitting.
0:27:15.492695 INFO: Resetting torch num_threads to 32
0:27:15.495475 PROGRESS: === Extracted 5876 precursors and 33379 fragments ===
0:27:15.495862 INFO: === FDR correction performed with classifier version -1 ===
0:27:15.496337 PROGRESS: ============================= Precursor FDR =============================
0:27:15.496422 PROGRESS: Total precursors accumulated: 0
0:27:15.496482 PROGRESS: Target precursors: 0 (0.00%)
0:27:15.496534 PROGRESS: Decoy precursors: 0 (0.00%)
0:27:15.496583 PROGRESS: 
0:27:15.496629 PROGRESS: Precursor Summary:
0:27:15.496743 PROGRESS: 
0:27:15.496806 PROGRESS: Protein Summary:
0:27:15.496886 PROGRESS: =========================================================================
0:27:15.497140 INFO: Target number of precursors not reached yet.
0:27:15.584916 INFO: Starting optimization step 2.
0:27:15.585137 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:27:15.585225 INFO: Using rust extraction backend
0:27:15.585292 PROGRESS: Extracting batch of 7852 precursors
0:27:15.600441 INFO: === Search parameters used ===
0:27:15.600577 INFO: rt_error       : 716.952392578125
0:27:15.600631 INFO: mobility_error : 0.1
0:27:15.600681 INFO: num_candidates : 1
0:27:15.600728 INFO: ms1_error      : 20
0:27:15.600775 INFO: ms2_error      : 20
0:27:15.600821 INFO: fwhm_rt        : 5
0:27:15.600865 INFO: quant_window   : 3
0:27:15.600909 INFO: ==============================================
0:27:15.717927 INFO: performing precursor FDR with 40 features
0:27:15.718038 INFO: Decoy channel: -1
0:27:15.718066 INFO: competitive: True
0:27:15.724703 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:15.728463 INFO: Estimating optimal hyperparameters - samples: 10,976, batch_size: 128, learning_rate: 1.77e-04
0:27:15.728592 INFO: Using random state 84620 for train-test-split
0:27:17.011496 INFO: Test AUC: 0.539
0:27:17.011608 INFO: Train AUC: 0.595
0:27:17.011638 INFO: AUC difference: 9.48%
0:27:17.011662 WARNING: AUC difference > 5%. This may indicate overfitting.
0:27:17.266511 INFO: Resetting torch num_threads to 32
0:27:17.270532 PROGRESS: === Extracted 13720 precursors and 78367 fragments ===
0:27:17.270927 INFO: === FDR correction performed with classifier version -1 ===
0:27:17.271425 PROGRESS: ============================= Precursor FDR =============================
0:27:17.271511 PROGRESS: Total precursors accumulated: 15
0:27:17.271573 PROGRESS: Target precursors: 15 (100.00%)
0:27:17.271627 PROGRESS: Decoy precursors: 0 (0.00%)
0:27:17.271675 PROGRESS: 
0:27:17.271728 PROGRESS: Precursor Summary:
0:27:17.272803 PROGRESS: Channel   0:	 0.050 FDR:    15; 0.010 FDR:    15; 0.001 FDR:    15
0:27:17.272888 PROGRESS: 
0:27:17.272946 PROGRESS: Protein Summary:
0:27:17.274118 PROGRESS: Channel   0:	 0.050 FDR:    15; 0.010 FDR:    15; 0.001 FDR:    15
0:27:17.274206 PROGRESS: =========================================================================
0:27:17.274525 INFO: Target number of precursors not reached yet.
0:27:17.373970 INFO: Starting optimization step 3.
0:27:17.374197 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:27:17.374283 INFO: Using rust extraction backend
0:27:17.374349 PROGRESS: Extracting batch of 15661 precursors
0:27:17.403086 INFO: === Search parameters used ===
0:27:17.403259 INFO: rt_error       : 716.952392578125
0:27:17.403328 INFO: mobility_error : 0.1
0:27:17.403378 INFO: num_candidates : 1
0:27:17.403425 INFO: ms1_error      : 20
0:27:17.403471 INFO: ms2_error      : 20
0:27:17.403515 INFO: fwhm_rt        : 5
0:27:17.403558 INFO: quant_window   : 3
0:27:17.403603 INFO: ==============================================
0:27:17.577502 INFO: performing precursor FDR with 40 features
0:27:17.577615 INFO: Decoy channel: -1
0:27:17.577641 INFO: competitive: True
0:27:17.588179 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:17.594984 INFO: Estimating optimal hyperparameters - samples: 23,483, batch_size: 128, learning_rate: 1.77e-04
0:27:17.595160 INFO: Using random state 575310 for train-test-split
0:27:20.470201 INFO: Test AUC: 0.558
0:27:20.470327 INFO: Train AUC: 0.604
0:27:20.470372 INFO: AUC difference: 7.57%
0:27:20.470399 WARNING: AUC difference > 5%. This may indicate overfitting.
0:27:20.719918 INFO: Resetting torch num_threads to 32
0:27:20.726202 PROGRESS: === Extracted 29354 precursors and 167736 fragments ===
0:27:20.726675 INFO: === FDR correction performed with classifier version -1 ===
0:27:20.727213 PROGRESS: ============================= Precursor FDR =============================
0:27:20.727305 PROGRESS: Total precursors accumulated: 13
0:27:20.727373 PROGRESS: Target precursors: 13 (100.00%)
0:27:20.727434 PROGRESS: Decoy precursors: 0 (0.00%)
0:27:20.727491 PROGRESS: 
0:27:20.727550 PROGRESS: Precursor Summary:
0:27:20.728618 PROGRESS: Channel   0:	 0.050 FDR:    13; 0.010 FDR:    13; 0.001 FDR:    13
0:27:20.728708 PROGRESS: 
0:27:20.728770 PROGRESS: Protein Summary:
0:27:20.729941 PROGRESS: Channel   0:	 0.050 FDR:    13; 0.010 FDR:    13; 0.001 FDR:    13
0:27:20.730042 PROGRESS: =========================================================================
0:27:20.730538 INFO: Target number of precursors not reached yet.
0:27:20.852923 INFO: Starting optimization step 4.
0:27:20.853165 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:27:20.853256 INFO: Using rust extraction backend
0:27:20.853329 PROGRESS: Extracting batch of 31339 precursors
0:27:20.908760 INFO: === Search parameters used ===
0:27:20.908967 INFO: rt_error       : 716.952392578125
0:27:20.909029 INFO: mobility_error : 0.1
0:27:20.909084 INFO: num_candidates : 1
0:27:20.909137 INFO: ms1_error      : 20
0:27:20.909199 INFO: ms2_error      : 20
0:27:20.909252 INFO: fwhm_rt        : 5
0:27:20.909302 INFO: quant_window   : 3
0:27:20.909349 INFO: ==============================================
0:27:21.217825 INFO: performing precursor FDR with 40 features
0:27:21.217939 INFO: Decoy channel: -1
0:27:21.217965 INFO: competitive: True
0:27:21.238742 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:21.252177 INFO: Estimating optimal hyperparameters - samples: 48,522, batch_size: 198, learning_rate: 2.20e-04
0:27:21.252374 INFO: Using random state 982583 for train-test-split
0:27:24.950956 INFO: Test AUC: 0.564
0:27:24.951065 INFO: Train AUC: 0.611
0:27:24.951097 INFO: AUC difference: 7.56%
0:27:24.951121 WARNING: AUC difference > 5%. This may indicate overfitting.
0:27:25.207860 INFO: Resetting torch num_threads to 32
0:27:25.218801 PROGRESS: === Extracted 60653 precursors and 346339 fragments ===
0:27:25.219369 INFO: === FDR correction performed with classifier version -1 ===
0:27:25.219977 PROGRESS: ============================= Precursor FDR =============================
0:27:25.220074 PROGRESS: Total precursors accumulated: 72
0:27:25.220140 PROGRESS: Target precursors: 72 (100.00%)
0:27:25.220198 PROGRESS: Decoy precursors: 0 (0.00%)
0:27:25.220250 PROGRESS: 
0:27:25.220307 PROGRESS: Precursor Summary:
0:27:25.221381 PROGRESS: Channel   0:	 0.050 FDR:    72; 0.010 FDR:    72; 0.001 FDR:    72
0:27:25.221471 PROGRESS: 
0:27:25.221532 PROGRESS: Protein Summary:
0:27:25.222747 PROGRESS: Channel   0:	 0.050 FDR:    71; 0.010 FDR:    71; 0.001 FDR:    71
0:27:25.222843 PROGRESS: =========================================================================
0:27:25.223708 INFO: Target number of precursors not reached yet.
0:27:25.389773 INFO: Starting optimization step 5.
0:27:25.390016 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:27:25.390106 INFO: Using rust extraction backend
0:27:25.390197 PROGRESS: Extracting batch of 62709 precursors
0:27:25.499210 INFO: === Search parameters used ===
0:27:25.499439 INFO: rt_error       : 716.952392578125
0:27:25.499499 INFO: mobility_error : 0.1
0:27:25.499550 INFO: num_candidates : 1
0:27:25.499597 INFO: ms1_error      : 20
0:27:25.499656 INFO: ms2_error      : 20
0:27:25.499702 INFO: fwhm_rt        : 5
0:27:25.499746 INFO: quant_window   : 3
0:27:25.499790 INFO: ==============================================
0:27:26.079969 INFO: performing precursor FDR with 40 features
0:27:26.080086 INFO: Decoy channel: -1
0:27:26.080112 INFO: competitive: True
0:27:26.125059 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:26.155571 INFO: Estimating optimal hyperparameters - samples: 98,611, batch_size: 403, learning_rate: 3.14e-04
0:27:26.155867 INFO: Using random state 284904 for train-test-split
0:27:31.652918 INFO: Test AUC: 0.585
0:27:31.653034 INFO: Train AUC: 0.607
0:27:31.653066 INFO: AUC difference: 3.56%
0:27:31.943916 INFO: Resetting torch num_threads to 32
0:27:31.966087 PROGRESS: === Extracted 123264 precursors and 703907 fragments ===
0:27:31.966734 INFO: === FDR correction performed with classifier version -1 ===
0:27:31.967286 PROGRESS: ============================= Precursor FDR =============================
0:27:31.967374 PROGRESS: Total precursors accumulated: 105
0:27:31.967436 PROGRESS: Target precursors: 104 (99.05%)
0:27:31.967491 PROGRESS: Decoy precursors: 1 (0.95%)
0:27:31.967539 PROGRESS: 
0:27:31.967585 PROGRESS: Precursor Summary:
0:27:31.968566 PROGRESS: Channel   0:	 0.050 FDR:   104; 0.010 FDR:   104; 0.001 FDR:    92
0:27:31.968652 PROGRESS: 
0:27:31.968711 PROGRESS: Protein Summary:
0:27:31.969808 PROGRESS: Channel   0:	 0.050 FDR:   102; 0.010 FDR:   102; 0.001 FDR:    90
0:27:31.969906 PROGRESS: =========================================================================
0:27:31.972089 INFO: Target number of precursors not reached yet.
0:27:32.220636 INFO: Starting optimization step 6.
0:27:32.220891 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:27:32.220985 INFO: Using rust extraction backend
0:27:32.221058 PROGRESS: Extracting batch of 125408 precursors
0:27:32.438795 INFO: === Search parameters used ===
0:27:32.439039 INFO: rt_error       : 716.952392578125
0:27:32.439100 INFO: mobility_error : 0.1
0:27:32.439151 INFO: num_candidates : 1
0:27:32.439198 INFO: ms1_error      : 20
0:27:32.439245 INFO: ms2_error      : 20
0:27:32.439290 INFO: fwhm_rt        : 5
0:27:32.439333 INFO: quant_window   : 3
0:27:32.439376 INFO: ==============================================
0:27:33.572623 INFO: performing precursor FDR with 40 features
0:27:33.572747 INFO: Decoy channel: -1
0:27:33.572779 INFO: competitive: True
0:27:33.683209 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:33.771088 INFO: Estimating optimal hyperparameters - samples: 198,808, batch_size: 814, learning_rate: 4.46e-04
0:27:33.771631 INFO: Using random state 222793 for train-test-split
0:27:40.341144 INFO: Test AUC: 0.582
0:27:40.341312 INFO: Train AUC: 0.607
0:27:40.341347 INFO: AUC difference: 4.10%
0:27:40.663867 INFO: Resetting torch num_threads to 32
0:27:40.715741 PROGRESS: === Extracted 248510 precursors and 1418575 fragments ===
0:27:40.716391 INFO: === FDR correction performed with classifier version -1 ===
0:27:40.716979 PROGRESS: ============================= Precursor FDR =============================
0:27:40.717068 PROGRESS: Total precursors accumulated: 228
0:27:40.717130 PROGRESS: Target precursors: 226 (99.12%)
0:27:40.717182 PROGRESS: Decoy precursors: 2 (0.88%)
0:27:40.717239 PROGRESS: 
0:27:40.717290 PROGRESS: Precursor Summary:
0:27:40.718323 PROGRESS: Channel   0:	 0.050 FDR:   226; 0.010 FDR:   226; 0.001 FDR:    99
0:27:40.718436 PROGRESS: 
0:27:40.718497 PROGRESS: Protein Summary:
0:27:40.719672 PROGRESS: Channel   0:	 0.050 FDR:   207; 0.010 FDR:   207; 0.001 FDR:    95
0:27:40.719760 PROGRESS: =========================================================================
0:27:40.723495 INFO: Target number of precursors not reached yet.
0:27:41.130146 INFO: Starting optimization step 7.
0:27:41.130417 PROGRESS: === Extracting elution groups 127000 to 255000 ===
0:27:41.130511 INFO: Using rust extraction backend
0:27:41.130593 PROGRESS: Extracting batch of 250773 precursors
0:27:41.561504 INFO: === Search parameters used ===
0:27:41.561759 INFO: rt_error       : 716.952392578125
0:27:41.561829 INFO: mobility_error : 0.1
0:27:41.561881 INFO: num_candidates : 1
0:27:41.561939 INFO: ms1_error      : 20
0:27:41.561985 INFO: ms2_error      : 20
0:27:41.562031 INFO: fwhm_rt        : 5
0:27:41.562083 INFO: quant_window   : 3
0:27:41.562128 INFO: ==============================================
0:27:43.753644 INFO: performing precursor FDR with 40 features
0:27:43.753763 INFO: Decoy channel: -1
0:27:43.753792 INFO: competitive: True
0:27:44.001852 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:44.198011 INFO: Estimating optimal hyperparameters - samples: 399,173, batch_size: 1,635, learning_rate: 6.32e-04
0:27:44.198728 INFO: Using random state 798876 for train-test-split
0:27:54.696166 INFO: Test AUC: 0.586
0:27:54.696318 INFO: Train AUC: 0.605
0:27:54.696354 INFO: AUC difference: 3.11%
0:27:55.456688 INFO: Resetting torch num_threads to 32
0:27:55.558130 PROGRESS: === Extracted 498967 precursors and 2845688 fragments ===
0:27:55.558797 INFO: === FDR correction performed with classifier version -1 ===
0:27:55.559440 PROGRESS: ============================= Precursor FDR =============================
0:27:55.559534 PROGRESS: Total precursors accumulated: 460
0:27:55.559600 PROGRESS: Target precursors: 456 (99.13%)
0:27:55.559659 PROGRESS: Decoy precursors: 4 (0.87%)
0:27:55.559714 PROGRESS: 
0:27:55.559767 PROGRESS: Precursor Summary:
0:27:55.560833 PROGRESS: Channel   0:	 0.050 FDR:   456; 0.010 FDR:   456; 0.001 FDR:   212
0:27:55.560934 PROGRESS: 
0:27:55.560995 PROGRESS: Protein Summary:
0:27:55.562246 PROGRESS: Channel   0:	 0.050 FDR:   398; 0.010 FDR:   398; 0.001 FDR:   189
0:27:55.562339 PROGRESS: =========================================================================
0:27:55.569260 INFO: Target number of precursors not reached yet.
0:27:56.378249 INFO: Starting optimization step 8.
0:27:56.378516 PROGRESS: === Extracting elution groups 255000 to 511000 ===
0:27:56.378607 INFO: Using rust extraction backend
0:27:56.378680 PROGRESS: Extracting batch of 501436 precursors
0:27:57.242350 INFO: === Search parameters used ===
0:27:57.242598 INFO: rt_error       : 716.952392578125
0:27:57.242661 INFO: mobility_error : 0.1
0:27:57.242714 INFO: num_candidates : 1
0:27:57.242773 INFO: ms1_error      : 20
0:27:57.242826 INFO: ms2_error      : 20
0:27:57.242879 INFO: fwhm_rt        : 5
0:27:57.242927 INFO: quant_window   : 3
0:27:57.242974 INFO: ==============================================
0:28:01.744386 INFO: performing precursor FDR with 40 features
0:28:01.744502 INFO: Decoy channel: -1
0:28:01.744532 INFO: competitive: True
0:28:02.210701 INFO: Setting torch num_threads to 2 for FDR classification task
0:28:02.634227 INFO: Estimating optimal hyperparameters - samples: 799,811, batch_size: 3,276, learning_rate: 8.94e-04
0:28:02.635711 INFO: Using random state 367546 for train-test-split
0:28:19.141668 INFO: Test AUC: 0.594
0:28:19.141792 INFO: Train AUC: 0.604
0:28:19.141827 INFO: AUC difference: 1.76%
0:28:19.734539 INFO: Resetting torch num_threads to 32
0:28:19.893452 PROGRESS: === Extracted 999764 precursors and 5703766 fragments ===
0:28:19.894094 INFO: === FDR correction performed with classifier version -1 ===
0:28:19.894869 PROGRESS: ============================= Precursor FDR =============================
0:28:19.894984 PROGRESS: Total precursors accumulated: 1,030
0:28:19.895052 PROGRESS: Target precursors: 1,020 (99.03%)
0:28:19.895112 PROGRESS: Decoy precursors: 10 (0.97%)
0:28:19.895180 PROGRESS: 
0:28:19.895233 PROGRESS: Precursor Summary:
0:28:19.896432 PROGRESS: Channel   0:	 0.050 FDR: 1,020; 0.010 FDR: 1,020; 0.001 FDR:   351
0:28:19.896530 PROGRESS: 
0:28:19.896593 PROGRESS: Protein Summary:
0:28:19.898061 PROGRESS: Channel   0:	 0.050 FDR:   817; 0.010 FDR:   817; 0.001 FDR:   299
0:28:19.898158 PROGRESS: =========================================================================
0:28:19.910621 INFO: Target number of precursors reached.
0:28:20.548712 INFO: fragments_df: keeping 5000 of 5703766 [sum(precursor_idx_mask)=11316 sum(mass_error_mask)=5703766 stop_rank=5000
0:28:21.616064 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:28:21.826755 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:28:22.571231 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:28:22.571698 INFO: Using score_cutoff 10.043027382087708 (fac=0.99, q=1)
0:28:22.572046 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:28:22.572133 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:28:22.572193 INFO: Updating optimization_manager: score_cutoff        : 0 -> 10.043027382087708
0:28:22.572271 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:23.185518 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:24.599482 INFO: Updating optimization_manager: classifier_version  : -1 -> 8
0:28:24.599773 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:28:24.599881 INFO: Starting optimization step 9.
0:28:24.599945 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:28:24.600024 INFO: Using rust extraction backend
0:28:24.600090 PROGRESS: Extracting batch of 1001059 precursors
0:28:26.297474 INFO: === Search parameters used ===
0:28:26.297757 INFO: rt_error       : 716.952392578125
0:28:26.297822 INFO: mobility_error : 0.1
0:28:26.297876 INFO: num_candidates : 3
0:28:26.297924 INFO: ms1_error      : 20
0:28:26.297969 INFO: ms2_error      : 20
0:28:26.298027 INFO: fwhm_rt        : 3.0
0:28:26.298077 INFO: quant_window   : 3
0:28:26.298120 INFO: ==============================================
0:28:40.745386 INFO: performing precursor FDR with 40 features
0:28:40.745518 INFO: Decoy channel: -1
0:28:40.745547 INFO: competitive: True
0:28:41.618802 INFO: Setting torch num_threads to 2 for FDR classification task
0:28:43.040754 INFO: Estimating optimal hyperparameters - samples: 2,399,763, batch_size: 4,096, learning_rate: 1.00e-03
0:28:43.047016 INFO: Using random state 807166 for train-test-split
0:29:27.996026 INFO: Test AUC: 0.601
0:29:27.996254 INFO: Train AUC: 0.606
0:29:27.996294 INFO: AUC difference: 0.69%
0:29:29.199152 INFO: Resetting torch num_threads to 32
0:29:29.319252 PROGRESS: === Extracted 2999704 precursors and 17033380 fragments ===
0:29:29.319809 INFO: === FDR correction performed with classifier version 8 ===
0:29:29.320585 PROGRESS: ============================= Precursor FDR =============================
0:29:29.320687 PROGRESS: Total precursors accumulated: 1,496
0:29:29.320753 PROGRESS: Target precursors: 1,482 (99.06%)
0:29:29.320809 PROGRESS: Decoy precursors: 14 (0.94%)
0:29:29.320862 PROGRESS: 
0:29:29.320911 PROGRESS: Precursor Summary:
0:29:29.322223 PROGRESS: Channel   0:	 0.050 FDR: 1,482; 0.010 FDR: 1,482; 0.001 FDR:   471
0:29:29.322315 PROGRESS: 
0:29:29.322385 PROGRESS: Protein Summary:
0:29:29.324072 PROGRESS: Channel   0:	 0.050 FDR: 1,171; 0.010 FDR: 1,171; 0.001 FDR:   406
0:29:29.324172 PROGRESS: =========================================================================
0:29:29.381929 INFO: Target number of precursors reached.
0:29:31.163365 INFO: fragments_df: keeping 5000 of 17033380 [sum(precursor_idx_mask)=36334 sum(mass_error_mask)=17033380 stop_rank=5000
0:29:32.365056 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:29:32.604486 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:29:33.328120 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:29:33.328588 INFO: Using score_cutoff 5.897228056526184 (fac=0.99, q=1)
0:29:33.328958 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:29:33.329041 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:29:33.329099 INFO: Updating optimization_manager: score_cutoff        : 10.043027382087708 -> 5.897228056526184
0:29:33.329170 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:29:33.935128 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:29:35.272881 INFO: === checking if optimization conditions were reached ===
0:29:35.275223 INFO: Updating optimization_manager: ms2_error           : 20 -> 10.0
0:29:35.275374 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:29:35.275449 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:29:35.275515 INFO: ==============================================
0:29:35.275588 INFO: Starting optimization step 10.
0:29:35.275654 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:29:35.275726 INFO: Using rust extraction backend
0:29:35.275789 PROGRESS: Extracting batch of 1001059 precursors
0:29:36.999356 INFO: === Search parameters used ===
0:29:36.999703 INFO: rt_error       : 716.952392578125
0:29:36.999771 INFO: mobility_error : 0.1
0:29:36.999825 INFO: num_candidates : 3
0:29:36.999874 INFO: ms1_error      : 20
0:29:36.999932 INFO: ms2_error      : 10.0
0:29:36.999982 INFO: fwhm_rt        : 3.0
0:29:37.000028 INFO: quant_window   : 3
0:29:37.000072 INFO: ==============================================
0:29:50.764599 INFO: performing precursor FDR with 40 features
0:29:50.764821 INFO: Decoy channel: -1
0:29:50.764855 INFO: competitive: True
0:29:51.510958 INFO: Setting torch num_threads to 2 for FDR classification task
0:29:52.844102 INFO: Estimating optimal hyperparameters - samples: 2,401,928, batch_size: 4,096, learning_rate: 1.00e-03
0:29:52.849506 INFO: Using random state 687580 for train-test-split
0:30:38.271580 INFO: Test AUC: 0.608
0:30:38.271808 INFO: Train AUC: 0.612
0:30:38.271847 INFO: AUC difference: 0.53%
0:30:39.505168 INFO: Resetting torch num_threads to 32
0:30:39.611092 PROGRESS: === Extracted 3002410 precursors and 18705816 fragments ===
0:30:39.611636 INFO: === FDR correction performed with classifier version 9 ===
0:30:39.612362 PROGRESS: ============================= Precursor FDR =============================
0:30:39.612459 PROGRESS: Total precursors accumulated: 1,627
0:30:39.612528 PROGRESS: Target precursors: 1,611 (99.02%)
0:30:39.612592 PROGRESS: Decoy precursors: 16 (0.98%)
0:30:39.612647 PROGRESS: 
0:30:39.612699 PROGRESS: Precursor Summary:
0:30:39.614076 PROGRESS: Channel   0:	 0.050 FDR: 1,611; 0.010 FDR: 1,611; 0.001 FDR: 1,315
0:30:39.614172 PROGRESS: 
0:30:39.614239 PROGRESS: Protein Summary:
0:30:39.616099 PROGRESS: Channel   0:	 0.050 FDR: 1,283; 0.010 FDR: 1,283; 0.001 FDR: 1,049
0:30:39.616202 PROGRESS: =========================================================================
0:30:39.670578 INFO: Target number of precursors reached.
0:30:41.664184 INFO: fragments_df: keeping 5000 of 18705816 [sum(precursor_idx_mask)=41590 sum(mass_error_mask)=18705816 stop_rank=5000
0:30:42.801598 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:30:43.057310 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:30:43.722778 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:30:43.723222 INFO: Using score_cutoff 5.043196622371673 (fac=0.99, q=1)
0:30:43.723567 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:30:43.723662 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:30:43.723723 INFO: Updating optimization_manager: score_cutoff        : 5.897228056526184 -> 5.043196622371673
0:30:43.723787 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:30:44.335665 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:30:45.758885 INFO: === checking if optimization conditions were reached ===
0:30:45.761072 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:30:45.761241 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:30:45.761315 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:30:45.761378 INFO: ==============================================
0:30:45.761451 INFO: Starting optimization step 11.
0:30:45.761519 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:30:45.761587 INFO: Using rust extraction backend
0:30:45.761651 PROGRESS: Extracting batch of 1001059 precursors
0:30:47.460340 INFO: === Search parameters used ===
0:30:47.460585 INFO: rt_error       : 716.952392578125
0:30:47.460650 INFO: mobility_error : 0.1
0:30:47.460715 INFO: num_candidates : 3
0:30:47.460766 INFO: ms1_error      : 20
0:30:47.460812 INFO: ms2_error      : 10.0
0:30:47.460868 INFO: fwhm_rt        : 3.0
0:30:47.460915 INFO: quant_window   : 3
0:30:47.460960 INFO: ==============================================
0:31:00.932691 INFO: performing precursor FDR with 40 features
0:31:00.932832 INFO: Decoy channel: -1
0:31:00.932860 INFO: competitive: True
0:31:01.684739 INFO: Setting torch num_threads to 2 for FDR classification task
0:31:02.998507 INFO: Estimating optimal hyperparameters - samples: 2,401,939, batch_size: 4,096, learning_rate: 1.00e-03
0:31:03.004324 INFO: Using random state 37144 for train-test-split
0:31:48.770820 INFO: Test AUC: 0.607
0:31:48.771044 INFO: Train AUC: 0.611
0:31:48.771081 INFO: AUC difference: 0.62%
0:31:50.054806 INFO: Resetting torch num_threads to 32
0:31:50.160207 PROGRESS: === Extracted 3002424 precursors and 18766458 fragments ===
0:31:50.160779 INFO: === FDR correction performed with classifier version 10 ===
0:31:50.161585 PROGRESS: ============================= Precursor FDR =============================
0:31:50.161688 PROGRESS: Total precursors accumulated: 1,748
0:31:50.161754 PROGRESS: Target precursors: 1,731 (99.03%)
0:31:50.161810 PROGRESS: Decoy precursors: 17 (0.97%)
0:31:50.161863 PROGRESS: 
0:31:50.161916 PROGRESS: Precursor Summary:
0:31:50.163450 PROGRESS: Channel   0:	 0.050 FDR: 1,731; 0.010 FDR: 1,731; 0.001 FDR: 1,382
0:31:50.163551 PROGRESS: 
0:31:50.163616 PROGRESS: Protein Summary:
0:31:50.165584 PROGRESS: Channel   0:	 0.050 FDR: 1,328; 0.010 FDR: 1,328; 0.001 FDR: 1,094
0:31:50.165682 PROGRESS: =========================================================================
0:31:50.225043 INFO: Target number of precursors reached.
0:31:52.114787 INFO: fragments_df: keeping 5000 of 18766458 [sum(precursor_idx_mask)=46094 sum(mass_error_mask)=18766458 stop_rank=5000
0:31:53.250907 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:31:53.513850 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:31:54.237468 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:31:54.237913 INFO: Using score_cutoff 9.164764855384826 (fac=0.99, q=1)
0:31:54.238255 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:31:54.238339 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:31:54.238415 INFO: Updating optimization_manager: score_cutoff        : 5.043196622371673 -> 9.164764855384826
0:31:54.238482 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:31:54.855888 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:31:56.287225 INFO: === checking if optimization conditions were reached ===
0:31:56.289701 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:31:56.289853 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:31:56.289933 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:31:56.290004 INFO: ==============================================
0:31:56.290087 INFO: Starting optimization step 12.
0:31:56.290170 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:31:56.290250 INFO: Using rust extraction backend
0:31:56.290331 PROGRESS: Extracting batch of 1001059 precursors
0:31:57.979075 INFO: === Search parameters used ===
0:31:57.979337 INFO: rt_error       : 716.952392578125
0:31:57.979436 INFO: mobility_error : 0.1
0:31:57.979497 INFO: num_candidates : 3
0:31:57.979546 INFO: ms1_error      : 20
0:31:57.979593 INFO: ms2_error      : 10.0
0:31:57.979637 INFO: fwhm_rt        : 3.0
0:31:57.979680 INFO: quant_window   : 3
0:31:57.979725 INFO: ==============================================
0:32:11.556195 INFO: performing precursor FDR with 40 features
0:32:11.556358 INFO: Decoy channel: -1
0:32:11.556386 INFO: competitive: True
0:32:12.290210 INFO: Setting torch num_threads to 2 for FDR classification task
0:32:13.575024 INFO: Estimating optimal hyperparameters - samples: 2,401,872, batch_size: 4,096, learning_rate: 1.00e-03
0:32:13.580332 INFO: Using random state 29095 for train-test-split
0:32:59.473188 INFO: Test AUC: 0.611
0:32:59.473412 INFO: Train AUC: 0.614
0:32:59.473450 INFO: AUC difference: 0.52%
0:33:00.705204 INFO: Resetting torch num_threads to 32
0:33:00.808004 PROGRESS: === Extracted 3002340 precursors and 18630071 fragments ===
0:33:00.808543 INFO: === FDR correction performed with classifier version 11 ===
0:33:00.809358 PROGRESS: ============================= Precursor FDR =============================
0:33:00.809454 PROGRESS: Total precursors accumulated: 1,989
0:33:00.809524 PROGRESS: Target precursors: 1,970 (99.04%)
0:33:00.809584 PROGRESS: Decoy precursors: 19 (0.96%)
0:33:00.809639 PROGRESS: 
0:33:00.809693 PROGRESS: Precursor Summary:
0:33:00.811165 PROGRESS: Channel   0:	 0.050 FDR: 1,970; 0.010 FDR: 1,970; 0.001 FDR: 1,202
0:33:00.811264 PROGRESS: 
0:33:00.811332 PROGRESS: Protein Summary:
0:33:00.813277 PROGRESS: Channel   0:	 0.050 FDR: 1,508; 0.010 FDR: 1,508; 0.001 FDR:   969
0:33:00.813375 PROGRESS: =========================================================================
0:33:00.868689 INFO: Target number of precursors reached.
0:33:02.785383 INFO: fragments_df: keeping 5000 of 18630071 [sum(precursor_idx_mask)=51232 sum(mass_error_mask)=18630071 stop_rank=5000
0:33:03.979842 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:33:04.288072 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:33:05.014158 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:33:05.014635 INFO: Using score_cutoff 6.4430755627155305 (fac=0.99, q=1)
0:33:05.014969 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:33:05.015053 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:33:05.015113 INFO: Updating optimization_manager: score_cutoff        : 9.164764855384826 -> 6.4430755627155305
0:33:05.015181 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:33:05.632530 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:33:07.060859 INFO: === checking if optimization conditions were reached ===
0:33:07.063198 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:33:07.063369 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
0:33:07.063444 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:33:07.063510 INFO: ==============================================
0:33:07.063590 INFO: Starting optimization step 13.
0:33:07.063662 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:33:07.063740 INFO: Using rust extraction backend
0:33:07.063818 PROGRESS: Extracting batch of 1001059 precursors
0:33:08.737664 INFO: === Search parameters used ===
0:33:08.738003 INFO: rt_error       : 716.952392578125
0:33:08.738071 INFO: mobility_error : 0.1
0:33:08.738123 INFO: num_candidates : 3
0:33:08.738172 INFO: ms1_error      : 20
0:33:08.738223 INFO: ms2_error      : 10.0
0:33:08.738276 INFO: fwhm_rt        : 3.0
0:33:08.738325 INFO: quant_window   : 3
0:33:08.738393 INFO: ==============================================
0:33:22.736904 INFO: performing precursor FDR with 40 features
0:33:22.737029 INFO: Decoy channel: -1
0:33:22.737058 INFO: competitive: True
0:33:23.469541 INFO: Setting torch num_threads to 2 for FDR classification task
0:33:24.821281 INFO: Estimating optimal hyperparameters - samples: 2,401,892, batch_size: 4,096, learning_rate: 1.00e-03
0:33:24.826513 INFO: Using random state 169664 for train-test-split
0:34:11.972538 INFO: Test AUC: 0.612
0:34:11.972977 INFO: Train AUC: 0.616
0:34:11.973032 INFO: AUC difference: 0.55%
0:34:13.196587 INFO: Resetting torch num_threads to 32
0:34:13.313562 PROGRESS: === Extracted 3002365 precursors and 18667164 fragments ===
0:34:13.314112 INFO: === FDR correction performed with classifier version 12 ===
0:34:13.314940 PROGRESS: ============================= Precursor FDR =============================
0:34:13.315038 PROGRESS: Total precursors accumulated: 1,994
0:34:13.315106 PROGRESS: Target precursors: 1,975 (99.05%)
0:34:13.315164 PROGRESS: Decoy precursors: 19 (0.95%)
0:34:13.315217 PROGRESS: 
0:34:13.315270 PROGRESS: Precursor Summary:
0:34:13.316750 PROGRESS: Channel   0:	 0.050 FDR: 1,975; 0.010 FDR: 1,975; 0.001 FDR: 1,400
0:34:13.316850 PROGRESS: 
0:34:13.316914 PROGRESS: Protein Summary:
0:34:13.318915 PROGRESS: Channel   0:	 0.050 FDR: 1,536; 0.010 FDR: 1,536; 0.001 FDR: 1,110
0:34:13.319030 PROGRESS: =========================================================================
0:34:13.379447 INFO: Target number of precursors reached.
0:34:15.305772 INFO: fragments_df: keeping 5000 of 18667164 [sum(precursor_idx_mask)=50917 sum(mass_error_mask)=18667164 stop_rank=5000
0:34:16.468875 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:34:16.769448 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:34:17.456703 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:34:17.457169 INFO: Using score_cutoff 5.720113153839112 (fac=0.99, q=1)
0:34:17.457515 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:34:17.457598 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:34:17.457658 INFO: Updating optimization_manager: score_cutoff        : 6.4430755627155305 -> 5.720113153839112
0:34:17.457724 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:34:18.068701 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:34:19.512833 INFO: === checking if optimization conditions were reached ===
0:34:19.515049 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:34:19.515214 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
0:34:19.515292 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:34:19.515360 INFO: ==============================================
0:34:19.515441 PROGRESS: Optimization finished for ms2_error.
0:34:20.552726 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:34:21.152640 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:34:22.634742 INFO: Starting optimization step 0.
0:34:22.634983 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:34:22.635090 INFO: Using rust extraction backend
0:34:22.635171 PROGRESS: Extracting batch of 1001059 precursors
0:34:24.376064 INFO: === Search parameters used ===
0:34:24.376409 INFO: rt_error       : 716.952392578125
0:34:24.376496 INFO: mobility_error : 0.1
0:34:24.376557 INFO: num_candidates : 3
0:34:24.376619 INFO: ms1_error      : 20
0:34:24.376668 INFO: ms2_error      : 10.0
0:34:24.376720 INFO: fwhm_rt        : 3.0
0:34:24.376774 INFO: quant_window   : 3
0:34:24.376822 INFO: ==============================================
0:34:38.027611 INFO: performing precursor FDR with 40 features
0:34:38.027814 INFO: Decoy channel: -1
0:34:38.027844 INFO: competitive: True
0:34:38.751502 INFO: Setting torch num_threads to 2 for FDR classification task
0:34:40.085335 INFO: Estimating optimal hyperparameters - samples: 2,401,931, batch_size: 4,096, learning_rate: 1.00e-03
0:34:40.090416 INFO: Using random state 73838 for train-test-split
0:35:24.451607 INFO: Test AUC: 0.612
0:35:24.451829 INFO: Train AUC: 0.617
0:35:24.451864 INFO: AUC difference: 0.80%
0:35:26.173359 INFO: Resetting torch num_threads to 32
0:35:26.282066 PROGRESS: === Extracted 3002414 precursors and 18731623 fragments ===
0:35:26.282567 INFO: === FDR correction performed with classifier version 13 ===
0:35:26.283379 PROGRESS: ============================= Precursor FDR =============================
0:35:26.283473 PROGRESS: Total precursors accumulated: 1,886
0:35:26.283548 PROGRESS: Target precursors: 1,868 (99.05%)
0:35:26.283604 PROGRESS: Decoy precursors: 18 (0.95%)
0:35:26.283656 PROGRESS: 
0:35:26.283704 PROGRESS: Precursor Summary:
0:35:26.285142 PROGRESS: Channel   0:	 0.050 FDR: 1,868; 0.010 FDR: 1,868; 0.001 FDR: 1,308
0:35:26.285244 PROGRESS: 
0:35:26.285303 PROGRESS: Protein Summary:
0:35:26.287237 PROGRESS: Channel   0:	 0.050 FDR: 1,443; 0.010 FDR: 1,443; 0.001 FDR: 1,040
0:35:26.287340 PROGRESS: =========================================================================
0:35:26.351318 INFO: Target number of precursors reached.
0:35:28.277274 INFO: fragments_df: keeping 5000 of 18731623 [sum(precursor_idx_mask)=48828 sum(mass_error_mask)=18731623 stop_rank=5000
0:35:29.422135 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:35:29.703421 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:35:30.427941 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:35:30.428411 INFO: Using score_cutoff 7.115149834442138 (fac=0.99, q=1)
0:35:30.428743 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:35:30.428831 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:35:30.428895 INFO: Updating optimization_manager: score_cutoff        : 5.720113153839112 -> 7.115149834442138
0:35:30.428969 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:35:31.040161 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:35:32.438889 INFO: === checking if optimization conditions were reached ===
0:35:32.439144 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:35:32.442090 INFO: Updating optimization_manager: rt_error            : 716.952392578125 -> 981.8728139951008
0:35:32.442251 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 981.8728.
0:35:32.442330 INFO: ==============================================
0:35:32.442431 INFO: Starting optimization step 1.
0:35:32.442505 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:35:32.442578 INFO: Using rust extraction backend
0:35:32.442644 PROGRESS: Extracting batch of 1001059 precursors
0:35:34.138977 INFO: === Search parameters used ===
0:35:34.139231 INFO: rt_error       : 981.8728139951008
0:35:34.139300 INFO: mobility_error : 0.1
0:35:34.139357 INFO: num_candidates : 3
0:35:34.139408 INFO: ms1_error      : 20
0:35:34.139455 INFO: ms2_error      : 10.0
0:35:34.139503 INFO: fwhm_rt        : 3.0
0:35:34.139551 INFO: quant_window   : 3
0:35:34.139600 INFO: ==============================================
0:35:48.639261 INFO: performing precursor FDR with 40 features
0:35:48.639410 INFO: Decoy channel: -1
0:35:48.639440 INFO: competitive: True
0:35:49.356149 INFO: Setting torch num_threads to 2 for FDR classification task
0:35:50.708089 INFO: Estimating optimal hyperparameters - samples: 2,401,966, batch_size: 4,096, learning_rate: 1.00e-03
0:35:50.713213 INFO: Using random state 73838 for train-test-split
0:36:37.656077 INFO: Test AUC: 0.612
0:36:37.656223 INFO: Train AUC: 0.618
0:36:37.656260 INFO: AUC difference: 1.01%
0:36:38.924824 INFO: Resetting torch num_threads to 32
0:36:39.022645 PROGRESS: === Extracted 3002458 precursors and 18844231 fragments ===
0:36:39.023150 INFO: === FDR correction performed with classifier version 13 ===
0:36:39.023944 PROGRESS: ============================= Precursor FDR =============================
0:36:39.024040 PROGRESS: Total precursors accumulated: 1,993
0:36:39.024112 PROGRESS: Target precursors: 1,974 (99.05%)
0:36:39.024171 PROGRESS: Decoy precursors: 19 (0.95%)
0:36:39.024229 PROGRESS: 
0:36:39.024293 PROGRESS: Precursor Summary:
0:36:39.025792 PROGRESS: Channel   0:	 0.050 FDR: 1,974; 0.010 FDR: 1,974; 0.001 FDR: 1,166
0:36:39.025893 PROGRESS: 
0:36:39.025955 PROGRESS: Protein Summary:
0:36:39.027904 PROGRESS: Channel   0:	 0.050 FDR: 1,516; 0.010 FDR: 1,516; 0.001 FDR:   938
0:36:39.028009 PROGRESS: =========================================================================
0:36:39.081427 INFO: Target number of precursors reached.
0:36:41.133394 INFO: fragments_df: keeping 5000 of 18844231 [sum(precursor_idx_mask)=52081 sum(mass_error_mask)=18844231 stop_rank=5000
0:36:42.244823 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:36:42.538365 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:36:43.261700 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:36:43.262151 INFO: Using score_cutoff 8.90230312614441 (fac=0.99, q=1)
0:36:43.262497 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:36:43.262588 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:36:43.262648 INFO: Updating optimization_manager: score_cutoff        : 7.115149834442138 -> 8.90230312614441
0:36:43.262708 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:43.897407 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:45.267442 INFO: === checking if optimization conditions were reached ===
0:36:45.267690 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:36:45.271069 INFO: Updating optimization_manager: rt_error            : 981.8728139951008 -> 1056.7525266874966
0:36:45.271207 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 1056.7525.
0:36:45.271281 INFO: ==============================================
0:36:45.271359 INFO: Starting optimization step 2.
0:36:45.271423 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:36:45.271511 INFO: Using rust extraction backend
0:36:45.271582 PROGRESS: Extracting batch of 1001059 precursors
0:36:46.972461 INFO: === Search parameters used ===
0:36:46.972718 INFO: rt_error       : 1056.7525266874966
0:36:46.972778 INFO: mobility_error : 0.1
0:36:46.972828 INFO: num_candidates : 3
0:36:46.972874 INFO: ms1_error      : 20
0:36:46.972918 INFO: ms2_error      : 10.0
0:36:46.972959 INFO: fwhm_rt        : 3.0
0:36:46.973000 INFO: quant_window   : 3
0:36:46.973041 INFO: ==============================================
0:37:01.118112 INFO: performing precursor FDR with 40 features
0:37:01.118241 INFO: Decoy channel: -1
0:37:01.118270 INFO: competitive: True
0:37:01.867361 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:03.269154 INFO: Estimating optimal hyperparameters - samples: 2,401,957, batch_size: 4,096, learning_rate: 1.00e-03
0:37:03.275344 INFO: Using random state 73838 for train-test-split
0:37:49.186022 INFO: Test AUC: 0.613
0:37:49.186165 INFO: Train AUC: 0.617
0:37:49.186202 INFO: AUC difference: 0.64%
0:37:50.419941 INFO: Resetting torch num_threads to 32
0:37:50.518173 PROGRESS: === Extracted 3002447 precursors and 18843471 fragments ===
0:37:50.518751 INFO: === FDR correction performed with classifier version 13 ===
0:37:50.519692 PROGRESS: ============================= Precursor FDR =============================
0:37:50.519810 PROGRESS: Total precursors accumulated: 2,005
0:37:50.519881 PROGRESS: Target precursors: 1,986 (99.05%)
0:37:50.519955 PROGRESS: Decoy precursors: 19 (0.95%)
0:37:50.520012 PROGRESS: 
0:37:50.520066 PROGRESS: Precursor Summary:
0:37:50.521700 PROGRESS: Channel   0:	 0.050 FDR: 1,986; 0.010 FDR: 1,986; 0.001 FDR: 1,205
0:37:50.521807 PROGRESS: 
0:37:50.521871 PROGRESS: Protein Summary:
0:37:50.523875 PROGRESS: Channel   0:	 0.050 FDR: 1,525; 0.010 FDR: 1,525; 0.001 FDR:   962
0:37:50.523980 PROGRESS: =========================================================================
0:37:50.578414 INFO: Target number of precursors reached.
0:37:52.550148 INFO: fragments_df: keeping 5000 of 18843471 [sum(precursor_idx_mask)=51977 sum(mass_error_mask)=18843471 stop_rank=5000
0:37:53.615209 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:37:53.866764 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:37:54.579436 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:37:54.579915 INFO: Using score_cutoff 6.8816516826152805 (fac=0.99, q=1)
0:37:54.580255 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:37:54.580347 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:37:54.580410 INFO: Updating optimization_manager: score_cutoff        : 8.90230312614441 -> 6.8816516826152805
0:37:54.580477 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:37:55.199856 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:37:56.568402 INFO: === checking if optimization conditions were reached ===
0:37:56.568676 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:37:56.571907 INFO: Updating optimization_manager: rt_error            : 1056.7525266874966 -> 1188.4930865782599
0:37:56.572055 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 1188.4931.
0:37:56.572129 INFO: ==============================================
0:37:56.572207 INFO: Starting optimization step 3.
0:37:56.572272 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:37:56.572338 INFO: Using rust extraction backend
0:37:56.572408 PROGRESS: Extracting batch of 1001059 precursors
0:37:58.295928 INFO: === Search parameters used ===
0:37:58.296191 INFO: rt_error       : 1188.4930865782599
0:37:58.296259 INFO: mobility_error : 0.1
0:37:58.296317 INFO: num_candidates : 3
0:37:58.296372 INFO: ms1_error      : 20
0:37:58.296422 INFO: ms2_error      : 10.0
0:37:58.296471 INFO: fwhm_rt        : 3.0
0:37:58.296518 INFO: quant_window   : 3
0:37:58.296563 INFO: ==============================================
0:38:12.670942 INFO: performing precursor FDR with 40 features
0:38:12.671074 INFO: Decoy channel: -1
0:38:12.671104 INFO: competitive: True
0:38:13.402114 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:14.732932 INFO: Estimating optimal hyperparameters - samples: 2,401,958, batch_size: 4,096, learning_rate: 1.00e-03
0:38:14.738048 INFO: Using random state 73838 for train-test-split
0:39:00.226605 INFO: Test AUC: 0.611
0:39:00.226741 INFO: Train AUC: 0.617
0:39:00.226777 INFO: AUC difference: 0.84%
0:39:01.459605 INFO: Resetting torch num_threads to 32
0:39:01.555472 PROGRESS: === Extracted 3002448 precursors and 18843079 fragments ===
0:39:01.555979 INFO: === FDR correction performed with classifier version 13 ===
0:39:01.556789 PROGRESS: ============================= Precursor FDR =============================
0:39:01.556896 PROGRESS: Total precursors accumulated: 1,886
0:39:01.556962 PROGRESS: Target precursors: 1,868 (99.05%)
0:39:01.557019 PROGRESS: Decoy precursors: 18 (0.95%)
0:39:01.557070 PROGRESS: 
0:39:01.557120 PROGRESS: Precursor Summary:
0:39:01.558635 PROGRESS: Channel   0:	 0.050 FDR: 1,868; 0.010 FDR: 1,868; 0.001 FDR: 1,398
0:39:01.558733 PROGRESS: 
0:39:01.558792 PROGRESS: Protein Summary:
0:39:01.560775 PROGRESS: Channel   0:	 0.050 FDR: 1,426; 0.010 FDR: 1,426; 0.001 FDR: 1,109
0:39:01.560870 PROGRESS: =========================================================================
0:39:01.616109 INFO: Target number of precursors reached.
0:39:03.551095 INFO: fragments_df: keeping 5000 of 18843079 [sum(precursor_idx_mask)=49755 sum(mass_error_mask)=18843079 stop_rank=5000
0:39:04.647938 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:04.966524 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:05.713377 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:05.713870 INFO: Using score_cutoff 9.349170832157135 (fac=0.99, q=1)
0:39:05.714286 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:05.714399 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:05.714467 INFO: Updating optimization_manager: score_cutoff        : 6.8816516826152805 -> 9.349170832157135
0:39:05.714533 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:06.329741 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:07.708862 INFO: === checking if optimization conditions were reached ===
0:39:07.709107 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:39:07.712251 INFO: Updating optimization_manager: rt_error            : 1188.4930865782599 -> 563.7278968102689
0:39:07.712395 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 563.7279.
0:39:07.712466 INFO: ==============================================
0:39:07.712538 INFO: Starting optimization step 4.
0:39:07.712600 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:39:07.712668 INFO: Using rust extraction backend
0:39:07.712728 PROGRESS: Extracting batch of 1001059 precursors
0:39:09.407252 INFO: === Search parameters used ===
0:39:09.407510 INFO: rt_error       : 563.7278968102689
0:39:09.407574 INFO: mobility_error : 0.1
0:39:09.407629 INFO: num_candidates : 3
0:39:09.407683 INFO: ms1_error      : 20
0:39:09.407730 INFO: ms2_error      : 10.0
0:39:09.407773 INFO: fwhm_rt        : 3.0
0:39:09.407816 INFO: quant_window   : 3
0:39:09.407860 INFO: ==============================================
0:39:22.255437 INFO: performing precursor FDR with 40 features
0:39:22.255564 INFO: Decoy channel: -1
0:39:22.255593 INFO: competitive: True
0:39:23.006590 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:24.368780 INFO: Estimating optimal hyperparameters - samples: 2,401,712, batch_size: 4,096, learning_rate: 1.00e-03
0:39:24.373960 INFO: Using random state 73838 for train-test-split
0:40:09.873897 INFO: Test AUC: 0.611
0:40:09.874053 INFO: Train AUC: 0.616
0:40:09.874091 INFO: AUC difference: 0.80%
0:40:11.172688 INFO: Resetting torch num_threads to 32
0:40:11.269895 PROGRESS: === Extracted 3002141 precursors and 18396831 fragments ===
0:40:11.270483 INFO: === FDR correction performed with classifier version 13 ===
0:40:11.271393 PROGRESS: ============================= Precursor FDR =============================
0:40:11.271501 PROGRESS: Total precursors accumulated: 1,900
0:40:11.271565 PROGRESS: Target precursors: 1,882 (99.05%)
0:40:11.271620 PROGRESS: Decoy precursors: 18 (0.95%)
0:40:11.271670 PROGRESS: 
0:40:11.271718 PROGRESS: Precursor Summary:
0:40:11.273297 PROGRESS: Channel   0:	 0.050 FDR: 1,882; 0.010 FDR: 1,882; 0.001 FDR: 1,323
0:40:11.273395 PROGRESS: 
0:40:11.273453 PROGRESS: Protein Summary:
0:40:11.275493 PROGRESS: Channel   0:	 0.050 FDR: 1,451; 0.010 FDR: 1,451; 0.001 FDR: 1,046
0:40:11.275595 PROGRESS: =========================================================================
0:40:11.332546 INFO: Target number of precursors reached.
0:40:13.216708 INFO: fragments_df: keeping 5000 of 18396831 [sum(precursor_idx_mask)=49667 sum(mass_error_mask)=18396831 stop_rank=5000
0:40:14.303517 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:14.583692 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:15.313461 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:15.313914 INFO: Using score_cutoff 9.159051708984375 (fac=0.99, q=1)
0:40:15.314235 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:15.314321 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:15.314402 INFO: Updating optimization_manager: score_cutoff        : 9.349170832157135 -> 9.159051708984375
0:40:15.314470 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:15.923710 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:17.331279 INFO: === checking if optimization conditions were reached ===
0:40:17.331548 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:40:17.334574 INFO: Updating optimization_manager: rt_error            : 563.7278968102689 -> 665.8478005984172
0:40:17.334689 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 665.8478.
0:40:17.334772 INFO: ==============================================
0:40:17.334863 INFO: Starting optimization step 5.
0:40:17.334930 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:40:17.335003 INFO: Using rust extraction backend
0:40:17.335067 PROGRESS: Extracting batch of 1001059 precursors
0:40:19.022497 INFO: === Search parameters used ===
0:40:19.022758 INFO: rt_error       : 665.8478005984172
0:40:19.022827 INFO: mobility_error : 0.1
0:40:19.022885 INFO: num_candidates : 3
0:40:19.022937 INFO: ms1_error      : 20
0:40:19.022987 INFO: ms2_error      : 10.0
0:40:19.023035 INFO: fwhm_rt        : 3.0
0:40:19.023083 INFO: quant_window   : 3
0:40:19.023145 INFO: ==============================================
0:40:32.186666 INFO: performing precursor FDR with 40 features
0:40:32.186791 INFO: Decoy channel: -1
0:40:32.186820 INFO: competitive: True
0:40:32.915723 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:34.236621 INFO: Estimating optimal hyperparameters - samples: 2,401,838, batch_size: 4,096, learning_rate: 1.00e-03
0:40:34.241994 INFO: Using random state 73838 for train-test-split
0:41:20.440888 INFO: Test AUC: 0.612
0:41:20.441115 INFO: Train AUC: 0.616
0:41:20.441155 INFO: AUC difference: 0.72%
0:41:21.750651 INFO: Resetting torch num_threads to 32
0:41:21.924429 PROGRESS: === Extracted 3002298 precursors and 18559264 fragments ===
0:41:21.925093 INFO: === FDR correction performed with classifier version 13 ===
0:41:21.926142 PROGRESS: ============================= Precursor FDR =============================
0:41:21.926245 PROGRESS: Total precursors accumulated: 1,889
0:41:21.926312 PROGRESS: Target precursors: 1,871 (99.05%)
0:41:21.926393 PROGRESS: Decoy precursors: 18 (0.95%)
0:41:21.926451 PROGRESS: 
0:41:21.926500 PROGRESS: Precursor Summary:
0:41:21.928013 PROGRESS: Channel   0:	 0.050 FDR: 1,871; 0.010 FDR: 1,871; 0.001 FDR: 1,359
0:41:21.928106 PROGRESS: 
0:41:21.928166 PROGRESS: Protein Summary:
0:41:21.930465 PROGRESS: Channel   0:	 0.050 FDR: 1,425; 0.010 FDR: 1,425; 0.001 FDR: 1,076
0:41:21.930573 PROGRESS: =========================================================================
0:41:22.010004 INFO: Target number of precursors reached.
0:41:24.021683 INFO: fragments_df: keeping 5000 of 18559264 [sum(precursor_idx_mask)=49421 sum(mass_error_mask)=18559264 stop_rank=5000
0:41:25.257068 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:25.527752 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:26.253489 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:26.253954 INFO: Using score_cutoff 9.162384495735168 (fac=0.99, q=1)
0:41:26.254310 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:26.254412 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:26.254478 INFO: Updating optimization_manager: score_cutoff        : 9.159051708984375 -> 9.162384495735168
0:41:26.254544 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:26.873224 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:28.273101 INFO: === checking if optimization conditions were reached ===
0:41:28.273390 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
0:41:28.276643 INFO: Updating optimization_manager: rt_error            : 665.8478005984172 -> 602.9239048762283
0:41:28.276779 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 602.9239.
0:41:28.276855 INFO: ==============================================
0:41:28.276945 INFO: Starting optimization step 6.
0:41:28.277014 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:41:28.277102 INFO: Using rust extraction backend
0:41:28.277178 PROGRESS: Extracting batch of 1001059 precursors
0:41:29.984915 INFO: === Search parameters used ===
0:41:29.985180 INFO: rt_error       : 602.9239048762283
0:41:29.985248 INFO: mobility_error : 0.1
0:41:29.985304 INFO: num_candidates : 3
0:41:29.985359 INFO: ms1_error      : 20
0:41:29.985410 INFO: ms2_error      : 10.0
0:41:29.985459 INFO: fwhm_rt        : 3.0
0:41:29.985523 INFO: quant_window   : 3
0:41:29.985571 INFO: ==============================================
0:41:43.646335 INFO: performing precursor FDR with 40 features
0:41:43.646502 INFO: Decoy channel: -1
0:41:43.646536 INFO: competitive: True
0:41:44.474443 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:46.071343 INFO: Estimating optimal hyperparameters - samples: 2,401,761, batch_size: 4,096, learning_rate: 1.00e-03
0:41:46.076549 INFO: Using random state 73838 for train-test-split
0:42:33.919438 INFO: Test AUC: 0.611
0:42:33.919705 INFO: Train AUC: 0.616
0:42:33.919745 INFO: AUC difference: 0.76%
0:42:35.194008 INFO: Resetting torch num_threads to 32
0:42:35.292975 PROGRESS: === Extracted 3002202 precursors and 18465267 fragments ===
0:42:35.293516 INFO: === FDR correction performed with classifier version 13 ===
0:42:35.294315 PROGRESS: ============================= Precursor FDR =============================
0:42:35.294426 PROGRESS: Total precursors accumulated: 1,939
0:42:35.294507 PROGRESS: Target precursors: 1,920 (99.02%)
0:42:35.294568 PROGRESS: Decoy precursors: 19 (0.98%)
0:42:35.294624 PROGRESS: 
0:42:35.294677 PROGRESS: Precursor Summary:
0:42:35.296184 PROGRESS: Channel   0:	 0.050 FDR: 1,920; 0.010 FDR: 1,920; 0.001 FDR: 1,512
0:42:35.296279 PROGRESS: 
0:42:35.296342 PROGRESS: Protein Summary:
0:42:35.298315 PROGRESS: Channel   0:	 0.050 FDR: 1,461; 0.010 FDR: 1,461; 0.001 FDR: 1,184
0:42:35.298424 PROGRESS: =========================================================================
0:42:35.353403 INFO: Target number of precursors reached.
0:42:37.308755 INFO: fragments_df: keeping 5000 of 18465267 [sum(precursor_idx_mask)=50419 sum(mass_error_mask)=18465267 stop_rank=5000
0:42:38.469107 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:42:38.764169 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:42:39.509223 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:42:39.509690 INFO: Using score_cutoff 8.897834938430787 (fac=0.99, q=1)
0:42:39.510042 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:42:39.510128 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:42:39.510189 INFO: Updating optimization_manager: score_cutoff        : 9.162384495735168 -> 8.897834938430787
0:42:39.510254 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:42:40.127424 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:42:41.532148 INFO: === checking if optimization conditions were reached ===
0:42:41.532492 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
0:42:41.535655 INFO: Updating optimization_manager: rt_error            : 602.9239048762283 -> 631.349952155061
0:42:41.535768 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 631.3500.
0:42:41.535839 INFO: ==============================================
0:42:41.535920 INFO: Starting optimization step 7.
0:42:41.535984 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:42:41.536064 INFO: Using rust extraction backend
0:42:41.536138 PROGRESS: Extracting batch of 1001059 precursors
0:42:43.238636 INFO: === Search parameters used ===
0:42:43.238917 INFO: rt_error       : 631.349952155061
0:42:43.238984 INFO: mobility_error : 0.1
0:42:43.239040 INFO: num_candidates : 3
0:42:43.239089 INFO: ms1_error      : 20
0:42:43.239135 INFO: ms2_error      : 10.0
0:42:43.239191 INFO: fwhm_rt        : 3.0
0:42:43.239237 INFO: quant_window   : 3
0:42:43.239282 INFO: ==============================================
0:42:56.658089 INFO: performing precursor FDR with 40 features
0:42:56.658280 INFO: Decoy channel: -1
0:42:56.658309 INFO: competitive: True
0:42:57.385306 INFO: Setting torch num_threads to 2 for FDR classification task
0:42:58.726764 INFO: Estimating optimal hyperparameters - samples: 2,401,819, batch_size: 4,096, learning_rate: 1.00e-03
0:42:58.731814 INFO: Using random state 73838 for train-test-split
0:43:47.195573 INFO: Test AUC: 0.611
0:43:47.195805 INFO: Train AUC: 0.617
0:43:47.195840 INFO: AUC difference: 1.05%
0:43:48.421366 INFO: Resetting torch num_threads to 32
0:43:48.520299 PROGRESS: === Extracted 3002274 precursors and 18515107 fragments ===
0:43:48.520840 INFO: === FDR correction performed with classifier version 13 ===
0:43:48.521650 PROGRESS: ============================= Precursor FDR =============================
0:43:48.521746 PROGRESS: Total precursors accumulated: 1,993
0:43:48.521812 PROGRESS: Target precursors: 1,974 (99.05%)
0:43:48.521869 PROGRESS: Decoy precursors: 19 (0.95%)
0:43:48.521921 PROGRESS: 
0:43:48.521971 PROGRESS: Precursor Summary:
0:43:48.523463 PROGRESS: Channel   0:	 0.050 FDR: 1,974; 0.010 FDR: 1,974; 0.001 FDR: 1,320
0:43:48.523572 PROGRESS: 
0:43:48.523632 PROGRESS: Protein Summary:
0:43:48.525603 PROGRESS: Channel   0:	 0.050 FDR: 1,560; 0.010 FDR: 1,560; 0.001 FDR: 1,055
0:43:48.525701 PROGRESS: =========================================================================
0:43:48.580181 INFO: Target number of precursors reached.
0:43:50.477568 INFO: fragments_df: keeping 5000 of 18515107 [sum(precursor_idx_mask)=49706 sum(mass_error_mask)=18515107 stop_rank=5000
0:43:51.649693 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:43:52.012586 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:43:52.748049 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:43:52.748509 INFO: Using score_cutoff 4.626805318450927 (fac=0.99, q=1)
0:43:52.748843 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:43:52.748924 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:43:52.748981 INFO: Updating optimization_manager: score_cutoff        : 8.897834938430787 -> 4.626805318450927
0:43:52.749041 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:43:53.359427 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:43:54.723656 INFO: === checking if optimization conditions were reached ===
0:43:54.724001 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
0:43:54.725375 INFO: Updating optimization_manager: rt_error            : 631.349952155061 -> 1056.7525266874966
0:43:54.725536 INFO: Updating optimization_manager: classifier_version  : 13 -> 16
0:43:54.725653 INFO: Updating optimization_manager: score_cutoff        : 4.626805318450927 -> 6.8816516826152805
0:43:54.725759 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:43:54.725857 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:43:54.725954 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 1056.7525 found after 8 searches.
0:43:54.726023 INFO: ==============================================
0:43:54.726109 PROGRESS: Optimization finished for rt_error.
0:43:55.976962 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:43:56.575939 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:43:58.013082 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:43:58.013415 PROGRESS: ==============================================
0:43:58.013522 PROGRESS: ms2_error      : 10.0000
0:43:58.013589 PROGRESS: rt_error       : 1056.7525
0:43:58.013641 PROGRESS: ==============================================
0:43:58.031794 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:04.603658 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:30.237306 INFO: Using rust extraction backend
0:44:30.237866 PROGRESS: Extracting batch of 10770831 precursors
0:44:53.288466 INFO: === Search parameters used ===
0:44:53.289219 INFO: rt_error       : 1056.7525266874966
0:44:53.289297 INFO: mobility_error : 0.1
0:44:53.289360 INFO: num_candidates : 3
0:44:53.289422 INFO: ms1_error      : 20
0:44:53.289484 INFO: ms2_error      : 10.0
0:44:53.289545 INFO: fwhm_rt        : 3.0
0:44:53.289603 INFO: quant_window   : 3
0:44:53.289654 INFO: ==============================================
0:45:59.820060 INFO: Removed 4124310 precursors with score below cutoff 6.8816516826152805
0:46:28.046336 INFO: performing precursor FDR with 40 features
0:46:28.046574 INFO: Decoy channel: -1
0:46:28.046618 INFO: competitive: True
0:46:31.123179 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:42.981701 INFO: Estimating optimal hyperparameters - samples: 22,550,541, batch_size: 4,096, learning_rate: 1.00e-03
0:46:43.051308 INFO: Using random state 701056 for train-test-split
0:53:52.503791 INFO: Test AUC: 0.615
0:53:52.504084 INFO: Train AUC: 0.615
0:53:52.504132 INFO: AUC difference: 0.10%
0:53:59.709260 INFO: Resetting torch num_threads to 32
0:54:01.569371 PROGRESS: ============================= Precursor FDR =============================
0:54:01.569877 PROGRESS: Total precursors accumulated: 20,887
0:54:01.569967 PROGRESS: Target precursors: 20,681 (99.01%)
0:54:01.570030 PROGRESS: Decoy precursors: 206 (0.99%)
0:54:01.570086 PROGRESS: 
0:54:01.570138 PROGRESS: Precursor Summary:
0:54:01.574891 PROGRESS: Channel   0:	 0.050 FDR: 20,681; 0.010 FDR: 20,681; 0.001 FDR: 11,361
0:54:01.575014 PROGRESS: 
0:54:01.575079 PROGRESS: Protein Summary:
0:54:01.582774 PROGRESS: Channel   0:	 0.050 FDR: 6,704; 0.010 FDR: 6,704; 0.001 FDR: 4,226
0:54:01.582912 PROGRESS: =========================================================================
0:54:01.720240 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1/psm.parquet
0:54:01.784653 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1/frag.parquet
0:54:01.862390 INFO: Finished workflow for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1
0:54:02.336027 PROGRESS: Loading raw file 2/6: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2 
0:54:02.336175 INFO: Quantification results path: /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant
0:54:02.336265 INFO: Creating folder /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2/figures
0:54:02.336458 INFO: Initializing TimingManager
0:54:02.336937 INFO: Initializing RawFileManager
0:54:09.308401 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
0:54:09.309562 INFO: Determining DIA cycle
0:54:09.322039 INFO: Found cycle with start 0.00 min and length 20.
0:54:09.380075 INFO: RT (min)            : 0.0 - 23.9
0:54:09.380162 INFO: RT duration (sec)   : 1433.9
0:54:09.380193 INFO: RT duration (min)   : 23.9
0:54:09.380216 INFO: Cycle len (scans)   : 20
0:54:09.380238 INFO: Cycle len (sec)     : 1.02
0:54:09.380260 INFO: Number of cycles    : 1409
0:54:09.380283 INFO: MS2 range (m/z)     : 400.4 - 800.6
0:54:09.380312 INFO: Creating DIA data object took: 7.04326319694519
0:54:10.129629 INFO: Creating DIA data NG object took: 0.7491939067840576
0:54:11.926096 INFO: Initializing CalibrationManager
0:54:11.926470 INFO: Setting up calibration estimators ..
0:54:11.926550 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:54:11.926651 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'}' ..
0:54:11.926775 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:54:11.926833 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:54:11.926904 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}}' ..
0:54:11.926977 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:54:11.927029 INFO: Done setting up calibration estimators.
0:54:11.927142 INFO: Initializing OptimizationManager
0:54:11.927278 INFO: initial parameter: ms1_error = 20
0:54:11.927338 INFO: initial parameter: ms2_error = 20
0:54:11.927391 INFO: initial parameter: rt_error = 717.0044555664062
0:54:11.927445 INFO: initial parameter: mobility_error = 0.1
0:54:11.927493 INFO: initial parameter: num_candidates = 1
0:54:11.927536 INFO: initial parameter: fwhm_rt = 5
0:54:11.927583 INFO: initial parameter: fwhm_mobility = 0.01
0:54:11.927626 INFO: initial parameter: score_cutoff = 0
0:54:11.927668 INFO: initial parameter: classifier_version = -1
0:54:11.927742 PROGRESS: Initializing workflow 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2
0:54:11.928039 INFO: FDRManager: loading saved state not requested, will be initialized.
0:54:11.928083 INFO: Initializing FDRManager
0:54:11.928126 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
0:54:13.320742 PROGRESS: Initializing spectral library: 5,415,345 target precursors potentially observable (2,595,411 removed)
0:54:14.159635 INFO: Updating optimization_manager: ms2_error           : 20 -> 20
0:54:14.160064 INFO: Updating optimization_manager: rt_error            : 717.0044555664062 -> 717.0044555664062
0:54:14.160168 PROGRESS: Starting initial search for precursors.
0:54:14.160263 INFO: Starting optimization step 0.
0:54:14.160326 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:54:14.160394 INFO: Using rust extraction backend
0:54:14.160458 PROGRESS: Extracting batch of 1960 precursors
0:54:14.165143 INFO: === Search parameters used ===
0:54:14.165241 INFO: rt_error       : 717.0044555664062
0:54:14.165291 INFO: mobility_error : 0.1
0:54:14.165336 INFO: num_candidates : 1
0:54:14.165379 INFO: ms1_error      : 20
0:54:14.165421 INFO: ms2_error      : 20
0:54:14.165462 INFO: fwhm_rt        : 5
0:54:14.165504 INFO: quant_window   : 3
0:54:14.165545 INFO: ==============================================
0:54:14.199197 INFO: performing precursor FDR with 40 features
0:54:14.199277 INFO: Decoy channel: -1
0:54:14.199304 INFO: competitive: True
0:54:14.200673 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:14.202824 INFO: Estimating optimal hyperparameters - samples: 1,565, batch_size: 128, learning_rate: 1.77e-04
0:54:14.203667 INFO: Using random state 999549 for train-test-split
0:54:14.356223 INFO: Test AUC: 0.516
0:54:14.356303 INFO: Train AUC: 0.552
0:54:14.356332 INFO: AUC difference: 6.52%
0:54:14.356354 WARNING: AUC difference > 5%. This may indicate overfitting.
0:54:14.605853 INFO: Resetting torch num_threads to 32
0:54:14.607415 PROGRESS: === Extracted 1957 precursors and 11486 fragments ===
0:54:14.607776 INFO: === FDR correction performed with classifier version -1 ===
0:54:14.608265 PROGRESS: ============================= Precursor FDR =============================
0:54:14.608356 PROGRESS: Total precursors accumulated: 13
0:54:14.608418 PROGRESS: Target precursors: 13 (100.00%)
0:54:14.608471 PROGRESS: Decoy precursors: 0 (0.00%)
0:54:14.608517 PROGRESS: 
0:54:14.608563 PROGRESS: Precursor Summary:
0:54:14.609608 PROGRESS: Channel   0:	 0.050 FDR:    13; 0.010 FDR:    13; 0.001 FDR:    13
0:54:14.609692 PROGRESS: 
0:54:14.609751 PROGRESS: Protein Summary:
0:54:14.610909 PROGRESS: Channel   0:	 0.050 FDR:    13; 0.010 FDR:    13; 0.001 FDR:    13
0:54:14.611001 PROGRESS: =========================================================================
0:54:14.611199 INFO: Target number of precursors not reached yet.
0:54:14.688785 INFO: Starting optimization step 1.
0:54:14.688981 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:54:14.689077 INFO: Using rust extraction backend
0:54:14.689141 PROGRESS: Extracting batch of 3921 precursors
0:54:14.697587 INFO: === Search parameters used ===
0:54:14.697736 INFO: rt_error       : 717.0044555664062
0:54:14.697790 INFO: mobility_error : 0.1
0:54:14.697836 INFO: num_candidates : 1
0:54:14.697880 INFO: ms1_error      : 20
0:54:14.697922 INFO: ms2_error      : 20
0:54:14.697965 INFO: fwhm_rt        : 5
0:54:14.698011 INFO: quant_window   : 3
0:54:14.698053 INFO: ==============================================
0:54:14.758390 INFO: performing precursor FDR with 40 features
0:54:14.758487 INFO: Decoy channel: -1
0:54:14.758513 INFO: competitive: True
0:54:14.764041 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:14.766604 INFO: Estimating optimal hyperparameters - samples: 4,698, batch_size: 128, learning_rate: 1.77e-04
0:54:14.766695 INFO: Using random state 562829 for train-test-split
0:54:15.227633 INFO: Test AUC: 0.551
0:54:15.227735 INFO: Train AUC: 0.574
0:54:15.227765 INFO: AUC difference: 4.00%
0:54:15.478828 INFO: Resetting torch num_threads to 32
0:54:15.481683 PROGRESS: === Extracted 5873 precursors and 34675 fragments ===
0:54:15.482054 INFO: === FDR correction performed with classifier version -1 ===
0:54:15.482581 PROGRESS: ============================= Precursor FDR =============================
0:54:15.482675 PROGRESS: Total precursors accumulated: 7
0:54:15.482736 PROGRESS: Target precursors: 7 (100.00%)
0:54:15.482792 PROGRESS: Decoy precursors: 0 (0.00%)
0:54:15.482839 PROGRESS: 
0:54:15.482884 PROGRESS: Precursor Summary:
0:54:15.483936 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
0:54:15.484022 PROGRESS: 
0:54:15.484077 PROGRESS: Protein Summary:
0:54:15.485229 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
0:54:15.485316 PROGRESS: =========================================================================
0:54:15.485567 INFO: Target number of precursors not reached yet.
0:54:15.567413 INFO: Starting optimization step 2.
0:54:15.567624 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:54:15.567705 INFO: Using rust extraction backend
0:54:15.567767 PROGRESS: Extracting batch of 7852 precursors
0:54:15.582912 INFO: === Search parameters used ===
0:54:15.583069 INFO: rt_error       : 717.0044555664062
0:54:15.583135 INFO: mobility_error : 0.1
0:54:15.583185 INFO: num_candidates : 1
0:54:15.583231 INFO: ms1_error      : 20
0:54:15.583275 INFO: ms2_error      : 20
0:54:15.583317 INFO: fwhm_rt        : 5
0:54:15.583358 INFO: quant_window   : 3
0:54:15.583398 INFO: ==============================================
0:54:15.697327 INFO: performing precursor FDR with 40 features
0:54:15.697431 INFO: Decoy channel: -1
0:54:15.697457 INFO: competitive: True
0:54:15.704074 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:15.708715 INFO: Estimating optimal hyperparameters - samples: 10,973, batch_size: 128, learning_rate: 1.77e-04
0:54:15.708843 INFO: Using random state 197388 for train-test-split
0:54:16.766035 INFO: Test AUC: 0.551
0:54:16.766142 INFO: Train AUC: 0.581
0:54:16.766172 INFO: AUC difference: 5.21%
0:54:16.766193 WARNING: AUC difference > 5%. This may indicate overfitting.
0:54:17.020318 INFO: Resetting torch num_threads to 32
0:54:17.024430 PROGRESS: === Extracted 13717 precursors and 81169 fragments ===
0:54:17.024838 INFO: === FDR correction performed with classifier version -1 ===
0:54:17.025393 PROGRESS: ============================= Precursor FDR =============================
0:54:17.025490 PROGRESS: Total precursors accumulated: 6
0:54:17.025563 PROGRESS: Target precursors: 6 (100.00%)
0:54:17.025628 PROGRESS: Decoy precursors: 0 (0.00%)
0:54:17.025690 PROGRESS: 
0:54:17.025745 PROGRESS: Precursor Summary:
0:54:17.026810 PROGRESS: Channel   0:	 0.050 FDR:     6; 0.010 FDR:     6; 0.001 FDR:     6
0:54:17.026908 PROGRESS: 
0:54:17.026979 PROGRESS: Protein Summary:
0:54:17.028124 PROGRESS: Channel   0:	 0.050 FDR:     6; 0.010 FDR:     6; 0.001 FDR:     6
0:54:17.028216 PROGRESS: =========================================================================
0:54:17.028549 INFO: Target number of precursors not reached yet.
0:54:17.120731 INFO: Starting optimization step 3.
0:54:17.120958 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:54:17.121054 INFO: Using rust extraction backend
0:54:17.121122 PROGRESS: Extracting batch of 15661 precursors
0:54:17.149826 INFO: === Search parameters used ===
0:54:17.150001 INFO: rt_error       : 717.0044555664062
0:54:17.150059 INFO: mobility_error : 0.1
0:54:17.150110 INFO: num_candidates : 1
0:54:17.150156 INFO: ms1_error      : 20
0:54:17.150215 INFO: ms2_error      : 20
0:54:17.150262 INFO: fwhm_rt        : 5
0:54:17.150307 INFO: quant_window   : 3
0:54:17.150359 INFO: ==============================================
0:54:17.335816 INFO: performing precursor FDR with 40 features
0:54:17.335927 INFO: Decoy channel: -1
0:54:17.335955 INFO: competitive: True
0:54:17.348228 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:17.354895 INFO: Estimating optimal hyperparameters - samples: 23,492, batch_size: 128, learning_rate: 1.77e-04
0:54:17.355061 INFO: Using random state 627300 for train-test-split
0:54:19.709261 INFO: Test AUC: 0.556
0:54:19.709377 INFO: Train AUC: 0.601
0:54:19.709408 INFO: AUC difference: 7.39%
0:54:19.709431 WARNING: AUC difference > 5%. This may indicate overfitting.
0:54:19.967132 INFO: Resetting torch num_threads to 32
0:54:19.973696 PROGRESS: === Extracted 29365 precursors and 173642 fragments ===
0:54:19.974151 INFO: === FDR correction performed with classifier version -1 ===
0:54:19.974696 PROGRESS: ============================= Precursor FDR =============================
0:54:19.974792 PROGRESS: Total precursors accumulated: 29
0:54:19.974857 PROGRESS: Target precursors: 29 (100.00%)
0:54:19.974913 PROGRESS: Decoy precursors: 0 (0.00%)
0:54:19.974964 PROGRESS: 
0:54:19.975012 PROGRESS: Precursor Summary:
0:54:19.976067 PROGRESS: Channel   0:	 0.050 FDR:    29; 0.010 FDR:    29; 0.001 FDR:    29
0:54:19.976153 PROGRESS: 
0:54:19.976214 PROGRESS: Protein Summary:
0:54:19.977390 PROGRESS: Channel   0:	 0.050 FDR:    29; 0.010 FDR:    29; 0.001 FDR:    29
0:54:19.977482 PROGRESS: =========================================================================
0:54:19.977971 INFO: Target number of precursors not reached yet.
0:54:20.089237 INFO: Starting optimization step 4.
0:54:20.089476 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:54:20.089566 INFO: Using rust extraction backend
0:54:20.089633 PROGRESS: Extracting batch of 31339 precursors
0:54:20.145482 INFO: === Search parameters used ===
0:54:20.145727 INFO: rt_error       : 717.0044555664062
0:54:20.145787 INFO: mobility_error : 0.1
0:54:20.145849 INFO: num_candidates : 1
0:54:20.145895 INFO: ms1_error      : 20
0:54:20.145942 INFO: ms2_error      : 20
0:54:20.145985 INFO: fwhm_rt        : 5
0:54:20.146028 INFO: quant_window   : 3
0:54:20.146071 INFO: ==============================================
0:54:20.467132 INFO: performing precursor FDR with 40 features
0:54:20.467243 INFO: Decoy channel: -1
0:54:20.467269 INFO: competitive: True
0:54:20.489125 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:20.506111 INFO: Estimating optimal hyperparameters - samples: 48,539, batch_size: 198, learning_rate: 2.20e-04
0:54:20.506393 INFO: Using random state 425283 for train-test-split
0:54:24.037023 INFO: Test AUC: 0.575
0:54:24.037135 INFO: Train AUC: 0.605
0:54:24.037168 INFO: AUC difference: 4.93%
0:54:24.305052 INFO: Resetting torch num_threads to 32
0:54:24.317758 PROGRESS: === Extracted 60674 precursors and 358690 fragments ===
0:54:24.318333 INFO: === FDR correction performed with classifier version -1 ===
0:54:24.318959 PROGRESS: ============================= Precursor FDR =============================
0:54:24.319061 PROGRESS: Total precursors accumulated: 32
0:54:24.319134 PROGRESS: Target precursors: 32 (100.00%)
0:54:24.319195 PROGRESS: Decoy precursors: 0 (0.00%)
0:54:24.319254 PROGRESS: 
0:54:24.319315 PROGRESS: Precursor Summary:
0:54:24.320381 PROGRESS: Channel   0:	 0.050 FDR:    32; 0.010 FDR:    32; 0.001 FDR:    32
0:54:24.320492 PROGRESS: 
0:54:24.320556 PROGRESS: Protein Summary:
0:54:24.321741 PROGRESS: Channel   0:	 0.050 FDR:    32; 0.010 FDR:    32; 0.001 FDR:    32
0:54:24.321844 PROGRESS: =========================================================================
0:54:24.322810 INFO: Target number of precursors not reached yet.
0:54:24.490264 INFO: Starting optimization step 5.
0:54:24.490520 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:54:24.490620 INFO: Using rust extraction backend
0:54:24.490690 PROGRESS: Extracting batch of 62709 precursors
0:54:24.600460 INFO: === Search parameters used ===
0:54:24.600712 INFO: rt_error       : 717.0044555664062
0:54:24.600783 INFO: mobility_error : 0.1
0:54:24.600846 INFO: num_candidates : 1
0:54:24.600898 INFO: ms1_error      : 20
0:54:24.600947 INFO: ms2_error      : 20
0:54:24.600996 INFO: fwhm_rt        : 5
0:54:24.601043 INFO: quant_window   : 3
0:54:24.601090 INFO: ==============================================
0:54:25.178422 INFO: performing precursor FDR with 40 features
0:54:25.178537 INFO: Decoy channel: -1
0:54:25.178564 INFO: competitive: True
0:54:25.225982 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:25.255988 INFO: Estimating optimal hyperparameters - samples: 98,659, batch_size: 404, learning_rate: 3.14e-04
0:54:25.256249 INFO: Using random state 375067 for train-test-split
0:54:29.697755 INFO: Test AUC: 0.577
0:54:29.697866 INFO: Train AUC: 0.605
0:54:29.697898 INFO: AUC difference: 4.64%
0:54:29.982009 INFO: Resetting torch num_threads to 32
0:54:30.004545 PROGRESS: === Extracted 123324 precursors and 729945 fragments ===
0:54:30.005162 INFO: === FDR correction performed with classifier version -1 ===
0:54:30.005795 PROGRESS: ============================= Precursor FDR =============================
0:54:30.005893 PROGRESS: Total precursors accumulated: 51
0:54:30.005968 PROGRESS: Target precursors: 51 (100.00%)
0:54:30.006029 PROGRESS: Decoy precursors: 0 (0.00%)
0:54:30.006084 PROGRESS: 
0:54:30.006150 PROGRESS: Precursor Summary:
0:54:30.007249 PROGRESS: Channel   0:	 0.050 FDR:    51; 0.010 FDR:    51; 0.001 FDR:    51
0:54:30.007352 PROGRESS: 
0:54:30.007416 PROGRESS: Protein Summary:
0:54:30.008711 PROGRESS: Channel   0:	 0.050 FDR:    51; 0.010 FDR:    51; 0.001 FDR:    51
0:54:30.008808 PROGRESS: =========================================================================
0:54:30.011138 INFO: Target number of precursors not reached yet.
0:54:30.256573 INFO: Starting optimization step 6.
0:54:30.256833 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:54:30.256922 INFO: Using rust extraction backend
0:54:30.256991 PROGRESS: Extracting batch of 125408 precursors
0:54:30.473758 INFO: === Search parameters used ===
0:54:30.474015 INFO: rt_error       : 717.0044555664062
0:54:30.474104 INFO: mobility_error : 0.1
0:54:30.474167 INFO: num_candidates : 1
0:54:30.474218 INFO: ms1_error      : 20
0:54:30.474266 INFO: ms2_error      : 20
0:54:30.474314 INFO: fwhm_rt        : 5
0:54:30.474375 INFO: quant_window   : 3
0:54:30.474431 INFO: ==============================================
0:54:31.597313 INFO: performing precursor FDR with 40 features
0:54:31.597439 INFO: Decoy channel: -1
0:54:31.597469 INFO: competitive: True
0:54:31.702533 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:31.783089 INFO: Estimating optimal hyperparameters - samples: 198,905, batch_size: 814, learning_rate: 4.46e-04
0:54:31.783489 INFO: Using random state 525844 for train-test-split
0:54:38.056355 INFO: Test AUC: 0.580
0:54:38.056476 INFO: Train AUC: 0.603
0:54:38.056510 INFO: AUC difference: 3.82%
0:54:38.390539 INFO: Resetting torch num_threads to 32
0:54:38.466737 PROGRESS: === Extracted 248632 precursors and 1471920 fragments ===
0:54:38.467390 INFO: === FDR correction performed with classifier version -1 ===
0:54:38.467983 PROGRESS: ============================= Precursor FDR =============================
0:54:38.468076 PROGRESS: Total precursors accumulated: 249
0:54:38.468142 PROGRESS: Target precursors: 247 (99.20%)
0:54:38.468206 PROGRESS: Decoy precursors: 2 (0.80%)
0:54:38.468261 PROGRESS: 
0:54:38.468309 PROGRESS: Precursor Summary:
0:54:38.469329 PROGRESS: Channel   0:	 0.050 FDR:   247; 0.010 FDR:   247; 0.001 FDR:   231
0:54:38.469424 PROGRESS: 
0:54:38.469481 PROGRESS: Protein Summary:
0:54:38.470662 PROGRESS: Channel   0:	 0.050 FDR:   231; 0.010 FDR:   231; 0.001 FDR:   215
0:54:38.470755 PROGRESS: =========================================================================
0:54:38.474566 INFO: Target number of precursors not reached yet.
0:54:38.984785 INFO: Starting optimization step 7.
0:54:38.985049 PROGRESS: === Extracting elution groups 127000 to 255000 ===
0:54:38.985137 INFO: Using rust extraction backend
0:54:38.985202 PROGRESS: Extracting batch of 250773 precursors
0:54:39.422426 INFO: === Search parameters used ===
0:54:39.422711 INFO: rt_error       : 717.0044555664062
0:54:39.422782 INFO: mobility_error : 0.1
0:54:39.422842 INFO: num_candidates : 1
0:54:39.422891 INFO: ms1_error      : 20
0:54:39.422949 INFO: ms2_error      : 20
0:54:39.422997 INFO: fwhm_rt        : 5
0:54:39.423040 INFO: quant_window   : 3
0:54:39.423081 INFO: ==============================================
0:54:41.718916 INFO: performing precursor FDR with 40 features
0:54:41.719051 INFO: Decoy channel: -1
0:54:41.719078 INFO: competitive: True
0:54:41.903850 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:42.085780 INFO: Estimating optimal hyperparameters - samples: 399,352, batch_size: 1,635, learning_rate: 6.32e-04
0:54:42.086424 INFO: Using random state 701809 for train-test-split
0:54:51.765995 INFO: Test AUC: 0.586
0:54:51.766118 INFO: Train AUC: 0.604
0:54:51.766151 INFO: AUC difference: 2.88%
0:54:52.165678 INFO: Resetting torch num_threads to 32
0:54:52.247236 PROGRESS: === Extracted 499191 precursors and 2954746 fragments ===
0:54:52.247908 INFO: === FDR correction performed with classifier version -1 ===
0:54:52.248577 PROGRESS: ============================= Precursor FDR =============================
0:54:52.248677 PROGRESS: Total precursors accumulated: 539
0:54:52.248743 PROGRESS: Target precursors: 534 (99.07%)
0:54:52.248803 PROGRESS: Decoy precursors: 5 (0.93%)
0:54:52.248858 PROGRESS: 
0:54:52.248907 PROGRESS: Precursor Summary:
0:54:52.250035 PROGRESS: Channel   0:	 0.050 FDR:   534; 0.010 FDR:   534; 0.001 FDR:   331
0:54:52.250142 PROGRESS: 
0:54:52.250207 PROGRESS: Protein Summary:
0:54:52.251564 PROGRESS: Channel   0:	 0.050 FDR:   458; 0.010 FDR:   458; 0.001 FDR:   292
0:54:52.251661 PROGRESS: =========================================================================
0:54:52.258227 INFO: Target number of precursors not reached yet.
0:54:52.953788 INFO: Starting optimization step 8.
0:54:52.954040 PROGRESS: === Extracting elution groups 255000 to 511000 ===
0:54:52.954136 INFO: Using rust extraction backend
0:54:52.954217 PROGRESS: Extracting batch of 501436 precursors
0:54:53.815275 INFO: === Search parameters used ===
0:54:53.815555 INFO: rt_error       : 717.0044555664062
0:54:53.815641 INFO: mobility_error : 0.1
0:54:53.815717 INFO: num_candidates : 1
0:54:53.815809 INFO: ms1_error      : 20
0:54:53.815878 INFO: ms2_error      : 20
0:54:53.815944 INFO: fwhm_rt        : 5
0:54:53.816011 INFO: quant_window   : 3
0:54:53.816077 INFO: ==============================================
0:54:58.041695 INFO: performing precursor FDR with 40 features
0:54:58.041814 INFO: Decoy channel: -1
0:54:58.041841 INFO: competitive: True
0:54:58.445407 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:58.872611 INFO: Estimating optimal hyperparameters - samples: 800,116, batch_size: 3,277, learning_rate: 8.94e-04
0:54:58.873924 INFO: Using random state 197096 for train-test-split
0:55:15.528256 INFO: Test AUC: 0.595
0:55:15.528407 INFO: Train AUC: 0.604
0:55:15.528442 INFO: AUC difference: 1.51%
0:55:16.104891 INFO: Resetting torch num_threads to 32
0:55:16.298855 PROGRESS: === Extracted 1000146 precursors and 5925911 fragments ===
0:55:16.299520 INFO: === FDR correction performed with classifier version -1 ===
0:55:16.300349 PROGRESS: ============================= Precursor FDR =============================
0:55:16.300448 PROGRESS: Total precursors accumulated: 1,264
0:55:16.300525 PROGRESS: Target precursors: 1,252 (99.05%)
0:55:16.300592 PROGRESS: Decoy precursors: 12 (0.95%)
0:55:16.300653 PROGRESS: 
0:55:16.300710 PROGRESS: Precursor Summary:
0:55:16.302023 PROGRESS: Channel   0:	 0.050 FDR: 1,252; 0.010 FDR: 1,252; 0.001 FDR:   705
0:55:16.302120 PROGRESS: 
0:55:16.302182 PROGRESS: Protein Summary:
0:55:16.303868 PROGRESS: Channel   0:	 0.050 FDR:   999; 0.010 FDR:   999; 0.001 FDR:   589
0:55:16.303975 PROGRESS: =========================================================================
0:55:16.316696 INFO: Target number of precursors reached.
0:55:16.990039 INFO: fragments_df: keeping 5000 of 5925911 [sum(precursor_idx_mask)=13773 sum(mass_error_mask)=5925911 stop_rank=5000
0:55:18.048043 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:55:18.270691 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:55:18.999675 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:55:19.000115 INFO: Using score_cutoff 9.683880602645875 (fac=0.99, q=1)
0:55:19.000440 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:55:19.000525 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:55:19.000586 INFO: Updating optimization_manager: score_cutoff        : 0 -> 9.683880602645875
0:55:19.000656 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:55:19.615513 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:55:21.021620 INFO: Updating optimization_manager: classifier_version  : -1 -> 8
0:55:21.021857 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:55:21.021979 INFO: Starting optimization step 9.
0:55:21.022059 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:55:21.022140 INFO: Using rust extraction backend
0:55:21.022212 PROGRESS: Extracting batch of 1001059 precursors
0:55:22.717142 INFO: === Search parameters used ===
0:55:22.717438 INFO: rt_error       : 717.0044555664062
0:55:22.717509 INFO: mobility_error : 0.1
0:55:22.717566 INFO: num_candidates : 3
0:55:22.717619 INFO: ms1_error      : 20
0:55:22.717670 INFO: ms2_error      : 20
0:55:22.717721 INFO: fwhm_rt        : 3.0
0:55:22.717780 INFO: quant_window   : 3
0:55:22.717828 INFO: ==============================================
0:55:36.995973 INFO: performing precursor FDR with 40 features
0:55:36.996100 INFO: Decoy channel: -1
0:55:36.996130 INFO: competitive: True
0:55:37.828138 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:39.134473 INFO: Estimating optimal hyperparameters - samples: 2,400,635, batch_size: 4,096, learning_rate: 1.00e-03
0:55:39.139144 INFO: Using random state 472655 for train-test-split
0:56:23.482974 INFO: Test AUC: 0.600
0:56:23.483139 INFO: Train AUC: 0.606
0:56:23.483175 INFO: AUC difference: 0.93%
0:56:24.695512 INFO: Resetting torch num_threads to 32
0:56:24.808960 PROGRESS: === Extracted 3000794 precursors and 17806947 fragments ===
0:56:24.809472 INFO: === FDR correction performed with classifier version 8 ===
0:56:24.810322 PROGRESS: ============================= Precursor FDR =============================
0:56:24.810462 PROGRESS: Total precursors accumulated: 1,394
0:56:24.810535 PROGRESS: Target precursors: 1,381 (99.07%)
0:56:24.810604 PROGRESS: Decoy precursors: 13 (0.93%)
0:56:24.810661 PROGRESS: 
0:56:24.810722 PROGRESS: Precursor Summary:
0:56:24.812120 PROGRESS: Channel   0:	 0.050 FDR: 1,381; 0.010 FDR: 1,381; 0.001 FDR:   670
0:56:24.812224 PROGRESS: 
0:56:24.812291 PROGRESS: Protein Summary:
0:56:24.814021 PROGRESS: Channel   0:	 0.050 FDR: 1,114; 0.010 FDR: 1,114; 0.001 FDR:   567
0:56:24.814126 PROGRESS: =========================================================================
0:56:24.871298 INFO: Target number of precursors reached.
0:56:26.755946 INFO: fragments_df: keeping 5000 of 17806947 [sum(precursor_idx_mask)=35096 sum(mass_error_mask)=17806947 stop_rank=5000
0:56:28.094212 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:56:28.337486 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:56:29.053095 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:56:29.053538 INFO: Using score_cutoff 6.936412582397461 (fac=0.99, q=1)
0:56:29.053861 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:56:29.053949 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:56:29.054017 INFO: Updating optimization_manager: score_cutoff        : 9.683880602645875 -> 6.936412582397461
0:56:29.054082 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:56:29.662282 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:56:31.096020 INFO: === checking if optimization conditions were reached ===
0:56:31.098457 INFO: Updating optimization_manager: ms2_error           : 20 -> 10.0
0:56:31.098626 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:56:31.098706 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:56:31.098782 INFO: ==============================================
0:56:31.098868 INFO: Starting optimization step 10.
0:56:31.098945 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:56:31.099031 INFO: Using rust extraction backend
0:56:31.099105 PROGRESS: Extracting batch of 1001059 precursors
0:56:32.789892 INFO: === Search parameters used ===
0:56:32.790336 INFO: rt_error       : 717.0044555664062
0:56:32.790439 INFO: mobility_error : 0.1
0:56:32.790512 INFO: num_candidates : 3
0:56:32.790565 INFO: ms1_error      : 20
0:56:32.790614 INFO: ms2_error      : 10.0
0:56:32.790666 INFO: fwhm_rt        : 3.0
0:56:32.790717 INFO: quant_window   : 3
0:56:32.790764 INFO: ==============================================
0:56:46.228892 INFO: performing precursor FDR with 40 features
0:56:46.229044 INFO: Decoy channel: -1
0:56:46.229073 INFO: competitive: True
0:56:46.963401 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:48.226073 INFO: Estimating optimal hyperparameters - samples: 2,402,130, batch_size: 4,096, learning_rate: 1.00e-03
0:56:48.231202 INFO: Using random state 140036 for train-test-split
0:57:33.486380 INFO: Test AUC: 0.609
0:57:33.486602 INFO: Train AUC: 0.612
0:57:33.486644 INFO: AUC difference: 0.52%
0:57:34.738304 INFO: Resetting torch num_threads to 32
0:57:34.833090 PROGRESS: === Extracted 3002663 precursors and 19573191 fragments ===
0:57:34.833658 INFO: === FDR correction performed with classifier version 9 ===
0:57:34.834538 PROGRESS: ============================= Precursor FDR =============================
0:57:34.834665 PROGRESS: Total precursors accumulated: 1,846
0:57:34.834748 PROGRESS: Target precursors: 1,828 (99.02%)
0:57:34.834823 PROGRESS: Decoy precursors: 18 (0.98%)
0:57:34.834882 PROGRESS: 
0:57:34.834937 PROGRESS: Precursor Summary:
0:57:34.836473 PROGRESS: Channel   0:	 0.050 FDR: 1,828; 0.010 FDR: 1,828; 0.001 FDR: 1,122
0:57:34.836579 PROGRESS: 
0:57:34.836649 PROGRESS: Protein Summary:
0:57:34.838605 PROGRESS: Channel   0:	 0.050 FDR: 1,442; 0.010 FDR: 1,442; 0.001 FDR:   919
0:57:34.838723 PROGRESS: =========================================================================
0:57:34.894052 INFO: Target number of precursors reached.
0:57:36.917550 INFO: fragments_df: keeping 5000 of 19573191 [sum(precursor_idx_mask)=48012 sum(mass_error_mask)=19573191 stop_rank=5000
0:57:38.257993 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:57:38.545604 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:57:39.270491 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:57:39.270988 INFO: Using score_cutoff 5.032026190853119 (fac=0.99, q=1)
0:57:39.271349 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:57:39.271446 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:57:39.271509 INFO: Updating optimization_manager: score_cutoff        : 6.936412582397461 -> 5.032026190853119
0:57:39.271592 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:57:39.878920 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:57:41.208739 INFO: === checking if optimization conditions were reached ===
0:57:41.211057 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:57:41.211222 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:57:41.211308 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:57:41.211382 INFO: ==============================================
0:57:41.211467 INFO: Starting optimization step 11.
0:57:41.211553 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:57:41.211655 INFO: Using rust extraction backend
0:57:41.211737 PROGRESS: Extracting batch of 1001059 precursors
0:57:42.897091 INFO: === Search parameters used ===
0:57:42.897355 INFO: rt_error       : 717.0044555664062
0:57:42.897418 INFO: mobility_error : 0.1
0:57:42.897482 INFO: num_candidates : 3
0:57:42.897542 INFO: ms1_error      : 20
0:57:42.897592 INFO: ms2_error      : 10.0
0:57:42.897639 INFO: fwhm_rt        : 3.0
0:57:42.897685 INFO: quant_window   : 3
0:57:42.897730 INFO: ==============================================
0:57:56.615294 INFO: performing precursor FDR with 40 features
0:57:56.615547 INFO: Decoy channel: -1
0:57:56.615579 INFO: competitive: True
0:57:57.357452 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:58.663265 INFO: Estimating optimal hyperparameters - samples: 2,402,171, batch_size: 4,096, learning_rate: 1.00e-03
0:57:58.668078 INFO: Using random state 768970 for train-test-split
0:58:45.457986 INFO: Test AUC: 0.610
0:58:45.458222 INFO: Train AUC: 0.614
0:58:45.458260 INFO: AUC difference: 0.58%
0:58:46.675634 INFO: Resetting torch num_threads to 32
0:58:46.777934 PROGRESS: === Extracted 3002714 precursors and 19674302 fragments ===
0:58:46.778518 INFO: === FDR correction performed with classifier version 10 ===
0:58:46.779398 PROGRESS: ============================= Precursor FDR =============================
0:58:46.779515 PROGRESS: Total precursors accumulated: 1,965
0:58:46.779589 PROGRESS: Target precursors: 1,946 (99.03%)
0:58:46.779659 PROGRESS: Decoy precursors: 19 (0.97%)
0:58:46.779720 PROGRESS: 
0:58:46.779781 PROGRESS: Precursor Summary:
0:58:46.781349 PROGRESS: Channel   0:	 0.050 FDR: 1,946; 0.010 FDR: 1,946; 0.001 FDR: 1,041
0:58:46.781454 PROGRESS: 
0:58:46.781528 PROGRESS: Protein Summary:
0:58:46.783545 PROGRESS: Channel   0:	 0.050 FDR: 1,459; 0.010 FDR: 1,459; 0.001 FDR:   845
0:58:46.783652 PROGRESS: =========================================================================
0:58:46.841815 INFO: Target number of precursors reached.
0:58:48.920922 INFO: fragments_df: keeping 5000 of 19674302 [sum(precursor_idx_mask)=52801 sum(mass_error_mask)=19674302 stop_rank=5000
0:58:50.244894 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:58:51.217807 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:58:51.935155 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:58:51.935601 INFO: Using score_cutoff 9.00777625608444 (fac=0.99, q=1)
0:58:51.935927 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:58:51.936019 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:58:51.936086 INFO: Updating optimization_manager: score_cutoff        : 5.032026190853119 -> 9.00777625608444
0:58:51.936156 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:58:52.559001 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:58:53.960120 INFO: === checking if optimization conditions were reached ===
0:58:53.963001 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:58:53.963205 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:58:53.963309 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:58:53.963419 INFO: ==============================================
0:58:53.963519 INFO: Starting optimization step 12.
0:58:53.963619 PROGRESS: === Extracting elution groups 0 to 511000 ===
0:58:53.963707 INFO: Using rust extraction backend
0:58:53.963788 PROGRESS: Extracting batch of 1001059 precursors
0:58:55.666721 INFO: === Search parameters used ===
0:58:55.667005 INFO: rt_error       : 717.0044555664062
0:58:55.667081 INFO: mobility_error : 0.1
0:58:55.667143 INFO: num_candidates : 3
0:58:55.667200 INFO: ms1_error      : 20
0:58:55.667253 INFO: ms2_error      : 10.0
0:58:55.667307 INFO: fwhm_rt        : 3.0
0:58:55.667360 INFO: quant_window   : 3
0:58:55.667412 INFO: ==============================================
0:59:09.167146 INFO: performing precursor FDR with 40 features
0:59:09.167394 INFO: Decoy channel: -1
0:59:09.167426 INFO: competitive: True
0:59:09.921787 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:11.202653 INFO: Estimating optimal hyperparameters - samples: 2,402,120, batch_size: 4,096, learning_rate: 1.00e-03
0:59:11.207775 INFO: Using random state 907818 for train-test-split
0:59:57.892341 INFO: Test AUC: 0.610
0:59:57.892611 INFO: Train AUC: 0.616
0:59:57.892649 INFO: AUC difference: 0.88%
0:59:59.169945 INFO: Resetting torch num_threads to 32
0:59:59.267191 PROGRESS: === Extracted 3002650 precursors and 19516324 fragments ===
0:59:59.267755 INFO: === FDR correction performed with classifier version 11 ===
0:59:59.268600 PROGRESS: ============================= Precursor FDR =============================
0:59:59.268702 PROGRESS: Total precursors accumulated: 1,991
0:59:59.268777 PROGRESS: Target precursors: 1,972 (99.05%)
0:59:59.268841 PROGRESS: Decoy precursors: 19 (0.95%)
0:59:59.268900 PROGRESS: 
0:59:59.268960 PROGRESS: Precursor Summary:
0:59:59.270551 PROGRESS: Channel   0:	 0.050 FDR: 1,972; 0.010 FDR: 1,972; 0.001 FDR: 1,241
0:59:59.270658 PROGRESS: 
0:59:59.270737 PROGRESS: Protein Summary:
0:59:59.272769 PROGRESS: Channel   0:	 0.050 FDR: 1,499; 0.010 FDR: 1,499; 0.001 FDR:   995
0:59:59.272872 PROGRESS: =========================================================================
0:59:59.327414 INFO: Target number of precursors reached.
1:00:01.339915 INFO: fragments_df: keeping 5000 of 19516324 [sum(precursor_idx_mask)=52745 sum(mass_error_mask)=19516324 stop_rank=5000
1:00:02.547309 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:00:02.845888 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:00:03.564026 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:00:03.564480 INFO: Using score_cutoff 6.780782021141052 (fac=0.99, q=1)
1:00:03.564827 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:00:03.564916 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:00:03.564981 INFO: Updating optimization_manager: score_cutoff        : 9.00777625608444 -> 6.780782021141052
1:00:03.565053 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:00:04.180542 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:00:05.549054 INFO: === checking if optimization conditions were reached ===
1:00:05.551265 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:00:05.551407 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
1:00:05.551484 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:00:05.551564 INFO: ==============================================
1:00:05.551665 INFO: Starting optimization step 13.
1:00:05.551749 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:00:05.551836 INFO: Using rust extraction backend
1:00:05.551912 PROGRESS: Extracting batch of 1001059 precursors
1:00:07.240498 INFO: === Search parameters used ===
1:00:07.240885 INFO: rt_error       : 717.0044555664062
1:00:07.240952 INFO: mobility_error : 0.1
1:00:07.241016 INFO: num_candidates : 3
1:00:07.241068 INFO: ms1_error      : 20
1:00:07.241117 INFO: ms2_error      : 10.0
1:00:07.241163 INFO: fwhm_rt        : 3.0
1:00:07.241211 INFO: quant_window   : 3
1:00:07.241256 INFO: ==============================================
1:00:20.812776 INFO: performing precursor FDR with 40 features
1:00:20.813009 INFO: Decoy channel: -1
1:00:20.813039 INFO: competitive: True
1:00:21.555245 INFO: Setting torch num_threads to 2 for FDR classification task
1:00:22.876930 INFO: Estimating optimal hyperparameters - samples: 2,402,120, batch_size: 4,096, learning_rate: 1.00e-03
1:00:22.882070 INFO: Using random state 432967 for train-test-split
1:01:09.052866 INFO: Test AUC: 0.613
1:01:09.053128 INFO: Train AUC: 0.616
1:01:09.053166 INFO: AUC difference: 0.56%
1:01:10.271200 INFO: Resetting torch num_threads to 32
1:01:10.380841 PROGRESS: === Extracted 3002651 precursors and 19547853 fragments ===
1:01:10.381376 INFO: === FDR correction performed with classifier version 12 ===
1:01:10.382284 PROGRESS: ============================= Precursor FDR =============================
1:01:10.382399 PROGRESS: Total precursors accumulated: 2,043
1:01:10.382474 PROGRESS: Target precursors: 2,023 (99.02%)
1:01:10.382539 PROGRESS: Decoy precursors: 20 (0.98%)
1:01:10.382596 PROGRESS: 
1:01:10.382652 PROGRESS: Precursor Summary:
1:01:10.384174 PROGRESS: Channel   0:	 0.050 FDR: 2,023; 0.010 FDR: 2,023; 0.001 FDR: 1,083
1:01:10.384273 PROGRESS: 
1:01:10.384340 PROGRESS: Protein Summary:
1:01:10.386340 PROGRESS: Channel   0:	 0.050 FDR: 1,586; 0.010 FDR: 1,586; 0.001 FDR:   878
1:01:10.386479 PROGRESS: =========================================================================
1:01:10.440331 INFO: Target number of precursors reached.
1:01:12.453327 INFO: fragments_df: keeping 5000 of 19547853 [sum(precursor_idx_mask)=52849 sum(mass_error_mask)=19547853 stop_rank=5000
1:01:13.219006 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:01:13.523071 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:01:14.236035 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:01:14.236475 INFO: Using score_cutoff 5.11399337310791 (fac=0.99, q=1)
1:01:14.236815 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:01:14.236906 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:01:14.236969 INFO: Updating optimization_manager: score_cutoff        : 6.780782021141052 -> 5.11399337310791
1:01:14.237033 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:01:14.532032 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:01:15.223499 INFO: === checking if optimization conditions were reached ===
1:01:15.225696 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:01:15.225841 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
1:01:15.225941 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:01:15.226012 INFO: ==============================================
1:01:15.226093 PROGRESS: Optimization finished for ms2_error.
1:01:15.964206 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:01:16.257977 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:01:16.943515 INFO: Starting optimization step 0.
1:01:16.943776 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:01:16.943906 INFO: Using rust extraction backend
1:01:16.943998 PROGRESS: Extracting batch of 499623 precursors
1:01:17.797277 INFO: === Search parameters used ===
1:01:17.797527 INFO: rt_error       : 717.0044555664062
1:01:17.797591 INFO: mobility_error : 0.1
1:01:17.797655 INFO: num_candidates : 3
1:01:17.797710 INFO: ms1_error      : 20
1:01:17.797774 INFO: ms2_error      : 10.0
1:01:17.797825 INFO: fwhm_rt        : 3.0
1:01:17.797876 INFO: quant_window   : 3
1:01:17.797925 INFO: ==============================================
1:01:24.339186 INFO: performing precursor FDR with 40 features
1:01:24.339310 INFO: Decoy channel: -1
1:01:24.339338 INFO: competitive: True
1:01:24.689004 INFO: Setting torch num_threads to 2 for FDR classification task
1:01:25.279831 INFO: Estimating optimal hyperparameters - samples: 1,198,912, batch_size: 4,096, learning_rate: 1.00e-03
1:01:25.282250 INFO: Using random state 617173 for train-test-split
1:01:47.839708 INFO: Test AUC: 0.611
1:01:47.839969 INFO: Train AUC: 0.620
1:01:47.840008 INFO: AUC difference: 1.52%
1:01:48.574858 INFO: Resetting torch num_threads to 32
1:01:48.624368 PROGRESS: === Extracted 1498640 precursors and 9806333 fragments ===
1:01:48.624901 INFO: === FDR correction performed with classifier version 13 ===
1:01:48.625596 PROGRESS: ============================= Precursor FDR =============================
1:01:48.625710 PROGRESS: Total precursors accumulated: 1,096
1:01:48.625800 PROGRESS: Target precursors: 1,086 (99.09%)
1:01:48.625868 PROGRESS: Decoy precursors: 10 (0.91%)
1:01:48.625923 PROGRESS: 
1:01:48.625976 PROGRESS: Precursor Summary:
1:01:48.627318 PROGRESS: Channel   0:	 0.050 FDR: 1,086; 0.010 FDR: 1,086; 0.001 FDR:   694
1:01:48.627424 PROGRESS: 
1:01:48.627489 PROGRESS: Protein Summary:
1:01:48.629137 PROGRESS: Channel   0:	 0.050 FDR:   923; 0.010 FDR:   923; 0.001 FDR:   596
1:01:48.629238 PROGRESS: =========================================================================
1:01:48.666026 INFO: Target number of precursors reached.
1:01:49.712478 INFO: fragments_df: keeping 5000 of 9806333 [sum(precursor_idx_mask)=28892 sum(mass_error_mask)=9806333 stop_rank=5000
1:01:50.433505 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:01:50.629552 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:01:51.347146 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:01:51.347670 INFO: Using score_cutoff 6.994717656612396 (fac=0.99, q=1)
1:01:51.348017 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:01:51.348102 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:01:51.348164 INFO: Updating optimization_manager: score_cutoff        : 5.11399337310791 -> 6.994717656612396
1:01:51.348230 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:01:51.642101 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:01:52.326995 INFO: === checking if optimization conditions were reached ===
1:01:52.327224 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:01:52.329694 INFO: Updating optimization_manager: rt_error            : 717.0044555664062 -> 960.1201391938225
1:01:52.329824 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 960.1201.
1:01:52.329905 INFO: ==============================================
1:01:52.329989 INFO: Starting optimization step 1.
1:01:52.330058 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:01:52.330151 INFO: Using rust extraction backend
1:01:52.330237 PROGRESS: Extracting batch of 499623 precursors
1:01:53.193317 INFO: === Search parameters used ===
1:01:53.193586 INFO: rt_error       : 960.1201391938225
1:01:53.193653 INFO: mobility_error : 0.1
1:01:53.193709 INFO: num_candidates : 3
1:01:53.193761 INFO: ms1_error      : 20
1:01:53.193812 INFO: ms2_error      : 10.0
1:01:53.193861 INFO: fwhm_rt        : 3.0
1:01:53.193909 INFO: quant_window   : 3
1:01:53.193957 INFO: ==============================================
1:02:00.200840 INFO: performing precursor FDR with 40 features
1:02:00.200989 INFO: Decoy channel: -1
1:02:00.201017 INFO: competitive: True
1:02:00.569904 INFO: Setting torch num_threads to 2 for FDR classification task
1:02:01.207342 INFO: Estimating optimal hyperparameters - samples: 1,198,908, batch_size: 4,096, learning_rate: 1.00e-03
1:02:01.209903 INFO: Using random state 617173 for train-test-split
1:02:23.916397 INFO: Test AUC: 0.612
1:02:23.916638 INFO: Train AUC: 0.620
1:02:23.916675 INFO: AUC difference: 1.28%
1:02:24.638222 INFO: Resetting torch num_threads to 32
1:02:24.687593 PROGRESS: === Extracted 1498636 precursors and 9841125 fragments ===
1:02:24.688135 INFO: === FDR correction performed with classifier version 13 ===
1:02:24.688834 PROGRESS: ============================= Precursor FDR =============================
1:02:24.688943 PROGRESS: Total precursors accumulated: 1,046
1:02:24.689015 PROGRESS: Target precursors: 1,036 (99.04%)
1:02:24.689078 PROGRESS: Decoy precursors: 10 (0.96%)
1:02:24.689146 PROGRESS: 
1:02:24.689202 PROGRESS: Precursor Summary:
1:02:24.690537 PROGRESS: Channel   0:	 0.050 FDR: 1,036; 0.010 FDR: 1,036; 0.001 FDR:   698
1:02:24.690643 PROGRESS: 
1:02:24.690707 PROGRESS: Protein Summary:
1:02:24.692330 PROGRESS: Channel   0:	 0.050 FDR:   880; 0.010 FDR:   880; 0.001 FDR:   591
1:02:24.692429 PROGRESS: =========================================================================
1:02:24.724411 INFO: Target number of precursors reached.
1:02:25.792585 INFO: fragments_df: keeping 5000 of 9841125 [sum(precursor_idx_mask)=27669 sum(mass_error_mask)=9841125 stop_rank=5000
1:02:26.533007 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:02:26.712903 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:02:27.431432 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:02:27.431884 INFO: Using score_cutoff 7.964563246250152 (fac=0.99, q=1)
1:02:27.432235 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:02:27.432325 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:02:27.432391 INFO: Updating optimization_manager: score_cutoff        : 6.994717656612396 -> 7.964563246250152
1:02:27.432469 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:02:27.729749 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:02:28.434572 INFO: === checking if optimization conditions were reached ===
1:02:28.434840 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:02:28.437367 INFO: Updating optimization_manager: rt_error            : 960.1201391938225 -> 1138.987677992983
1:02:28.437502 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 1138.9877.
1:02:28.437578 INFO: ==============================================
1:02:28.437664 INFO: Starting optimization step 2.
1:02:28.437736 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:02:28.437832 INFO: Using rust extraction backend
1:02:28.437911 PROGRESS: Extracting batch of 499623 precursors
1:02:29.299886 INFO: === Search parameters used ===
1:02:29.300351 INFO: rt_error       : 1138.987677992983
1:02:29.300421 INFO: mobility_error : 0.1
1:02:29.300482 INFO: num_candidates : 3
1:02:29.300536 INFO: ms1_error      : 20
1:02:29.300586 INFO: ms2_error      : 10.0
1:02:29.300637 INFO: fwhm_rt        : 3.0
1:02:29.300687 INFO: quant_window   : 3
1:02:29.300735 INFO: ==============================================
1:02:36.259313 INFO: performing precursor FDR with 40 features
1:02:36.259444 INFO: Decoy channel: -1
1:02:36.259472 INFO: competitive: True
1:02:36.627116 INFO: Setting torch num_threads to 2 for FDR classification task
1:02:37.255788 INFO: Estimating optimal hyperparameters - samples: 1,198,911, batch_size: 4,096, learning_rate: 1.00e-03
1:02:37.258389 INFO: Using random state 617173 for train-test-split
1:03:00.079038 INFO: Test AUC: 0.612
1:03:00.079275 INFO: Train AUC: 0.620
1:03:00.079312 INFO: AUC difference: 1.16%
1:03:00.836727 INFO: Resetting torch num_threads to 32
1:03:00.888256 PROGRESS: === Extracted 1498639 precursors and 9838682 fragments ===
1:03:00.888810 INFO: === FDR correction performed with classifier version 13 ===
1:03:00.889482 PROGRESS: ============================= Precursor FDR =============================
1:03:00.889587 PROGRESS: Total precursors accumulated: 1,063
1:03:00.889657 PROGRESS: Target precursors: 1,053 (99.06%)
1:03:00.889719 PROGRESS: Decoy precursors: 10 (0.94%)
1:03:00.889771 PROGRESS: 
1:03:00.889825 PROGRESS: Precursor Summary:
1:03:00.891113 PROGRESS: Channel   0:	 0.050 FDR: 1,053; 0.010 FDR: 1,053; 0.001 FDR:   671
1:03:00.891223 PROGRESS: 
1:03:00.891284 PROGRESS: Protein Summary:
1:03:00.892848 PROGRESS: Channel   0:	 0.050 FDR:   901; 0.010 FDR:   901; 0.001 FDR:   569
1:03:00.892942 PROGRESS: =========================================================================
1:03:00.930532 INFO: Target number of precursors reached.
1:03:01.926785 INFO: fragments_df: keeping 5000 of 9838682 [sum(precursor_idx_mask)=27418 sum(mass_error_mask)=9838682 stop_rank=5000
1:03:02.675426 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:03:02.872501 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:03:03.601272 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:03:03.601707 INFO: Using score_cutoff 5.859967931556702 (fac=0.99, q=1)
1:03:03.602039 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:03:03.602132 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:03:03.602196 INFO: Updating optimization_manager: score_cutoff        : 7.964563246250152 -> 5.859967931556702
1:03:03.602258 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:03:03.904287 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:03:04.615560 INFO: === checking if optimization conditions were reached ===
1:03:04.615842 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:03:04.618501 INFO: Updating optimization_manager: rt_error            : 1138.987677992983 -> 1076.2152015189408
1:03:04.618642 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 1076.2152.
1:03:04.618723 INFO: ==============================================
1:03:04.618806 INFO: Starting optimization step 3.
1:03:04.618884 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:03:04.618975 INFO: Using rust extraction backend
1:03:04.619053 PROGRESS: Extracting batch of 499623 precursors
1:03:05.485272 INFO: === Search parameters used ===
1:03:05.485620 INFO: rt_error       : 1076.2152015189408
1:03:05.485689 INFO: mobility_error : 0.1
1:03:05.485748 INFO: num_candidates : 3
1:03:05.485808 INFO: ms1_error      : 20
1:03:05.485859 INFO: ms2_error      : 10.0
1:03:05.485910 INFO: fwhm_rt        : 3.0
1:03:05.485959 INFO: quant_window   : 3
1:03:05.486021 INFO: ==============================================
1:03:12.405310 INFO: performing precursor FDR with 40 features
1:03:12.405436 INFO: Decoy channel: -1
1:03:12.405465 INFO: competitive: True
1:03:12.767106 INFO: Setting torch num_threads to 2 for FDR classification task
1:03:13.390119 INFO: Estimating optimal hyperparameters - samples: 1,198,912, batch_size: 4,096, learning_rate: 1.00e-03
1:03:13.392737 INFO: Using random state 617173 for train-test-split
1:03:36.024394 INFO: Test AUC: 0.612
1:03:36.024553 INFO: Train AUC: 0.620
1:03:36.024588 INFO: AUC difference: 1.31%
1:03:36.746092 INFO: Resetting torch num_threads to 32
1:03:36.794576 PROGRESS: === Extracted 1498641 precursors and 9839242 fragments ===
1:03:36.795093 INFO: === FDR correction performed with classifier version 13 ===
1:03:36.795748 PROGRESS: ============================= Precursor FDR =============================
1:03:36.795856 PROGRESS: Total precursors accumulated: 1,066
1:03:36.795938 PROGRESS: Target precursors: 1,056 (99.06%)
1:03:36.795998 PROGRESS: Decoy precursors: 10 (0.94%)
1:03:36.796052 PROGRESS: 
1:03:36.796105 PROGRESS: Precursor Summary:
1:03:36.797382 PROGRESS: Channel   0:	 0.050 FDR: 1,056; 0.010 FDR: 1,056; 0.001 FDR:   758
1:03:36.797481 PROGRESS: 
1:03:36.797552 PROGRESS: Protein Summary:
1:03:36.799160 PROGRESS: Channel   0:	 0.050 FDR:   901; 0.010 FDR:   901; 0.001 FDR:   645
1:03:36.799263 PROGRESS: =========================================================================
1:03:36.834867 INFO: Target number of precursors reached.
1:03:37.875876 INFO: fragments_df: keeping 5000 of 9839242 [sum(precursor_idx_mask)=27921 sum(mass_error_mask)=9839242 stop_rank=5000
1:03:38.725406 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:03:38.922471 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:03:39.642073 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:03:39.642714 INFO: Using score_cutoff 6.177160537004471 (fac=0.99, q=1)
1:03:39.643062 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:03:39.643154 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:03:39.643227 INFO: Updating optimization_manager: score_cutoff        : 5.859967931556702 -> 6.177160537004471
1:03:39.643299 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:03:39.937525 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:03:40.622503 INFO: === checking if optimization conditions were reached ===
1:03:40.622784 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:03:40.625616 INFO: Updating optimization_manager: rt_error            : 1076.2152015189408 -> 1003.7472239015904
1:03:40.625752 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 1003.7472.
1:03:40.625833 INFO: ==============================================
1:03:40.625924 INFO: Starting optimization step 4.
1:03:40.626006 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:03:40.626096 INFO: Using rust extraction backend
1:03:40.626175 PROGRESS: Extracting batch of 499623 precursors
1:03:41.479475 INFO: === Search parameters used ===
1:03:41.479738 INFO: rt_error       : 1003.7472239015904
1:03:41.479805 INFO: mobility_error : 0.1
1:03:41.479875 INFO: num_candidates : 3
1:03:41.479928 INFO: ms1_error      : 20
1:03:41.479980 INFO: ms2_error      : 10.0
1:03:41.480051 INFO: fwhm_rt        : 3.0
1:03:41.480103 INFO: quant_window   : 3
1:03:41.480150 INFO: ==============================================
1:03:48.313302 INFO: performing precursor FDR with 40 features
1:03:48.313425 INFO: Decoy channel: -1
1:03:48.313455 INFO: competitive: True
1:03:48.657214 INFO: Setting torch num_threads to 2 for FDR classification task
1:03:49.257581 INFO: Estimating optimal hyperparameters - samples: 1,198,911, batch_size: 4,096, learning_rate: 1.00e-03
1:03:49.260070 INFO: Using random state 617173 for train-test-split
1:04:11.672060 INFO: Test AUC: 0.613
1:04:11.672268 INFO: Train AUC: 0.619
1:04:11.672307 INFO: AUC difference: 1.08%
1:04:12.405356 INFO: Resetting torch num_threads to 32
1:04:12.506369 PROGRESS: === Extracted 1498639 precursors and 9839732 fragments ===
1:04:12.506979 INFO: === FDR correction performed with classifier version 13 ===
1:04:12.507624 PROGRESS: ============================= Precursor FDR =============================
1:04:12.507732 PROGRESS: Total precursors accumulated: 947
1:04:12.507807 PROGRESS: Target precursors: 938 (99.05%)
1:04:12.507867 PROGRESS: Decoy precursors: 9 (0.95%)
1:04:12.507926 PROGRESS: 
1:04:12.507981 PROGRESS: Precursor Summary:
1:04:12.509191 PROGRESS: Channel   0:	 0.050 FDR:   938; 0.010 FDR:   938; 0.001 FDR:   369
1:04:12.509291 PROGRESS: 
1:04:12.509354 PROGRESS: Protein Summary:
1:04:12.510861 PROGRESS: Channel   0:	 0.050 FDR:   808; 0.010 FDR:   808; 0.001 FDR:   325
1:04:12.510964 PROGRESS: =========================================================================
1:04:12.542043 INFO: Target number of precursors not reached yet.
1:04:13.343600 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:04:13.635478 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:04:14.323907 INFO: === skipping optimization until target number of precursors are found ===
1:04:14.324222 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
1:04:14.324358 INFO: Starting optimization step 5.
1:04:14.324441 PROGRESS: === Extracting elution groups 255000 to 511000 ===
1:04:14.324533 INFO: Using rust extraction backend
1:04:14.324615 PROGRESS: Extracting batch of 501436 precursors
1:04:15.180246 INFO: === Search parameters used ===
1:04:15.180501 INFO: rt_error       : 1003.7472239015904
1:04:15.180574 INFO: mobility_error : 0.1
1:04:15.180634 INFO: num_candidates : 3
1:04:15.180687 INFO: ms1_error      : 20
1:04:15.180745 INFO: ms2_error      : 10.0
1:04:15.180797 INFO: fwhm_rt        : 3.0
1:04:15.180858 INFO: quant_window   : 3
1:04:15.180919 INFO: ==============================================
1:04:22.543482 INFO: performing precursor FDR with 40 features
1:04:22.543588 INFO: Decoy channel: -1
1:04:22.543627 INFO: competitive: True
1:04:23.735040 INFO: Setting torch num_threads to 2 for FDR classification task
1:04:25.000959 INFO: Estimating optimal hyperparameters - samples: 2,402,156, batch_size: 4,096, learning_rate: 1.00e-03
1:04:25.005824 INFO: Using random state 617173 for train-test-split
1:05:11.334867 INFO: Test AUC: 0.612
1:05:11.335088 INFO: Train AUC: 0.617
1:05:11.335124 INFO: AUC difference: 0.78%
1:05:12.568839 INFO: Resetting torch num_threads to 32
1:05:13.100169 PROGRESS: === Extracted 3002696 precursors and 19720925 fragments ===
1:05:13.100854 INFO: === FDR correction performed with classifier version 13 ===
1:05:13.101765 PROGRESS: ============================= Precursor FDR =============================
1:05:13.101861 PROGRESS: Total precursors accumulated: 1,966
1:05:13.101928 PROGRESS: Target precursors: 1,947 (99.03%)
1:05:13.101991 PROGRESS: Decoy precursors: 19 (0.97%)
1:05:13.102041 PROGRESS: 
1:05:13.102090 PROGRESS: Precursor Summary:
1:05:13.103613 PROGRESS: Channel   0:	 0.050 FDR: 1,947; 0.010 FDR: 1,947; 0.001 FDR: 1,151
1:05:13.103710 PROGRESS: 
1:05:13.103776 PROGRESS: Protein Summary:
1:05:13.105734 PROGRESS: Channel   0:	 0.050 FDR: 1,476; 0.010 FDR: 1,476; 0.001 FDR:   934
1:05:13.105834 PROGRESS: =========================================================================
1:05:13.134450 INFO: Target number of precursors reached.
1:05:15.299155 INFO: fragments_df: keeping 5000 of 19720925 [sum(precursor_idx_mask)=52597 sum(mass_error_mask)=19720925 stop_rank=5000
1:05:16.494065 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:05:16.786608 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:05:17.500926 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:05:17.501403 INFO: Using score_cutoff 8.878416332244873 (fac=0.99, q=1)
1:05:17.501763 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:05:17.501846 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:05:17.501906 INFO: Updating optimization_manager: score_cutoff        : 6.177160537004471 -> 8.878416332244873
1:05:17.501970 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:05:18.143668 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:05:19.568773 INFO: === checking if optimization conditions were reached ===
1:05:19.569044 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:05:19.572272 INFO: Updating optimization_manager: rt_error            : 1003.7472239015904 -> 1082.7078143446704
1:05:19.572416 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 1082.7078.
1:05:19.572491 INFO: ==============================================
1:05:19.572583 INFO: Starting optimization step 6.
1:05:19.572651 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:05:19.572731 INFO: Using rust extraction backend
1:05:19.572812 PROGRESS: Extracting batch of 1001059 precursors
1:05:21.307904 INFO: === Search parameters used ===
1:05:21.308442 INFO: rt_error       : 1082.7078143446704
1:05:21.308509 INFO: mobility_error : 0.1
1:05:21.308566 INFO: num_candidates : 3
1:05:21.308620 INFO: ms1_error      : 20
1:05:21.308667 INFO: ms2_error      : 10.0
1:05:21.308713 INFO: fwhm_rt        : 3.0
1:05:21.308770 INFO: quant_window   : 3
1:05:21.308818 INFO: ==============================================
1:05:36.018219 INFO: performing precursor FDR with 40 features
1:05:36.018484 INFO: Decoy channel: -1
1:05:36.018514 INFO: competitive: True
1:05:36.753356 INFO: Setting torch num_threads to 2 for FDR classification task
1:05:38.067210 INFO: Estimating optimal hyperparameters - samples: 2,402,165, batch_size: 4,096, learning_rate: 1.00e-03
1:05:38.072521 INFO: Using random state 617173 for train-test-split
1:06:24.165260 INFO: Test AUC: 0.612
1:06:24.165489 INFO: Train AUC: 0.616
1:06:24.165528 INFO: AUC difference: 0.75%
1:06:25.400650 INFO: Resetting torch num_threads to 32
1:06:25.572539 PROGRESS: === Extracted 3002707 precursors and 19719856 fragments ===
1:06:25.573111 INFO: === FDR correction performed with classifier version 13 ===
1:06:25.574029 PROGRESS: ============================= Precursor FDR =============================
1:06:25.574144 PROGRESS: Total precursors accumulated: 2,046
1:06:25.574227 PROGRESS: Target precursors: 2,026 (99.02%)
1:06:25.574291 PROGRESS: Decoy precursors: 20 (0.98%)
1:06:25.574365 PROGRESS: 
1:06:25.574421 PROGRESS: Precursor Summary:
1:06:25.576049 PROGRESS: Channel   0:	 0.050 FDR: 2,026; 0.010 FDR: 2,026; 0.001 FDR: 1,420
1:06:25.576149 PROGRESS: 
1:06:25.576209 PROGRESS: Protein Summary:
1:06:25.578273 PROGRESS: Channel   0:	 0.050 FDR: 1,551; 0.010 FDR: 1,551; 0.001 FDR: 1,117
1:06:25.578394 PROGRESS: =========================================================================
1:06:25.637185 INFO: Target number of precursors reached.
1:06:27.709075 INFO: fragments_df: keeping 5000 of 19719856 [sum(precursor_idx_mask)=53378 sum(mass_error_mask)=19719856 stop_rank=5000
1:06:28.654494 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:06:28.914010 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:06:29.634752 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:06:29.635231 INFO: Using score_cutoff 5.358060861825943 (fac=0.99, q=1)
1:06:29.635578 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:06:29.635667 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:06:29.635725 INFO: Updating optimization_manager: score_cutoff        : 8.878416332244873 -> 5.358060861825943
1:06:29.635793 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:06:29.930575 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:06:30.633701 INFO: === checking if optimization conditions were reached ===
1:06:30.633958 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
1:06:30.637393 INFO: Updating optimization_manager: rt_error            : 1082.7078143446704 -> 1037.8615294369706
1:06:30.637533 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 1037.8615.
1:06:30.637609 INFO: ==============================================
1:06:30.637700 INFO: Starting optimization step 7.
1:06:30.637773 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:06:30.637865 INFO: Using rust extraction backend
1:06:30.637948 PROGRESS: Extracting batch of 499623 precursors
1:06:31.499182 INFO: === Search parameters used ===
1:06:31.499520 INFO: rt_error       : 1037.8615294369706
1:06:31.499589 INFO: mobility_error : 0.1
1:06:31.499643 INFO: num_candidates : 3
1:06:31.499708 INFO: ms1_error      : 20
1:06:31.499793 INFO: ms2_error      : 10.0
1:06:31.499868 INFO: fwhm_rt        : 3.0
1:06:31.499945 INFO: quant_window   : 3
1:06:31.500018 INFO: ==============================================
1:06:38.452162 INFO: performing precursor FDR with 40 features
1:06:38.452346 INFO: Decoy channel: -1
1:06:38.452378 INFO: competitive: True
1:06:38.806364 INFO: Setting torch num_threads to 2 for FDR classification task
1:06:39.407884 INFO: Estimating optimal hyperparameters - samples: 1,198,914, batch_size: 4,096, learning_rate: 1.00e-03
1:06:39.410417 INFO: Using random state 617173 for train-test-split
1:07:02.123938 INFO: Test AUC: 0.611
1:07:02.124161 INFO: Train AUC: 0.620
1:07:02.124197 INFO: AUC difference: 1.50%
1:07:02.874369 INFO: Resetting torch num_threads to 32
1:07:02.923747 PROGRESS: === Extracted 1498643 precursors and 9839326 fragments ===
1:07:02.924282 INFO: === FDR correction performed with classifier version 13 ===
1:07:02.924916 PROGRESS: ============================= Precursor FDR =============================
1:07:02.925015 PROGRESS: Total precursors accumulated: 1,088
1:07:02.925092 PROGRESS: Target precursors: 1,078 (99.08%)
1:07:02.925151 PROGRESS: Decoy precursors: 10 (0.92%)
1:07:02.925208 PROGRESS: 
1:07:02.925259 PROGRESS: Precursor Summary:
1:07:02.926516 PROGRESS: Channel   0:	 0.050 FDR: 1,078; 0.010 FDR: 1,078; 0.001 FDR:   710
1:07:02.926621 PROGRESS: 
1:07:02.926687 PROGRESS: Protein Summary:
1:07:02.928279 PROGRESS: Channel   0:	 0.050 FDR:   922; 0.010 FDR:   922; 0.001 FDR:   602
1:07:02.928374 PROGRESS: =========================================================================
1:07:02.954363 INFO: Target number of precursors reached.
1:07:04.009242 INFO: fragments_df: keeping 5000 of 9839326 [sum(precursor_idx_mask)=28535 sum(mass_error_mask)=9839326 stop_rank=5000
1:07:04.782858 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:07:04.978069 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:07:05.695480 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:07:05.695924 INFO: Using score_cutoff 6.043320241355896 (fac=0.99, q=1)
1:07:05.696253 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:07:05.696335 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:07:05.696397 INFO: Updating optimization_manager: score_cutoff        : 5.358060861825943 -> 6.043320241355896
1:07:05.696458 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:07:05.989453 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:07:06.679509 INFO: === checking if optimization conditions were reached ===
1:07:06.679782 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
1:07:06.680770 INFO: Updating optimization_manager: rt_error            : 1037.8615294369706 -> 717.0044555664062
1:07:06.680935 INFO: Updating optimization_manager: classifier_version  : 13 -> 14
1:07:06.681039 INFO: Updating optimization_manager: score_cutoff        : 6.043320241355896 -> 6.994717656612396
1:07:06.681132 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:07:06.681224 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:07:06.681322 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 717.0045 found after 7 searches.
1:07:06.681391 INFO: ==============================================
1:07:06.681474 PROGRESS: Optimization finished for rt_error.
1:07:07.377088 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:07:07.676100 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:07:08.373557 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:07:08.373809 PROGRESS: ==============================================
1:07:08.373901 PROGRESS: ms2_error      : 10.0000
1:07:08.373975 PROGRESS: rt_error       : 717.0045
1:07:08.374036 PROGRESS: ==============================================
1:07:08.376435 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:07:14.933307 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:07:39.808822 INFO: Using rust extraction backend
1:07:39.809353 PROGRESS: Extracting batch of 10770831 precursors
1:08:02.732245 INFO: === Search parameters used ===
1:08:02.732913 INFO: rt_error       : 717.0044555664062
1:08:02.732992 INFO: mobility_error : 0.1
1:08:02.733055 INFO: num_candidates : 3
1:08:02.733114 INFO: ms1_error      : 20
1:08:02.733175 INFO: ms2_error      : 10.0
1:08:02.733231 INFO: fwhm_rt        : 3.0
1:08:02.733284 INFO: quant_window   : 3
1:08:02.733348 INFO: ==============================================
1:08:59.023218 INFO: Removed 3510714 precursors with score below cutoff 6.994717656612396
1:09:29.273759 INFO: performing precursor FDR with 40 features
1:09:29.274006 INFO: Decoy channel: -1
1:09:29.274039 INFO: competitive: True
1:09:32.281906 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:44.088188 INFO: Estimating optimal hyperparameters - samples: 23,041,418, batch_size: 4,096, learning_rate: 1.00e-03
1:09:44.158502 INFO: Using random state 894141 for train-test-split
1:17:06.084581 INFO: Test AUC: 0.614
1:17:06.084864 INFO: Train AUC: 0.614
1:17:06.084911 INFO: AUC difference: 0.09%
1:17:12.875597 INFO: Resetting torch num_threads to 32
1:17:14.812343 PROGRESS: ============================= Precursor FDR =============================
1:17:14.812640 PROGRESS: Total precursors accumulated: 22,500
1:17:14.812717 PROGRESS: Target precursors: 22,278 (99.01%)
1:17:14.812782 PROGRESS: Decoy precursors: 222 (0.99%)
1:17:14.812845 PROGRESS: 
1:17:14.812899 PROGRESS: Precursor Summary:
1:17:14.817849 PROGRESS: Channel   0:	 0.050 FDR: 22,278; 0.010 FDR: 22,278; 0.001 FDR: 13,653
1:17:14.817979 PROGRESS: 
1:17:14.818051 PROGRESS: Protein Summary:
1:17:14.826051 PROGRESS: Channel   0:	 0.050 FDR: 6,677; 0.010 FDR: 6,677; 0.001 FDR: 4,740
1:17:14.826199 PROGRESS: =========================================================================
1:17:14.952309 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2/psm.parquet
1:17:14.996207 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2/frag.parquet
1:17:15.081128 INFO: Finished workflow for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2
1:17:15.643607 PROGRESS: Loading raw file 3/6: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3 
1:17:15.643764 INFO: Quantification results path: /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant
1:17:15.643858 INFO: Creating folder /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3/figures
1:17:15.644038 INFO: Initializing TimingManager
1:17:15.644488 INFO: Initializing RawFileManager
1:17:22.376553 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
1:17:22.377632 INFO: Determining DIA cycle
1:17:22.390023 INFO: Found cycle with start 0.00 min and length 20.
1:17:22.416953 INFO: RT (min)            : 0.0 - 23.9
1:17:22.417054 INFO: RT duration (sec)   : 1433.6
1:17:22.417093 INFO: RT duration (min)   : 23.9
1:17:22.417120 INFO: Cycle len (scans)   : 20
1:17:22.417142 INFO: Cycle len (sec)     : 1.02
1:17:22.417164 INFO: Number of cycles    : 1405
1:17:22.417184 INFO: MS2 range (m/z)     : 400.4 - 800.6
1:17:22.417214 INFO: Creating DIA data object took: 6.772620677947998
1:17:23.141917 INFO: Creating DIA data NG object took: 0.7245767116546631
1:17:24.723267 INFO: Initializing CalibrationManager
1:17:24.723543 INFO: Setting up calibration estimators ..
1:17:24.723613 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:17:24.723707 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'}' ..
1:17:24.723820 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:17:24.723882 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:17:24.723945 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}}' ..
1:17:24.724000 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:17:24.724050 INFO: Done setting up calibration estimators.
1:17:24.724157 INFO: Initializing OptimizationManager
1:17:24.724295 INFO: initial parameter: ms1_error = 20
1:17:24.724358 INFO: initial parameter: ms2_error = 20
1:17:24.724414 INFO: initial parameter: rt_error = 716.8717651367188
1:17:24.724461 INFO: initial parameter: mobility_error = 0.1
1:17:24.724506 INFO: initial parameter: num_candidates = 1
1:17:24.724551 INFO: initial parameter: fwhm_rt = 5
1:17:24.724596 INFO: initial parameter: fwhm_mobility = 0.01
1:17:24.724649 INFO: initial parameter: score_cutoff = 0
1:17:24.724704 INFO: initial parameter: classifier_version = -1
1:17:24.724777 PROGRESS: Initializing workflow 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3
1:17:24.725007 INFO: FDRManager: loading saved state not requested, will be initialized.
1:17:24.725044 INFO: Initializing FDRManager
1:17:24.725083 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
1:17:26.078483 PROGRESS: Initializing spectral library: 5,415,345 target precursors potentially observable (2,595,411 removed)
1:17:26.882846 INFO: Updating optimization_manager: ms2_error           : 20 -> 20
1:17:26.883279 INFO: Updating optimization_manager: rt_error            : 716.8717651367188 -> 716.8717651367188
1:17:26.883385 PROGRESS: Starting initial search for precursors.
1:17:26.883477 INFO: Starting optimization step 0.
1:17:26.883540 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:17:26.883605 INFO: Using rust extraction backend
1:17:26.883667 PROGRESS: Extracting batch of 1960 precursors
1:17:26.888470 INFO: === Search parameters used ===
1:17:26.888571 INFO: rt_error       : 716.8717651367188
1:17:26.888625 INFO: mobility_error : 0.1
1:17:26.888671 INFO: num_candidates : 1
1:17:26.888716 INFO: ms1_error      : 20
1:17:26.888758 INFO: ms2_error      : 20
1:17:26.888801 INFO: fwhm_rt        : 5
1:17:26.888841 INFO: quant_window   : 3
1:17:26.888882 INFO: ==============================================
1:17:26.920715 INFO: performing precursor FDR with 40 features
1:17:26.920787 INFO: Decoy channel: -1
1:17:26.920812 INFO: competitive: True
1:17:26.922030 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:26.924068 INFO: Estimating optimal hyperparameters - samples: 1,565, batch_size: 128, learning_rate: 1.77e-04
1:17:26.924908 INFO: Using random state 260608 for train-test-split
1:17:27.072071 INFO: Test AUC: 0.484
1:17:27.072159 INFO: Train AUC: 0.569
1:17:27.072192 INFO: AUC difference: 14.89%
1:17:27.072217 WARNING: AUC difference > 5%. This may indicate overfitting.
1:17:28.097160 INFO: Resetting torch num_threads to 32
1:17:28.098873 PROGRESS: === Extracted 1957 precursors and 11243 fragments ===
1:17:28.099259 INFO: === FDR correction performed with classifier version -1 ===
1:17:28.099745 PROGRESS: ============================= Precursor FDR =============================
1:17:28.099834 PROGRESS: Total precursors accumulated: 2
1:17:28.099897 PROGRESS: Target precursors: 2 (100.00%)
1:17:28.099955 PROGRESS: Decoy precursors: 0 (0.00%)
1:17:28.100006 PROGRESS: 
1:17:28.100055 PROGRESS: Precursor Summary:
1:17:28.101111 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:17:28.101201 PROGRESS: 
1:17:28.101260 PROGRESS: Protein Summary:
1:17:28.102443 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:17:28.102535 PROGRESS: =========================================================================
1:17:28.102754 INFO: Target number of precursors not reached yet.
1:17:28.180178 INFO: Starting optimization step 1.
1:17:28.180391 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:17:28.180484 INFO: Using rust extraction backend
1:17:28.180565 PROGRESS: Extracting batch of 3921 precursors
1:17:28.189466 INFO: === Search parameters used ===
1:17:28.189596 INFO: rt_error       : 716.8717651367188
1:17:28.189654 INFO: mobility_error : 0.1
1:17:28.189705 INFO: num_candidates : 1
1:17:28.189760 INFO: ms1_error      : 20
1:17:28.189816 INFO: ms2_error      : 20
1:17:28.189862 INFO: fwhm_rt        : 5
1:17:28.189907 INFO: quant_window   : 3
1:17:28.189968 INFO: ==============================================
1:17:28.246144 INFO: performing precursor FDR with 40 features
1:17:28.246238 INFO: Decoy channel: -1
1:17:28.246265 INFO: competitive: True
1:17:28.250665 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:28.253042 INFO: Estimating optimal hyperparameters - samples: 4,702, batch_size: 128, learning_rate: 1.77e-04
1:17:28.253144 INFO: Using random state 36003 for train-test-split
1:17:28.706967 INFO: Test AUC: 0.536
1:17:28.707046 INFO: Train AUC: 0.575
1:17:28.707075 INFO: AUC difference: 6.89%
1:17:28.707096 WARNING: AUC difference > 5%. This may indicate overfitting.
1:17:28.949251 INFO: Resetting torch num_threads to 32
1:17:28.952089 PROGRESS: === Extracted 5878 precursors and 34192 fragments ===
1:17:28.952449 INFO: === FDR correction performed with classifier version -1 ===
1:17:28.952916 PROGRESS: ============================= Precursor FDR =============================
1:17:28.953000 PROGRESS: Total precursors accumulated: 0
1:17:28.953062 PROGRESS: Target precursors: 0 (0.00%)
1:17:28.953114 PROGRESS: Decoy precursors: 0 (0.00%)
1:17:28.953161 PROGRESS: 
1:17:28.953206 PROGRESS: Precursor Summary:
1:17:28.953327 PROGRESS: 
1:17:28.953392 PROGRESS: Protein Summary:
1:17:28.953471 PROGRESS: =========================================================================
1:17:28.953708 INFO: Target number of precursors not reached yet.
1:17:29.035440 INFO: Starting optimization step 2.
1:17:29.035657 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:17:29.035744 INFO: Using rust extraction backend
1:17:29.035814 PROGRESS: Extracting batch of 7852 precursors
1:17:29.050914 INFO: === Search parameters used ===
1:17:29.051053 INFO: rt_error       : 716.8717651367188
1:17:29.051106 INFO: mobility_error : 0.1
1:17:29.051152 INFO: num_candidates : 1
1:17:29.051194 INFO: ms1_error      : 20
1:17:29.051236 INFO: ms2_error      : 20
1:17:29.051277 INFO: fwhm_rt        : 5
1:17:29.051317 INFO: quant_window   : 3
1:17:29.051358 INFO: ==============================================
1:17:29.164468 INFO: performing precursor FDR with 40 features
1:17:29.164571 INFO: Decoy channel: -1
1:17:29.164596 INFO: competitive: True
1:17:29.170546 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:29.174105 INFO: Estimating optimal hyperparameters - samples: 10,976, batch_size: 128, learning_rate: 1.77e-04
1:17:29.174213 INFO: Using random state 103454 for train-test-split
1:17:30.241633 INFO: Test AUC: 0.541
1:17:30.241719 INFO: Train AUC: 0.590
1:17:30.241748 INFO: AUC difference: 8.21%
1:17:30.241770 WARNING: AUC difference > 5%. This may indicate overfitting.
1:17:30.487168 INFO: Resetting torch num_threads to 32
1:17:30.492393 PROGRESS: === Extracted 13720 precursors and 79741 fragments ===
1:17:30.492788 INFO: === FDR correction performed with classifier version -1 ===
1:17:30.493263 PROGRESS: ============================= Precursor FDR =============================
1:17:30.493349 PROGRESS: Total precursors accumulated: 0
1:17:30.493416 PROGRESS: Target precursors: 0 (0.00%)
1:17:30.493472 PROGRESS: Decoy precursors: 0 (0.00%)
1:17:30.493520 PROGRESS: 
1:17:30.493567 PROGRESS: Precursor Summary:
1:17:30.493677 PROGRESS: 
1:17:30.493738 PROGRESS: Protein Summary:
1:17:30.493813 PROGRESS: =========================================================================
1:17:30.494138 INFO: Target number of precursors not reached yet.
1:17:30.586182 INFO: Starting optimization step 3.
1:17:30.586446 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:17:30.586536 INFO: Using rust extraction backend
1:17:30.586599 PROGRESS: Extracting batch of 15661 precursors
1:17:30.615247 INFO: === Search parameters used ===
1:17:30.615431 INFO: rt_error       : 716.8717651367188
1:17:30.615492 INFO: mobility_error : 0.1
1:17:30.615539 INFO: num_candidates : 1
1:17:30.615585 INFO: ms1_error      : 20
1:17:30.615631 INFO: ms2_error      : 20
1:17:30.615675 INFO: fwhm_rt        : 5
1:17:30.615718 INFO: quant_window   : 3
1:17:30.615760 INFO: ==============================================
1:17:30.790166 INFO: performing precursor FDR with 40 features
1:17:30.790280 INFO: Decoy channel: -1
1:17:30.790312 INFO: competitive: True
1:17:30.801563 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:30.808291 INFO: Estimating optimal hyperparameters - samples: 23,492, batch_size: 128, learning_rate: 1.77e-04
1:17:30.808496 INFO: Using random state 799783 for train-test-split
1:17:33.120709 INFO: Test AUC: 0.568
1:17:33.120802 INFO: Train AUC: 0.602
1:17:33.120834 INFO: AUC difference: 5.75%
1:17:33.120858 WARNING: AUC difference > 5%. This may indicate overfitting.
1:17:33.374317 INFO: Resetting torch num_threads to 32
1:17:33.380468 PROGRESS: === Extracted 29366 precursors and 170961 fragments ===
1:17:33.380897 INFO: === FDR correction performed with classifier version -1 ===
1:17:33.381391 PROGRESS: ============================= Precursor FDR =============================
1:17:33.381488 PROGRESS: Total precursors accumulated: 0
1:17:33.381550 PROGRESS: Target precursors: 0 (0.00%)
1:17:33.381603 PROGRESS: Decoy precursors: 0 (0.00%)
1:17:33.381651 PROGRESS: 
1:17:33.381698 PROGRESS: Precursor Summary:
1:17:33.381811 PROGRESS: 
1:17:33.381874 PROGRESS: Protein Summary:
1:17:33.381952 PROGRESS: =========================================================================
1:17:33.382413 INFO: Target number of precursors not reached yet.
1:17:33.493266 INFO: Starting optimization step 4.
1:17:33.493512 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:17:33.493594 INFO: Using rust extraction backend
1:17:33.493659 PROGRESS: Extracting batch of 31339 precursors
1:17:33.549306 INFO: === Search parameters used ===
1:17:33.549552 INFO: rt_error       : 716.8717651367188
1:17:33.549618 INFO: mobility_error : 0.1
1:17:33.549675 INFO: num_candidates : 1
1:17:33.549728 INFO: ms1_error      : 20
1:17:33.549774 INFO: ms2_error      : 20
1:17:33.549819 INFO: fwhm_rt        : 5
1:17:33.549875 INFO: quant_window   : 3
1:17:33.549923 INFO: ==============================================
1:17:33.852041 INFO: performing precursor FDR with 40 features
1:17:33.852150 INFO: Decoy channel: -1
1:17:33.852178 INFO: competitive: True
1:17:33.873762 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:33.887521 INFO: Estimating optimal hyperparameters - samples: 48,536, batch_size: 198, learning_rate: 2.20e-04
1:17:33.887718 INFO: Using random state 340714 for train-test-split
1:17:37.436859 INFO: Test AUC: 0.578
1:17:37.436953 INFO: Train AUC: 0.606
1:17:37.436983 INFO: AUC difference: 4.67%
1:17:37.699569 INFO: Resetting torch num_threads to 32
1:17:37.710016 PROGRESS: === Extracted 60671 precursors and 354328 fragments ===
1:17:37.710615 INFO: === FDR correction performed with classifier version -1 ===
1:17:37.711161 PROGRESS: ============================= Precursor FDR =============================
1:17:37.711253 PROGRESS: Total precursors accumulated: 0
1:17:37.711316 PROGRESS: Target precursors: 0 (0.00%)
1:17:37.711371 PROGRESS: Decoy precursors: 0 (0.00%)
1:17:37.711421 PROGRESS: 
1:17:37.711468 PROGRESS: Precursor Summary:
1:17:37.711590 PROGRESS: 
1:17:37.711654 PROGRESS: Protein Summary:
1:17:37.711730 PROGRESS: =========================================================================
1:17:37.712642 INFO: Target number of precursors not reached yet.
1:17:37.862984 INFO: Starting optimization step 5.
1:17:37.863238 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:17:37.863322 INFO: Using rust extraction backend
1:17:37.863392 PROGRESS: Extracting batch of 62709 precursors
1:17:37.972557 INFO: === Search parameters used ===
1:17:37.972809 INFO: rt_error       : 716.8717651367188
1:17:37.972881 INFO: mobility_error : 0.1
1:17:37.972934 INFO: num_candidates : 1
1:17:37.972991 INFO: ms1_error      : 20
1:17:37.973038 INFO: ms2_error      : 20
1:17:37.973082 INFO: fwhm_rt        : 5
1:17:37.973125 INFO: quant_window   : 3
1:17:37.973168 INFO: ==============================================
1:17:38.540353 INFO: performing precursor FDR with 40 features
1:17:38.540471 INFO: Decoy channel: -1
1:17:38.540497 INFO: competitive: True
1:17:38.585489 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:38.617450 INFO: Estimating optimal hyperparameters - samples: 98,648, batch_size: 404, learning_rate: 3.14e-04
1:17:38.617765 INFO: Using random state 767220 for train-test-split
1:17:42.962273 INFO: Test AUC: 0.582
1:17:42.962390 INFO: Train AUC: 0.605
1:17:42.962424 INFO: AUC difference: 3.81%
1:17:43.247499 INFO: Resetting torch num_threads to 32
1:17:43.268439 PROGRESS: === Extracted 123310 precursors and 720780 fragments ===
1:17:43.269071 INFO: === FDR correction performed with classifier version -1 ===
1:17:43.269627 PROGRESS: ============================= Precursor FDR =============================
1:17:43.269717 PROGRESS: Total precursors accumulated: 0
1:17:43.269780 PROGRESS: Target precursors: 0 (0.00%)
1:17:43.269836 PROGRESS: Decoy precursors: 0 (0.00%)
1:17:43.269887 PROGRESS: 
1:17:43.269939 PROGRESS: Precursor Summary:
1:17:43.270065 PROGRESS: 
1:17:43.270131 PROGRESS: Protein Summary:
1:17:43.270211 PROGRESS: =========================================================================
1:17:43.272347 INFO: Target number of precursors not reached yet.
1:17:43.506660 INFO: Starting optimization step 6.
1:17:43.506921 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:17:43.507013 INFO: Using rust extraction backend
1:17:43.507082 PROGRESS: Extracting batch of 125408 precursors
1:17:43.724042 INFO: === Search parameters used ===
1:17:43.724301 INFO: rt_error       : 716.8717651367188
1:17:43.724367 INFO: mobility_error : 0.1
1:17:43.724417 INFO: num_candidates : 1
1:17:43.724466 INFO: ms1_error      : 20
1:17:43.724518 INFO: ms2_error      : 20
1:17:43.724563 INFO: fwhm_rt        : 5
1:17:43.724607 INFO: quant_window   : 3
1:17:43.724653 INFO: ==============================================
1:17:44.790602 INFO: performing precursor FDR with 40 features
1:17:44.790717 INFO: Decoy channel: -1
1:17:44.790745 INFO: competitive: True
1:17:44.885725 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:44.959933 INFO: Estimating optimal hyperparameters - samples: 198,881, batch_size: 814, learning_rate: 4.46e-04
1:17:44.960342 INFO: Using random state 127885 for train-test-split
1:17:51.330470 INFO: Test AUC: 0.582
1:17:51.330586 INFO: Train AUC: 0.607
1:17:51.330619 INFO: AUC difference: 4.12%
1:17:51.660165 INFO: Resetting torch num_threads to 32
1:17:51.704472 PROGRESS: === Extracted 248602 precursors and 1452903 fragments ===
1:17:51.705116 INFO: === FDR correction performed with classifier version -1 ===
1:17:51.705742 PROGRESS: ============================= Precursor FDR =============================
1:17:51.705841 PROGRESS: Total precursors accumulated: 250
1:17:51.705910 PROGRESS: Target precursors: 248 (99.20%)
1:17:51.705972 PROGRESS: Decoy precursors: 2 (0.80%)
1:17:51.706030 PROGRESS: 
1:17:51.706084 PROGRESS: Precursor Summary:
1:17:51.707156 PROGRESS: Channel   0:	 0.050 FDR:   248; 0.010 FDR:   248; 0.001 FDR:   223
1:17:51.707256 PROGRESS: 
1:17:51.707321 PROGRESS: Protein Summary:
1:17:51.708544 PROGRESS: Channel   0:	 0.050 FDR:   230; 0.010 FDR:   230; 0.001 FDR:   207
1:17:51.708642 PROGRESS: =========================================================================
1:17:51.712507 INFO: Target number of precursors not reached yet.
1:17:52.102030 INFO: Starting optimization step 7.
1:17:52.102274 PROGRESS: === Extracting elution groups 127000 to 255000 ===
1:17:52.102394 INFO: Using rust extraction backend
1:17:52.102484 PROGRESS: Extracting batch of 250773 precursors
1:17:52.534546 INFO: === Search parameters used ===
1:17:52.534810 INFO: rt_error       : 716.8717651367188
1:17:52.534886 INFO: mobility_error : 0.1
1:17:52.534949 INFO: num_candidates : 1
1:17:52.535006 INFO: ms1_error      : 20
1:17:52.535056 INFO: ms2_error      : 20
1:17:52.535105 INFO: fwhm_rt        : 5
1:17:52.535152 INFO: quant_window   : 3
1:17:52.535199 INFO: ==============================================
1:17:54.654280 INFO: performing precursor FDR with 40 features
1:17:54.654427 INFO: Decoy channel: -1
1:17:54.654456 INFO: competitive: True
1:17:54.836344 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:55.011610 INFO: Estimating optimal hyperparameters - samples: 399,285, batch_size: 1,635, learning_rate: 6.32e-04
1:17:55.012271 INFO: Using random state 694332 for train-test-split
1:18:05.014534 INFO: Test AUC: 0.588
1:18:05.014658 INFO: Train AUC: 0.605
1:18:05.014692 INFO: AUC difference: 2.78%
1:18:05.404857 INFO: Resetting torch num_threads to 32
1:18:05.483378 PROGRESS: === Extracted 499107 precursors and 2915440 fragments ===
1:18:05.484012 INFO: === FDR correction performed with classifier version -1 ===
1:18:05.484697 PROGRESS: ============================= Precursor FDR =============================
1:18:05.484804 PROGRESS: Total precursors accumulated: 590
1:18:05.484878 PROGRESS: Target precursors: 585 (99.15%)
1:18:05.484951 PROGRESS: Decoy precursors: 5 (0.85%)
1:18:05.485007 PROGRESS: 
1:18:05.485062 PROGRESS: Precursor Summary:
1:18:05.486207 PROGRESS: Channel   0:	 0.050 FDR:   585; 0.010 FDR:   585; 0.001 FDR:   488
1:18:05.486306 PROGRESS: 
1:18:05.486383 PROGRESS: Protein Summary:
1:18:05.487768 PROGRESS: Channel   0:	 0.050 FDR:   507; 0.010 FDR:   507; 0.001 FDR:   427
1:18:05.487865 PROGRESS: =========================================================================
1:18:05.494473 INFO: Target number of precursors not reached yet.
1:18:06.145557 INFO: Starting optimization step 8.
1:18:06.145806 PROGRESS: === Extracting elution groups 255000 to 511000 ===
1:18:06.145895 INFO: Using rust extraction backend
1:18:06.145967 PROGRESS: Extracting batch of 501436 precursors
1:18:07.002403 INFO: === Search parameters used ===
1:18:07.002647 INFO: rt_error       : 716.8717651367188
1:18:07.002712 INFO: mobility_error : 0.1
1:18:07.002769 INFO: num_candidates : 1
1:18:07.002820 INFO: ms1_error      : 20
1:18:07.002866 INFO: ms2_error      : 20
1:18:07.002915 INFO: fwhm_rt        : 5
1:18:07.002962 INFO: quant_window   : 3
1:18:07.003010 INFO: ==============================================
1:18:11.027993 INFO: performing precursor FDR with 40 features
1:18:11.028115 INFO: Decoy channel: -1
1:18:11.028143 INFO: competitive: True
1:18:11.399603 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:11.800484 INFO: Estimating optimal hyperparameters - samples: 800,052, batch_size: 3,277, learning_rate: 8.94e-04
1:18:11.801934 INFO: Using random state 863705 for train-test-split
1:18:29.076647 INFO: Test AUC: 0.593
1:18:29.076799 INFO: Train AUC: 0.602
1:18:29.076833 INFO: AUC difference: 1.61%
1:18:29.633950 INFO: Resetting torch num_threads to 32
1:18:29.817757 PROGRESS: === Extracted 1000066 precursors and 5848205 fragments ===
1:18:29.818419 INFO: === FDR correction performed with classifier version -1 ===
1:18:29.819252 PROGRESS: ============================= Precursor FDR =============================
1:18:29.819346 PROGRESS: Total precursors accumulated: 1,381
1:18:29.819412 PROGRESS: Target precursors: 1,368 (99.06%)
1:18:29.819467 PROGRESS: Decoy precursors: 13 (0.94%)
1:18:29.819519 PROGRESS: 
1:18:29.819569 PROGRESS: Precursor Summary:
1:18:29.820928 PROGRESS: Channel   0:	 0.050 FDR: 1,368; 0.010 FDR: 1,368; 0.001 FDR: 1,012
1:18:29.821027 PROGRESS: 
1:18:29.821085 PROGRESS: Protein Summary:
1:18:29.823462 PROGRESS: Channel   0:	 0.050 FDR: 1,087; 0.010 FDR: 1,087; 0.001 FDR:   823
1:18:29.823565 PROGRESS: =========================================================================
1:18:29.835468 INFO: Target number of precursors reached.
1:18:30.480152 INFO: fragments_df: keeping 5000 of 5848205 [sum(precursor_idx_mask)=14900 sum(mass_error_mask)=5848205 stop_rank=5000
1:18:31.585090 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:18:31.815641 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:18:32.542740 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:18:32.543208 INFO: Using score_cutoff 8.90564762020111 (fac=0.99, q=1)
1:18:32.543548 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:18:32.543631 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:18:32.543694 INFO: Updating optimization_manager: score_cutoff        : 0 -> 8.90564762020111
1:18:32.543763 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:18:33.139718 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:18:34.431373 INFO: Updating optimization_manager: classifier_version  : -1 -> 8
1:18:34.431606 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:18:34.431713 INFO: Starting optimization step 9.
1:18:34.431784 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:18:34.431879 INFO: Using rust extraction backend
1:18:34.431946 PROGRESS: Extracting batch of 1001059 precursors
1:18:36.132010 INFO: === Search parameters used ===
1:18:36.132278 INFO: rt_error       : 716.8717651367188
1:18:36.132344 INFO: mobility_error : 0.1
1:18:36.132403 INFO: num_candidates : 3
1:18:36.132456 INFO: ms1_error      : 20
1:18:36.132508 INFO: ms2_error      : 20
1:18:36.132569 INFO: fwhm_rt        : 3.0
1:18:36.132614 INFO: quant_window   : 3
1:18:36.132659 INFO: ==============================================
1:18:49.930284 INFO: performing precursor FDR with 40 features
1:18:49.930443 INFO: Decoy channel: -1
1:18:49.930472 INFO: competitive: True
1:18:50.655479 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:51.965935 INFO: Estimating optimal hyperparameters - samples: 2,400,404, batch_size: 4,096, learning_rate: 1.00e-03
1:18:51.971218 INFO: Using random state 277247 for train-test-split
1:19:37.641871 INFO: Test AUC: 0.602
1:19:37.642017 INFO: Train AUC: 0.605
1:19:37.642060 INFO: AUC difference: 0.57%
1:19:38.840584 INFO: Resetting torch num_threads to 32
1:19:38.953481 PROGRESS: === Extracted 3000505 precursors and 17468711 fragments ===
1:19:38.954008 INFO: === FDR correction performed with classifier version 8 ===
1:19:38.954811 PROGRESS: ============================= Precursor FDR =============================
1:19:38.954921 PROGRESS: Total precursors accumulated: 1,525
1:19:38.955000 PROGRESS: Target precursors: 1,510 (99.02%)
1:19:38.955059 PROGRESS: Decoy precursors: 15 (0.98%)
1:19:38.955108 PROGRESS: 
1:19:38.955161 PROGRESS: Precursor Summary:
1:19:38.956616 PROGRESS: Channel   0:	 0.050 FDR: 1,510; 0.010 FDR: 1,510; 0.001 FDR: 1,174
1:19:38.956718 PROGRESS: 
1:19:38.956777 PROGRESS: Protein Summary:
1:19:38.958676 PROGRESS: Channel   0:	 0.050 FDR: 1,195; 0.010 FDR: 1,195; 0.001 FDR:   944
1:19:38.958778 PROGRESS: =========================================================================
1:19:39.016994 INFO: Target number of precursors reached.
1:19:40.911744 INFO: fragments_df: keeping 5000 of 17468711 [sum(precursor_idx_mask)=38085 sum(mass_error_mask)=17468711 stop_rank=5000
1:19:42.067981 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:19:42.311775 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:19:43.032041 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:19:43.032492 INFO: Using score_cutoff 8.372590529823302 (fac=0.99, q=1)
1:19:43.032829 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:19:43.032912 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:19:43.032971 INFO: Updating optimization_manager: score_cutoff        : 8.90564762020111 -> 8.372590529823302
1:19:43.033029 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:19:43.635102 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:19:44.971955 INFO: === checking if optimization conditions were reached ===
1:19:44.974186 INFO: Updating optimization_manager: ms2_error           : 20 -> 10.0
1:19:44.974343 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:19:44.974435 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:19:44.974496 INFO: ==============================================
1:19:44.974565 INFO: Starting optimization step 10.
1:19:44.974627 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:19:44.974699 INFO: Using rust extraction backend
1:19:44.974764 PROGRESS: Extracting batch of 1001059 precursors
1:19:46.663217 INFO: === Search parameters used ===
1:19:46.663496 INFO: rt_error       : 716.8717651367188
1:19:46.663573 INFO: mobility_error : 0.1
1:19:46.663660 INFO: num_candidates : 3
1:19:46.663720 INFO: ms1_error      : 20
1:19:46.663773 INFO: ms2_error      : 10.0
1:19:46.663824 INFO: fwhm_rt        : 3.0
1:19:46.663871 INFO: quant_window   : 3
1:19:46.663914 INFO: ==============================================
1:20:00.130686 INFO: performing precursor FDR with 40 features
1:20:00.130807 INFO: Decoy channel: -1
1:20:00.130836 INFO: competitive: True
1:20:00.871566 INFO: Setting torch num_threads to 2 for FDR classification task
1:20:02.200174 INFO: Estimating optimal hyperparameters - samples: 2,402,056, batch_size: 4,096, learning_rate: 1.00e-03
1:20:02.204951 INFO: Using random state 231448 for train-test-split
1:20:48.455960 INFO: Test AUC: 0.608
1:20:48.456123 INFO: Train AUC: 0.612
1:20:48.456158 INFO: AUC difference: 0.57%
1:20:49.680499 INFO: Resetting torch num_threads to 32
1:20:49.793937 PROGRESS: === Extracted 3002571 precursors and 19171359 fragments ===
1:20:49.794479 INFO: === FDR correction performed with classifier version 9 ===
1:20:49.795360 PROGRESS: ============================= Precursor FDR =============================
1:20:49.795480 PROGRESS: Total precursors accumulated: 1,969
1:20:49.795551 PROGRESS: Target precursors: 1,950 (99.04%)
1:20:49.795610 PROGRESS: Decoy precursors: 19 (0.96%)
1:20:49.795659 PROGRESS: 
1:20:49.795712 PROGRESS: Precursor Summary:
1:20:49.797326 PROGRESS: Channel   0:	 0.050 FDR: 1,950; 0.010 FDR: 1,950; 0.001 FDR: 1,260
1:20:49.797430 PROGRESS: 
1:20:49.797494 PROGRESS: Protein Summary:
1:20:49.799503 PROGRESS: Channel   0:	 0.050 FDR: 1,491; 0.010 FDR: 1,491; 0.001 FDR: 1,010
1:20:49.799603 PROGRESS: =========================================================================
1:20:49.855438 INFO: Target number of precursors reached.
1:20:51.785046 INFO: fragments_df: keeping 5000 of 19171359 [sum(precursor_idx_mask)=52197 sum(mass_error_mask)=19171359 stop_rank=5000
1:20:52.868779 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:20:53.163578 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:20:53.888130 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:20:53.888624 INFO: Using score_cutoff 8.95686896238327 (fac=0.99, q=1)
1:20:53.888972 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:20:53.889056 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:20:53.889113 INFO: Updating optimization_manager: score_cutoff        : 8.372590529823302 -> 8.95686896238327
1:20:53.889177 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:20:54.497616 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:20:55.869941 INFO: === checking if optimization conditions were reached ===
1:20:55.872267 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:20:55.872422 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:20:55.872496 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:20:55.872559 INFO: ==============================================
1:20:55.872639 INFO: Starting optimization step 11.
1:20:55.872709 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:20:55.872802 INFO: Using rust extraction backend
1:20:55.872892 PROGRESS: Extracting batch of 1001059 precursors
1:20:57.579273 INFO: === Search parameters used ===
1:20:57.579648 INFO: rt_error       : 716.8717651367188
1:20:57.579719 INFO: mobility_error : 0.1
1:20:57.579777 INFO: num_candidates : 3
1:20:57.579828 INFO: ms1_error      : 20
1:20:57.579878 INFO: ms2_error      : 10.0
1:20:57.579935 INFO: fwhm_rt        : 3.0
1:20:57.579985 INFO: quant_window   : 3
1:20:57.580034 INFO: ==============================================
1:21:11.375051 INFO: performing precursor FDR with 40 features
1:21:11.375175 INFO: Decoy channel: -1
1:21:11.375204 INFO: competitive: True
1:21:12.113552 INFO: Setting torch num_threads to 2 for FDR classification task
1:21:13.402319 INFO: Estimating optimal hyperparameters - samples: 2,402,042, batch_size: 4,096, learning_rate: 1.00e-03
1:21:13.407570 INFO: Using random state 800347 for train-test-split
1:21:59.636251 INFO: Test AUC: 0.610
1:21:59.636439 INFO: Train AUC: 0.614
1:21:59.636475 INFO: AUC difference: 0.64%
1:22:00.874765 INFO: Resetting torch num_threads to 32
1:22:00.980867 PROGRESS: === Extracted 3002553 precursors and 19145784 fragments ===
1:22:00.981410 INFO: === FDR correction performed with classifier version 10 ===
1:22:00.982407 PROGRESS: ============================= Precursor FDR =============================
1:22:00.982520 PROGRESS: Total precursors accumulated: 1,980
1:22:00.982591 PROGRESS: Target precursors: 1,961 (99.04%)
1:22:00.982661 PROGRESS: Decoy precursors: 19 (0.96%)
1:22:00.982716 PROGRESS: 
1:22:00.982774 PROGRESS: Precursor Summary:
1:22:00.984396 PROGRESS: Channel   0:	 0.050 FDR: 1,961; 0.010 FDR: 1,961; 0.001 FDR: 1,455
1:22:00.984497 PROGRESS: 
1:22:00.984566 PROGRESS: Protein Summary:
1:22:00.986644 PROGRESS: Channel   0:	 0.050 FDR: 1,491; 0.010 FDR: 1,491; 0.001 FDR: 1,146
1:22:00.986763 PROGRESS: =========================================================================
1:22:01.042920 INFO: Target number of precursors reached.
1:22:03.048425 INFO: fragments_df: keeping 5000 of 19145784 [sum(precursor_idx_mask)=52613 sum(mass_error_mask)=19145784 stop_rank=5000
1:22:04.399057 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:22:04.655770 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:22:05.374344 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:22:05.374817 INFO: Using score_cutoff 9.352065605163574 (fac=0.99, q=1)
1:22:05.375143 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:22:05.375238 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:22:05.375305 INFO: Updating optimization_manager: score_cutoff        : 8.95686896238327 -> 9.352065605163574
1:22:05.375375 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:22:05.997732 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:22:07.358537 INFO: === checking if optimization conditions were reached ===
1:22:07.360990 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:22:07.361154 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:22:07.361229 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:22:07.361310 INFO: ==============================================
1:22:07.361397 INFO: Starting optimization step 12.
1:22:07.361476 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:22:07.361568 INFO: Using rust extraction backend
1:22:07.361650 PROGRESS: Extracting batch of 1001059 precursors
1:22:09.054731 INFO: === Search parameters used ===
1:22:09.054997 INFO: rt_error       : 716.8717651367188
1:22:09.055065 INFO: mobility_error : 0.1
1:22:09.055120 INFO: num_candidates : 3
1:22:09.055167 INFO: ms1_error      : 20
1:22:09.055213 INFO: ms2_error      : 10.0
1:22:09.055257 INFO: fwhm_rt        : 3.0
1:22:09.055300 INFO: quant_window   : 3
1:22:09.055346 INFO: ==============================================
1:22:22.575649 INFO: performing precursor FDR with 40 features
1:22:22.575804 INFO: Decoy channel: -1
1:22:22.575834 INFO: competitive: True
1:22:23.324485 INFO: Setting torch num_threads to 2 for FDR classification task
1:22:24.647599 INFO: Estimating optimal hyperparameters - samples: 2,402,044, batch_size: 4,096, learning_rate: 1.00e-03
1:22:24.652879 INFO: Using random state 828436 for train-test-split
1:23:10.579430 INFO: Test AUC: 0.612
1:23:10.579575 INFO: Train AUC: 0.615
1:23:10.579612 INFO: AUC difference: 0.46%
1:23:11.809168 INFO: Resetting torch num_threads to 32
1:23:11.904138 PROGRESS: === Extracted 3002555 precursors and 19139413 fragments ===
1:23:11.904674 INFO: === FDR correction performed with classifier version 11 ===
1:23:11.905528 PROGRESS: ============================= Precursor FDR =============================
1:23:11.905646 PROGRESS: Total precursors accumulated: 2,090
1:23:11.905733 PROGRESS: Target precursors: 2,070 (99.04%)
1:23:11.905811 PROGRESS: Decoy precursors: 20 (0.96%)
1:23:11.905899 PROGRESS: 
1:23:11.905972 PROGRESS: Precursor Summary:
1:23:11.907554 PROGRESS: Channel   0:	 0.050 FDR: 2,070; 0.010 FDR: 2,070; 0.001 FDR: 1,335
1:23:11.907668 PROGRESS: 
1:23:11.907748 PROGRESS: Protein Summary:
1:23:11.909814 PROGRESS: Channel   0:	 0.050 FDR: 1,588; 0.010 FDR: 1,588; 0.001 FDR: 1,079
1:23:11.909925 PROGRESS: =========================================================================
1:23:11.963539 INFO: Target number of precursors reached.
1:23:13.984063 INFO: fragments_df: keeping 5000 of 19139413 [sum(precursor_idx_mask)=55216 sum(mass_error_mask)=19139413 stop_rank=5000
1:23:14.755106 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:15.065192 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:15.787522 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:15.787986 INFO: Using score_cutoff 8.187026964855194 (fac=0.99, q=1)
1:23:15.788320 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:15.788413 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:15.788477 INFO: Updating optimization_manager: score_cutoff        : 9.352065605163574 -> 8.187026964855194
1:23:15.788545 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:16.087028 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:16.767544 INFO: === checking if optimization conditions were reached ===
1:23:16.769703 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:23:16.769856 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
1:23:16.769932 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:23:16.770001 INFO: ==============================================
1:23:16.770081 INFO: Starting optimization step 13.
1:23:16.770149 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:23:16.770235 INFO: Using rust extraction backend
1:23:16.770321 PROGRESS: Extracting batch of 499623 precursors
1:23:17.624333 INFO: === Search parameters used ===
1:23:17.624624 INFO: rt_error       : 716.8717651367188
1:23:17.624687 INFO: mobility_error : 0.1
1:23:17.624743 INFO: num_candidates : 3
1:23:17.624794 INFO: ms1_error      : 20
1:23:17.624843 INFO: ms2_error      : 10.0
1:23:17.624899 INFO: fwhm_rt        : 3.0
1:23:17.624947 INFO: quant_window   : 3
1:23:17.625019 INFO: ==============================================
1:23:24.116017 INFO: performing precursor FDR with 40 features
1:23:24.116145 INFO: Decoy channel: -1
1:23:24.116174 INFO: competitive: True
1:23:24.462577 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:25.086208 INFO: Estimating optimal hyperparameters - samples: 1,198,851, batch_size: 4,096, learning_rate: 1.00e-03
1:23:25.088696 INFO: Using random state 414462 for train-test-split
1:23:47.214083 INFO: Test AUC: 0.611
1:23:47.214278 INFO: Train AUC: 0.619
1:23:47.214318 INFO: AUC difference: 1.33%
1:23:47.951799 INFO: Resetting torch num_threads to 32
1:23:48.004641 PROGRESS: === Extracted 1498564 precursors and 9551829 fragments ===
1:23:48.005152 INFO: === FDR correction performed with classifier version 12 ===
1:23:48.005791 PROGRESS: ============================= Precursor FDR =============================
1:23:48.005890 PROGRESS: Total precursors accumulated: 1,052
1:23:48.005960 PROGRESS: Target precursors: 1,042 (99.05%)
1:23:48.006030 PROGRESS: Decoy precursors: 10 (0.95%)
1:23:48.006094 PROGRESS: 
1:23:48.006172 PROGRESS: Precursor Summary:
1:23:48.007458 PROGRESS: Channel   0:	 0.050 FDR: 1,042; 0.010 FDR: 1,042; 0.001 FDR:   634
1:23:48.007561 PROGRESS: 
1:23:48.007634 PROGRESS: Protein Summary:
1:23:48.009224 PROGRESS: Channel   0:	 0.050 FDR:   890; 0.010 FDR:   890; 0.001 FDR:   546
1:23:48.009327 PROGRESS: =========================================================================
1:23:48.036518 INFO: Target number of precursors reached.
1:23:49.035588 INFO: fragments_df: keeping 5000 of 9551829 [sum(precursor_idx_mask)=26831 sum(mass_error_mask)=9551829 stop_rank=5000
1:23:49.770686 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:49.966930 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:50.685339 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:50.685859 INFO: Using score_cutoff 6.4762056097984315 (fac=0.99, q=1)
1:23:50.686245 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:50.686333 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:50.686415 INFO: Updating optimization_manager: score_cutoff        : 8.187026964855194 -> 6.4762056097984315
1:23:50.686478 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:50.982449 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:51.666973 INFO: === checking if optimization conditions were reached ===
1:23:51.669160 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:23:51.669304 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
1:23:51.669378 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:23:51.669443 INFO: ==============================================
1:23:51.669527 PROGRESS: Optimization finished for ms2_error.
1:23:52.395835 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:52.700922 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:53.379512 INFO: Starting optimization step 0.
1:23:53.379754 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:23:53.379853 INFO: Using rust extraction backend
1:23:53.379939 PROGRESS: Extracting batch of 499623 precursors
1:23:54.239173 INFO: === Search parameters used ===
1:23:54.239485 INFO: rt_error       : 716.8717651367188
1:23:54.239549 INFO: mobility_error : 0.1
1:23:54.239617 INFO: num_candidates : 3
1:23:54.239668 INFO: ms1_error      : 20
1:23:54.239713 INFO: ms2_error      : 10.0
1:23:54.239761 INFO: fwhm_rt        : 3.0
1:23:54.239804 INFO: quant_window   : 3
1:23:54.239848 INFO: ==============================================
1:24:01.696531 INFO: performing precursor FDR with 40 features
1:24:01.696651 INFO: Decoy channel: -1
1:24:01.696679 INFO: competitive: True
1:24:02.053800 INFO: Setting torch num_threads to 2 for FDR classification task
1:24:02.678821 INFO: Estimating optimal hyperparameters - samples: 1,198,852, batch_size: 4,096, learning_rate: 1.00e-03
1:24:02.681216 INFO: Using random state 532988 for train-test-split
1:24:24.987056 INFO: Test AUC: 0.612
1:24:24.987241 INFO: Train AUC: 0.620
1:24:24.987277 INFO: AUC difference: 1.34%
1:24:25.709227 INFO: Resetting torch num_threads to 32
1:24:25.759945 PROGRESS: === Extracted 1498566 precursors and 9574290 fragments ===
1:24:25.760460 INFO: === FDR correction performed with classifier version 13 ===
1:24:25.761112 PROGRESS: ============================= Precursor FDR =============================
1:24:25.761212 PROGRESS: Total precursors accumulated: 1,150
1:24:25.761280 PROGRESS: Target precursors: 1,139 (99.04%)
1:24:25.761340 PROGRESS: Decoy precursors: 11 (0.96%)
1:24:25.761394 PROGRESS: 
1:24:25.761447 PROGRESS: Precursor Summary:
1:24:25.762772 PROGRESS: Channel   0:	 0.050 FDR: 1,139; 0.010 FDR: 1,139; 0.001 FDR:   817
1:24:25.762873 PROGRESS: 
1:24:25.762939 PROGRESS: Protein Summary:
1:24:25.764553 PROGRESS: Channel   0:	 0.050 FDR:   963; 0.010 FDR:   963; 0.001 FDR:   697
1:24:25.764659 PROGRESS: =========================================================================
1:24:25.792379 INFO: Target number of precursors reached.
1:24:26.852017 INFO: fragments_df: keeping 5000 of 9574290 [sum(precursor_idx_mask)=29763 sum(mass_error_mask)=9574290 stop_rank=5000
1:24:27.579484 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:24:27.787781 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:24:28.506930 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:24:28.507405 INFO: Using score_cutoff 7.711953224372864 (fac=0.99, q=1)
1:24:28.507741 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:24:28.507838 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:24:28.507900 INFO: Updating optimization_manager: score_cutoff        : 6.4762056097984315 -> 7.711953224372864
1:24:28.507964 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:24:28.807146 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:24:29.507376 INFO: === checking if optimization conditions were reached ===
1:24:29.507646 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:24:29.510174 INFO: Updating optimization_manager: rt_error            : 716.8717651367188 -> 868.1295090370324
1:24:29.510304 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 868.1295.
1:24:29.510399 INFO: ==============================================
1:24:29.510488 INFO: Starting optimization step 1.
1:24:29.510557 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:24:29.510639 INFO: Using rust extraction backend
1:24:29.510712 PROGRESS: Extracting batch of 499623 precursors
1:24:30.375572 INFO: === Search parameters used ===
1:24:30.375892 INFO: rt_error       : 868.1295090370324
1:24:30.375959 INFO: mobility_error : 0.1
1:24:30.376021 INFO: num_candidates : 3
1:24:30.376070 INFO: ms1_error      : 20
1:24:30.376121 INFO: ms2_error      : 10.0
1:24:30.376169 INFO: fwhm_rt        : 3.0
1:24:30.376216 INFO: quant_window   : 3
1:24:30.376269 INFO: ==============================================
1:24:37.313168 INFO: performing precursor FDR with 40 features
1:24:37.313339 INFO: Decoy channel: -1
1:24:37.313369 INFO: competitive: True
1:24:37.668634 INFO: Setting torch num_threads to 2 for FDR classification task
1:24:38.261261 INFO: Estimating optimal hyperparameters - samples: 1,198,877, batch_size: 4,096, learning_rate: 1.00e-03
1:24:38.263656 INFO: Using random state 532988 for train-test-split
1:25:00.650392 INFO: Test AUC: 0.612
1:25:00.650552 INFO: Train AUC: 0.620
1:25:00.650586 INFO: AUC difference: 1.20%
1:25:01.385425 INFO: Resetting torch num_threads to 32
1:25:01.435585 PROGRESS: === Extracted 1498597 precursors and 9626538 fragments ===
1:25:01.436076 INFO: === FDR correction performed with classifier version 13 ===
1:25:01.436718 PROGRESS: ============================= Precursor FDR =============================
1:25:01.436818 PROGRESS: Total precursors accumulated: 1,049
1:25:01.436895 PROGRESS: Target precursors: 1,039 (99.05%)
1:25:01.436957 PROGRESS: Decoy precursors: 10 (0.95%)
1:25:01.437015 PROGRESS: 
1:25:01.437073 PROGRESS: Precursor Summary:
1:25:01.438345 PROGRESS: Channel   0:	 0.050 FDR: 1,039; 0.010 FDR: 1,039; 0.001 FDR:   799
1:25:01.438473 PROGRESS: 
1:25:01.438543 PROGRESS: Protein Summary:
1:25:01.440152 PROGRESS: Channel   0:	 0.050 FDR:   895; 0.010 FDR:   895; 0.001 FDR:   684
1:25:01.440252 PROGRESS: =========================================================================
1:25:01.466610 INFO: Target number of precursors reached.
1:25:02.449741 INFO: fragments_df: keeping 5000 of 9626538 [sum(precursor_idx_mask)=26248 sum(mass_error_mask)=9626538 stop_rank=5000
1:25:03.183524 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:25:04.281257 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:25:05.003364 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:25:05.003803 INFO: Using score_cutoff 5.832120046234131 (fac=0.99, q=1)
1:25:05.004114 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:25:05.004197 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:25:05.004260 INFO: Updating optimization_manager: score_cutoff        : 7.711953224372864 -> 5.832120046234131
1:25:05.004330 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:05.292690 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:05.992797 INFO: === checking if optimization conditions were reached ===
1:25:05.993057 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:25:05.995624 INFO: Updating optimization_manager: rt_error            : 868.1295090370324 -> 1089.7595737797865
1:25:05.995764 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 1089.7596.
1:25:05.995838 INFO: ==============================================
1:25:05.995916 INFO: Starting optimization step 2.
1:25:05.995987 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:25:05.996057 INFO: Using rust extraction backend
1:25:05.996130 PROGRESS: Extracting batch of 499623 precursors
1:25:06.857430 INFO: === Search parameters used ===
1:25:06.857698 INFO: rt_error       : 1089.7595737797865
1:25:06.857765 INFO: mobility_error : 0.1
1:25:06.857822 INFO: num_candidates : 3
1:25:06.857874 INFO: ms1_error      : 20
1:25:06.857930 INFO: ms2_error      : 10.0
1:25:06.857978 INFO: fwhm_rt        : 3.0
1:25:06.858026 INFO: quant_window   : 3
1:25:06.858073 INFO: ==============================================
1:25:13.932021 INFO: performing precursor FDR with 40 features
1:25:13.932148 INFO: Decoy channel: -1
1:25:13.932174 INFO: competitive: True
1:25:14.313819 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:14.931393 INFO: Estimating optimal hyperparameters - samples: 1,198,883, batch_size: 4,096, learning_rate: 1.00e-03
1:25:14.933871 INFO: Using random state 532988 for train-test-split
1:25:37.742786 INFO: Test AUC: 0.613
1:25:37.742966 INFO: Train AUC: 0.620
1:25:37.743001 INFO: AUC difference: 1.15%
1:25:38.458279 INFO: Resetting torch num_threads to 32
1:25:38.510947 PROGRESS: === Extracted 1498604 precursors and 9641499 fragments ===
1:25:38.511464 INFO: === FDR correction performed with classifier version 13 ===
1:25:38.512165 PROGRESS: ============================= Precursor FDR =============================
1:25:38.512271 PROGRESS: Total precursors accumulated: 1,060
1:25:38.512342 PROGRESS: Target precursors: 1,050 (99.06%)
1:25:38.512406 PROGRESS: Decoy precursors: 10 (0.94%)
1:25:38.512463 PROGRESS: 
1:25:38.512517 PROGRESS: Precursor Summary:
1:25:38.513857 PROGRESS: Channel   0:	 0.050 FDR: 1,050; 0.010 FDR: 1,050; 0.001 FDR:   567
1:25:38.513956 PROGRESS: 
1:25:38.514020 PROGRESS: Protein Summary:
1:25:38.515662 PROGRESS: Channel   0:	 0.050 FDR:   892; 0.010 FDR:   892; 0.001 FDR:   483
1:25:38.515777 PROGRESS: =========================================================================
1:25:38.545429 INFO: Target number of precursors reached.
1:25:39.535990 INFO: fragments_df: keeping 5000 of 9641499 [sum(precursor_idx_mask)=27343 sum(mass_error_mask)=9641499 stop_rank=5000
1:25:40.267367 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:25:40.460187 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:25:41.184046 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:25:41.184511 INFO: Using score_cutoff 6.599885101604461 (fac=0.99, q=1)
1:25:41.184852 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:25:41.184952 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:25:41.185031 INFO: Updating optimization_manager: score_cutoff        : 5.832120046234131 -> 6.599885101604461
1:25:41.185117 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:41.481742 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:42.199864 INFO: === checking if optimization conditions were reached ===
1:25:42.200128 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:25:42.202836 INFO: Updating optimization_manager: rt_error            : 1089.7595737797865 -> 1314.7188059329455
1:25:42.202975 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 1314.7188.
1:25:42.203056 INFO: ==============================================
1:25:42.203143 INFO: Starting optimization step 3.
1:25:42.203228 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:25:42.203318 INFO: Using rust extraction backend
1:25:42.203399 PROGRESS: Extracting batch of 499623 precursors
1:25:43.067528 INFO: === Search parameters used ===
1:25:43.067818 INFO: rt_error       : 1314.7188059329455
1:25:43.067889 INFO: mobility_error : 0.1
1:25:43.067945 INFO: num_candidates : 3
1:25:43.068027 INFO: ms1_error      : 20
1:25:43.068076 INFO: ms2_error      : 10.0
1:25:43.068125 INFO: fwhm_rt        : 3.0
1:25:43.068174 INFO: quant_window   : 3
1:25:43.068222 INFO: ==============================================
1:25:50.156843 INFO: performing precursor FDR with 40 features
1:25:50.156968 INFO: Decoy channel: -1
1:25:50.156996 INFO: competitive: True
1:25:50.510408 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:51.109284 INFO: Estimating optimal hyperparameters - samples: 1,198,884, batch_size: 4,096, learning_rate: 1.00e-03
1:25:51.111878 INFO: Using random state 532988 for train-test-split
1:26:14.054217 INFO: Test AUC: 0.613
1:26:14.054345 INFO: Train AUC: 0.620
1:26:14.054396 INFO: AUC difference: 1.05%
1:26:14.783783 INFO: Resetting torch num_threads to 32
1:26:14.832850 PROGRESS: === Extracted 1498605 precursors and 9640565 fragments ===
1:26:14.833389 INFO: === FDR correction performed with classifier version 13 ===
1:26:14.834130 PROGRESS: ============================= Precursor FDR =============================
1:26:14.834260 PROGRESS: Total precursors accumulated: 1,082
1:26:14.834349 PROGRESS: Target precursors: 1,072 (99.08%)
1:26:14.834445 PROGRESS: Decoy precursors: 10 (0.92%)
1:26:14.834523 PROGRESS: 
1:26:14.834608 PROGRESS: Precursor Summary:
1:26:14.835953 PROGRESS: Channel   0:	 0.050 FDR: 1,072; 0.010 FDR: 1,072; 0.001 FDR:   781
1:26:14.836069 PROGRESS: 
1:26:14.836157 PROGRESS: Protein Summary:
1:26:14.837834 PROGRESS: Channel   0:	 0.050 FDR:   917; 0.010 FDR:   917; 0.001 FDR:   661
1:26:14.837943 PROGRESS: =========================================================================
1:26:14.863976 INFO: Target number of precursors reached.
1:26:15.861223 INFO: fragments_df: keeping 5000 of 9640565 [sum(precursor_idx_mask)=27858 sum(mass_error_mask)=9640565 stop_rank=5000
1:26:16.576321 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:26:16.772016 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:26:17.491705 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:26:17.492148 INFO: Using score_cutoff 7.069002348947525 (fac=0.99, q=1)
1:26:17.492480 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:26:17.492570 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:26:17.492638 INFO: Updating optimization_manager: score_cutoff        : 6.599885101604461 -> 7.069002348947525
1:26:17.492701 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:26:17.785657 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:26:18.471445 INFO: === checking if optimization conditions were reached ===
1:26:18.471708 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:26:18.474291 INFO: Updating optimization_manager: rt_error            : 1314.7188059329455 -> 1210.4917950199683
1:26:18.474447 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 1210.4918.
1:26:18.474526 INFO: ==============================================
1:26:18.474625 INFO: Starting optimization step 4.
1:26:18.474696 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:26:18.474783 INFO: Using rust extraction backend
1:26:18.474860 PROGRESS: Extracting batch of 499623 precursors
1:26:19.328000 INFO: === Search parameters used ===
1:26:19.328275 INFO: rt_error       : 1210.4917950199683
1:26:19.328343 INFO: mobility_error : 0.1
1:26:19.328408 INFO: num_candidates : 3
1:26:19.328462 INFO: ms1_error      : 20
1:26:19.328515 INFO: ms2_error      : 10.0
1:26:19.328573 INFO: fwhm_rt        : 3.0
1:26:19.328624 INFO: quant_window   : 3
1:26:19.328684 INFO: ==============================================
1:26:26.182142 INFO: performing precursor FDR with 40 features
1:26:26.182270 INFO: Decoy channel: -1
1:26:26.182310 INFO: competitive: True
1:26:26.550448 INFO: Setting torch num_threads to 2 for FDR classification task
1:26:27.174153 INFO: Estimating optimal hyperparameters - samples: 1,198,882, batch_size: 4,096, learning_rate: 1.00e-03
1:26:27.176699 INFO: Using random state 532988 for train-test-split
1:26:49.647524 INFO: Test AUC: 0.612
1:26:49.647662 INFO: Train AUC: 0.620
1:26:49.647697 INFO: AUC difference: 1.30%
1:26:50.396504 INFO: Resetting torch num_threads to 32
1:26:50.444568 PROGRESS: === Extracted 1498603 precursors and 9640601 fragments ===
1:26:50.445032 INFO: === FDR correction performed with classifier version 13 ===
1:26:50.445655 PROGRESS: ============================= Precursor FDR =============================
1:26:50.445754 PROGRESS: Total precursors accumulated: 1,061
1:26:50.445824 PROGRESS: Target precursors: 1,051 (99.06%)
1:26:50.445884 PROGRESS: Decoy precursors: 10 (0.94%)
1:26:50.445941 PROGRESS: 
1:26:50.445997 PROGRESS: Precursor Summary:
1:26:50.447264 PROGRESS: Channel   0:	 0.050 FDR: 1,051; 0.010 FDR: 1,051; 0.001 FDR:   797
1:26:50.447379 PROGRESS: 
1:26:50.447453 PROGRESS: Protein Summary:
1:26:50.449036 PROGRESS: Channel   0:	 0.050 FDR:   889; 0.010 FDR:   889; 0.001 FDR:   678
1:26:50.449133 PROGRESS: =========================================================================
1:26:50.475402 INFO: Target number of precursors reached.
1:26:51.508190 INFO: fragments_df: keeping 5000 of 9640601 [sum(precursor_idx_mask)=27689 sum(mass_error_mask)=9640601 stop_rank=5000
1:26:52.187584 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:26:52.379680 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:26:53.097888 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:26:53.098318 INFO: Using score_cutoff 7.741780815124511 (fac=0.99, q=1)
1:26:53.098635 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:26:53.098722 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:26:53.098782 INFO: Updating optimization_manager: score_cutoff        : 7.069002348947525 -> 7.741780815124511
1:26:53.098845 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:26:53.391214 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:26:54.071930 INFO: === checking if optimization conditions were reached ===
1:26:54.072171 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:26:54.074722 INFO: Updating optimization_manager: rt_error            : 1210.4917950199683 -> 1189.111035439574
1:26:54.075016 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 1189.1110.
1:26:54.075095 INFO: ==============================================
1:26:54.075174 INFO: Starting optimization step 5.
1:26:54.075241 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:26:54.075311 INFO: Using rust extraction backend
1:26:54.075377 PROGRESS: Extracting batch of 499623 precursors
1:26:54.932042 INFO: === Search parameters used ===
1:26:54.932490 INFO: rt_error       : 1189.111035439574
1:26:54.932570 INFO: mobility_error : 0.1
1:26:54.932629 INFO: num_candidates : 3
1:26:54.932683 INFO: ms1_error      : 20
1:26:54.932730 INFO: ms2_error      : 10.0
1:26:54.932777 INFO: fwhm_rt        : 3.0
1:26:54.932824 INFO: quant_window   : 3
1:26:54.932871 INFO: ==============================================
1:27:01.762408 INFO: performing precursor FDR with 40 features
1:27:01.762533 INFO: Decoy channel: -1
1:27:01.762562 INFO: competitive: True
1:27:02.120642 INFO: Setting torch num_threads to 2 for FDR classification task
1:27:02.734011 INFO: Estimating optimal hyperparameters - samples: 1,198,883, batch_size: 4,096, learning_rate: 1.00e-03
1:27:02.736450 INFO: Using random state 532988 for train-test-split
1:27:24.621073 INFO: Test AUC: 0.612
1:27:24.621202 INFO: Train AUC: 0.620
1:27:24.621237 INFO: AUC difference: 1.27%
1:27:25.341688 INFO: Resetting torch num_threads to 32
1:27:25.390838 PROGRESS: === Extracted 1498604 precursors and 9641166 fragments ===
1:27:25.391314 INFO: === FDR correction performed with classifier version 13 ===
1:27:25.391972 PROGRESS: ============================= Precursor FDR =============================
1:27:25.392077 PROGRESS: Total precursors accumulated: 1,134
1:27:25.392156 PROGRESS: Target precursors: 1,123 (99.03%)
1:27:25.392220 PROGRESS: Decoy precursors: 11 (0.97%)
1:27:25.392280 PROGRESS: 
1:27:25.392348 PROGRESS: Precursor Summary:
1:27:25.393619 PROGRESS: Channel   0:	 0.050 FDR: 1,123; 0.010 FDR: 1,123; 0.001 FDR:   605
1:27:25.393719 PROGRESS: 
1:27:25.393785 PROGRESS: Protein Summary:
1:27:25.395403 PROGRESS: Channel   0:	 0.050 FDR:   950; 0.010 FDR:   950; 0.001 FDR:   521
1:27:25.395506 PROGRESS: =========================================================================
1:27:25.421040 INFO: Target number of precursors reached.
1:27:26.442079 INFO: fragments_df: keeping 5000 of 9641166 [sum(precursor_idx_mask)=29306 sum(mass_error_mask)=9641166 stop_rank=5000
1:27:27.121677 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:27:27.329659 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:27:28.045519 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:27:28.045967 INFO: Using score_cutoff 7.337295945167542 (fac=0.99, q=1)
1:27:28.046277 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:27:28.046376 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:27:28.046444 INFO: Updating optimization_manager: score_cutoff        : 7.741780815124511 -> 7.337295945167542
1:27:28.046504 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:27:28.337861 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:27:29.028238 INFO: === checking if optimization conditions were reached ===
1:27:29.028499 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
1:27:29.029402 INFO: Updating optimization_manager: rt_error            : 1189.111035439574 -> 716.8717651367188
1:27:29.029553 INFO: Updating optimization_manager: classifier_version  : 13 -> 14
1:27:29.029657 INFO: Updating optimization_manager: score_cutoff        : 7.337295945167542 -> 7.711953224372864
1:27:29.029759 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:27:29.029843 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:27:29.029929 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 716.8718 found after 6 searches.
1:27:29.029992 INFO: ==============================================
1:27:29.030061 PROGRESS: Optimization finished for rt_error.
1:27:29.687471 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:27:29.978910 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:27:30.667786 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:27:30.668041 PROGRESS: ==============================================
1:27:30.668128 PROGRESS: ms2_error      : 10.0000
1:27:30.668194 PROGRESS: rt_error       : 716.8718
1:27:30.668252 PROGRESS: ==============================================
1:27:30.668890 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:27:37.206346 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:28:02.059607 INFO: Using rust extraction backend
1:28:02.060178 PROGRESS: Extracting batch of 10770831 precursors
1:28:25.077387 INFO: === Search parameters used ===
1:28:25.077875 INFO: rt_error       : 716.8717651367188
1:28:25.077959 INFO: mobility_error : 0.1
1:28:25.078036 INFO: num_candidates : 3
1:28:25.078098 INFO: ms1_error      : 20
1:28:25.078158 INFO: ms2_error      : 10.0
1:28:25.078217 INFO: fwhm_rt        : 3.0
1:28:25.078280 INFO: quant_window   : 3
1:28:25.078336 INFO: ==============================================
1:29:20.560495 INFO: Removed 5769203 precursors with score below cutoff 7.711953224372864
1:29:50.190605 INFO: performing precursor FDR with 40 features
1:29:50.190785 INFO: Decoy channel: -1
1:29:50.190819 INFO: competitive: True
1:29:53.023220 INFO: Setting torch num_threads to 2 for FDR classification task
1:30:03.780498 INFO: Estimating optimal hyperparameters - samples: 21,234,627, batch_size: 4,096, learning_rate: 1.00e-03
1:30:03.844855 INFO: Using random state 296887 for train-test-split
1:36:49.693186 INFO: Test AUC: 0.614
1:36:49.693453 INFO: Train AUC: 0.614
1:36:49.693498 INFO: AUC difference: 0.11%
1:36:56.058795 INFO: Resetting torch num_threads to 32
1:36:57.871225 PROGRESS: ============================= Precursor FDR =============================
1:36:57.871535 PROGRESS: Total precursors accumulated: 22,927
1:36:57.871614 PROGRESS: Target precursors: 22,700 (99.01%)
1:36:57.871680 PROGRESS: Decoy precursors: 227 (0.99%)
1:36:57.871744 PROGRESS: 
1:36:57.871817 PROGRESS: Precursor Summary:
1:36:57.876994 PROGRESS: Channel   0:	 0.050 FDR: 22,700; 0.010 FDR: 22,695; 0.001 FDR: 14,408
1:36:57.877131 PROGRESS: 
1:36:57.877208 PROGRESS: Protein Summary:
1:36:57.885746 PROGRESS: Channel   0:	 0.050 FDR: 6,984; 0.010 FDR: 6,983; 0.001 FDR: 4,817
1:36:57.885885 PROGRESS: =========================================================================
1:36:58.058397 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3/psm.parquet
1:36:58.103256 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3/frag.parquet
1:36:58.183871 INFO: Finished workflow for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3
1:36:58.639704 PROGRESS: Loading raw file 4/6: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1 
1:36:58.639860 INFO: Quantification results path: /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant
1:36:58.639950 INFO: Creating folder /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1/figures
1:36:58.640118 INFO: Initializing TimingManager
1:36:58.640542 INFO: Initializing RawFileManager
1:37:04.886301 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
1:37:04.887398 INFO: Determining DIA cycle
1:37:04.900080 INFO: Found cycle with start 0.00 min and length 20.
1:37:04.922684 INFO: RT (min)            : 0.0 - 23.9
1:37:04.922775 INFO: RT duration (sec)   : 1433.8
1:37:04.922809 INFO: RT duration (min)   : 23.9
1:37:04.922836 INFO: Cycle len (scans)   : 20
1:37:04.922860 INFO: Cycle len (sec)     : 1.04
1:37:04.922882 INFO: Number of cycles    : 1376
1:37:04.922905 INFO: MS2 range (m/z)     : 400.4 - 800.6
1:37:04.922933 INFO: Creating DIA data object took: 6.282289505004883
1:37:05.524081 INFO: Creating DIA data NG object took: 0.6010148525238037
1:37:07.067772 INFO: Initializing CalibrationManager
1:37:07.068042 INFO: Setting up calibration estimators ..
1:37:07.068116 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:37:07.068211 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'}' ..
1:37:07.068303 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:37:07.068367 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:37:07.068434 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}}' ..
1:37:07.068496 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:37:07.068551 INFO: Done setting up calibration estimators.
1:37:07.068678 INFO: Initializing OptimizationManager
1:37:07.068810 INFO: initial parameter: ms1_error = 20
1:37:07.068874 INFO: initial parameter: ms2_error = 20
1:37:07.068930 INFO: initial parameter: rt_error = 716.9457397460938
1:37:07.068985 INFO: initial parameter: mobility_error = 0.1
1:37:07.069039 INFO: initial parameter: num_candidates = 1
1:37:07.069086 INFO: initial parameter: fwhm_rt = 5
1:37:07.069139 INFO: initial parameter: fwhm_mobility = 0.01
1:37:07.069185 INFO: initial parameter: score_cutoff = 0
1:37:07.069235 INFO: initial parameter: classifier_version = -1
1:37:07.069315 PROGRESS: Initializing workflow 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1
1:37:07.069559 INFO: FDRManager: loading saved state not requested, will be initialized.
1:37:07.069601 INFO: Initializing FDRManager
1:37:07.069645 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
1:37:08.363317 PROGRESS: Initializing spectral library: 5,415,345 target precursors potentially observable (2,595,411 removed)
1:37:09.184001 INFO: Updating optimization_manager: ms2_error           : 20 -> 20
1:37:09.184389 INFO: Updating optimization_manager: rt_error            : 716.9457397460938 -> 716.9457397460938
1:37:09.184501 PROGRESS: Starting initial search for precursors.
1:37:09.184594 INFO: Starting optimization step 0.
1:37:09.184677 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:37:09.184762 INFO: Using rust extraction backend
1:37:09.184826 PROGRESS: Extracting batch of 1960 precursors
1:37:09.189557 INFO: === Search parameters used ===
1:37:09.189676 INFO: rt_error       : 716.9457397460938
1:37:09.189734 INFO: mobility_error : 0.1
1:37:09.189785 INFO: num_candidates : 1
1:37:09.189834 INFO: ms1_error      : 20
1:37:09.189883 INFO: ms2_error      : 20
1:37:09.189930 INFO: fwhm_rt        : 5
1:37:09.189987 INFO: quant_window   : 3
1:37:09.190034 INFO: ==============================================
1:37:09.223595 INFO: performing precursor FDR with 40 features
1:37:09.223671 INFO: Decoy channel: -1
1:37:09.223699 INFO: competitive: True
1:37:09.224935 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:09.226814 INFO: Estimating optimal hyperparameters - samples: 1,565, batch_size: 128, learning_rate: 1.77e-04
1:37:09.227647 INFO: Using random state 271132 for train-test-split
1:37:09.379347 INFO: Test AUC: 0.458
1:37:09.379436 INFO: Train AUC: 0.598
1:37:09.379468 INFO: AUC difference: 23.35%
1:37:09.379491 WARNING: AUC difference > 5%. This may indicate overfitting.
1:37:09.627185 INFO: Resetting torch num_threads to 32
1:37:09.628682 PROGRESS: === Extracted 1957 precursors and 10806 fragments ===
1:37:09.629192 INFO: === FDR correction performed with classifier version -1 ===
1:37:09.629692 PROGRESS: ============================= Precursor FDR =============================
1:37:09.629786 PROGRESS: Total precursors accumulated: 1
1:37:09.629850 PROGRESS: Target precursors: 1 (100.00%)
1:37:09.629904 PROGRESS: Decoy precursors: 0 (0.00%)
1:37:09.629956 PROGRESS: 
1:37:09.630002 PROGRESS: Precursor Summary:
1:37:09.631082 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:37:09.631179 PROGRESS: 
1:37:09.631245 PROGRESS: Protein Summary:
1:37:09.632417 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:37:09.632506 PROGRESS: =========================================================================
1:37:09.632723 INFO: Target number of precursors not reached yet.
1:37:09.709615 INFO: Starting optimization step 1.
1:37:09.709820 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:37:09.709916 INFO: Using rust extraction backend
1:37:09.709983 PROGRESS: Extracting batch of 3921 precursors
1:37:09.718550 INFO: === Search parameters used ===
1:37:09.718701 INFO: rt_error       : 716.9457397460938
1:37:09.718757 INFO: mobility_error : 0.1
1:37:09.718809 INFO: num_candidates : 1
1:37:09.718857 INFO: ms1_error      : 20
1:37:09.718923 INFO: ms2_error      : 20
1:37:09.718970 INFO: fwhm_rt        : 5
1:37:09.719016 INFO: quant_window   : 3
1:37:09.719066 INFO: ==============================================
1:37:09.791336 INFO: performing precursor FDR with 40 features
1:37:09.791427 INFO: Decoy channel: -1
1:37:09.791454 INFO: competitive: True
1:37:09.795616 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:09.797886 INFO: Estimating optimal hyperparameters - samples: 4,696, batch_size: 128, learning_rate: 1.77e-04
1:37:09.797970 INFO: Using random state 318893 for train-test-split
1:37:10.259219 INFO: Test AUC: 0.527
1:37:10.259309 INFO: Train AUC: 0.588
1:37:10.259338 INFO: AUC difference: 10.33%
1:37:10.259361 WARNING: AUC difference > 5%. This may indicate overfitting.
1:37:10.501632 INFO: Resetting torch num_threads to 32
1:37:10.504474 PROGRESS: === Extracted 5870 precursors and 32486 fragments ===
1:37:10.504847 INFO: === FDR correction performed with classifier version -1 ===
1:37:10.505328 PROGRESS: ============================= Precursor FDR =============================
1:37:10.505414 PROGRESS: Total precursors accumulated: 2
1:37:10.505473 PROGRESS: Target precursors: 2 (100.00%)
1:37:10.505524 PROGRESS: Decoy precursors: 0 (0.00%)
1:37:10.505573 PROGRESS: 
1:37:10.505622 PROGRESS: Precursor Summary:
1:37:10.506678 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:37:10.506769 PROGRESS: 
1:37:10.506826 PROGRESS: Protein Summary:
1:37:10.507973 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:37:10.508058 PROGRESS: =========================================================================
1:37:10.508317 INFO: Target number of precursors not reached yet.
1:37:10.589995 INFO: Starting optimization step 2.
1:37:10.590204 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:37:10.590286 INFO: Using rust extraction backend
1:37:10.590347 PROGRESS: Extracting batch of 7852 precursors
1:37:10.605435 INFO: === Search parameters used ===
1:37:10.605575 INFO: rt_error       : 716.9457397460938
1:37:10.605640 INFO: mobility_error : 0.1
1:37:10.605685 INFO: num_candidates : 1
1:37:10.605741 INFO: ms1_error      : 20
1:37:10.605783 INFO: ms2_error      : 20
1:37:10.605829 INFO: fwhm_rt        : 5
1:37:10.605871 INFO: quant_window   : 3
1:37:10.605911 INFO: ==============================================
1:37:10.709852 INFO: performing precursor FDR with 40 features
1:37:10.709956 INFO: Decoy channel: -1
1:37:10.709982 INFO: competitive: True
1:37:10.716223 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:10.721125 INFO: Estimating optimal hyperparameters - samples: 10,968, batch_size: 128, learning_rate: 1.77e-04
1:37:10.721247 INFO: Using random state 343139 for train-test-split
1:37:11.829190 INFO: Test AUC: 0.567
1:37:11.829300 INFO: Train AUC: 0.590
1:37:11.829333 INFO: AUC difference: 3.78%
1:37:12.084160 INFO: Resetting torch num_threads to 32
1:37:12.088111 PROGRESS: === Extracted 13711 precursors and 75765 fragments ===
1:37:12.088519 INFO: === FDR correction performed with classifier version -1 ===
1:37:12.089025 PROGRESS: ============================= Precursor FDR =============================
1:37:12.089117 PROGRESS: Total precursors accumulated: 7
1:37:12.089183 PROGRESS: Target precursors: 7 (100.00%)
1:37:12.089236 PROGRESS: Decoy precursors: 0 (0.00%)
1:37:12.089287 PROGRESS: 
1:37:12.089335 PROGRESS: Precursor Summary:
1:37:12.090386 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
1:37:12.090480 PROGRESS: 
1:37:12.090540 PROGRESS: Protein Summary:
1:37:12.091707 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
1:37:12.091796 PROGRESS: =========================================================================
1:37:12.092124 INFO: Target number of precursors not reached yet.
1:37:12.184340 INFO: Starting optimization step 3.
1:37:12.184561 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:37:12.184644 INFO: Using rust extraction backend
1:37:12.184710 PROGRESS: Extracting batch of 15661 precursors
1:37:12.213732 INFO: === Search parameters used ===
1:37:12.213910 INFO: rt_error       : 716.9457397460938
1:37:12.213974 INFO: mobility_error : 0.1
1:37:12.214028 INFO: num_candidates : 1
1:37:12.214080 INFO: ms1_error      : 20
1:37:12.214127 INFO: ms2_error      : 20
1:37:12.214184 INFO: fwhm_rt        : 5
1:37:12.214231 INFO: quant_window   : 3
1:37:12.214276 INFO: ==============================================
1:37:12.388698 INFO: performing precursor FDR with 40 features
1:37:12.388810 INFO: Decoy channel: -1
1:37:12.388837 INFO: competitive: True
1:37:12.399917 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:12.407008 INFO: Estimating optimal hyperparameters - samples: 23,469, batch_size: 128, learning_rate: 1.77e-04
1:37:12.407176 INFO: Using random state 643547 for train-test-split
1:37:14.781051 INFO: Test AUC: 0.551
1:37:14.781142 INFO: Train AUC: 0.603
1:37:14.781171 INFO: AUC difference: 8.64%
1:37:14.781193 WARNING: AUC difference > 5%. This may indicate overfitting.
1:37:15.033415 INFO: Resetting torch num_threads to 32
1:37:15.040853 PROGRESS: === Extracted 29337 precursors and 162433 fragments ===
1:37:15.041331 INFO: === FDR correction performed with classifier version -1 ===
1:37:15.041824 PROGRESS: ============================= Precursor FDR =============================
1:37:15.041909 PROGRESS: Total precursors accumulated: 0
1:37:15.041970 PROGRESS: Target precursors: 0 (0.00%)
1:37:15.042020 PROGRESS: Decoy precursors: 0 (0.00%)
1:37:15.042066 PROGRESS: 
1:37:15.042110 PROGRESS: Precursor Summary:
1:37:15.042225 PROGRESS: 
1:37:15.042285 PROGRESS: Protein Summary:
1:37:15.042371 PROGRESS: =========================================================================
1:37:15.042831 INFO: Target number of precursors not reached yet.
1:37:15.153046 INFO: Starting optimization step 4.
1:37:15.153286 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:37:15.153380 INFO: Using rust extraction backend
1:37:15.153445 PROGRESS: Extracting batch of 31339 precursors
1:37:15.209079 INFO: === Search parameters used ===
1:37:15.209305 INFO: rt_error       : 716.9457397460938
1:37:15.209374 INFO: mobility_error : 0.1
1:37:15.209433 INFO: num_candidates : 1
1:37:15.209479 INFO: ms1_error      : 20
1:37:15.209522 INFO: ms2_error      : 20
1:37:15.209563 INFO: fwhm_rt        : 5
1:37:15.209605 INFO: quant_window   : 3
1:37:15.209645 INFO: ==============================================
1:37:15.497142 INFO: performing precursor FDR with 40 features
1:37:15.497256 INFO: Decoy channel: -1
1:37:15.497282 INFO: competitive: True
1:37:15.519021 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:15.532871 INFO: Estimating optimal hyperparameters - samples: 48,514, batch_size: 198, learning_rate: 2.20e-04
1:37:15.533081 INFO: Using random state 213735 for train-test-split
1:37:19.182145 INFO: Test AUC: 0.566
1:37:19.182263 INFO: Train AUC: 0.599
1:37:19.182295 INFO: AUC difference: 5.61%
1:37:19.182321 WARNING: AUC difference > 5%. This may indicate overfitting.
1:37:19.453305 INFO: Resetting torch num_threads to 32
1:37:19.464861 PROGRESS: === Extracted 60643 precursors and 335579 fragments ===
1:37:19.465404 INFO: === FDR correction performed with classifier version -1 ===
1:37:19.465970 PROGRESS: ============================= Precursor FDR =============================
1:37:19.466074 PROGRESS: Total precursors accumulated: 60
1:37:19.466145 PROGRESS: Target precursors: 60 (100.00%)
1:37:19.466203 PROGRESS: Decoy precursors: 0 (0.00%)
1:37:19.466252 PROGRESS: 
1:37:19.466305 PROGRESS: Precursor Summary:
1:37:19.467395 PROGRESS: Channel   0:	 0.050 FDR:    60; 0.010 FDR:    60; 0.001 FDR:    60
1:37:19.467490 PROGRESS: 
1:37:19.467549 PROGRESS: Protein Summary:
1:37:19.468736 PROGRESS: Channel   0:	 0.050 FDR:    59; 0.010 FDR:    59; 0.001 FDR:    59
1:37:19.468829 PROGRESS: =========================================================================
1:37:19.469975 INFO: Target number of precursors not reached yet.
1:37:19.623352 INFO: Starting optimization step 5.
1:37:19.623615 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:37:19.623698 INFO: Using rust extraction backend
1:37:19.623765 PROGRESS: Extracting batch of 62709 precursors
1:37:19.733445 INFO: === Search parameters used ===
1:37:19.733703 INFO: rt_error       : 716.9457397460938
1:37:19.733761 INFO: mobility_error : 0.1
1:37:19.733811 INFO: num_candidates : 1
1:37:19.733856 INFO: ms1_error      : 20
1:37:19.733898 INFO: ms2_error      : 20
1:37:19.733940 INFO: fwhm_rt        : 5
1:37:19.733982 INFO: quant_window   : 3
1:37:19.734023 INFO: ==============================================
1:37:20.269657 INFO: performing precursor FDR with 40 features
1:37:20.269773 INFO: Decoy channel: -1
1:37:20.269800 INFO: competitive: True
1:37:20.314862 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:20.344371 INFO: Estimating optimal hyperparameters - samples: 98,604, batch_size: 403, learning_rate: 3.14e-04
1:37:20.344697 INFO: Using random state 167763 for train-test-split
1:37:24.921880 INFO: Test AUC: 0.570
1:37:24.922002 INFO: Train AUC: 0.608
1:37:24.922035 INFO: AUC difference: 6.17%
1:37:24.922060 WARNING: AUC difference > 5%. This may indicate overfitting.
1:37:25.214106 INFO: Resetting torch num_threads to 32
1:37:25.235526 PROGRESS: === Extracted 123256 precursors and 683345 fragments ===
1:37:25.236137 INFO: === FDR correction performed with classifier version -1 ===
1:37:25.236693 PROGRESS: ============================= Precursor FDR =============================
1:37:25.236788 PROGRESS: Total precursors accumulated: 121
1:37:25.236857 PROGRESS: Target precursors: 120 (99.17%)
1:37:25.236919 PROGRESS: Decoy precursors: 1 (0.83%)
1:37:25.236979 PROGRESS: 
1:37:25.237032 PROGRESS: Precursor Summary:
1:37:25.238044 PROGRESS: Channel   0:	 0.050 FDR:   120; 0.010 FDR:   120; 0.001 FDR:   117
1:37:25.238151 PROGRESS: 
1:37:25.238216 PROGRESS: Protein Summary:
1:37:25.239341 PROGRESS: Channel   0:	 0.050 FDR:   118; 0.010 FDR:   118; 0.001 FDR:   115
1:37:25.239440 PROGRESS: =========================================================================
1:37:25.241634 INFO: Target number of precursors not reached yet.
1:37:25.476746 INFO: Starting optimization step 6.
1:37:25.477000 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:37:25.477092 INFO: Using rust extraction backend
1:37:25.477182 PROGRESS: Extracting batch of 125408 precursors
1:37:25.695079 INFO: === Search parameters used ===
1:37:25.695340 INFO: rt_error       : 716.9457397460938
1:37:25.695407 INFO: mobility_error : 0.1
1:37:25.695476 INFO: num_candidates : 1
1:37:25.695537 INFO: ms1_error      : 20
1:37:25.695586 INFO: ms2_error      : 20
1:37:25.695634 INFO: fwhm_rt        : 5
1:37:25.695681 INFO: quant_window   : 3
1:37:25.695729 INFO: ==============================================
1:37:26.726540 INFO: performing precursor FDR with 40 features
1:37:26.726666 INFO: Decoy channel: -1
1:37:26.726695 INFO: competitive: True
1:37:26.823239 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:26.903212 INFO: Estimating optimal hyperparameters - samples: 198,769, batch_size: 814, learning_rate: 4.46e-04
1:37:26.903628 INFO: Using random state 226486 for train-test-split
1:37:33.042015 INFO: Test AUC: 0.581
1:37:33.042130 INFO: Train AUC: 0.604
1:37:33.042163 INFO: AUC difference: 3.82%
1:37:33.363654 INFO: Resetting torch num_threads to 32
1:37:33.404351 PROGRESS: === Extracted 248462 precursors and 1376804 fragments ===
1:37:33.404966 INFO: === FDR correction performed with classifier version -1 ===
1:37:33.405541 PROGRESS: ============================= Precursor FDR =============================
1:37:33.405650 PROGRESS: Total precursors accumulated: 242
1:37:33.405718 PROGRESS: Target precursors: 240 (99.17%)
1:37:33.405779 PROGRESS: Decoy precursors: 2 (0.83%)
1:37:33.405834 PROGRESS: 
1:37:33.405885 PROGRESS: Precursor Summary:
1:37:33.406941 PROGRESS: Channel   0:	 0.050 FDR:   240; 0.010 FDR:   240; 0.001 FDR:   223
1:37:33.407040 PROGRESS: 
1:37:33.407103 PROGRESS: Protein Summary:
1:37:33.408282 PROGRESS: Channel   0:	 0.050 FDR:   228; 0.010 FDR:   228; 0.001 FDR:   211
1:37:33.408378 PROGRESS: =========================================================================
1:37:33.412186 INFO: Target number of precursors not reached yet.
1:37:33.797091 INFO: Starting optimization step 7.
1:37:33.797338 PROGRESS: === Extracting elution groups 127000 to 255000 ===
1:37:33.797429 INFO: Using rust extraction backend
1:37:33.797500 PROGRESS: Extracting batch of 250773 precursors
1:37:34.232008 INFO: === Search parameters used ===
1:37:34.232256 INFO: rt_error       : 716.9457397460938
1:37:34.232327 INFO: mobility_error : 0.1
1:37:34.232383 INFO: num_candidates : 1
1:37:34.232434 INFO: ms1_error      : 20
1:37:34.232484 INFO: ms2_error      : 20
1:37:34.232532 INFO: fwhm_rt        : 5
1:37:34.232600 INFO: quant_window   : 3
1:37:34.232651 INFO: ==============================================
1:37:36.228454 INFO: performing precursor FDR with 40 features
1:37:36.228565 INFO: Decoy channel: -1
1:37:36.228592 INFO: competitive: True
1:37:36.414472 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:36.593691 INFO: Estimating optimal hyperparameters - samples: 399,054, batch_size: 1,634, learning_rate: 6.32e-04
1:37:36.594421 INFO: Using random state 894127 for train-test-split
1:37:46.472409 INFO: Test AUC: 0.585
1:37:46.472541 INFO: Train AUC: 0.604
1:37:46.472575 INFO: AUC difference: 3.10%
1:37:46.879339 INFO: Resetting torch num_threads to 32
1:37:46.957929 PROGRESS: === Extracted 498818 precursors and 2761856 fragments ===
1:37:46.958590 INFO: === FDR correction performed with classifier version -1 ===
1:37:46.959234 PROGRESS: ============================= Precursor FDR =============================
1:37:46.959332 PROGRESS: Total precursors accumulated: 405
1:37:46.959407 PROGRESS: Target precursors: 401 (99.01%)
1:37:46.959473 PROGRESS: Decoy precursors: 4 (0.99%)
1:37:46.959529 PROGRESS: 
1:37:46.959590 PROGRESS: Precursor Summary:
1:37:46.960659 PROGRESS: Channel   0:	 0.050 FDR:   401; 0.010 FDR:   401; 0.001 FDR:   196
1:37:46.960756 PROGRESS: 
1:37:46.960824 PROGRESS: Protein Summary:
1:37:46.962415 PROGRESS: Channel   0:	 0.050 FDR:   350; 0.010 FDR:   350; 0.001 FDR:   176
1:37:46.962536 PROGRESS: =========================================================================
1:37:46.969095 INFO: Target number of precursors not reached yet.
1:37:47.626483 INFO: Starting optimization step 8.
1:37:47.626724 PROGRESS: === Extracting elution groups 255000 to 511000 ===
1:37:47.626826 INFO: Using rust extraction backend
1:37:47.626908 PROGRESS: Extracting batch of 501436 precursors
1:37:48.484103 INFO: === Search parameters used ===
1:37:48.484352 INFO: rt_error       : 716.9457397460938
1:37:48.484421 INFO: mobility_error : 0.1
1:37:48.484501 INFO: num_candidates : 1
1:37:48.484558 INFO: ms1_error      : 20
1:37:48.484616 INFO: ms2_error      : 20
1:37:48.484664 INFO: fwhm_rt        : 5
1:37:48.484711 INFO: quant_window   : 3
1:37:48.484763 INFO: ==============================================
1:37:52.464600 INFO: performing precursor FDR with 40 features
1:37:52.464718 INFO: Decoy channel: -1
1:37:52.464747 INFO: competitive: True
1:37:52.834293 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:53.238905 INFO: Estimating optimal hyperparameters - samples: 799,528, batch_size: 3,274, learning_rate: 8.94e-04
1:37:53.240289 INFO: Using random state 391565 for train-test-split
1:38:10.406390 INFO: Test AUC: 0.591
1:38:10.406555 INFO: Train AUC: 0.602
1:38:10.406592 INFO: AUC difference: 1.87%
1:38:10.974040 INFO: Resetting torch num_threads to 32
1:38:11.170455 PROGRESS: === Extracted 999411 precursors and 5536713 fragments ===
1:38:11.171115 INFO: === FDR correction performed with classifier version -1 ===
1:38:11.171901 PROGRESS: ============================= Precursor FDR =============================
1:38:11.171997 PROGRESS: Total precursors accumulated: 1,086
1:38:11.172061 PROGRESS: Target precursors: 1,076 (99.08%)
1:38:11.172133 PROGRESS: Decoy precursors: 10 (0.92%)
1:38:11.172203 PROGRESS: 
1:38:11.172257 PROGRESS: Precursor Summary:
1:38:11.173530 PROGRESS: Channel   0:	 0.050 FDR: 1,076; 0.010 FDR: 1,076; 0.001 FDR:   588
1:38:11.173624 PROGRESS: 
1:38:11.173682 PROGRESS: Protein Summary:
1:38:11.175278 PROGRESS: Channel   0:	 0.050 FDR:   866; 0.010 FDR:   866; 0.001 FDR:   494
1:38:11.175375 PROGRESS: =========================================================================
1:38:11.187268 INFO: Target number of precursors reached.
1:38:11.793209 INFO: fragments_df: keeping 5000 of 5536713 [sum(precursor_idx_mask)=11737 sum(mass_error_mask)=5536713 stop_rank=5000
1:38:12.822794 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:38:13.024582 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:38:13.762271 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:38:13.762731 INFO: Using score_cutoff 6.718695638179779 (fac=0.99, q=1)
1:38:13.763067 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:38:13.763154 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:38:13.763212 INFO: Updating optimization_manager: score_cutoff        : 0 -> 6.718695638179779
1:38:13.763278 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:38:14.380119 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:38:15.766628 INFO: Updating optimization_manager: classifier_version  : -1 -> 8
1:38:15.766868 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:38:15.766986 INFO: Starting optimization step 9.
1:38:15.767064 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:38:15.767147 INFO: Using rust extraction backend
1:38:15.767222 PROGRESS: Extracting batch of 1001059 precursors
1:38:17.489158 INFO: === Search parameters used ===
1:38:17.489468 INFO: rt_error       : 716.9457397460938
1:38:17.489542 INFO: mobility_error : 0.1
1:38:17.489603 INFO: num_candidates : 3
1:38:17.489674 INFO: ms1_error      : 20
1:38:17.489733 INFO: ms2_error      : 20
1:38:17.489783 INFO: fwhm_rt        : 3.0
1:38:17.489833 INFO: quant_window   : 3
1:38:17.489891 INFO: ==============================================
1:38:31.268346 INFO: performing precursor FDR with 40 features
1:38:31.268466 INFO: Decoy channel: -1
1:38:31.268497 INFO: competitive: True
1:38:32.040076 INFO: Setting torch num_threads to 2 for FDR classification task
1:38:33.393552 INFO: Estimating optimal hyperparameters - samples: 2,398,815, batch_size: 4,096, learning_rate: 1.00e-03
1:38:33.398410 INFO: Using random state 30138 for train-test-split
1:39:19.031595 INFO: Test AUC: 0.600
1:39:19.031783 INFO: Train AUC: 0.604
1:39:19.031819 INFO: AUC difference: 0.67%
1:39:20.267147 INFO: Resetting torch num_threads to 32
1:39:20.370949 PROGRESS: === Extracted 2998519 precursors and 16440017 fragments ===
1:39:20.371458 INFO: === FDR correction performed with classifier version 8 ===
1:39:20.372157 PROGRESS: ============================= Precursor FDR =============================
1:39:20.372261 PROGRESS: Total precursors accumulated: 1,373
1:39:20.372336 PROGRESS: Target precursors: 1,360 (99.05%)
1:39:20.372418 PROGRESS: Decoy precursors: 13 (0.95%)
1:39:20.372476 PROGRESS: 
1:39:20.372529 PROGRESS: Precursor Summary:
1:39:20.373846 PROGRESS: Channel   0:	 0.050 FDR: 1,360; 0.010 FDR: 1,360; 0.001 FDR: 1,102
1:39:20.373946 PROGRESS: 
1:39:20.374009 PROGRESS: Protein Summary:
1:39:20.375741 PROGRESS: Channel   0:	 0.050 FDR: 1,083; 0.010 FDR: 1,083; 0.001 FDR:   886
1:39:20.375844 PROGRESS: =========================================================================
1:39:20.452698 INFO: Target number of precursors reached.
1:39:22.171732 INFO: fragments_df: keeping 5000 of 16440017 [sum(precursor_idx_mask)=33565 sum(mass_error_mask)=16440017 stop_rank=5000
1:39:23.509763 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:39:23.738081 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:39:24.456505 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:39:24.456976 INFO: Using score_cutoff 6.484959275722503 (fac=0.99, q=1)
1:39:24.457291 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:39:24.457377 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:39:24.457439 INFO: Updating optimization_manager: score_cutoff        : 6.718695638179779 -> 6.484959275722503
1:39:24.457501 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:39:25.057654 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:39:26.491187 INFO: === checking if optimization conditions were reached ===
1:39:26.493409 INFO: Updating optimization_manager: ms2_error           : 20 -> 10.0
1:39:26.493573 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:39:26.493654 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:39:26.493730 INFO: ==============================================
1:39:26.493816 INFO: Starting optimization step 10.
1:39:26.493898 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:39:26.493988 INFO: Using rust extraction backend
1:39:26.494069 PROGRESS: Extracting batch of 1001059 precursors
1:39:28.186454 INFO: === Search parameters used ===
1:39:28.186720 INFO: rt_error       : 716.9457397460938
1:39:28.186816 INFO: mobility_error : 0.1
1:39:28.186875 INFO: num_candidates : 3
1:39:28.186928 INFO: ms1_error      : 20
1:39:28.186977 INFO: ms2_error      : 10.0
1:39:28.187025 INFO: fwhm_rt        : 3.0
1:39:28.187073 INFO: quant_window   : 3
1:39:28.187122 INFO: ==============================================
1:39:41.467955 INFO: performing precursor FDR with 40 features
1:39:41.468079 INFO: Decoy channel: -1
1:39:41.468107 INFO: competitive: True
1:39:42.227720 INFO: Setting torch num_threads to 2 for FDR classification task
1:39:43.532386 INFO: Estimating optimal hyperparameters - samples: 2,401,636, batch_size: 4,096, learning_rate: 1.00e-03
1:39:43.537207 INFO: Using random state 2811 for train-test-split
1:40:28.987828 INFO: Test AUC: 0.608
1:40:28.987968 INFO: Train AUC: 0.611
1:40:28.988076 INFO: AUC difference: 0.47%
1:40:30.215309 INFO: Resetting torch num_threads to 32
1:40:30.310506 PROGRESS: === Extracted 3002045 precursors and 17984293 fragments ===
1:40:30.311030 INFO: === FDR correction performed with classifier version 9 ===
1:40:30.311914 PROGRESS: ============================= Precursor FDR =============================
1:40:30.312023 PROGRESS: Total precursors accumulated: 1,850
1:40:30.312096 PROGRESS: Target precursors: 1,832 (99.03%)
1:40:30.312155 PROGRESS: Decoy precursors: 18 (0.97%)
1:40:30.312206 PROGRESS: 
1:40:30.312254 PROGRESS: Precursor Summary:
1:40:30.313776 PROGRESS: Channel   0:	 0.050 FDR: 1,832; 0.010 FDR: 1,832; 0.001 FDR: 1,172
1:40:30.313877 PROGRESS: 
1:40:30.313941 PROGRESS: Protein Summary:
1:40:30.315894 PROGRESS: Channel   0:	 0.050 FDR: 1,416; 0.010 FDR: 1,416; 0.001 FDR:   935
1:40:30.315998 PROGRESS: =========================================================================
1:40:30.370195 INFO: Target number of precursors reached.
1:40:32.305638 INFO: fragments_df: keeping 5000 of 17984293 [sum(precursor_idx_mask)=47188 sum(mass_error_mask)=17984293 stop_rank=5000
1:40:33.372906 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:40:33.607215 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:40:34.262855 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:40:34.263312 INFO: Using score_cutoff 6.359267071437835 (fac=0.99, q=1)
1:40:34.263622 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:40:34.263705 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:40:34.263766 INFO: Updating optimization_manager: score_cutoff        : 6.484959275722503 -> 6.359267071437835
1:40:34.263824 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:40:34.865007 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:40:36.259103 INFO: === checking if optimization conditions were reached ===
1:40:36.261199 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:40:36.261317 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:40:36.261389 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:40:36.261452 INFO: ==============================================
1:40:36.261529 INFO: Starting optimization step 11.
1:40:36.261592 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:40:36.261657 INFO: Using rust extraction backend
1:40:36.261718 PROGRESS: Extracting batch of 1001059 precursors
1:40:37.954434 INFO: === Search parameters used ===
1:40:37.954712 INFO: rt_error       : 716.9457397460938
1:40:37.954792 INFO: mobility_error : 0.1
1:40:37.954847 INFO: num_candidates : 3
1:40:37.954896 INFO: ms1_error      : 20
1:40:37.954943 INFO: ms2_error      : 10.0
1:40:37.954988 INFO: fwhm_rt        : 3.0
1:40:37.955031 INFO: quant_window   : 3
1:40:37.955074 INFO: ==============================================
1:40:51.190121 INFO: performing precursor FDR with 40 features
1:40:51.190251 INFO: Decoy channel: -1
1:40:51.190280 INFO: competitive: True
1:40:51.918335 INFO: Setting torch num_threads to 2 for FDR classification task
1:40:53.166455 INFO: Estimating optimal hyperparameters - samples: 2,401,581, batch_size: 4,096, learning_rate: 1.00e-03
1:40:53.171815 INFO: Using random state 347590 for train-test-split
1:41:38.635121 INFO: Test AUC: 0.608
1:41:38.635264 INFO: Train AUC: 0.613
1:41:38.635300 INFO: AUC difference: 0.93%
1:41:39.848176 INFO: Resetting torch num_threads to 32
1:41:39.939004 PROGRESS: === Extracted 3001977 precursors and 17933204 fragments ===
1:41:39.939490 INFO: === FDR correction performed with classifier version 10 ===
1:41:39.940237 PROGRESS: ============================= Precursor FDR =============================
1:41:39.940335 PROGRESS: Total precursors accumulated: 1,833
1:41:39.940404 PROGRESS: Target precursors: 1,815 (99.02%)
1:41:39.940465 PROGRESS: Decoy precursors: 18 (0.98%)
1:41:39.940521 PROGRESS: 
1:41:39.940574 PROGRESS: Precursor Summary:
1:41:39.941987 PROGRESS: Channel   0:	 0.050 FDR: 1,815; 0.010 FDR: 1,815; 0.001 FDR: 1,201
1:41:39.942086 PROGRESS: 
1:41:39.942160 PROGRESS: Protein Summary:
1:41:39.944036 PROGRESS: Channel   0:	 0.050 FDR: 1,407; 0.010 FDR: 1,407; 0.001 FDR:   959
1:41:39.944137 PROGRESS: =========================================================================
1:41:39.997684 INFO: Target number of precursors reached.
1:41:41.820586 INFO: fragments_df: keeping 5000 of 17933204 [sum(precursor_idx_mask)=46744 sum(mass_error_mask)=17933204 stop_rank=5000
1:41:42.883727 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:41:43.134871 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:41:43.831431 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:41:43.831867 INFO: Using score_cutoff 5.4447837641716 (fac=0.99, q=1)
1:41:43.832190 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:41:43.832273 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:41:43.832333 INFO: Updating optimization_manager: score_cutoff        : 6.359267071437835 -> 5.4447837641716
1:41:43.832396 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:41:44.436889 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:41:45.788774 INFO: === checking if optimization conditions were reached ===
1:41:45.790957 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:41:45.791085 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:41:45.791177 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:41:45.791260 INFO: ==============================================
1:41:45.791357 INFO: Starting optimization step 12.
1:41:45.791440 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:41:45.791525 INFO: Using rust extraction backend
1:41:45.791623 PROGRESS: Extracting batch of 1001059 precursors
1:41:47.485437 INFO: === Search parameters used ===
1:41:47.485685 INFO: rt_error       : 716.9457397460938
1:41:47.485780 INFO: mobility_error : 0.1
1:41:47.485835 INFO: num_candidates : 3
1:41:47.485885 INFO: ms1_error      : 20
1:41:47.485936 INFO: ms2_error      : 10.0
1:41:47.485984 INFO: fwhm_rt        : 3.0
1:41:47.486031 INFO: quant_window   : 3
1:41:47.486077 INFO: ==============================================
1:42:00.649643 INFO: performing precursor FDR with 40 features
1:42:00.649767 INFO: Decoy channel: -1
1:42:00.649796 INFO: competitive: True
1:42:01.389762 INFO: Setting torch num_threads to 2 for FDR classification task
1:42:02.720605 INFO: Estimating optimal hyperparameters - samples: 2,401,620, batch_size: 4,096, learning_rate: 1.00e-03
1:42:02.725883 INFO: Using random state 345095 for train-test-split
1:42:48.971159 INFO: Test AUC: 0.608
1:42:48.971362 INFO: Train AUC: 0.614
1:42:48.971403 INFO: AUC difference: 0.92%
1:42:50.189392 INFO: Resetting torch num_threads to 32
1:42:50.297028 PROGRESS: === Extracted 3002026 precursors and 17974812 fragments ===
1:42:50.297554 INFO: === FDR correction performed with classifier version 11 ===
1:42:50.298454 PROGRESS: ============================= Precursor FDR =============================
1:42:50.298565 PROGRESS: Total precursors accumulated: 1,922
1:42:50.298634 PROGRESS: Target precursors: 1,903 (99.01%)
1:42:50.298695 PROGRESS: Decoy precursors: 19 (0.99%)
1:42:50.298755 PROGRESS: 
1:42:50.298816 PROGRESS: Precursor Summary:
1:42:50.300416 PROGRESS: Channel   0:	 0.050 FDR: 1,903; 0.010 FDR: 1,903; 0.001 FDR: 1,369
1:42:50.300520 PROGRESS: 
1:42:50.300586 PROGRESS: Protein Summary:
1:42:50.302648 PROGRESS: Channel   0:	 0.050 FDR: 1,479; 0.010 FDR: 1,479; 0.001 FDR: 1,089
1:42:50.302768 PROGRESS: =========================================================================
1:42:50.357677 INFO: Target number of precursors reached.
1:42:52.265466 INFO: fragments_df: keeping 5000 of 17974812 [sum(precursor_idx_mask)=48441 sum(mass_error_mask)=17974812 stop_rank=5000
1:42:53.528307 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:42:53.813879 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:42:55.595712 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:42:55.596160 INFO: Using score_cutoff 5.5279201003074645 (fac=0.99, q=1)
1:42:55.596476 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:42:55.596562 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:42:55.596624 INFO: Updating optimization_manager: score_cutoff        : 5.4447837641716 -> 5.5279201003074645
1:42:55.596690 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:42:56.195129 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:42:57.539567 INFO: === checking if optimization conditions were reached ===
1:42:57.541701 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:42:57.541816 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
1:42:57.541892 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:42:57.541959 INFO: ==============================================
1:42:57.542032 INFO: Starting optimization step 13.
1:42:57.542099 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:42:57.542178 INFO: Using rust extraction backend
1:42:57.542246 PROGRESS: Extracting batch of 1001059 precursors
1:42:59.223038 INFO: === Search parameters used ===
1:42:59.223298 INFO: rt_error       : 716.9457397460938
1:42:59.223361 INFO: mobility_error : 0.1
1:42:59.223424 INFO: num_candidates : 3
1:42:59.223476 INFO: ms1_error      : 20
1:42:59.223526 INFO: ms2_error      : 10.0
1:42:59.223574 INFO: fwhm_rt        : 3.0
1:42:59.223622 INFO: quant_window   : 3
1:42:59.223669 INFO: ==============================================
1:43:12.649529 INFO: performing precursor FDR with 40 features
1:43:12.649696 INFO: Decoy channel: -1
1:43:12.649728 INFO: competitive: True
1:43:13.362985 INFO: Setting torch num_threads to 2 for FDR classification task
1:43:14.626369 INFO: Estimating optimal hyperparameters - samples: 2,401,696, batch_size: 4,096, learning_rate: 1.00e-03
1:43:14.631590 INFO: Using random state 702425 for train-test-split
1:44:01.289507 INFO: Test AUC: 0.612
1:44:01.289703 INFO: Train AUC: 0.616
1:44:01.289741 INFO: AUC difference: 0.71%
1:44:02.444983 INFO: Resetting torch num_threads to 32
1:44:02.548668 PROGRESS: === Extracted 3002121 precursors and 18064027 fragments ===
1:44:02.549238 INFO: === FDR correction performed with classifier version 12 ===
1:44:02.550098 PROGRESS: ============================= Precursor FDR =============================
1:44:02.550210 PROGRESS: Total precursors accumulated: 1,781
1:44:02.550280 PROGRESS: Target precursors: 1,764 (99.05%)
1:44:02.550338 PROGRESS: Decoy precursors: 17 (0.95%)
1:44:02.550412 PROGRESS: 
1:44:02.550462 PROGRESS: Precursor Summary:
1:44:02.552021 PROGRESS: Channel   0:	 0.050 FDR: 1,764; 0.010 FDR: 1,764; 0.001 FDR: 1,312
1:44:02.552121 PROGRESS: 
1:44:02.552183 PROGRESS: Protein Summary:
1:44:02.554195 PROGRESS: Channel   0:	 0.050 FDR: 1,381; 0.010 FDR: 1,381; 0.001 FDR: 1,047
1:44:02.554297 PROGRESS: =========================================================================
1:44:02.610312 INFO: Target number of precursors reached.
1:44:04.440665 INFO: fragments_df: keeping 5000 of 18064027 [sum(precursor_idx_mask)=45032 sum(mass_error_mask)=18064027 stop_rank=5000
1:44:05.631781 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:44:05.898344 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:44:06.593726 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:44:06.594214 INFO: Using score_cutoff 4.229773026752472 (fac=0.99, q=1)
1:44:06.594556 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:44:06.594647 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:44:06.594707 INFO: Updating optimization_manager: score_cutoff        : 5.5279201003074645 -> 4.229773026752472
1:44:06.594774 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:44:07.191496 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:44:08.536469 INFO: === checking if optimization conditions were reached ===
1:44:08.538680 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:44:08.538838 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
1:44:08.538917 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:44:08.538991 INFO: ==============================================
1:44:08.539077 PROGRESS: Optimization finished for ms2_error.
1:44:09.604081 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:44:10.200180 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:44:11.551069 INFO: Starting optimization step 0.
1:44:11.551304 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:44:11.551404 INFO: Using rust extraction backend
1:44:11.551491 PROGRESS: Extracting batch of 1001059 precursors
1:44:13.244804 INFO: === Search parameters used ===
1:44:13.245089 INFO: rt_error       : 716.9457397460938
1:44:13.245162 INFO: mobility_error : 0.1
1:44:13.245222 INFO: num_candidates : 3
1:44:13.245279 INFO: ms1_error      : 20
1:44:13.245328 INFO: ms2_error      : 10.0
1:44:13.245375 INFO: fwhm_rt        : 3.0
1:44:13.245422 INFO: quant_window   : 3
1:44:13.245468 INFO: ==============================================
1:44:26.507295 INFO: performing precursor FDR with 40 features
1:44:26.507417 INFO: Decoy channel: -1
1:44:26.507445 INFO: competitive: True
1:44:27.237313 INFO: Setting torch num_threads to 2 for FDR classification task
1:44:28.508220 INFO: Estimating optimal hyperparameters - samples: 2,401,718, batch_size: 4,096, learning_rate: 1.00e-03
1:44:28.513388 INFO: Using random state 846810 for train-test-split
1:45:14.939537 INFO: Test AUC: 0.611
1:45:14.939685 INFO: Train AUC: 0.617
1:45:14.939721 INFO: AUC difference: 1.11%
1:45:16.173615 INFO: Resetting torch num_threads to 32
1:45:16.271214 PROGRESS: === Extracted 3002148 precursors and 18105685 fragments ===
1:45:16.271714 INFO: === FDR correction performed with classifier version 13 ===
1:45:16.272539 PROGRESS: ============================= Precursor FDR =============================
1:45:16.272639 PROGRESS: Total precursors accumulated: 1,874
1:45:16.272712 PROGRESS: Target precursors: 1,856 (99.04%)
1:45:16.272774 PROGRESS: Decoy precursors: 18 (0.96%)
1:45:16.272837 PROGRESS: 
1:45:16.272889 PROGRESS: Precursor Summary:
1:45:16.274383 PROGRESS: Channel   0:	 0.050 FDR: 1,856; 0.010 FDR: 1,856; 0.001 FDR: 1,353
1:45:16.274484 PROGRESS: 
1:45:16.274546 PROGRESS: Protein Summary:
1:45:16.276497 PROGRESS: Channel   0:	 0.050 FDR: 1,440; 0.010 FDR: 1,440; 0.001 FDR: 1,064
1:45:16.276594 PROGRESS: =========================================================================
1:45:16.330891 INFO: Target number of precursors reached.
1:45:18.154602 INFO: fragments_df: keeping 5000 of 18105685 [sum(precursor_idx_mask)=47253 sum(mass_error_mask)=18105685 stop_rank=5000
1:45:19.231045 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:45:19.509097 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:45:20.232134 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:45:20.232630 INFO: Using score_cutoff 4.76042737197876 (fac=0.99, q=1)
1:45:20.232962 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:45:20.233049 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:45:20.233108 INFO: Updating optimization_manager: score_cutoff        : 4.229773026752472 -> 4.76042737197876
1:45:20.233176 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:45:20.832760 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:45:22.157580 INFO: === checking if optimization conditions were reached ===
1:45:22.157837 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:45:22.160693 INFO: Updating optimization_manager: rt_error            : 716.9457397460938 -> 984.0111846429264
1:45:22.160806 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 984.0112.
1:45:22.160877 INFO: ==============================================
1:45:22.160953 INFO: Starting optimization step 1.
1:45:22.161017 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:45:22.161096 INFO: Using rust extraction backend
1:45:22.161166 PROGRESS: Extracting batch of 1001059 precursors
1:45:23.846706 INFO: === Search parameters used ===
1:45:23.846986 INFO: rt_error       : 984.0111846429264
1:45:23.847054 INFO: mobility_error : 0.1
1:45:23.847117 INFO: num_candidates : 3
1:45:23.847172 INFO: ms1_error      : 20
1:45:23.847228 INFO: ms2_error      : 10.0
1:45:23.847283 INFO: fwhm_rt        : 3.0
1:45:23.847328 INFO: quant_window   : 3
1:45:23.847436 INFO: ==============================================
1:45:37.778817 INFO: performing precursor FDR with 40 features
1:45:37.778947 INFO: Decoy channel: -1
1:45:37.778976 INFO: competitive: True
1:45:38.504003 INFO: Setting torch num_threads to 2 for FDR classification task
1:45:39.831987 INFO: Estimating optimal hyperparameters - samples: 2,401,734, batch_size: 4,096, learning_rate: 1.00e-03
1:45:39.837092 INFO: Using random state 846810 for train-test-split
1:46:25.428258 INFO: Test AUC: 0.612
1:46:25.428400 INFO: Train AUC: 0.618
1:46:25.428437 INFO: AUC difference: 0.94%
1:46:26.662909 INFO: Resetting torch num_threads to 32
1:46:26.754328 PROGRESS: === Extracted 3002168 precursors and 18209267 fragments ===
1:46:26.754848 INFO: === FDR correction performed with classifier version 13 ===
1:46:26.755617 PROGRESS: ============================= Precursor FDR =============================
1:46:26.755715 PROGRESS: Total precursors accumulated: 1,871
1:46:26.755800 PROGRESS: Target precursors: 1,853 (99.04%)
1:46:26.755862 PROGRESS: Decoy precursors: 18 (0.96%)
1:46:26.755918 PROGRESS: 
1:46:26.755973 PROGRESS: Precursor Summary:
1:46:26.757404 PROGRESS: Channel   0:	 0.050 FDR: 1,853; 0.010 FDR: 1,853; 0.001 FDR: 1,199
1:46:26.757502 PROGRESS: 
1:46:26.757563 PROGRESS: Protein Summary:
1:46:26.759535 PROGRESS: Channel   0:	 0.050 FDR: 1,433; 0.010 FDR: 1,433; 0.001 FDR:   957
1:46:26.759637 PROGRESS: =========================================================================
1:46:26.813050 INFO: Target number of precursors reached.
1:46:28.659304 INFO: fragments_df: keeping 5000 of 18209267 [sum(precursor_idx_mask)=47434 sum(mass_error_mask)=18209267 stop_rank=5000
1:46:29.720805 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:46:29.995266 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:46:30.718071 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:46:30.718522 INFO: Using score_cutoff 4.676163697814942 (fac=0.99, q=1)
1:46:30.718846 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:46:30.718934 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:46:30.718999 INFO: Updating optimization_manager: score_cutoff        : 4.76042737197876 -> 4.676163697814942
1:46:30.719064 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:46:31.320543 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:46:32.661523 INFO: === checking if optimization conditions were reached ===
1:46:32.661762 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:46:32.664845 INFO: Updating optimization_manager: rt_error            : 984.0111846429264 -> 1250.4207189241872
1:46:32.664984 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 1250.4207.
1:46:32.665060 INFO: ==============================================
1:46:32.665143 INFO: Starting optimization step 2.
1:46:32.665216 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:46:32.665294 INFO: Using rust extraction backend
1:46:32.665365 PROGRESS: Extracting batch of 1001059 precursors
1:46:34.366481 INFO: === Search parameters used ===
1:46:34.366778 INFO: rt_error       : 1250.4207189241872
1:46:34.366853 INFO: mobility_error : 0.1
1:46:34.366919 INFO: num_candidates : 3
1:46:34.366984 INFO: ms1_error      : 20
1:46:34.367040 INFO: ms2_error      : 10.0
1:46:34.367098 INFO: fwhm_rt        : 3.0
1:46:34.367153 INFO: quant_window   : 3
1:46:34.367211 INFO: ==============================================
1:46:48.739794 INFO: performing precursor FDR with 40 features
1:46:48.739940 INFO: Decoy channel: -1
1:46:48.739970 INFO: competitive: True
1:46:49.449505 INFO: Setting torch num_threads to 2 for FDR classification task
1:46:50.765300 INFO: Estimating optimal hyperparameters - samples: 2,401,733, batch_size: 4,096, learning_rate: 1.00e-03
1:46:50.770440 INFO: Using random state 846810 for train-test-split
1:47:37.276704 INFO: Test AUC: 0.613
1:47:37.276891 INFO: Train AUC: 0.616
1:47:37.276926 INFO: AUC difference: 0.44%
1:47:38.502042 INFO: Resetting torch num_threads to 32
1:47:38.725980 PROGRESS: === Extracted 3002167 precursors and 18206245 fragments ===
1:47:38.726547 INFO: === FDR correction performed with classifier version 13 ===
1:47:38.727321 PROGRESS: ============================= Precursor FDR =============================
1:47:38.727435 PROGRESS: Total precursors accumulated: 1,847
1:47:38.727511 PROGRESS: Target precursors: 1,829 (99.03%)
1:47:38.727576 PROGRESS: Decoy precursors: 18 (0.97%)
1:47:38.727635 PROGRESS: 
1:47:38.727692 PROGRESS: Precursor Summary:
1:47:38.729138 PROGRESS: Channel   0:	 0.050 FDR: 1,829; 0.010 FDR: 1,829; 0.001 FDR: 1,291
1:47:38.729234 PROGRESS: 
1:47:38.729307 PROGRESS: Protein Summary:
1:47:38.731266 PROGRESS: Channel   0:	 0.050 FDR: 1,412; 0.010 FDR: 1,412; 0.001 FDR: 1,015
1:47:38.731375 PROGRESS: =========================================================================
1:47:38.790863 INFO: Target number of precursors reached.
1:47:40.635819 INFO: fragments_df: keeping 5000 of 18206245 [sum(precursor_idx_mask)=46498 sum(mass_error_mask)=18206245 stop_rank=5000
1:47:41.744503 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:47:41.985620 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:47:42.724330 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:47:42.724789 INFO: Using score_cutoff 4.869337153244018 (fac=0.99, q=1)
1:47:42.725122 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:47:42.725209 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:47:42.725271 INFO: Updating optimization_manager: score_cutoff        : 4.676163697814942 -> 4.869337153244018
1:47:42.725335 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:47:43.316886 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:47:44.638996 INFO: === checking if optimization conditions were reached ===
1:47:44.639272 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:47:44.642504 INFO: Updating optimization_manager: rt_error            : 1250.4207189241872 -> 1043.1175124910774
1:47:44.642647 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 1043.1175.
1:47:44.642744 INFO: ==============================================
1:47:44.642832 INFO: Starting optimization step 3.
1:47:44.642906 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:47:44.642989 INFO: Using rust extraction backend
1:47:44.643072 PROGRESS: Extracting batch of 1001059 precursors
1:47:46.348530 INFO: === Search parameters used ===
1:47:46.348906 INFO: rt_error       : 1043.1175124910774
1:47:46.348983 INFO: mobility_error : 0.1
1:47:46.349043 INFO: num_candidates : 3
1:47:46.349102 INFO: ms1_error      : 20
1:47:46.349163 INFO: ms2_error      : 10.0
1:47:46.349218 INFO: fwhm_rt        : 3.0
1:47:46.349266 INFO: quant_window   : 3
1:47:46.349318 INFO: ==============================================
1:48:00.532006 INFO: performing precursor FDR with 40 features
1:48:00.532155 INFO: Decoy channel: -1
1:48:00.532187 INFO: competitive: True
1:48:01.246753 INFO: Setting torch num_threads to 2 for FDR classification task
1:48:02.488831 INFO: Estimating optimal hyperparameters - samples: 2,401,722, batch_size: 4,096, learning_rate: 1.00e-03
1:48:02.494187 INFO: Using random state 846810 for train-test-split
1:48:48.193959 INFO: Test AUC: 0.613
1:48:48.194146 INFO: Train AUC: 0.616
1:48:48.194182 INFO: AUC difference: 0.58%
1:48:49.496165 INFO: Resetting torch num_threads to 32
1:48:49.776500 PROGRESS: === Extracted 3002153 precursors and 18207586 fragments ===
1:48:49.777063 INFO: === FDR correction performed with classifier version 13 ===
1:48:49.777863 PROGRESS: ============================= Precursor FDR =============================
1:48:49.777973 PROGRESS: Total precursors accumulated: 1,541
1:48:49.778048 PROGRESS: Target precursors: 1,526 (99.03%)
1:48:49.778113 PROGRESS: Decoy precursors: 15 (0.97%)
1:48:49.778167 PROGRESS: 
1:48:49.778226 PROGRESS: Precursor Summary:
1:48:49.779687 PROGRESS: Channel   0:	 0.050 FDR: 1,526; 0.010 FDR: 1,526; 0.001 FDR: 1,072
1:48:49.779796 PROGRESS: 
1:48:49.779864 PROGRESS: Protein Summary:
1:48:49.781694 PROGRESS: Channel   0:	 0.050 FDR: 1,237; 0.010 FDR: 1,237; 0.001 FDR:   870
1:48:49.781795 PROGRESS: =========================================================================
1:48:49.842105 INFO: Target number of precursors reached.
1:48:51.795037 INFO: fragments_df: keeping 5000 of 18207586 [sum(precursor_idx_mask)=38458 sum(mass_error_mask)=18207586 stop_rank=5000
1:48:52.886250 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:48:53.126149 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:48:53.848308 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:48:53.848760 INFO: Using score_cutoff 4.064962134361267 (fac=0.99, q=1)
1:48:53.849097 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:48:53.849183 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:48:53.849254 INFO: Updating optimization_manager: score_cutoff        : 4.869337153244018 -> 4.064962134361267
1:48:53.849323 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:48:54.450479 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:48:55.836771 INFO: === checking if optimization conditions were reached ===
1:48:55.837033 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:48:55.839986 INFO: Updating optimization_manager: rt_error            : 1043.1175124910774 -> 1159.0576118050453
1:48:55.840121 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 1159.0576.
1:48:55.840194 INFO: ==============================================
1:48:55.840275 INFO: Starting optimization step 4.
1:48:55.840348 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:48:55.840432 INFO: Using rust extraction backend
1:48:55.840513 PROGRESS: Extracting batch of 1001059 precursors
1:48:57.544197 INFO: === Search parameters used ===
1:48:57.544562 INFO: rt_error       : 1159.0576118050453
1:48:57.544629 INFO: mobility_error : 0.1
1:48:57.544693 INFO: num_candidates : 3
1:48:57.544744 INFO: ms1_error      : 20
1:48:57.544790 INFO: ms2_error      : 10.0
1:48:57.544835 INFO: fwhm_rt        : 3.0
1:48:57.544881 INFO: quant_window   : 3
1:48:57.544935 INFO: ==============================================
1:49:11.738026 INFO: performing precursor FDR with 40 features
1:49:11.738176 INFO: Decoy channel: -1
1:49:11.738205 INFO: competitive: True
1:49:12.469796 INFO: Setting torch num_threads to 2 for FDR classification task
1:49:13.775873 INFO: Estimating optimal hyperparameters - samples: 2,401,721, batch_size: 4,096, learning_rate: 1.00e-03
1:49:13.781187 INFO: Using random state 846810 for train-test-split
1:50:00.739739 INFO: Test AUC: 0.611
1:50:00.739931 INFO: Train AUC: 0.617
1:50:00.739967 INFO: AUC difference: 0.94%
1:50:01.984392 INFO: Resetting torch num_threads to 32
1:50:02.077417 PROGRESS: === Extracted 3002152 precursors and 18205330 fragments ===
1:50:02.077971 INFO: === FDR correction performed with classifier version 13 ===
1:50:02.078790 PROGRESS: ============================= Precursor FDR =============================
1:50:02.078889 PROGRESS: Total precursors accumulated: 1,860
1:50:02.078959 PROGRESS: Target precursors: 1,842 (99.03%)
1:50:02.079018 PROGRESS: Decoy precursors: 18 (0.97%)
1:50:02.079069 PROGRESS: 
1:50:02.079118 PROGRESS: Precursor Summary:
1:50:02.080587 PROGRESS: Channel   0:	 0.050 FDR: 1,842; 0.010 FDR: 1,842; 0.001 FDR: 1,487
1:50:02.080679 PROGRESS: 
1:50:02.080746 PROGRESS: Protein Summary:
1:50:02.082725 PROGRESS: Channel   0:	 0.050 FDR: 1,441; 0.010 FDR: 1,441; 0.001 FDR: 1,159
1:50:02.082824 PROGRESS: =========================================================================
1:50:02.142670 INFO: Target number of precursors reached.
1:50:04.079719 INFO: fragments_df: keeping 5000 of 18205330 [sum(precursor_idx_mask)=46846 sum(mass_error_mask)=18205330 stop_rank=5000
1:50:05.340968 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:50:05.616267 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:50:06.341527 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:50:06.342001 INFO: Using score_cutoff 5.201613366651535 (fac=0.99, q=1)
1:50:06.342347 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:50:06.342450 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:50:06.342510 INFO: Updating optimization_manager: score_cutoff        : 4.064962134361267 -> 5.201613366651535
1:50:06.342581 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:50:06.980710 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:50:08.350427 INFO: === checking if optimization conditions were reached ===
1:50:08.350693 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:50:08.353952 INFO: Updating optimization_manager: rt_error            : 1159.0576118050453 -> 1204.2679839201635
1:50:08.354088 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 1204.2680.
1:50:08.354174 INFO: ==============================================
1:50:08.354279 INFO: Starting optimization step 5.
1:50:08.354369 PROGRESS: === Extracting elution groups 0 to 511000 ===
1:50:08.354471 INFO: Using rust extraction backend
1:50:08.354555 PROGRESS: Extracting batch of 1001059 precursors
1:50:10.054958 INFO: === Search parameters used ===
1:50:10.055346 INFO: rt_error       : 1204.2679839201635
1:50:10.055413 INFO: mobility_error : 0.1
1:50:10.055466 INFO: num_candidates : 3
1:50:10.055514 INFO: ms1_error      : 20
1:50:10.055561 INFO: ms2_error      : 10.0
1:50:10.055606 INFO: fwhm_rt        : 3.0
1:50:10.055665 INFO: quant_window   : 3
1:50:10.055712 INFO: ==============================================
1:50:24.137111 INFO: performing precursor FDR with 40 features
1:50:24.137234 INFO: Decoy channel: -1
1:50:24.137264 INFO: competitive: True
1:50:24.847221 INFO: Setting torch num_threads to 2 for FDR classification task
1:50:26.146629 INFO: Estimating optimal hyperparameters - samples: 2,401,724, batch_size: 4,096, learning_rate: 1.00e-03
1:50:26.151967 INFO: Using random state 846810 for train-test-split
1:51:10.021645 INFO: Test AUC: 0.612
1:51:10.021788 INFO: Train AUC: 0.617
1:51:10.021827 INFO: AUC difference: 0.77%
1:51:11.233464 INFO: Resetting torch num_threads to 32
1:51:11.324095 PROGRESS: === Extracted 3002155 precursors and 18206130 fragments ===
1:51:11.324634 INFO: === FDR correction performed with classifier version 13 ===
1:51:11.325477 PROGRESS: ============================= Precursor FDR =============================
1:51:11.325593 PROGRESS: Total precursors accumulated: 1,821
1:51:11.325668 PROGRESS: Target precursors: 1,803 (99.01%)
1:51:11.325733 PROGRESS: Decoy precursors: 18 (0.99%)
1:51:11.325793 PROGRESS: 
1:51:11.325845 PROGRESS: Precursor Summary:
1:51:11.327397 PROGRESS: Channel   0:	 0.050 FDR: 1,803; 0.010 FDR: 1,803; 0.001 FDR: 1,171
1:51:11.327511 PROGRESS: 
1:51:11.327575 PROGRESS: Protein Summary:
1:51:11.329540 PROGRESS: Channel   0:	 0.050 FDR: 1,400; 0.010 FDR: 1,400; 0.001 FDR:   940
1:51:11.329645 PROGRESS: =========================================================================
1:51:11.382878 INFO: Target number of precursors reached.
1:51:13.314645 INFO: fragments_df: keeping 5000 of 18206130 [sum(precursor_idx_mask)=45841 sum(mass_error_mask)=18206130 stop_rank=5000
1:51:14.396381 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:51:14.666391 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:51:15.388175 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:51:15.388634 INFO: Using score_cutoff 4.387591334152222 (fac=0.99, q=1)
1:51:15.388963 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:51:15.389049 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:51:15.389112 INFO: Updating optimization_manager: score_cutoff        : 5.201613366651535 -> 4.387591334152222
1:51:15.389173 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:51:15.993019 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:51:17.326773 INFO: === checking if optimization conditions were reached ===
1:51:17.327044 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
1:51:17.328172 INFO: Updating optimization_manager: rt_error            : 1204.2679839201635 -> 716.9457397460938
1:51:17.328337 INFO: Updating optimization_manager: classifier_version  : 13 -> 14
1:51:17.328448 INFO: Updating optimization_manager: score_cutoff        : 4.387591334152222 -> 4.76042737197876
1:51:17.328554 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:51:17.328658 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:51:17.328757 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 716.9457 found after 6 searches.
1:51:17.328828 INFO: ==============================================
1:51:17.328916 PROGRESS: Optimization finished for rt_error.
1:51:18.567347 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:51:19.163628 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:51:20.494038 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:51:20.494306 PROGRESS: ==============================================
1:51:20.494411 PROGRESS: ms2_error      : 10.0000
1:51:20.494490 PROGRESS: rt_error       : 716.9457
1:51:20.494547 PROGRESS: ==============================================
1:51:20.495410 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:51:27.062930 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:51:51.275421 INFO: Using rust extraction backend
1:51:51.275885 PROGRESS: Extracting batch of 10770831 precursors
1:52:14.229247 INFO: === Search parameters used ===
1:52:14.229851 INFO: rt_error       : 716.9457397460938
1:52:14.229930 INFO: mobility_error : 0.1
1:52:14.230003 INFO: num_candidates : 3
1:52:14.230064 INFO: ms1_error      : 20
1:52:14.230132 INFO: ms2_error      : 10.0
1:52:14.230195 INFO: fwhm_rt        : 3.0
1:52:14.230254 INFO: quant_window   : 3
1:52:14.230304 INFO: ==============================================
1:53:08.838127 INFO: Removed 1115782 precursors with score below cutoff 4.76042737197876
1:53:42.800612 INFO: performing precursor FDR with 40 features
1:53:42.800860 INFO: Decoy channel: -1
1:53:42.800894 INFO: competitive: True
1:53:46.120038 INFO: Setting torch num_threads to 2 for FDR classification task
1:53:58.849030 INFO: Estimating optimal hyperparameters - samples: 24,957,362, batch_size: 4,096, learning_rate: 1.00e-03
1:53:58.925026 INFO: Using random state 495265 for train-test-split
2:02:00.850470 INFO: Test AUC: 0.616
2:02:00.850754 INFO: Train AUC: 0.616
2:02:00.850814 INFO: AUC difference: 0.06%
2:02:07.969479 INFO: Resetting torch num_threads to 32
2:02:09.758092 PROGRESS: ============================= Precursor FDR =============================
2:02:09.758361 PROGRESS: Total precursors accumulated: 20,386
2:02:09.758443 PROGRESS: Target precursors: 20,185 (99.01%)
2:02:09.758513 PROGRESS: Decoy precursors: 201 (0.99%)
2:02:09.758567 PROGRESS: 
2:02:09.758616 PROGRESS: Precursor Summary:
2:02:09.762892 PROGRESS: Channel   0:	 0.050 FDR: 20,185; 0.010 FDR: 20,185; 0.001 FDR: 8,180
2:02:09.763000 PROGRESS: 
2:02:09.763062 PROGRESS: Protein Summary:
2:02:09.770014 PROGRESS: Channel   0:	 0.050 FDR: 6,104; 0.010 FDR: 6,104; 0.001 FDR: 3,201
2:02:09.770134 PROGRESS: =========================================================================
2:02:09.959721 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1/psm.parquet
2:02:10.003200 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1/frag.parquet
2:02:10.081462 INFO: Finished workflow for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1
2:02:10.520354 PROGRESS: Loading raw file 5/6: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2 
2:02:10.520504 INFO: Quantification results path: /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant
2:02:10.520584 INFO: Creating folder /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2/figures
2:02:10.520751 INFO: Initializing TimingManager
2:02:10.521164 INFO: Initializing RawFileManager
2:02:17.119322 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:02:17.120373 INFO: Determining DIA cycle
2:02:17.132762 INFO: Found cycle with start 0.00 min and length 20.
2:02:17.155915 INFO: RT (min)            : 0.0 - 23.9
2:02:17.156003 INFO: RT duration (sec)   : 1433.8
2:02:17.156041 INFO: RT duration (min)   : 23.9
2:02:17.156069 INFO: Cycle len (scans)   : 20
2:02:17.156107 INFO: Cycle len (sec)     : 1.04
2:02:17.156129 INFO: Number of cycles    : 1381
2:02:17.156152 INFO: MS2 range (m/z)     : 400.4 - 800.6
2:02:17.156180 INFO: Creating DIA data object took: 6.634917497634888
2:02:17.759226 INFO: Creating DIA data NG object took: 0.6029300689697266
2:02:19.409245 INFO: Initializing CalibrationManager
2:02:19.409580 INFO: Setting up calibration estimators ..
2:02:19.409650 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:02:19.409741 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'}' ..
2:02:19.409832 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:02:19.409894 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:02:19.409959 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}}' ..
2:02:19.410022 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:02:19.410078 INFO: Done setting up calibration estimators.
2:02:19.410193 INFO: Initializing OptimizationManager
2:02:19.410333 INFO: initial parameter: ms1_error = 20
2:02:19.410416 INFO: initial parameter: ms2_error = 20
2:02:19.410479 INFO: initial parameter: rt_error = 716.953369140625
2:02:19.410532 INFO: initial parameter: mobility_error = 0.1
2:02:19.410581 INFO: initial parameter: num_candidates = 1
2:02:19.410628 INFO: initial parameter: fwhm_rt = 5
2:02:19.410674 INFO: initial parameter: fwhm_mobility = 0.01
2:02:19.410721 INFO: initial parameter: score_cutoff = 0
2:02:19.410775 INFO: initial parameter: classifier_version = -1
2:02:19.410855 PROGRESS: Initializing workflow 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2
2:02:19.411113 INFO: FDRManager: loading saved state not requested, will be initialized.
2:02:19.411153 INFO: Initializing FDRManager
2:02:19.411200 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2:02:20.675321 PROGRESS: Initializing spectral library: 5,415,345 target precursors potentially observable (2,595,411 removed)
2:02:21.469548 INFO: Updating optimization_manager: ms2_error           : 20 -> 20
2:02:21.469942 INFO: Updating optimization_manager: rt_error            : 716.953369140625 -> 716.953369140625
2:02:21.470050 PROGRESS: Starting initial search for precursors.
2:02:21.470147 INFO: Starting optimization step 0.
2:02:21.470217 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:02:21.470293 INFO: Using rust extraction backend
2:02:21.470387 PROGRESS: Extracting batch of 1960 precursors
2:02:21.476388 INFO: === Search parameters used ===
2:02:21.476502 INFO: rt_error       : 716.953369140625
2:02:21.476557 INFO: mobility_error : 0.1
2:02:21.476607 INFO: num_candidates : 1
2:02:21.476663 INFO: ms1_error      : 20
2:02:21.476710 INFO: ms2_error      : 20
2:02:21.476755 INFO: fwhm_rt        : 5
2:02:21.476799 INFO: quant_window   : 3
2:02:21.476844 INFO: ==============================================
2:02:21.515180 INFO: performing precursor FDR with 40 features
2:02:21.515263 INFO: Decoy channel: -1
2:02:21.515290 INFO: competitive: True
2:02:21.516569 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:21.518657 INFO: Estimating optimal hyperparameters - samples: 1,564, batch_size: 128, learning_rate: 1.77e-04
2:02:21.519632 INFO: Using random state 684577 for train-test-split
2:02:21.671017 INFO: Test AUC: 0.476
2:02:21.671104 INFO: Train AUC: 0.600
2:02:21.671134 INFO: AUC difference: 20.66%
2:02:21.671157 WARNING: AUC difference > 5%. This may indicate overfitting.
2:02:21.914994 INFO: Resetting torch num_threads to 32
2:02:21.916599 PROGRESS: === Extracted 1956 precursors and 10657 fragments ===
2:02:21.916961 INFO: === FDR correction performed with classifier version -1 ===
2:02:21.917452 PROGRESS: ============================= Precursor FDR =============================
2:02:21.917547 PROGRESS: Total precursors accumulated: 69
2:02:21.917609 PROGRESS: Target precursors: 69 (100.00%)
2:02:21.917663 PROGRESS: Decoy precursors: 0 (0.00%)
2:02:21.917713 PROGRESS: 
2:02:21.917764 PROGRESS: Precursor Summary:
2:02:21.918858 PROGRESS: Channel   0:	 0.050 FDR:    69; 0.010 FDR:    69; 0.001 FDR:    69
2:02:21.918954 PROGRESS: 
2:02:21.919014 PROGRESS: Protein Summary:
2:02:21.920193 PROGRESS: Channel   0:	 0.050 FDR:    68; 0.010 FDR:    68; 0.001 FDR:    68
2:02:21.920281 PROGRESS: =========================================================================
2:02:21.920530 INFO: Target number of precursors not reached yet.
2:02:21.997801 INFO: Starting optimization step 1.
2:02:21.998011 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:02:21.998100 INFO: Using rust extraction backend
2:02:21.998165 PROGRESS: Extracting batch of 3921 precursors
2:02:22.006993 INFO: === Search parameters used ===
2:02:22.007128 INFO: rt_error       : 716.953369140625
2:02:22.007185 INFO: mobility_error : 0.1
2:02:22.007240 INFO: num_candidates : 1
2:02:22.007289 INFO: ms1_error      : 20
2:02:22.007335 INFO: ms2_error      : 20
2:02:22.007381 INFO: fwhm_rt        : 5
2:02:22.007427 INFO: quant_window   : 3
2:02:22.007470 INFO: ==============================================
2:02:22.079316 INFO: performing precursor FDR with 40 features
2:02:22.079412 INFO: Decoy channel: -1
2:02:22.079437 INFO: competitive: True
2:02:22.083651 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:22.085964 INFO: Estimating optimal hyperparameters - samples: 4,693, batch_size: 128, learning_rate: 1.77e-04
2:02:22.086048 INFO: Using random state 30644 for train-test-split
2:02:22.562119 INFO: Test AUC: 0.529
2:02:22.562213 INFO: Train AUC: 0.610
2:02:22.562246 INFO: AUC difference: 13.32%
2:02:22.562269 WARNING: AUC difference > 5%. This may indicate overfitting.
2:02:22.808201 INFO: Resetting torch num_threads to 32
2:02:22.811049 PROGRESS: === Extracted 5867 precursors and 32352 fragments ===
2:02:22.811419 INFO: === FDR correction performed with classifier version -1 ===
2:02:22.811910 PROGRESS: ============================= Precursor FDR =============================
2:02:22.812007 PROGRESS: Total precursors accumulated: 2
2:02:22.812084 PROGRESS: Target precursors: 2 (100.00%)
2:02:22.812145 PROGRESS: Decoy precursors: 0 (0.00%)
2:02:22.812199 PROGRESS: 
2:02:22.812253 PROGRESS: Precursor Summary:
2:02:22.813311 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
2:02:22.813401 PROGRESS: 
2:02:22.813463 PROGRESS: Protein Summary:
2:02:22.814648 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
2:02:22.814749 PROGRESS: =========================================================================
2:02:22.815026 INFO: Target number of precursors not reached yet.
2:02:22.896945 INFO: Starting optimization step 2.
2:02:22.897150 PROGRESS: === Extracting elution groups 3000 to 7000 ===
2:02:22.897236 INFO: Using rust extraction backend
2:02:22.897310 PROGRESS: Extracting batch of 7852 precursors
2:02:22.912566 INFO: === Search parameters used ===
2:02:22.912729 INFO: rt_error       : 716.953369140625
2:02:22.912790 INFO: mobility_error : 0.1
2:02:22.912843 INFO: num_candidates : 1
2:02:22.912895 INFO: ms1_error      : 20
2:02:22.912945 INFO: ms2_error      : 20
2:02:22.912995 INFO: fwhm_rt        : 5
2:02:22.913043 INFO: quant_window   : 3
2:02:22.913092 INFO: ==============================================
2:02:23.040933 INFO: performing precursor FDR with 40 features
2:02:23.041044 INFO: Decoy channel: -1
2:02:23.041073 INFO: competitive: True
2:02:23.047324 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:23.051678 INFO: Estimating optimal hyperparameters - samples: 10,968, batch_size: 128, learning_rate: 1.77e-04
2:02:23.051808 INFO: Using random state 935443 for train-test-split
2:02:24.155838 INFO: Test AUC: 0.562
2:02:24.155950 INFO: Train AUC: 0.596
2:02:24.155980 INFO: AUC difference: 5.75%
2:02:24.156003 WARNING: AUC difference > 5%. This may indicate overfitting.
2:02:24.400312 INFO: Resetting torch num_threads to 32
2:02:24.404313 PROGRESS: === Extracted 13711 precursors and 75581 fragments ===
2:02:24.404699 INFO: === FDR correction performed with classifier version -1 ===
2:02:24.405207 PROGRESS: ============================= Precursor FDR =============================
2:02:24.405298 PROGRESS: Total precursors accumulated: 14
2:02:24.405360 PROGRESS: Target precursors: 14 (100.00%)
2:02:24.405415 PROGRESS: Decoy precursors: 0 (0.00%)
2:02:24.405465 PROGRESS: 
2:02:24.405513 PROGRESS: Precursor Summary:
2:02:24.406570 PROGRESS: Channel   0:	 0.050 FDR:    14; 0.010 FDR:    14; 0.001 FDR:    14
2:02:24.406664 PROGRESS: 
2:02:24.406726 PROGRESS: Protein Summary:
2:02:24.407897 PROGRESS: Channel   0:	 0.050 FDR:    14; 0.010 FDR:    14; 0.001 FDR:    14
2:02:24.407986 PROGRESS: =========================================================================
2:02:24.408316 INFO: Target number of precursors not reached yet.
2:02:24.500382 INFO: Starting optimization step 3.
2:02:24.500622 PROGRESS: === Extracting elution groups 7000 to 15000 ===
2:02:24.500717 INFO: Using rust extraction backend
2:02:24.500784 PROGRESS: Extracting batch of 15661 precursors
2:02:24.529529 INFO: === Search parameters used ===
2:02:24.529742 INFO: rt_error       : 716.953369140625
2:02:24.529803 INFO: mobility_error : 0.1
2:02:24.529863 INFO: num_candidates : 1
2:02:24.529911 INFO: ms1_error      : 20
2:02:24.529962 INFO: ms2_error      : 20
2:02:24.530011 INFO: fwhm_rt        : 5
2:02:24.530057 INFO: quant_window   : 3
2:02:24.530101 INFO: ==============================================
2:02:24.694901 INFO: performing precursor FDR with 40 features
2:02:24.695013 INFO: Decoy channel: -1
2:02:24.695041 INFO: competitive: True
2:02:24.707510 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:24.714284 INFO: Estimating optimal hyperparameters - samples: 23,476, batch_size: 128, learning_rate: 1.77e-04
2:02:24.714473 INFO: Using random state 924173 for train-test-split
2:02:27.092740 INFO: Test AUC: 0.561
2:02:27.092854 INFO: Train AUC: 0.602
2:02:27.092886 INFO: AUC difference: 6.94%
2:02:27.092909 WARNING: AUC difference > 5%. This may indicate overfitting.
2:02:27.350937 INFO: Resetting torch num_threads to 32
2:02:27.357381 PROGRESS: === Extracted 29345 precursors and 162210 fragments ===
2:02:27.357795 INFO: === FDR correction performed with classifier version -1 ===
2:02:27.358322 PROGRESS: ============================= Precursor FDR =============================
2:02:27.358436 PROGRESS: Total precursors accumulated: 8
2:02:27.358509 PROGRESS: Target precursors: 8 (100.00%)
2:02:27.358572 PROGRESS: Decoy precursors: 0 (0.00%)
2:02:27.358629 PROGRESS: 
2:02:27.358684 PROGRESS: Precursor Summary:
2:02:27.359767 PROGRESS: Channel   0:	 0.050 FDR:     8; 0.010 FDR:     8; 0.001 FDR:     8
2:02:27.359865 PROGRESS: 
2:02:27.359930 PROGRESS: Protein Summary:
2:02:27.361140 PROGRESS: Channel   0:	 0.050 FDR:     8; 0.010 FDR:     8; 0.001 FDR:     8
2:02:27.361241 PROGRESS: =========================================================================
2:02:27.361727 INFO: Target number of precursors not reached yet.
2:02:27.473170 INFO: Starting optimization step 4.
2:02:27.473413 PROGRESS: === Extracting elution groups 15000 to 31000 ===
2:02:27.473503 INFO: Using rust extraction backend
2:02:27.473574 PROGRESS: Extracting batch of 31339 precursors
2:02:27.529637 INFO: === Search parameters used ===
2:02:27.529891 INFO: rt_error       : 716.953369140625
2:02:27.529958 INFO: mobility_error : 0.1
2:02:27.530018 INFO: num_candidates : 1
2:02:27.530070 INFO: ms1_error      : 20
2:02:27.530118 INFO: ms2_error      : 20
2:02:27.530166 INFO: fwhm_rt        : 5
2:02:27.530213 INFO: quant_window   : 3
2:02:27.530260 INFO: ==============================================
2:02:27.816952 INFO: performing precursor FDR with 40 features
2:02:27.817063 INFO: Decoy channel: -1
2:02:27.817090 INFO: competitive: True
2:02:27.838518 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:27.852825 INFO: Estimating optimal hyperparameters - samples: 48,516, batch_size: 198, learning_rate: 2.20e-04
2:02:27.853039 INFO: Using random state 336063 for train-test-split
2:02:31.523917 INFO: Test AUC: 0.572
2:02:31.524010 INFO: Train AUC: 0.605
2:02:31.524040 INFO: AUC difference: 5.43%
2:02:31.524064 WARNING: AUC difference > 5%. This may indicate overfitting.
2:02:31.787406 INFO: Resetting torch num_threads to 32
2:02:31.798694 PROGRESS: === Extracted 60645 precursors and 335407 fragments ===
2:02:31.799308 INFO: === FDR correction performed with classifier version -1 ===
2:02:31.799858 PROGRESS: ============================= Precursor FDR =============================
2:02:31.799951 PROGRESS: Total precursors accumulated: 0
2:02:31.800016 PROGRESS: Target precursors: 0 (0.00%)
2:02:31.800073 PROGRESS: Decoy precursors: 0 (0.00%)
2:02:31.800122 PROGRESS: 
2:02:31.800172 PROGRESS: Precursor Summary:
2:02:31.800302 PROGRESS: 
2:02:31.800369 PROGRESS: Protein Summary:
2:02:31.800450 PROGRESS: =========================================================================
2:02:31.801351 INFO: Target number of precursors not reached yet.
2:02:31.954387 INFO: Starting optimization step 5.
2:02:31.954630 PROGRESS: === Extracting elution groups 31000 to 63000 ===
2:02:31.954723 INFO: Using rust extraction backend
2:02:31.954791 PROGRESS: Extracting batch of 62709 precursors
2:02:32.064830 INFO: === Search parameters used ===
2:02:32.065110 INFO: rt_error       : 716.953369140625
2:02:32.065176 INFO: mobility_error : 0.1
2:02:32.065229 INFO: num_candidates : 1
2:02:32.065278 INFO: ms1_error      : 20
2:02:32.065323 INFO: ms2_error      : 20
2:02:32.065368 INFO: fwhm_rt        : 5
2:02:32.065413 INFO: quant_window   : 3
2:02:32.065456 INFO: ==============================================
2:02:32.622237 INFO: performing precursor FDR with 40 features
2:02:32.622361 INFO: Decoy channel: -1
2:02:32.622393 INFO: competitive: True
2:02:32.674659 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:32.709636 INFO: Estimating optimal hyperparameters - samples: 98,611, batch_size: 403, learning_rate: 3.14e-04
2:02:32.709955 INFO: Using random state 492976 for train-test-split
2:02:37.260867 INFO: Test AUC: 0.574
2:02:37.260995 INFO: Train AUC: 0.610
2:02:37.261029 INFO: AUC difference: 5.79%
2:02:37.261055 WARNING: AUC difference > 5%. This may indicate overfitting.
2:02:37.548005 INFO: Resetting torch num_threads to 32
2:02:37.570040 PROGRESS: === Extracted 123264 precursors and 683149 fragments ===
2:02:37.570704 INFO: === FDR correction performed with classifier version -1 ===
2:02:37.571331 PROGRESS: ============================= Precursor FDR =============================
2:02:37.571429 PROGRESS: Total precursors accumulated: 24
2:02:37.571501 PROGRESS: Target precursors: 24 (100.00%)
2:02:37.571562 PROGRESS: Decoy precursors: 0 (0.00%)
2:02:37.571622 PROGRESS: 
2:02:37.571681 PROGRESS: Precursor Summary:
2:02:37.572734 PROGRESS: Channel   0:	 0.050 FDR:    24; 0.010 FDR:    24; 0.001 FDR:    24
2:02:37.572836 PROGRESS: 
2:02:37.572899 PROGRESS: Protein Summary:
2:02:37.574059 PROGRESS: Channel   0:	 0.050 FDR:    24; 0.010 FDR:    24; 0.001 FDR:    24
2:02:37.574153 PROGRESS: =========================================================================
2:02:37.576427 INFO: Target number of precursors not reached yet.
2:02:37.813608 INFO: Starting optimization step 6.
2:02:37.813869 PROGRESS: === Extracting elution groups 63000 to 127000 ===
2:02:37.813961 INFO: Using rust extraction backend
2:02:37.814034 PROGRESS: Extracting batch of 125408 precursors
2:02:38.031125 INFO: === Search parameters used ===
2:02:38.031402 INFO: rt_error       : 716.953369140625
2:02:38.031477 INFO: mobility_error : 0.1
2:02:38.031536 INFO: num_candidates : 1
2:02:38.031594 INFO: ms1_error      : 20
2:02:38.031664 INFO: ms2_error      : 20
2:02:38.031714 INFO: fwhm_rt        : 5
2:02:38.031762 INFO: quant_window   : 3
2:02:38.031811 INFO: ==============================================
2:02:39.073296 INFO: performing precursor FDR with 40 features
2:02:39.073444 INFO: Decoy channel: -1
2:02:39.073473 INFO: competitive: True
2:02:39.169885 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:39.250454 INFO: Estimating optimal hyperparameters - samples: 198,800, batch_size: 814, learning_rate: 4.46e-04
2:02:39.250905 INFO: Using random state 737143 for train-test-split
2:02:45.566984 INFO: Test AUC: 0.582
2:02:45.567100 INFO: Train AUC: 0.606
2:02:45.567133 INFO: AUC difference: 3.88%
2:02:45.894612 INFO: Resetting torch num_threads to 32
2:02:45.944285 PROGRESS: === Extracted 248501 precursors and 1377373 fragments ===
2:02:45.944932 INFO: === FDR correction performed with classifier version -1 ===
2:02:45.945523 PROGRESS: ============================= Precursor FDR =============================
2:02:45.945634 PROGRESS: Total precursors accumulated: 209
2:02:45.945709 PROGRESS: Target precursors: 207 (99.04%)
2:02:45.945771 PROGRESS: Decoy precursors: 2 (0.96%)
2:02:45.945832 PROGRESS: 
2:02:45.945885 PROGRESS: Precursor Summary:
2:02:45.946912 PROGRESS: Channel   0:	 0.050 FDR:   207; 0.010 FDR:   207; 0.001 FDR:   151
2:02:45.947012 PROGRESS: 
2:02:45.947074 PROGRESS: Protein Summary:
2:02:45.948230 PROGRESS: Channel   0:	 0.050 FDR:   189; 0.010 FDR:   189; 0.001 FDR:   142
2:02:45.948326 PROGRESS: =========================================================================
2:02:45.952087 INFO: Target number of precursors not reached yet.
2:02:46.357387 INFO: Starting optimization step 7.
2:02:46.357666 PROGRESS: === Extracting elution groups 127000 to 255000 ===
2:02:46.357775 INFO: Using rust extraction backend
2:02:46.357847 PROGRESS: Extracting batch of 250773 precursors
2:02:46.791504 INFO: === Search parameters used ===
2:02:46.791752 INFO: rt_error       : 716.953369140625
2:02:46.791825 INFO: mobility_error : 0.1
2:02:46.791882 INFO: num_candidates : 1
2:02:46.791932 INFO: ms1_error      : 20
2:02:46.791978 INFO: ms2_error      : 20
2:02:46.792024 INFO: fwhm_rt        : 5
2:02:46.792085 INFO: quant_window   : 3
2:02:46.792137 INFO: ==============================================
2:02:48.821098 INFO: performing precursor FDR with 40 features
2:02:48.821221 INFO: Decoy channel: -1
2:02:48.821251 INFO: competitive: True
2:02:49.002258 INFO: Setting torch num_threads to 2 for FDR classification task
2:02:49.174917 INFO: Estimating optimal hyperparameters - samples: 399,092, batch_size: 1,634, learning_rate: 6.32e-04
2:02:49.175569 INFO: Using random state 31201 for train-test-split
2:02:59.351859 INFO: Test AUC: 0.588
2:02:59.351992 INFO: Train AUC: 0.605
2:02:59.352026 INFO: AUC difference: 2.86%
2:02:59.751313 INFO: Resetting torch num_threads to 32
2:02:59.831244 PROGRESS: === Extracted 498866 precursors and 2764750 fragments ===
2:02:59.831898 INFO: === FDR correction performed with classifier version -1 ===
2:02:59.832544 PROGRESS: ============================= Precursor FDR =============================
2:02:59.832638 PROGRESS: Total precursors accumulated: 516
2:02:59.832711 PROGRESS: Target precursors: 511 (99.03%)
2:02:59.832770 PROGRESS: Decoy precursors: 5 (0.97%)
2:02:59.832822 PROGRESS: 
2:02:59.832872 PROGRESS: Precursor Summary:
2:02:59.833970 PROGRESS: Channel   0:	 0.050 FDR:   511; 0.010 FDR:   511; 0.001 FDR:   388
2:02:59.834067 PROGRESS: 
2:02:59.834128 PROGRESS: Protein Summary:
2:02:59.835446 PROGRESS: Channel   0:	 0.050 FDR:   439; 0.010 FDR:   439; 0.001 FDR:   334
2:02:59.835543 PROGRESS: =========================================================================
2:02:59.842124 INFO: Target number of precursors not reached yet.
2:03:00.538807 INFO: Starting optimization step 8.
2:03:00.539052 PROGRESS: === Extracting elution groups 255000 to 511000 ===
2:03:00.539148 INFO: Using rust extraction backend
2:03:00.539219 PROGRESS: Extracting batch of 501436 precursors
2:03:01.397875 INFO: === Search parameters used ===
2:03:01.398153 INFO: rt_error       : 716.953369140625
2:03:01.398220 INFO: mobility_error : 0.1
2:03:01.398273 INFO: num_candidates : 1
2:03:01.398319 INFO: ms1_error      : 20
2:03:01.398375 INFO: ms2_error      : 20
2:03:01.398427 INFO: fwhm_rt        : 5
2:03:01.398472 INFO: quant_window   : 3
2:03:01.398527 INFO: ==============================================
2:03:05.456742 INFO: performing precursor FDR with 40 features
2:03:05.456868 INFO: Decoy channel: -1
2:03:05.456896 INFO: competitive: True
2:03:05.811052 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:06.192163 INFO: Estimating optimal hyperparameters - samples: 799,640, batch_size: 3,275, learning_rate: 8.94e-04
2:03:06.193290 INFO: Using random state 599560 for train-test-split
2:03:23.390471 INFO: Test AUC: 0.591
2:03:23.390616 INFO: Train AUC: 0.604
2:03:23.390652 INFO: AUC difference: 2.14%
2:03:23.954539 INFO: Resetting torch num_threads to 32
2:03:24.106503 PROGRESS: === Extracted 999550 precursors and 5543290 fragments ===
2:03:24.107168 INFO: === FDR correction performed with classifier version -1 ===
2:03:24.107915 PROGRESS: ============================= Precursor FDR =============================
2:03:24.108010 PROGRESS: Total precursors accumulated: 1,117
2:03:24.108078 PROGRESS: Target precursors: 1,106 (99.02%)
2:03:24.108136 PROGRESS: Decoy precursors: 11 (0.98%)
2:03:24.108190 PROGRESS: 
2:03:24.108242 PROGRESS: Precursor Summary:
2:03:24.109490 PROGRESS: Channel   0:	 0.050 FDR: 1,106; 0.010 FDR: 1,106; 0.001 FDR:   802
2:03:24.109586 PROGRESS: 
2:03:24.109646 PROGRESS: Protein Summary:
2:03:24.111245 PROGRESS: Channel   0:	 0.050 FDR:   871; 0.010 FDR:   871; 0.001 FDR:   647
2:03:24.111345 PROGRESS: =========================================================================
2:03:24.123062 INFO: Target number of precursors reached.
2:03:24.710302 INFO: fragments_df: keeping 5000 of 5543290 [sum(precursor_idx_mask)=12235 sum(mass_error_mask)=5543290 stop_rank=5000
2:03:25.719795 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:03:25.921767 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:03:26.643907 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:03:26.644367 INFO: Using score_cutoff 10.182723790168762 (fac=0.99, q=1)
2:03:26.644687 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:03:26.644770 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:03:26.644831 INFO: Updating optimization_manager: score_cutoff        : 0 -> 10.182723790168762
2:03:26.644898 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:03:27.256589 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:03:28.654791 INFO: Updating optimization_manager: classifier_version  : -1 -> 8
2:03:28.655043 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:03:28.655156 INFO: Starting optimization step 9.
2:03:28.655236 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:03:28.655350 INFO: Using rust extraction backend
2:03:28.655473 PROGRESS: Extracting batch of 1001059 precursors
2:03:30.362688 INFO: === Search parameters used ===
2:03:30.362968 INFO: rt_error       : 716.953369140625
2:03:30.363056 INFO: mobility_error : 0.1
2:03:30.363124 INFO: num_candidates : 3
2:03:30.363191 INFO: ms1_error      : 20
2:03:30.363247 INFO: ms2_error      : 20
2:03:30.363297 INFO: fwhm_rt        : 3.0
2:03:30.363341 INFO: quant_window   : 3
2:03:30.363382 INFO: ==============================================
2:03:43.996259 INFO: performing precursor FDR with 40 features
2:03:43.996389 INFO: Decoy channel: -1
2:03:43.996419 INFO: competitive: True
2:03:44.718193 INFO: Setting torch num_threads to 2 for FDR classification task
2:03:46.035725 INFO: Estimating optimal hyperparameters - samples: 2,399,013, batch_size: 4,096, learning_rate: 1.00e-03
2:03:46.041039 INFO: Using random state 415403 for train-test-split
2:04:31.804807 INFO: Test AUC: 0.601
2:04:31.804986 INFO: Train AUC: 0.605
2:04:31.805034 INFO: AUC difference: 0.67%
2:04:33.031584 INFO: Resetting torch num_threads to 32
2:04:33.304250 PROGRESS: === Extracted 2998767 precursors and 16457008 fragments ===
2:04:33.304853 INFO: === FDR correction performed with classifier version 8 ===
2:04:33.305674 PROGRESS: ============================= Precursor FDR =============================
2:04:33.305787 PROGRESS: Total precursors accumulated: 1,323
2:04:33.305857 PROGRESS: Target precursors: 1,310 (99.02%)
2:04:33.305916 PROGRESS: Decoy precursors: 13 (0.98%)
2:04:33.305968 PROGRESS: 
2:04:33.306017 PROGRESS: Precursor Summary:
2:04:33.307387 PROGRESS: Channel   0:	 0.050 FDR: 1,310; 0.010 FDR: 1,310; 0.001 FDR:   464
2:04:33.307488 PROGRESS: 
2:04:33.307549 PROGRESS: Protein Summary:
2:04:33.309222 PROGRESS: Channel   0:	 0.050 FDR: 1,023; 0.010 FDR: 1,023; 0.001 FDR:   396
2:04:33.309317 PROGRESS: =========================================================================
2:04:33.364116 INFO: Target number of precursors reached.
2:04:35.076310 INFO: fragments_df: keeping 5000 of 16457008 [sum(precursor_idx_mask)=32678 sum(mass_error_mask)=16457008 stop_rank=5000
2:04:36.180593 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:04:36.405215 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:04:37.126093 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:04:37.126551 INFO: Using score_cutoff 9.052047027397155 (fac=0.99, q=1)
2:04:37.126884 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:04:37.126970 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:04:37.127031 INFO: Updating optimization_manager: score_cutoff        : 10.182723790168762 -> 9.052047027397155
2:04:37.127087 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:04:37.741493 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:04:39.112391 INFO: === checking if optimization conditions were reached ===
2:04:39.114638 INFO: Updating optimization_manager: ms2_error           : 20 -> 10.0
2:04:39.114792 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
2:04:39.114873 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:04:39.114938 INFO: ==============================================
2:04:39.115016 INFO: Starting optimization step 10.
2:04:39.115084 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:04:39.115156 INFO: Using rust extraction backend
2:04:39.115223 PROGRESS: Extracting batch of 1001059 precursors
2:04:40.836426 INFO: === Search parameters used ===
2:04:40.836722 INFO: rt_error       : 716.953369140625
2:04:40.836824 INFO: mobility_error : 0.1
2:04:40.836885 INFO: num_candidates : 3
2:04:40.836935 INFO: ms1_error      : 20
2:04:40.836982 INFO: ms2_error      : 10.0
2:04:40.837028 INFO: fwhm_rt        : 3.0
2:04:40.837072 INFO: quant_window   : 3
2:04:40.837118 INFO: ==============================================
2:04:54.269190 INFO: performing precursor FDR with 40 features
2:04:54.269357 INFO: Decoy channel: -1
2:04:54.269386 INFO: competitive: True
2:04:54.995423 INFO: Setting torch num_threads to 2 for FDR classification task
2:04:56.311743 INFO: Estimating optimal hyperparameters - samples: 2,401,637, batch_size: 4,096, learning_rate: 1.00e-03
2:04:56.316952 INFO: Using random state 228643 for train-test-split
2:05:42.024324 INFO: Test AUC: 0.607
2:05:42.024499 INFO: Train AUC: 0.610
2:05:42.024538 INFO: AUC difference: 0.53%
2:05:43.229285 INFO: Resetting torch num_threads to 32
2:05:43.330379 PROGRESS: === Extracted 3002047 precursors and 17983969 fragments ===
2:05:43.330918 INFO: === FDR correction performed with classifier version 9 ===
2:05:43.331869 PROGRESS: ============================= Precursor FDR =============================
2:05:43.331979 PROGRESS: Total precursors accumulated: 1,836
2:05:43.332047 PROGRESS: Target precursors: 1,818 (99.02%)
2:05:43.332108 PROGRESS: Decoy precursors: 18 (0.98%)
2:05:43.332164 PROGRESS: 
2:05:43.332217 PROGRESS: Precursor Summary:
2:05:43.333796 PROGRESS: Channel   0:	 0.050 FDR: 1,818; 0.010 FDR: 1,818; 0.001 FDR: 1,236
2:05:43.333903 PROGRESS: 
2:05:43.333971 PROGRESS: Protein Summary:
2:05:43.335984 PROGRESS: Channel   0:	 0.050 FDR: 1,391; 0.010 FDR: 1,391; 0.001 FDR:   996
2:05:43.336091 PROGRESS: =========================================================================
2:05:43.392974 INFO: Target number of precursors reached.
2:05:45.275494 INFO: fragments_df: keeping 5000 of 17983969 [sum(precursor_idx_mask)=47502 sum(mass_error_mask)=17983969 stop_rank=5000
2:05:46.469820 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:05:46.751351 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:05:47.472982 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:05:47.473442 INFO: Using score_cutoff 8.792714037895202 (fac=0.99, q=1)
2:05:47.473768 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:05:47.473854 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:05:47.473917 INFO: Updating optimization_manager: score_cutoff        : 9.052047027397155 -> 8.792714037895202
2:05:47.473982 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:05:48.085656 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:05:49.463028 INFO: === checking if optimization conditions were reached ===
2:05:49.465222 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:05:49.465370 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
2:05:49.465448 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:05:49.465515 INFO: ==============================================
2:05:49.465597 INFO: Starting optimization step 11.
2:05:49.465667 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:05:49.465740 INFO: Using rust extraction backend
2:05:49.465813 PROGRESS: Extracting batch of 1001059 precursors
2:05:51.162079 INFO: === Search parameters used ===
2:05:51.162385 INFO: rt_error       : 716.953369140625
2:05:51.162492 INFO: mobility_error : 0.1
2:05:51.162554 INFO: num_candidates : 3
2:05:51.162603 INFO: ms1_error      : 20
2:05:51.162654 INFO: ms2_error      : 10.0
2:05:51.162703 INFO: fwhm_rt        : 3.0
2:05:51.162750 INFO: quant_window   : 3
2:05:51.162797 INFO: ==============================================
2:06:04.508122 INFO: performing precursor FDR with 40 features
2:06:04.508256 INFO: Decoy channel: -1
2:06:04.508284 INFO: competitive: True
2:06:05.256924 INFO: Setting torch num_threads to 2 for FDR classification task
2:06:06.579165 INFO: Estimating optimal hyperparameters - samples: 2,401,647, batch_size: 4,096, learning_rate: 1.00e-03
2:06:06.583861 INFO: Using random state 490359 for train-test-split
2:06:52.818199 INFO: Test AUC: 0.608
2:06:52.818334 INFO: Train AUC: 0.612
2:06:52.818387 INFO: AUC difference: 0.69%
2:06:54.056057 INFO: Resetting torch num_threads to 32
2:06:54.150604 PROGRESS: === Extracted 3002059 precursors and 17989090 fragments ===
2:06:54.151118 INFO: === FDR correction performed with classifier version 10 ===
2:06:54.151922 PROGRESS: ============================= Precursor FDR =============================
2:06:54.152026 PROGRESS: Total precursors accumulated: 1,768
2:06:54.152097 PROGRESS: Target precursors: 1,751 (99.04%)
2:06:54.152155 PROGRESS: Decoy precursors: 17 (0.96%)
2:06:54.152210 PROGRESS: 
2:06:54.152263 PROGRESS: Precursor Summary:
2:06:54.153711 PROGRESS: Channel   0:	 0.050 FDR: 1,751; 0.010 FDR: 1,751; 0.001 FDR:   776
2:06:54.153808 PROGRESS: 
2:06:54.153869 PROGRESS: Protein Summary:
2:06:54.155717 PROGRESS: Channel   0:	 0.050 FDR: 1,335; 0.010 FDR: 1,335; 0.001 FDR:   649
2:06:54.155818 PROGRESS: =========================================================================
2:06:54.210304 INFO: Target number of precursors reached.
2:06:56.079093 INFO: fragments_df: keeping 5000 of 17989090 [sum(precursor_idx_mask)=45558 sum(mass_error_mask)=17989090 stop_rank=5000
2:06:57.162323 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:06:57.432358 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:06:58.153687 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:06:58.154128 INFO: Using score_cutoff 8.794443225860595 (fac=0.99, q=1)
2:06:58.154442 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:06:58.154528 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:06:58.154590 INFO: Updating optimization_manager: score_cutoff        : 8.792714037895202 -> 8.794443225860595
2:06:58.154646 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:06:58.756408 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:07:00.158556 INFO: === checking if optimization conditions were reached ===
2:07:00.160688 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:07:00.160832 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
2:07:00.160902 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:07:00.160968 INFO: ==============================================
2:07:00.161045 INFO: Starting optimization step 12.
2:07:00.161107 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:07:00.161171 INFO: Using rust extraction backend
2:07:00.161246 PROGRESS: Extracting batch of 1001059 precursors
2:07:01.852597 INFO: === Search parameters used ===
2:07:01.852878 INFO: rt_error       : 716.953369140625
2:07:01.852945 INFO: mobility_error : 0.1
2:07:01.853001 INFO: num_candidates : 3
2:07:01.853056 INFO: ms1_error      : 20
2:07:01.853120 INFO: ms2_error      : 10.0
2:07:01.853167 INFO: fwhm_rt        : 3.0
2:07:01.853211 INFO: quant_window   : 3
2:07:01.853257 INFO: ==============================================
2:07:15.160031 INFO: performing precursor FDR with 40 features
2:07:15.160152 INFO: Decoy channel: -1
2:07:15.160181 INFO: competitive: True
2:07:15.915445 INFO: Setting torch num_threads to 2 for FDR classification task
2:07:17.239297 INFO: Estimating optimal hyperparameters - samples: 2,401,653, batch_size: 4,096, learning_rate: 1.00e-03
2:07:17.245826 INFO: Using random state 806157 for train-test-split
2:08:02.796504 INFO: Test AUC: 0.609
2:08:02.796643 INFO: Train AUC: 0.614
2:08:02.796679 INFO: AUC difference: 0.93%
2:08:05.251377 INFO: Resetting torch num_threads to 32
2:08:05.352660 PROGRESS: === Extracted 3002067 precursors and 17992427 fragments ===
2:08:05.353168 INFO: === FDR correction performed with classifier version 11 ===
2:08:05.354033 PROGRESS: ============================= Precursor FDR =============================
2:08:05.354146 PROGRESS: Total precursors accumulated: 1,921
2:08:05.354220 PROGRESS: Target precursors: 1,902 (99.01%)
2:08:05.354287 PROGRESS: Decoy precursors: 19 (0.99%)
2:08:05.354346 PROGRESS: 
2:08:05.354419 PROGRESS: Precursor Summary:
2:08:05.355981 PROGRESS: Channel   0:	 0.050 FDR: 1,902; 0.010 FDR: 1,902; 0.001 FDR: 1,130
2:08:05.356086 PROGRESS: 
2:08:05.356155 PROGRESS: Protein Summary:
2:08:05.358118 PROGRESS: Channel   0:	 0.050 FDR: 1,464; 0.010 FDR: 1,464; 0.001 FDR:   919
2:08:05.358232 PROGRESS: =========================================================================
2:08:05.411541 INFO: Target number of precursors reached.
2:08:07.297859 INFO: fragments_df: keeping 5000 of 17992427 [sum(precursor_idx_mask)=48785 sum(mass_error_mask)=17992427 stop_rank=5000
2:08:08.355220 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:08:08.606796 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:08:09.270175 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:08:09.270732 INFO: Using score_cutoff 6.455452172470093 (fac=0.99, q=1)
2:08:09.271089 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:08:09.271178 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:08:09.271244 INFO: Updating optimization_manager: score_cutoff        : 8.794443225860595 -> 6.455452172470093
2:08:09.271308 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:08:09.885619 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:08:11.267639 INFO: === checking if optimization conditions were reached ===
2:08:11.270172 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:08:11.270331 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
2:08:11.270425 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:08:11.270497 INFO: ==============================================
2:08:11.270574 INFO: Starting optimization step 13.
2:08:11.270646 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:08:11.270736 INFO: Using rust extraction backend
2:08:11.270813 PROGRESS: Extracting batch of 1001059 precursors
2:08:12.969581 INFO: === Search parameters used ===
2:08:12.969908 INFO: rt_error       : 716.953369140625
2:08:12.969970 INFO: mobility_error : 0.1
2:08:12.970021 INFO: num_candidates : 3
2:08:12.970068 INFO: ms1_error      : 20
2:08:12.970112 INFO: ms2_error      : 10.0
2:08:12.970154 INFO: fwhm_rt        : 3.0
2:08:12.970197 INFO: quant_window   : 3
2:08:12.970239 INFO: ==============================================
2:08:26.013036 INFO: performing precursor FDR with 40 features
2:08:26.013250 INFO: Decoy channel: -1
2:08:26.013282 INFO: competitive: True
2:08:26.774164 INFO: Setting torch num_threads to 2 for FDR classification task
2:08:28.098670 INFO: Estimating optimal hyperparameters - samples: 2,401,665, batch_size: 4,096, learning_rate: 1.00e-03
2:08:28.104033 INFO: Using random state 58057 for train-test-split
2:09:14.332074 INFO: Test AUC: 0.612
2:09:14.332320 INFO: Train AUC: 0.616
2:09:14.332359 INFO: AUC difference: 0.65%
2:09:15.610476 INFO: Resetting torch num_threads to 32
2:09:15.715297 PROGRESS: === Extracted 3002082 precursors and 18020340 fragments ===
2:09:15.715859 INFO: === FDR correction performed with classifier version 12 ===
2:09:15.716795 PROGRESS: ============================= Precursor FDR =============================
2:09:15.716907 PROGRESS: Total precursors accumulated: 1,877
2:09:15.716978 PROGRESS: Target precursors: 1,859 (99.04%)
2:09:15.717040 PROGRESS: Decoy precursors: 18 (0.96%)
2:09:15.717097 PROGRESS: 
2:09:15.717152 PROGRESS: Precursor Summary:
2:09:15.718827 PROGRESS: Channel   0:	 0.050 FDR: 1,859; 0.010 FDR: 1,859; 0.001 FDR: 1,340
2:09:15.718939 PROGRESS: 
2:09:15.719005 PROGRESS: Protein Summary:
2:09:15.721136 PROGRESS: Channel   0:	 0.050 FDR: 1,421; 0.010 FDR: 1,421; 0.001 FDR: 1,070
2:09:15.721269 PROGRESS: =========================================================================
2:09:15.777987 INFO: Target number of precursors reached.
2:09:17.631808 INFO: fragments_df: keeping 5000 of 18020340 [sum(precursor_idx_mask)=48256 sum(mass_error_mask)=18020340 stop_rank=5000
2:09:18.734179 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:09:19.021984 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:09:19.747721 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:09:19.748189 INFO: Using score_cutoff 8.324280634117127 (fac=0.99, q=1)
2:09:19.748538 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:09:19.748626 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:09:19.748695 INFO: Updating optimization_manager: score_cutoff        : 6.455452172470093 -> 8.324280634117127
2:09:19.748757 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:09:20.361291 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:09:21.740750 INFO: === checking if optimization conditions were reached ===
2:09:21.743002 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:09:21.743174 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
2:09:21.743272 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:09:21.743360 INFO: ==============================================
2:09:21.743452 PROGRESS: Optimization finished for ms2_error.
2:09:22.773669 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:09:23.387706 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:09:24.794865 INFO: Starting optimization step 0.
2:09:24.795126 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:09:24.795237 INFO: Using rust extraction backend
2:09:24.795316 PROGRESS: Extracting batch of 1001059 precursors
2:09:26.494152 INFO: === Search parameters used ===
2:09:26.494451 INFO: rt_error       : 716.953369140625
2:09:26.494533 INFO: mobility_error : 0.1
2:09:26.494592 INFO: num_candidates : 3
2:09:26.494646 INFO: ms1_error      : 20
2:09:26.494698 INFO: ms2_error      : 10.0
2:09:26.494751 INFO: fwhm_rt        : 3.0
2:09:26.494802 INFO: quant_window   : 3
2:09:26.494853 INFO: ==============================================
2:09:39.724994 INFO: performing precursor FDR with 40 features
2:09:39.725191 INFO: Decoy channel: -1
2:09:39.725223 INFO: competitive: True
2:09:40.508728 INFO: Setting torch num_threads to 2 for FDR classification task
2:09:41.864042 INFO: Estimating optimal hyperparameters - samples: 2,401,657, batch_size: 4,096, learning_rate: 1.00e-03
2:09:41.869369 INFO: Using random state 512663 for train-test-split
2:10:27.524336 INFO: Test AUC: 0.614
2:10:27.524535 INFO: Train AUC: 0.618
2:10:27.524572 INFO: AUC difference: 0.71%
2:10:28.791499 INFO: Resetting torch num_threads to 32
2:10:28.896811 PROGRESS: === Extracted 3002072 precursors and 17992583 fragments ===
2:10:28.897475 INFO: === FDR correction performed with classifier version 13 ===
2:10:28.898417 PROGRESS: ============================= Precursor FDR =============================
2:10:28.898533 PROGRESS: Total precursors accumulated: 1,781
2:10:28.898608 PROGRESS: Target precursors: 1,764 (99.05%)
2:10:28.898670 PROGRESS: Decoy precursors: 17 (0.95%)
2:10:28.898735 PROGRESS: 
2:10:28.898790 PROGRESS: Precursor Summary:
2:10:28.900371 PROGRESS: Channel   0:	 0.050 FDR: 1,764; 0.010 FDR: 1,764; 0.001 FDR:   517
2:10:28.900474 PROGRESS: 
2:10:28.900539 PROGRESS: Protein Summary:
2:10:28.902380 PROGRESS: Channel   0:	 0.050 FDR: 1,344; 0.010 FDR: 1,344; 0.001 FDR:   441
2:10:28.902492 PROGRESS: =========================================================================
2:10:28.957716 INFO: Target number of precursors reached.
2:10:30.746067 INFO: fragments_df: keeping 5000 of 17992583 [sum(precursor_idx_mask)=46027 sum(mass_error_mask)=17992583 stop_rank=5000
2:10:31.830828 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:10:32.106538 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:10:32.832601 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:10:32.833155 INFO: Using score_cutoff 8.959738961219788 (fac=0.99, q=1)
2:10:32.833499 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:10:32.833589 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:10:32.833655 INFO: Updating optimization_manager: score_cutoff        : 8.324280634117127 -> 8.959738961219788
2:10:32.833720 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:10:33.459114 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:10:34.817497 INFO: === checking if optimization conditions were reached ===
2:10:34.817798 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:10:34.821049 INFO: Updating optimization_manager: rt_error            : 716.953369140625 -> 624.8115988764649
2:10:34.821183 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 624.8116.
2:10:34.821254 INFO: ==============================================
2:10:34.821331 INFO: Starting optimization step 1.
2:10:34.821402 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:10:34.821474 INFO: Using rust extraction backend
2:10:34.821540 PROGRESS: Extracting batch of 1001059 precursors
2:10:36.517070 INFO: === Search parameters used ===
2:10:36.517344 INFO: rt_error       : 624.8115988764649
2:10:36.517409 INFO: mobility_error : 0.1
2:10:36.517460 INFO: num_candidates : 3
2:10:36.517512 INFO: ms1_error      : 20
2:10:36.517558 INFO: ms2_error      : 10.0
2:10:36.517629 INFO: fwhm_rt        : 3.0
2:10:36.517675 INFO: quant_window   : 3
2:10:36.517715 INFO: ==============================================
2:10:49.440716 INFO: performing precursor FDR with 40 features
2:10:49.440933 INFO: Decoy channel: -1
2:10:49.440964 INFO: competitive: True
2:10:50.193224 INFO: Setting torch num_threads to 2 for FDR classification task
2:10:51.517590 INFO: Estimating optimal hyperparameters - samples: 2,401,598, batch_size: 4,096, learning_rate: 1.00e-03
2:10:51.522857 INFO: Using random state 512663 for train-test-split
2:11:35.292895 INFO: Test AUC: 0.612
2:11:35.293145 INFO: Train AUC: 0.617
2:11:35.293185 INFO: AUC difference: 0.81%
2:11:36.491937 INFO: Resetting torch num_threads to 32
2:11:36.588378 PROGRESS: === Extracted 3001998 precursors and 17871956 fragments ===
2:11:36.588948 INFO: === FDR correction performed with classifier version 13 ===
2:11:36.589818 PROGRESS: ============================= Precursor FDR =============================
2:11:36.589936 PROGRESS: Total precursors accumulated: 1,859
2:11:36.590019 PROGRESS: Target precursors: 1,841 (99.03%)
2:11:36.590083 PROGRESS: Decoy precursors: 18 (0.97%)
2:11:36.590138 PROGRESS: 
2:11:36.590191 PROGRESS: Precursor Summary:
2:11:36.591723 PROGRESS: Channel   0:	 0.050 FDR: 1,841; 0.010 FDR: 1,841; 0.001 FDR: 1,341
2:11:36.591831 PROGRESS: 
2:11:36.591899 PROGRESS: Protein Summary:
2:11:36.593838 PROGRESS: Channel   0:	 0.050 FDR: 1,441; 0.010 FDR: 1,441; 0.001 FDR: 1,073
2:11:36.593937 PROGRESS: =========================================================================
2:11:36.647363 INFO: Target number of precursors reached.
2:11:38.513440 INFO: fragments_df: keeping 5000 of 17871956 [sum(precursor_idx_mask)=46949 sum(mass_error_mask)=17871956 stop_rank=5000
2:11:39.594191 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:11:39.896461 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:11:40.590261 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:11:40.590727 INFO: Using score_cutoff 4.880150436401367 (fac=0.99, q=1)
2:11:40.591064 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:11:40.591162 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:11:40.591227 INFO: Updating optimization_manager: score_cutoff        : 8.959738961219788 -> 4.880150436401367
2:11:40.591292 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:11:41.203592 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:11:42.554704 INFO: === checking if optimization conditions were reached ===
2:11:42.554982 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:11:42.558160 INFO: Updating optimization_manager: rt_error            : 624.8115988764649 -> 809.9163915823843
2:11:42.558295 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 809.9164.
2:11:42.558384 INFO: ==============================================
2:11:42.558469 INFO: Starting optimization step 2.
2:11:42.558538 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:11:42.558614 INFO: Using rust extraction backend
2:11:42.558679 PROGRESS: Extracting batch of 1001059 precursors
2:11:44.260616 INFO: === Search parameters used ===
2:11:44.261161 INFO: rt_error       : 809.9163915823843
2:11:44.261229 INFO: mobility_error : 0.1
2:11:44.261281 INFO: num_candidates : 3
2:11:44.261329 INFO: ms1_error      : 20
2:11:44.261376 INFO: ms2_error      : 10.0
2:11:44.261434 INFO: fwhm_rt        : 3.0
2:11:44.261479 INFO: quant_window   : 3
2:11:44.261522 INFO: ==============================================
2:11:58.004416 INFO: performing precursor FDR with 40 features
2:11:58.004624 INFO: Decoy channel: -1
2:11:58.004655 INFO: competitive: True
2:11:58.731077 INFO: Setting torch num_threads to 2 for FDR classification task
2:12:00.013747 INFO: Estimating optimal hyperparameters - samples: 2,401,754, batch_size: 4,096, learning_rate: 1.00e-03
2:12:00.018593 INFO: Using random state 512663 for train-test-split
2:12:46.429008 INFO: Test AUC: 0.612
2:12:46.429230 INFO: Train AUC: 0.618
2:12:46.429270 INFO: AUC difference: 1.00%
2:12:47.690742 INFO: Resetting torch num_threads to 32
2:12:47.767636 PROGRESS: === Extracted 3002193 precursors and 18182516 fragments ===
2:12:47.768136 INFO: === FDR correction performed with classifier version 13 ===
2:12:47.768617 PROGRESS: ============================= Precursor FDR =============================
2:12:47.768720 PROGRESS: Total precursors accumulated: 0
2:12:47.768791 PROGRESS: Target precursors: 0 (0.00%)
2:12:47.768848 PROGRESS: Decoy precursors: 0 (0.00%)
2:12:47.768897 PROGRESS: 
2:12:47.768945 PROGRESS: Precursor Summary:
2:12:47.769066 PROGRESS: 
2:12:47.769130 PROGRESS: Protein Summary:
2:12:47.769211 PROGRESS: =========================================================================
2:12:47.823097 INFO: Target number of precursors not reached yet.
2:12:48.858017 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:12:49.471363 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:12:50.882113 INFO: === skipping optimization until target number of precursors are found ===
2:12:50.882346 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
2:12:50.882491 INFO: Starting optimization step 3.
2:12:50.882579 PROGRESS: === Extracting elution groups 511000 to 1023000 ===
2:12:50.882656 INFO: Using rust extraction backend
2:12:50.882727 PROGRESS: Extracting batch of 1003103 precursors
2:12:52.579383 INFO: === Search parameters used ===
2:12:52.579667 INFO: rt_error       : 809.9163915823843
2:12:52.579736 INFO: mobility_error : 0.1
2:12:52.579796 INFO: num_candidates : 3
2:12:52.579862 INFO: ms1_error      : 20
2:12:52.579911 INFO: ms2_error      : 10.0
2:12:52.579974 INFO: fwhm_rt        : 3.0
2:12:52.580024 INFO: quant_window   : 3
2:12:52.580070 INFO: ==============================================
2:13:07.143295 INFO: performing precursor FDR with 40 features
2:13:07.143526 INFO: Decoy channel: -1
2:13:07.143558 INFO: competitive: True
2:13:09.593151 INFO: Setting torch num_threads to 2 for FDR classification task
2:13:12.234760 INFO: Estimating optimal hyperparameters - samples: 4,808,416, batch_size: 4,096, learning_rate: 1.00e-03
2:13:12.244899 INFO: Using random state 512663 for train-test-split
2:14:48.017517 INFO: Test AUC: 0.614
2:14:48.017766 INFO: Train AUC: 0.616
2:14:48.017807 INFO: AUC difference: 0.34%
2:14:50.184440 INFO: Resetting torch num_threads to 32
2:14:51.423960 PROGRESS: === Extracted 6010521 precursors and 36400846 fragments ===
2:14:51.424919 INFO: === FDR correction performed with classifier version 13 ===
2:14:51.426028 PROGRESS: ============================= Precursor FDR =============================
2:14:51.426134 PROGRESS: Total precursors accumulated: 2,602
2:14:51.426208 PROGRESS: Target precursors: 2,577 (99.04%)
2:14:51.426268 PROGRESS: Decoy precursors: 25 (0.96%)
2:14:51.426322 PROGRESS: 
2:14:51.426390 PROGRESS: Precursor Summary:
2:14:51.427921 PROGRESS: Channel   0:	 0.050 FDR: 2,577; 0.010 FDR: 2,577; 0.001 FDR:     3
2:14:51.428026 PROGRESS: 
2:14:51.428096 PROGRESS: Protein Summary:
2:14:51.430037 PROGRESS: Channel   0:	 0.050 FDR: 1,822; 0.010 FDR: 1,822; 0.001 FDR:     3
2:14:51.430138 PROGRESS: =========================================================================
2:14:51.491523 INFO: Target number of precursors reached.
2:14:55.446859 INFO: fragments_df: keeping 5000 of 36400846 [sum(precursor_idx_mask)=66541 sum(mass_error_mask)=36400846 stop_rank=5000
2:14:56.635740 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:14:56.954096 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:14:57.611089 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:14:57.611549 INFO: Using score_cutoff 6.439223693847656 (fac=0.99, q=1)
2:14:57.611903 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:14:57.611988 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:14:57.612056 INFO: Updating optimization_manager: score_cutoff        : 4.880150436401367 -> 6.439223693847656
2:14:57.612138 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:14:58.272028 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:14:59.617584 INFO: === checking if optimization conditions were reached ===
2:14:59.617830 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:14:59.621377 INFO: Updating optimization_manager: rt_error            : 809.9163915823843 -> 1144.7623734313097
2:14:59.621524 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 1144.7624.
2:14:59.621601 INFO: ==============================================
2:14:59.621691 INFO: Starting optimization step 4.
2:14:59.621763 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:14:59.621861 INFO: Using rust extraction backend
2:14:59.621951 PROGRESS: Extracting batch of 1001059 precursors
2:15:01.349329 INFO: === Search parameters used ===
2:15:01.349886 INFO: rt_error       : 1144.7623734313097
2:15:01.349984 INFO: mobility_error : 0.1
2:15:01.350046 INFO: num_candidates : 3
2:15:01.350100 INFO: ms1_error      : 20
2:15:01.350156 INFO: ms2_error      : 10.0
2:15:01.350213 INFO: fwhm_rt        : 3.0
2:15:01.350286 INFO: quant_window   : 3
2:15:01.350337 INFO: ==============================================
2:15:15.827632 INFO: performing precursor FDR with 40 features
2:15:15.827853 INFO: Decoy channel: -1
2:15:15.827887 INFO: competitive: True
2:15:16.532479 INFO: Setting torch num_threads to 2 for FDR classification task
2:15:17.849468 INFO: Estimating optimal hyperparameters - samples: 2,401,763, batch_size: 4,096, learning_rate: 1.00e-03
2:15:17.854879 INFO: Using random state 512663 for train-test-split
2:16:03.676639 INFO: Test AUC: 0.614
2:16:03.676875 INFO: Train AUC: 0.618
2:16:03.676915 INFO: AUC difference: 0.67%
2:16:04.932902 INFO: Resetting torch num_threads to 32
2:16:05.025221 PROGRESS: === Extracted 3002204 precursors and 18224533 fragments ===
2:16:05.025747 INFO: === FDR correction performed with classifier version 13 ===
2:16:05.026525 PROGRESS: ============================= Precursor FDR =============================
2:16:05.026630 PROGRESS: Total precursors accumulated: 1,824
2:16:05.026702 PROGRESS: Target precursors: 1,806 (99.01%)
2:16:05.026768 PROGRESS: Decoy precursors: 18 (0.99%)
2:16:05.026824 PROGRESS: 
2:16:05.026886 PROGRESS: Precursor Summary:
2:16:05.028339 PROGRESS: Channel   0:	 0.050 FDR: 1,806; 0.010 FDR: 1,806; 0.001 FDR: 1,298
2:16:05.028435 PROGRESS: 
2:16:05.028499 PROGRESS: Protein Summary:
2:16:05.030422 PROGRESS: Channel   0:	 0.050 FDR: 1,387; 0.010 FDR: 1,387; 0.001 FDR: 1,039
2:16:05.030531 PROGRESS: =========================================================================
2:16:05.082919 INFO: Target number of precursors reached.
2:16:06.983337 INFO: fragments_df: keeping 5000 of 18224533 [sum(precursor_idx_mask)=47008 sum(mass_error_mask)=18224533 stop_rank=5000
2:16:08.339486 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:16:08.616056 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:16:09.347486 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:16:09.348052 INFO: Using score_cutoff 8.07547755432129 (fac=0.99, q=1)
2:16:09.348421 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:16:09.348510 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:16:09.348572 INFO: Updating optimization_manager: score_cutoff        : 6.439223693847656 -> 8.07547755432129
2:16:09.348648 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:16:09.948222 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:16:11.286013 INFO: === checking if optimization conditions were reached ===
2:16:11.286284 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:16:11.289511 INFO: Updating optimization_manager: rt_error            : 1144.7623734313097 -> 1020.5944034727047
2:16:11.289673 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 1020.5944.
2:16:11.289753 INFO: ==============================================
2:16:11.289845 INFO: Starting optimization step 5.
2:16:11.289920 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:16:11.290016 INFO: Using rust extraction backend
2:16:11.290102 PROGRESS: Extracting batch of 1001059 precursors
2:16:12.993277 INFO: === Search parameters used ===
2:16:12.993560 INFO: rt_error       : 1020.5944034727047
2:16:12.993628 INFO: mobility_error : 0.1
2:16:12.993686 INFO: num_candidates : 3
2:16:12.993746 INFO: ms1_error      : 20
2:16:12.993803 INFO: ms2_error      : 10.0
2:16:12.993858 INFO: fwhm_rt        : 3.0
2:16:12.993906 INFO: quant_window   : 3
2:16:12.993956 INFO: ==============================================
2:16:26.761019 INFO: performing precursor FDR with 40 features
2:16:26.761138 INFO: Decoy channel: -1
2:16:26.761166 INFO: competitive: True
2:16:27.386765 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:28.626443 INFO: Estimating optimal hyperparameters - samples: 2,401,766, batch_size: 4,096, learning_rate: 1.00e-03
2:16:28.631873 INFO: Using random state 512663 for train-test-split
2:17:15.046243 INFO: Test AUC: 0.612
2:17:15.046465 INFO: Train AUC: 0.616
2:17:15.046503 INFO: AUC difference: 0.66%
2:17:16.243847 INFO: Resetting torch num_threads to 32
2:17:16.336196 PROGRESS: === Extracted 3002208 precursors and 18226349 fragments ===
2:17:16.336782 INFO: === FDR correction performed with classifier version 13 ===
2:17:16.337660 PROGRESS: ============================= Precursor FDR =============================
2:17:16.337772 PROGRESS: Total precursors accumulated: 1,936
2:17:16.337852 PROGRESS: Target precursors: 1,917 (99.02%)
2:17:16.337930 PROGRESS: Decoy precursors: 19 (0.98%)
2:17:16.337996 PROGRESS: 
2:17:16.338059 PROGRESS: Precursor Summary:
2:17:16.339665 PROGRESS: Channel   0:	 0.050 FDR: 1,917; 0.010 FDR: 1,917; 0.001 FDR: 1,226
2:17:16.339778 PROGRESS: 
2:17:16.339852 PROGRESS: Protein Summary:
2:17:16.341888 PROGRESS: Channel   0:	 0.050 FDR: 1,510; 0.010 FDR: 1,510; 0.001 FDR:   987
2:17:16.341994 PROGRESS: =========================================================================
2:17:16.394367 INFO: Target number of precursors reached.
2:17:18.253287 INFO: fragments_df: keeping 5000 of 18226349 [sum(precursor_idx_mask)=47770 sum(mass_error_mask)=18226349 stop_rank=5000
2:17:19.319639 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:17:19.605650 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:17:20.328533 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:17:20.329010 INFO: Using score_cutoff 4.749513708114624 (fac=0.99, q=1)
2:17:20.329354 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:17:20.329437 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:17:20.329497 INFO: Updating optimization_manager: score_cutoff        : 8.07547755432129 -> 4.749513708114624
2:17:20.329556 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:17:20.933822 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:17:22.338800 INFO: === checking if optimization conditions were reached ===
2:17:22.339060 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:17:22.342163 INFO: Updating optimization_manager: rt_error            : 1020.5944034727047 -> 1088.4202824943698
2:17:22.342301 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 1088.4203.
2:17:22.342392 INFO: ==============================================
2:17:22.342474 INFO: Starting optimization step 6.
2:17:22.342540 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:17:22.342882 INFO: Using rust extraction backend
2:17:22.342953 PROGRESS: Extracting batch of 1001059 precursors
2:17:24.031157 INFO: === Search parameters used ===
2:17:24.031435 INFO: rt_error       : 1088.4202824943698
2:17:24.031510 INFO: mobility_error : 0.1
2:17:24.031573 INFO: num_candidates : 3
2:17:24.031626 INFO: ms1_error      : 20
2:17:24.031675 INFO: ms2_error      : 10.0
2:17:24.031719 INFO: fwhm_rt        : 3.0
2:17:24.031763 INFO: quant_window   : 3
2:17:24.031807 INFO: ==============================================
2:17:37.635553 INFO: performing precursor FDR with 40 features
2:17:37.635674 INFO: Decoy channel: -1
2:17:37.635702 INFO: competitive: True
2:17:38.250385 INFO: Setting torch num_threads to 2 for FDR classification task
2:17:39.484053 INFO: Estimating optimal hyperparameters - samples: 2,401,767, batch_size: 4,096, learning_rate: 1.00e-03
2:17:39.489460 INFO: Using random state 512663 for train-test-split
2:18:24.873405 INFO: Test AUC: 0.611
2:18:24.873616 INFO: Train AUC: 0.617
2:18:24.873652 INFO: AUC difference: 0.96%
2:18:26.074882 INFO: Resetting torch num_threads to 32
2:18:26.308666 PROGRESS: === Extracted 3002209 precursors and 18225393 fragments ===
2:18:26.309289 INFO: === FDR correction performed with classifier version 13 ===
2:18:26.310138 PROGRESS: ============================= Precursor FDR =============================
2:18:26.310231 PROGRESS: Total precursors accumulated: 1,782
2:18:26.310296 PROGRESS: Target precursors: 1,765 (99.05%)
2:18:26.310364 PROGRESS: Decoy precursors: 17 (0.95%)
2:18:26.310422 PROGRESS: 
2:18:26.310472 PROGRESS: Precursor Summary:
2:18:26.311918 PROGRESS: Channel   0:	 0.050 FDR: 1,765; 0.010 FDR: 1,765; 0.001 FDR: 1,352
2:18:26.312012 PROGRESS: 
2:18:26.312083 PROGRESS: Protein Summary:
2:18:26.313992 PROGRESS: Channel   0:	 0.050 FDR: 1,355; 0.010 FDR: 1,355; 0.001 FDR: 1,078
2:18:26.314088 PROGRESS: =========================================================================
2:18:26.370043 INFO: Target number of precursors reached.
2:18:28.291735 INFO: fragments_df: keeping 5000 of 18225393 [sum(precursor_idx_mask)=45872 sum(mass_error_mask)=18225393 stop_rank=5000
2:18:29.407128 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:18:29.675003 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:18:30.396128 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:18:30.396592 INFO: Using score_cutoff 8.209182314300538 (fac=0.99, q=1)
2:18:30.396920 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:18:30.397005 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:18:30.397067 INFO: Updating optimization_manager: score_cutoff        : 4.749513708114624 -> 8.209182314300538
2:18:30.397125 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:18:31.012212 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:18:32.418739 INFO: === checking if optimization conditions were reached ===
2:18:32.418988 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:18:32.422004 INFO: Updating optimization_manager: rt_error            : 1088.4202824943698 -> 961.9567415297622
2:18:32.422141 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 961.9567.
2:18:32.422212 INFO: ==============================================
2:18:32.422297 INFO: Starting optimization step 7.
2:18:32.422399 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:18:32.422486 INFO: Using rust extraction backend
2:18:32.422554 PROGRESS: Extracting batch of 1001059 precursors
2:18:34.114412 INFO: === Search parameters used ===
2:18:34.114727 INFO: rt_error       : 961.9567415297622
2:18:34.114790 INFO: mobility_error : 0.1
2:18:34.114848 INFO: num_candidates : 3
2:18:34.114905 INFO: ms1_error      : 20
2:18:34.114957 INFO: ms2_error      : 10.0
2:18:34.115004 INFO: fwhm_rt        : 3.0
2:18:34.115049 INFO: quant_window   : 3
2:18:34.115099 INFO: ==============================================
2:18:47.801049 INFO: performing precursor FDR with 40 features
2:18:47.801246 INFO: Decoy channel: -1
2:18:47.801277 INFO: competitive: True
2:18:48.459464 INFO: Setting torch num_threads to 2 for FDR classification task
2:18:49.693818 INFO: Estimating optimal hyperparameters - samples: 2,401,779, batch_size: 4,096, learning_rate: 1.00e-03
2:18:49.699096 INFO: Using random state 512663 for train-test-split
2:19:34.707987 INFO: Test AUC: 0.612
2:19:34.708212 INFO: Train AUC: 0.618
2:19:34.708251 INFO: AUC difference: 0.90%
2:19:35.943332 INFO: Resetting torch num_threads to 32
2:19:36.093211 PROGRESS: === Extracted 3002224 precursors and 18229033 fragments ===
2:19:36.093754 INFO: === FDR correction performed with classifier version 13 ===
2:19:36.094612 PROGRESS: ============================= Precursor FDR =============================
2:19:36.094716 PROGRESS: Total precursors accumulated: 1,825
2:19:36.094787 PROGRESS: Target precursors: 1,807 (99.01%)
2:19:36.094860 PROGRESS: Decoy precursors: 18 (0.99%)
2:19:36.094916 PROGRESS: 
2:19:36.094972 PROGRESS: Precursor Summary:
2:19:36.096406 PROGRESS: Channel   0:	 0.050 FDR: 1,807; 0.010 FDR: 1,807; 0.001 FDR: 1,260
2:19:36.096509 PROGRESS: 
2:19:36.096572 PROGRESS: Protein Summary:
2:19:36.098460 PROGRESS: Channel   0:	 0.050 FDR: 1,389; 0.010 FDR: 1,389; 0.001 FDR: 1,015
2:19:36.098562 PROGRESS: =========================================================================
2:19:36.158570 INFO: Target number of precursors reached.
2:19:38.081423 INFO: fragments_df: keeping 5000 of 18229033 [sum(precursor_idx_mask)=47197 sum(mass_error_mask)=18229033 stop_rank=5000
2:19:39.336312 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:19:39.612764 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:19:40.334783 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:19:40.335236 INFO: Using score_cutoff 8.797085017204283 (fac=0.99, q=1)
2:19:40.335590 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:19:40.335685 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:19:40.335750 INFO: Updating optimization_manager: score_cutoff        : 8.209182314300538 -> 8.797085017204283
2:19:40.335814 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:19:40.952224 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:19:42.340489 INFO: === checking if optimization conditions were reached ===
2:19:42.340749 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
2:19:42.343819 INFO: Updating optimization_manager: rt_error            : 961.9567415297622 -> 1134.1529845299783
2:19:42.343956 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 1134.1530.
2:19:42.344055 INFO: ==============================================
2:19:42.344145 INFO: Starting optimization step 8.
2:19:42.344217 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:19:42.344298 INFO: Using rust extraction backend
2:19:42.344371 PROGRESS: Extracting batch of 1001059 precursors
2:19:44.038733 INFO: === Search parameters used ===
2:19:44.039016 INFO: rt_error       : 1134.1529845299783
2:19:44.039085 INFO: mobility_error : 0.1
2:19:44.039142 INFO: num_candidates : 3
2:19:44.039196 INFO: ms1_error      : 20
2:19:44.039251 INFO: ms2_error      : 10.0
2:19:44.039306 INFO: fwhm_rt        : 3.0
2:19:44.039353 INFO: quant_window   : 3
2:19:44.039400 INFO: ==============================================
2:19:57.869932 INFO: performing precursor FDR with 40 features
2:19:57.870078 INFO: Decoy channel: -1
2:19:57.870107 INFO: competitive: True
2:19:58.532547 INFO: Setting torch num_threads to 2 for FDR classification task
2:19:59.766687 INFO: Estimating optimal hyperparameters - samples: 2,401,763, batch_size: 4,096, learning_rate: 1.00e-03
2:19:59.772058 INFO: Using random state 512663 for train-test-split
2:20:45.774976 INFO: Test AUC: 0.613
2:20:45.775137 INFO: Train AUC: 0.618
2:20:45.775175 INFO: AUC difference: 0.72%
2:20:46.988879 INFO: Resetting torch num_threads to 32
2:20:47.229409 PROGRESS: === Extracted 3002204 precursors and 18223540 fragments ===
2:20:47.229929 INFO: === FDR correction performed with classifier version 13 ===
2:20:47.230736 PROGRESS: ============================= Precursor FDR =============================
2:20:47.230844 PROGRESS: Total precursors accumulated: 2,010
2:20:47.230916 PROGRESS: Target precursors: 1,991 (99.05%)
2:20:47.230972 PROGRESS: Decoy precursors: 19 (0.95%)
2:20:47.231022 PROGRESS: 
2:20:47.231072 PROGRESS: Precursor Summary:
2:20:47.232562 PROGRESS: Channel   0:	 0.050 FDR: 1,991; 0.010 FDR: 1,991; 0.001 FDR: 1,363
2:20:47.232656 PROGRESS: 
2:20:47.232712 PROGRESS: Protein Summary:
2:20:47.234699 PROGRESS: Channel   0:	 0.050 FDR: 1,528; 0.010 FDR: 1,528; 0.001 FDR: 1,087
2:20:47.234802 PROGRESS: =========================================================================
2:20:47.297286 INFO: Target number of precursors reached.
2:20:49.121131 INFO: fragments_df: keeping 5000 of 18223540 [sum(precursor_idx_mask)=50719 sum(mass_error_mask)=18223540 stop_rank=5000
2:20:50.340589 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:20:50.634973 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:20:51.354742 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:20:51.355212 INFO: Using score_cutoff 5.56776979637146 (fac=0.99, q=1)
2:20:51.355552 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:20:51.355638 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:20:51.355701 INFO: Updating optimization_manager: score_cutoff        : 8.797085017204283 -> 5.56776979637146
2:20:51.355764 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:20:51.971862 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:20:53.362051 INFO: === checking if optimization conditions were reached ===
2:20:53.362334 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
2:20:53.365574 INFO: Updating optimization_manager: rt_error            : 1134.1529845299783 -> 1068.1936693384177
2:20:53.365724 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 1068.1937.
2:20:53.365803 INFO: ==============================================
2:20:53.365887 INFO: Starting optimization step 9.
2:20:53.365957 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:20:53.366032 INFO: Using rust extraction backend
2:20:53.366102 PROGRESS: Extracting batch of 1001059 precursors
2:20:55.058300 INFO: === Search parameters used ===
2:20:55.058596 INFO: rt_error       : 1068.1936693384177
2:20:55.058667 INFO: mobility_error : 0.1
2:20:55.058724 INFO: num_candidates : 3
2:20:55.058781 INFO: ms1_error      : 20
2:20:55.058833 INFO: ms2_error      : 10.0
2:20:55.058883 INFO: fwhm_rt        : 3.0
2:20:55.058932 INFO: quant_window   : 3
2:20:55.058989 INFO: ==============================================
2:21:08.886443 INFO: performing precursor FDR with 40 features
2:21:08.886567 INFO: Decoy channel: -1
2:21:08.886596 INFO: competitive: True
2:21:09.546236 INFO: Setting torch num_threads to 2 for FDR classification task
2:21:10.787450 INFO: Estimating optimal hyperparameters - samples: 2,401,768, batch_size: 4,096, learning_rate: 1.00e-03
2:21:10.792315 INFO: Using random state 512663 for train-test-split
2:21:56.749279 INFO: Test AUC: 0.612
2:21:56.749431 INFO: Train AUC: 0.617
2:21:56.749468 INFO: AUC difference: 0.88%
2:21:57.971386 INFO: Resetting torch num_threads to 32
2:21:58.059864 PROGRESS: === Extracted 3002211 precursors and 18225360 fragments ===
2:21:58.060398 INFO: === FDR correction performed with classifier version 13 ===
2:21:58.061203 PROGRESS: ============================= Precursor FDR =============================
2:21:58.061315 PROGRESS: Total precursors accumulated: 1,818
2:21:58.061385 PROGRESS: Target precursors: 1,800 (99.01%)
2:21:58.061458 PROGRESS: Decoy precursors: 18 (0.99%)
2:21:58.061516 PROGRESS: 
2:21:58.061571 PROGRESS: Precursor Summary:
2:21:58.063043 PROGRESS: Channel   0:	 0.050 FDR: 1,800; 0.010 FDR: 1,780; 0.001 FDR: 1,077
2:21:58.063157 PROGRESS: 
2:21:58.063225 PROGRESS: Protein Summary:
2:21:58.065098 PROGRESS: Channel   0:	 0.050 FDR: 1,368; 0.010 FDR: 1,353; 0.001 FDR:   868
2:21:58.065204 PROGRESS: =========================================================================
2:21:58.121418 INFO: Target number of precursors reached.
2:21:59.970167 INFO: fragments_df: keeping 5000 of 18225360 [sum(precursor_idx_mask)=46612 sum(mass_error_mask)=18225360 stop_rank=5000
2:22:01.059195 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:22:01.335729 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:22:02.022226 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:22:02.022688 INFO: Using score_cutoff 8.96894316959381 (fac=0.99, q=1)
2:22:02.023024 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:22:02.023113 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:22:02.023183 INFO: Updating optimization_manager: score_cutoff        : 5.56776979637146 -> 8.96894316959381
2:22:02.023248 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:22:02.632682 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:22:03.991718 INFO: === checking if optimization conditions were reached ===
2:22:03.992002 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
2:22:03.995067 INFO: Updating optimization_manager: rt_error            : 1068.1936693384177 -> 842.9181129123065
2:22:03.995207 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 842.9181.
2:22:03.995283 INFO: ==============================================
2:22:03.995365 INFO: Starting optimization step 10.
2:22:03.995439 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:22:03.995517 INFO: Using rust extraction backend
2:22:03.995588 PROGRESS: Extracting batch of 1001059 precursors
2:22:05.696850 INFO: === Search parameters used ===
2:22:05.697137 INFO: rt_error       : 842.9181129123065
2:22:05.697206 INFO: mobility_error : 0.1
2:22:05.697264 INFO: num_candidates : 3
2:22:05.697315 INFO: ms1_error      : 20
2:22:05.697366 INFO: ms2_error      : 10.0
2:22:05.697417 INFO: fwhm_rt        : 3.0
2:22:05.697468 INFO: quant_window   : 3
2:22:05.697519 INFO: ==============================================
2:22:18.893126 INFO: performing precursor FDR with 40 features
2:22:18.893250 INFO: Decoy channel: -1
2:22:18.893280 INFO: competitive: True
2:22:19.547496 INFO: Setting torch num_threads to 2 for FDR classification task
2:22:20.779541 INFO: Estimating optimal hyperparameters - samples: 2,401,744, batch_size: 4,096, learning_rate: 1.00e-03
2:22:20.784439 INFO: Using random state 512663 for train-test-split
2:23:06.648294 INFO: Test AUC: 0.613
2:23:06.648427 INFO: Train AUC: 0.618
2:23:06.648462 INFO: AUC difference: 0.74%
2:23:07.863653 INFO: Resetting torch num_threads to 32
2:23:07.955909 PROGRESS: === Extracted 3002180 precursors and 18155861 fragments ===
2:23:07.956439 INFO: === FDR correction performed with classifier version 13 ===
2:23:07.957296 PROGRESS: ============================= Precursor FDR =============================
2:23:07.957407 PROGRESS: Total precursors accumulated: 2,050
2:23:07.957494 PROGRESS: Target precursors: 2,030 (99.02%)
2:23:07.957555 PROGRESS: Decoy precursors: 20 (0.98%)
2:23:07.957609 PROGRESS: 
2:23:07.957664 PROGRESS: Precursor Summary:
2:23:07.959276 PROGRESS: Channel   0:	 0.050 FDR: 2,030; 0.010 FDR: 2,030; 0.001 FDR: 1,277
2:23:07.959388 PROGRESS: 
2:23:07.959452 PROGRESS: Protein Summary:
2:23:07.961500 PROGRESS: Channel   0:	 0.050 FDR: 1,553; 0.010 FDR: 1,553; 0.001 FDR: 1,028
2:23:07.961603 PROGRESS: =========================================================================
2:23:08.013250 INFO: Target number of precursors reached.
2:23:09.821185 INFO: fragments_df: keeping 5000 of 18155861 [sum(precursor_idx_mask)=52180 sum(mass_error_mask)=18155861 stop_rank=5000
2:23:10.568115 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:23:10.867332 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:23:11.533273 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:23:11.533714 INFO: Using score_cutoff 6.688304774951934 (fac=0.99, q=1)
2:23:11.534045 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:23:11.534133 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:23:11.534199 INFO: Updating optimization_manager: score_cutoff        : 8.96894316959381 -> 6.688304774951934
2:23:11.534259 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:23:11.831069 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:23:12.515068 INFO: === checking if optimization conditions were reached ===
2:23:12.515369 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
2:23:12.518864 INFO: Updating optimization_manager: rt_error            : 842.9181129123065 -> 1033.9356235409969
2:23:12.519001 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 1033.9356.
2:23:12.519070 INFO: ==============================================
2:23:12.519147 INFO: Starting optimization step 11.
2:23:12.519211 PROGRESS: === Extracting elution groups 0 to 255000 ===
2:23:12.519282 INFO: Using rust extraction backend
2:23:12.519348 PROGRESS: Extracting batch of 499623 precursors
2:23:13.372499 INFO: === Search parameters used ===
2:23:13.372761 INFO: rt_error       : 1033.9356235409969
2:23:13.372830 INFO: mobility_error : 0.1
2:23:13.372882 INFO: num_candidates : 3
2:23:13.372929 INFO: ms1_error      : 20
2:23:13.372974 INFO: ms2_error      : 10.0
2:23:13.373019 INFO: fwhm_rt        : 3.0
2:23:13.373064 INFO: quant_window   : 3
2:23:13.373108 INFO: ==============================================
2:23:19.901945 INFO: performing precursor FDR with 40 features
2:23:19.902074 INFO: Decoy channel: -1
2:23:19.902102 INFO: competitive: True
2:23:20.211164 INFO: Setting torch num_threads to 2 for FDR classification task
2:23:20.774322 INFO: Estimating optimal hyperparameters - samples: 1,198,712, batch_size: 4,096, learning_rate: 1.00e-03
2:23:20.777112 INFO: Using random state 512663 for train-test-split
2:23:43.215044 INFO: Test AUC: 0.612
2:23:43.215199 INFO: Train AUC: 0.620
2:23:43.215234 INFO: AUC difference: 1.29%
2:23:43.956980 INFO: Resetting torch num_threads to 32
2:23:44.004122 PROGRESS: === Extracted 1498391 precursors and 9091914 fragments ===
2:23:44.004613 INFO: === FDR correction performed with classifier version 13 ===
2:23:44.005273 PROGRESS: ============================= Precursor FDR =============================
2:23:44.005378 PROGRESS: Total precursors accumulated: 951
2:23:44.005445 PROGRESS: Target precursors: 942 (99.05%)
2:23:44.005506 PROGRESS: Decoy precursors: 9 (0.95%)
2:23:44.005566 PROGRESS: 
2:23:44.005625 PROGRESS: Precursor Summary:
2:23:44.006894 PROGRESS: Channel   0:	 0.050 FDR:   942; 0.010 FDR:   942; 0.001 FDR:   776
2:23:44.006998 PROGRESS: 
2:23:44.007062 PROGRESS: Protein Summary:
2:23:44.008619 PROGRESS: Channel   0:	 0.050 FDR:   801; 0.010 FDR:   801; 0.001 FDR:   666
2:23:44.008718 PROGRESS: =========================================================================
2:23:44.038762 INFO: Target number of precursors not reached yet.
2:23:44.771276 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:23:45.068918 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:23:45.767961 INFO: === skipping optimization until target number of precursors are found ===
2:23:45.768228 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
2:23:45.768347 INFO: Starting optimization step 12.
2:23:45.768423 PROGRESS: === Extracting elution groups 255000 to 511000 ===
2:23:45.768505 INFO: Using rust extraction backend
2:23:45.768575 PROGRESS: Extracting batch of 501436 precursors
2:23:46.629323 INFO: === Search parameters used ===
2:23:46.629658 INFO: rt_error       : 1033.9356235409969
2:23:46.629733 INFO: mobility_error : 0.1
2:23:46.629792 INFO: num_candidates : 3
2:23:46.629853 INFO: ms1_error      : 20
2:23:46.629921 INFO: ms2_error      : 10.0
2:23:46.629970 INFO: fwhm_rt        : 3.0
2:23:46.630025 INFO: quant_window   : 3
2:23:46.630073 INFO: ==============================================
2:23:53.758216 INFO: performing precursor FDR with 40 features
2:23:53.758338 INFO: Decoy channel: -1
2:23:53.758385 INFO: competitive: True
2:23:54.910297 INFO: Setting torch num_threads to 2 for FDR classification task
2:23:56.182490 INFO: Estimating optimal hyperparameters - samples: 2,401,764, batch_size: 4,096, learning_rate: 1.00e-03
2:23:56.187907 INFO: Using random state 512663 for train-test-split
2:24:42.588920 INFO: Test AUC: 0.611
2:24:42.589124 INFO: Train AUC: 0.616
2:24:42.589162 INFO: AUC difference: 0.87%
2:24:43.825497 INFO: Resetting torch num_threads to 32
2:24:44.266600 PROGRESS: === Extracted 3002205 precursors and 18225866 fragments ===
2:24:44.267289 INFO: === FDR correction performed with classifier version 13 ===
2:24:44.268231 PROGRESS: ============================= Precursor FDR =============================
2:24:44.268332 PROGRESS: Total precursors accumulated: 1,857
2:24:44.268408 PROGRESS: Target precursors: 1,839 (99.03%)
2:24:44.268470 PROGRESS: Decoy precursors: 18 (0.97%)
2:24:44.268532 PROGRESS: 
2:24:44.268589 PROGRESS: Precursor Summary:
2:24:44.270084 PROGRESS: Channel   0:	 0.050 FDR: 1,839; 0.010 FDR: 1,839; 0.001 FDR: 1,410
2:24:44.270185 PROGRESS: 
2:24:44.270260 PROGRESS: Protein Summary:
2:24:44.272239 PROGRESS: Channel   0:	 0.050 FDR: 1,399; 0.010 FDR: 1,399; 0.001 FDR: 1,120
2:24:44.272346 PROGRESS: =========================================================================
2:24:44.299164 INFO: Target number of precursors reached.
2:24:46.237646 INFO: fragments_df: keeping 5000 of 18225866 [sum(precursor_idx_mask)=48079 sum(mass_error_mask)=18225866 stop_rank=5000
2:24:47.293894 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:24:47.572248 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:24:48.295325 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:24:48.295774 INFO: Using score_cutoff 9.090782782745361 (fac=0.99, q=1)
2:24:48.296106 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:24:48.296193 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:24:48.296255 INFO: Updating optimization_manager: score_cutoff        : 6.688304774951934 -> 9.090782782745361
2:24:48.296318 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:24:48.904584 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:24:50.286854 INFO: === checking if optimization conditions were reached ===
2:24:50.287128 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
2:24:50.290322 INFO: Updating optimization_manager: rt_error            : 1033.9356235409969 -> 735.2290683334388
2:24:50.290469 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 735.2291.
2:24:50.290550 INFO: ==============================================
2:24:50.290637 INFO: Starting optimization step 13.
2:24:50.290716 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:24:50.290816 INFO: Using rust extraction backend
2:24:50.290888 PROGRESS: Extracting batch of 1001059 precursors
2:24:51.991429 INFO: === Search parameters used ===
2:24:51.991727 INFO: rt_error       : 735.2290683334388
2:24:51.991799 INFO: mobility_error : 0.1
2:24:51.991858 INFO: num_candidates : 3
2:24:51.991912 INFO: ms1_error      : 20
2:24:51.991962 INFO: ms2_error      : 10.0
2:24:51.992011 INFO: fwhm_rt        : 3.0
2:24:51.992069 INFO: quant_window   : 3
2:24:51.992118 INFO: ==============================================
2:25:05.073325 INFO: performing precursor FDR with 40 features
2:25:05.073449 INFO: Decoy channel: -1
2:25:05.073478 INFO: competitive: True
2:25:05.747123 INFO: Setting torch num_threads to 2 for FDR classification task
2:25:06.988233 INFO: Estimating optimal hyperparameters - samples: 2,401,652, batch_size: 4,096, learning_rate: 1.00e-03
2:25:06.993500 INFO: Using random state 512663 for train-test-split
2:25:52.444084 INFO: Test AUC: 0.612
2:25:52.444219 INFO: Train AUC: 0.618
2:25:52.444254 INFO: AUC difference: 0.95%
2:25:53.660877 INFO: Resetting torch num_threads to 32
2:25:53.750117 PROGRESS: === Extracted 3002066 precursors and 18006748 fragments ===
2:25:53.750618 INFO: === FDR correction performed with classifier version 13 ===
2:25:53.751365 PROGRESS: ============================= Precursor FDR =============================
2:25:53.751462 PROGRESS: Total precursors accumulated: 1,794
2:25:53.751531 PROGRESS: Target precursors: 1,777 (99.05%)
2:25:53.751595 PROGRESS: Decoy precursors: 17 (0.95%)
2:25:53.751652 PROGRESS: 
2:25:53.751711 PROGRESS: Precursor Summary:
2:25:53.753096 PROGRESS: Channel   0:	 0.050 FDR: 1,777; 0.010 FDR: 1,777; 0.001 FDR: 1,267
2:25:53.753192 PROGRESS: 
2:25:53.753257 PROGRESS: Protein Summary:
2:25:53.755168 PROGRESS: Channel   0:	 0.050 FDR: 1,352; 0.010 FDR: 1,352; 0.001 FDR: 1,019
2:25:53.755270 PROGRESS: =========================================================================
2:25:53.805723 INFO: Target number of precursors reached.
2:25:55.628296 INFO: fragments_df: keeping 5000 of 18006748 [sum(precursor_idx_mask)=46613 sum(mass_error_mask)=18006748 stop_rank=5000
2:25:56.688253 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:25:56.917837 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:25:57.604887 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:25:57.605342 INFO: Using score_cutoff 9.336898412704468 (fac=0.99, q=1)
2:25:57.605649 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:25:57.605734 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:25:57.605796 INFO: Updating optimization_manager: score_cutoff        : 9.090782782745361 -> 9.336898412704468
2:25:57.605862 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:25:58.207388 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:25:59.563126 INFO: === checking if optimization conditions were reached ===
2:25:59.563421 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 5 ===
2:25:59.566429 INFO: Updating optimization_manager: rt_error            : 735.2290683334388 -> 585.0411248290177
2:25:59.566569 PROGRESS: ❌ rt_error       : optimization incomplete after 12 search(es). Will search with parameter 585.0411.
2:25:59.566646 INFO: ==============================================
2:25:59.566724 INFO: Starting optimization step 14.
2:25:59.566808 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:25:59.566883 INFO: Using rust extraction backend
2:25:59.566948 PROGRESS: Extracting batch of 1001059 precursors
2:26:01.259441 INFO: === Search parameters used ===
2:26:01.259721 INFO: rt_error       : 585.0411248290177
2:26:01.259800 INFO: mobility_error : 0.1
2:26:01.259860 INFO: num_candidates : 3
2:26:01.259915 INFO: ms1_error      : 20
2:26:01.259974 INFO: ms2_error      : 10.0
2:26:01.260026 INFO: fwhm_rt        : 3.0
2:26:01.260074 INFO: quant_window   : 3
2:26:01.260123 INFO: ==============================================
2:26:13.588535 INFO: performing precursor FDR with 40 features
2:26:13.588662 INFO: Decoy channel: -1
2:26:13.588692 INFO: competitive: True
2:26:14.285986 INFO: Setting torch num_threads to 2 for FDR classification task
2:26:15.576852 INFO: Estimating optimal hyperparameters - samples: 2,401,560, batch_size: 4,096, learning_rate: 1.00e-03
2:26:15.582083 INFO: Using random state 512663 for train-test-split
2:27:01.669788 INFO: Test AUC: 0.612
2:27:01.669957 INFO: Train AUC: 0.616
2:27:01.669993 INFO: AUC difference: 0.60%
2:27:02.863233 INFO: Resetting torch num_threads to 32
2:27:02.956478 PROGRESS: === Extracted 3001950 precursors and 17818605 fragments ===
2:27:02.956993 INFO: === FDR correction performed with classifier version 13 ===
2:27:02.957788 PROGRESS: ============================= Precursor FDR =============================
2:27:02.957888 PROGRESS: Total precursors accumulated: 1,931
2:27:02.957973 PROGRESS: Target precursors: 1,912 (99.02%)
2:27:02.958035 PROGRESS: Decoy precursors: 19 (0.98%)
2:27:02.958092 PROGRESS: 
2:27:02.958152 PROGRESS: Precursor Summary:
2:27:02.959645 PROGRESS: Channel   0:	 0.050 FDR: 1,912; 0.010 FDR: 1,912; 0.001 FDR: 1,304
2:27:02.959753 PROGRESS: 
2:27:02.959826 PROGRESS: Protein Summary:
2:27:02.961776 PROGRESS: Channel   0:	 0.050 FDR: 1,455; 0.010 FDR: 1,455; 0.001 FDR: 1,049
2:27:02.961890 PROGRESS: =========================================================================
2:27:03.014787 INFO: Target number of precursors reached.
2:27:04.824790 INFO: fragments_df: keeping 5000 of 17818605 [sum(precursor_idx_mask)=49800 sum(mass_error_mask)=17818605 stop_rank=5000
2:27:05.903455 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:27:06.188484 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:27:06.896840 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:27:06.897306 INFO: Using score_cutoff 8.982964641666412 (fac=0.99, q=1)
2:27:06.897642 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:27:06.897736 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:27:06.897803 INFO: Updating optimization_manager: score_cutoff        : 9.336898412704468 -> 8.982964641666412
2:27:06.897875 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:27:07.515589 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:27:08.916169 INFO: === checking if optimization conditions were reached ===
2:27:08.916454 PROGRESS: === Optimization of rt_error has been performed 13 time(s); minimum number is 5 ===
2:27:08.919739 INFO: Updating optimization_manager: rt_error            : 585.0411248290177 -> 525.4214095038986
2:27:08.919885 PROGRESS: ❌ rt_error       : optimization incomplete after 13 search(es). Will search with parameter 525.4214.
2:27:08.919974 INFO: ==============================================
2:27:08.920066 INFO: Starting optimization step 15.
2:27:08.920146 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:27:08.920218 INFO: Using rust extraction backend
2:27:08.920290 PROGRESS: Extracting batch of 1001059 precursors
2:27:10.626270 INFO: === Search parameters used ===
2:27:10.626575 INFO: rt_error       : 525.4214095038986
2:27:10.626651 INFO: mobility_error : 0.1
2:27:10.626711 INFO: num_candidates : 3
2:27:10.626764 INFO: ms1_error      : 20
2:27:10.626818 INFO: ms2_error      : 10.0
2:27:10.626872 INFO: fwhm_rt        : 3.0
2:27:10.626922 INFO: quant_window   : 3
2:27:10.626971 INFO: ==============================================
2:27:22.871205 INFO: performing precursor FDR with 40 features
2:27:22.871331 INFO: Decoy channel: -1
2:27:22.871360 INFO: competitive: True
2:27:23.564332 INFO: Setting torch num_threads to 2 for FDR classification task
2:27:24.860384 INFO: Estimating optimal hyperparameters - samples: 2,401,472, batch_size: 4,096, learning_rate: 1.00e-03
2:27:24.865741 INFO: Using random state 512663 for train-test-split
2:28:10.204879 INFO: Test AUC: 0.611
2:28:10.205016 INFO: Train AUC: 0.616
2:28:10.205054 INFO: AUC difference: 0.75%
2:28:11.451036 INFO: Resetting torch num_threads to 32
2:28:11.542569 PROGRESS: === Extracted 3001840 precursors and 17720194 fragments ===
2:28:11.543052 INFO: === FDR correction performed with classifier version 13 ===
2:28:11.543825 PROGRESS: ============================= Precursor FDR =============================
2:28:11.543924 PROGRESS: Total precursors accumulated: 1,880
2:28:11.543993 PROGRESS: Target precursors: 1,862 (99.04%)
2:28:11.544055 PROGRESS: Decoy precursors: 18 (0.96%)
2:28:11.544111 PROGRESS: 
2:28:11.544175 PROGRESS: Precursor Summary:
2:28:11.545635 PROGRESS: Channel   0:	 0.050 FDR: 1,862; 0.010 FDR: 1,862; 0.001 FDR: 1,382
2:28:11.545731 PROGRESS: 
2:28:11.545796 PROGRESS: Protein Summary:
2:28:11.547794 PROGRESS: Channel   0:	 0.050 FDR: 1,459; 0.010 FDR: 1,459; 0.001 FDR: 1,107
2:28:11.547905 PROGRESS: =========================================================================
2:28:11.601043 INFO: Target number of precursors reached.
2:28:13.381648 INFO: fragments_df: keeping 5000 of 17720194 [sum(precursor_idx_mask)=47007 sum(mass_error_mask)=17720194 stop_rank=5000
2:28:14.444549 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:28:14.724190 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:28:15.444776 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:28:15.445227 INFO: Using score_cutoff 4.603549397277832 (fac=0.99, q=1)
2:28:15.445544 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:28:15.445631 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:28:15.445696 INFO: Updating optimization_manager: score_cutoff        : 8.982964641666412 -> 4.603549397277832
2:28:15.445759 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:28:16.046368 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:28:17.437412 INFO: === checking if optimization conditions were reached ===
2:28:17.437648 PROGRESS: === Optimization of rt_error has been performed 14 time(s); minimum number is 5 ===
2:28:17.440694 INFO: Updating optimization_manager: rt_error            : 525.4214095038986 -> 726.9132512437067
2:28:17.440828 PROGRESS: ❌ rt_error       : optimization incomplete after 14 search(es). Will search with parameter 726.9133.
2:28:17.440904 INFO: ==============================================
2:28:17.440978 INFO: Starting optimization step 16.
2:28:17.441043 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:28:17.441106 INFO: Using rust extraction backend
2:28:17.441172 PROGRESS: Extracting batch of 1001059 precursors
2:28:19.125692 INFO: === Search parameters used ===
2:28:19.126000 INFO: rt_error       : 726.9132512437067
2:28:19.126066 INFO: mobility_error : 0.1
2:28:19.126117 INFO: num_candidates : 3
2:28:19.126165 INFO: ms1_error      : 20
2:28:19.126209 INFO: ms2_error      : 10.0
2:28:19.126253 INFO: fwhm_rt        : 3.0
2:28:19.126297 INFO: quant_window   : 3
2:28:19.126340 INFO: ==============================================
2:28:31.797854 INFO: performing precursor FDR with 40 features
2:28:31.797981 INFO: Decoy channel: -1
2:28:31.798011 INFO: competitive: True
2:28:32.482728 INFO: Setting torch num_threads to 2 for FDR classification task
2:28:33.793037 INFO: Estimating optimal hyperparameters - samples: 2,401,688, batch_size: 4,096, learning_rate: 1.00e-03
2:28:33.798221 INFO: Using random state 512663 for train-test-split
2:29:18.724145 INFO: Test AUC: 0.614
2:29:18.724283 INFO: Train AUC: 0.617
2:29:18.724319 INFO: AUC difference: 0.64%
2:29:19.925845 INFO: Resetting torch num_threads to 32
2:29:20.019368 PROGRESS: === Extracted 3002111 precursors and 18045625 fragments ===
2:29:20.019846 INFO: === FDR correction performed with classifier version 13 ===
2:29:20.020620 PROGRESS: ============================= Precursor FDR =============================
2:29:20.020720 PROGRESS: Total precursors accumulated: 1,870
2:29:20.020795 PROGRESS: Target precursors: 1,852 (99.04%)
2:29:20.020869 PROGRESS: Decoy precursors: 18 (0.96%)
2:29:20.020926 PROGRESS: 
2:29:20.020988 PROGRESS: Precursor Summary:
2:29:20.022458 PROGRESS: Channel   0:	 0.050 FDR: 1,852; 0.010 FDR: 1,852; 0.001 FDR: 1,429
2:29:20.022557 PROGRESS: 
2:29:20.022622 PROGRESS: Protein Summary:
2:29:20.024587 PROGRESS: Channel   0:	 0.050 FDR: 1,427; 0.010 FDR: 1,427; 0.001 FDR: 1,138
2:29:20.024693 PROGRESS: =========================================================================
2:29:20.077129 INFO: Target number of precursors reached.
2:29:21.897634 INFO: fragments_df: keeping 5000 of 18045625 [sum(precursor_idx_mask)=47523 sum(mass_error_mask)=18045625 stop_rank=5000
2:29:22.934126 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:29:23.209212 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:29:23.902542 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:29:23.902996 INFO: Using score_cutoff 5.37408960814476 (fac=0.99, q=1)
2:29:23.903332 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:29:23.903418 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:29:23.903481 INFO: Updating optimization_manager: score_cutoff        : 4.603549397277832 -> 5.37408960814476
2:29:23.903546 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:29:24.510908 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:29:25.874449 INFO: === checking if optimization conditions were reached ===
2:29:25.874746 PROGRESS: === Optimization of rt_error has been performed 15 time(s); minimum number is 5 ===
2:29:25.877772 INFO: Updating optimization_manager: rt_error            : 726.9132512437067 -> 999.8239790086685
2:29:25.877901 PROGRESS: ❌ rt_error       : optimization incomplete after 15 search(es). Will search with parameter 999.8240.
2:29:25.877975 INFO: ==============================================
2:29:25.878059 INFO: Starting optimization step 17.
2:29:25.878124 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:29:25.878190 INFO: Using rust extraction backend
2:29:25.878255 PROGRESS: Extracting batch of 1001059 precursors
2:29:27.565924 INFO: === Search parameters used ===
2:29:27.566281 INFO: rt_error       : 999.8239790086685
2:29:27.566346 INFO: mobility_error : 0.1
2:29:27.566414 INFO: num_candidates : 3
2:29:27.566464 INFO: ms1_error      : 20
2:29:27.566511 INFO: ms2_error      : 10.0
2:29:27.566557 INFO: fwhm_rt        : 3.0
2:29:27.566600 INFO: quant_window   : 3
2:29:27.566645 INFO: ==============================================
2:29:40.981192 INFO: performing precursor FDR with 40 features
2:29:40.981323 INFO: Decoy channel: -1
2:29:40.981361 INFO: competitive: True
2:29:41.688417 INFO: Setting torch num_threads to 2 for FDR classification task
2:29:42.983895 INFO: Estimating optimal hyperparameters - samples: 2,401,774, batch_size: 4,096, learning_rate: 1.00e-03
2:29:42.988618 INFO: Using random state 512663 for train-test-split
2:30:27.373135 INFO: Test AUC: 0.613
2:30:27.373384 INFO: Train AUC: 0.618
2:30:27.373424 INFO: AUC difference: 0.85%
2:30:28.587727 INFO: Resetting torch num_threads to 32
2:30:28.812232 PROGRESS: === Extracted 3002218 precursors and 18227647 fragments ===
2:30:28.812774 INFO: === FDR correction performed with classifier version 13 ===
2:30:28.813613 PROGRESS: ============================= Precursor FDR =============================
2:30:28.813737 PROGRESS: Total precursors accumulated: 1,828
2:30:28.813814 PROGRESS: Target precursors: 1,810 (99.02%)
2:30:28.813874 PROGRESS: Decoy precursors: 18 (0.98%)
2:30:28.813931 PROGRESS: 
2:30:28.813987 PROGRESS: Precursor Summary:
2:30:28.815499 PROGRESS: Channel   0:	 0.050 FDR: 1,810; 0.010 FDR: 1,810; 0.001 FDR: 1,077
2:30:28.815607 PROGRESS: 
2:30:28.815671 PROGRESS: Protein Summary:
2:30:28.817579 PROGRESS: Channel   0:	 0.050 FDR: 1,387; 0.010 FDR: 1,387; 0.001 FDR:   888
2:30:28.817684 PROGRESS: =========================================================================
2:30:28.877010 INFO: Target number of precursors reached.
2:30:30.765718 INFO: fragments_df: keeping 5000 of 18227647 [sum(precursor_idx_mask)=47217 sum(mass_error_mask)=18227647 stop_rank=5000
2:30:31.927039 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:30:32.205946 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:30:34.456020 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:30:34.456612 INFO: Using score_cutoff 8.787429473304748 (fac=0.99, q=1)
2:30:34.456995 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:30:34.457086 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:30:34.457150 INFO: Updating optimization_manager: score_cutoff        : 5.37408960814476 -> 8.787429473304748
2:30:34.457218 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:30:35.064279 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:30:36.446484 INFO: === checking if optimization conditions were reached ===
2:30:36.446759 PROGRESS: === Optimization of rt_error has been performed 16 time(s); minimum number is 5 ===
2:30:36.450011 INFO: Updating optimization_manager: rt_error            : 999.8239790086685 -> 1096.496243328373
2:30:36.450145 PROGRESS: ❌ rt_error       : optimization incomplete after 16 search(es). Will search with parameter 1096.4962.
2:30:36.450223 INFO: ==============================================
2:30:36.450298 INFO: Starting optimization step 18.
2:30:36.450374 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:30:36.450458 INFO: Using rust extraction backend
2:30:36.450526 PROGRESS: Extracting batch of 1001059 precursors
2:30:38.162831 INFO: === Search parameters used ===
2:30:38.163350 INFO: rt_error       : 1096.496243328373
2:30:38.163416 INFO: mobility_error : 0.1
2:30:38.163475 INFO: num_candidates : 3
2:30:38.163526 INFO: ms1_error      : 20
2:30:38.163574 INFO: ms2_error      : 10.0
2:30:38.163619 INFO: fwhm_rt        : 3.0
2:30:38.163662 INFO: quant_window   : 3
2:30:38.163708 INFO: ==============================================
2:30:52.031586 INFO: performing precursor FDR with 40 features
2:30:52.031809 INFO: Decoy channel: -1
2:30:52.031840 INFO: competitive: True
2:30:52.705826 INFO: Setting torch num_threads to 2 for FDR classification task
2:30:53.979570 INFO: Estimating optimal hyperparameters - samples: 2,401,767, batch_size: 4,096, learning_rate: 1.00e-03
2:30:53.985760 INFO: Using random state 512663 for train-test-split
2:31:41.058790 INFO: Test AUC: 0.613
2:31:41.059041 INFO: Train AUC: 0.618
2:31:41.059079 INFO: AUC difference: 0.78%
2:31:42.298150 INFO: Resetting torch num_threads to 32
2:31:42.390114 PROGRESS: === Extracted 3002209 precursors and 18224831 fragments ===
2:31:42.390678 INFO: === FDR correction performed with classifier version 13 ===
2:31:42.391530 PROGRESS: ============================= Precursor FDR =============================
2:31:42.391642 PROGRESS: Total precursors accumulated: 1,831
2:31:42.391715 PROGRESS: Target precursors: 1,813 (99.02%)
2:31:42.391773 PROGRESS: Decoy precursors: 18 (0.98%)
2:31:42.391827 PROGRESS: 
2:31:42.391879 PROGRESS: Precursor Summary:
2:31:42.393455 PROGRESS: Channel   0:	 0.050 FDR: 1,813; 0.010 FDR: 1,813; 0.001 FDR: 1,355
2:31:42.393566 PROGRESS: 
2:31:42.393626 PROGRESS: Protein Summary:
2:31:42.395629 PROGRESS: Channel   0:	 0.050 FDR: 1,372; 0.010 FDR: 1,372; 0.001 FDR: 1,079
2:31:42.395733 PROGRESS: =========================================================================
2:31:42.449063 INFO: Target number of precursors reached.
2:31:44.274926 INFO: fragments_df: keeping 5000 of 18224831 [sum(precursor_idx_mask)=47323 sum(mass_error_mask)=18224831 stop_rank=5000
2:31:45.364391 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:31:45.637023 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:31:46.366826 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:31:46.367291 INFO: Using score_cutoff 9.080017197418213 (fac=0.99, q=1)
2:31:46.367635 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:31:46.367723 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:31:46.367787 INFO: Updating optimization_manager: score_cutoff        : 8.787429473304748 -> 9.080017197418213
2:31:46.367861 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:31:46.973696 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:31:48.360255 INFO: === checking if optimization conditions were reached ===
2:31:48.360515 PROGRESS: === Optimization of rt_error has been performed 17 time(s); minimum number is 5 ===
2:31:48.363680 INFO: Updating optimization_manager: rt_error            : 1096.496243328373 -> 880.5232746077367
2:31:48.363824 PROGRESS: ❌ rt_error       : optimization incomplete after 17 search(es). Will search with parameter 880.5233.
2:31:48.363901 INFO: ==============================================
2:31:48.363985 INFO: Starting optimization step 19.
2:31:48.364057 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:31:48.364153 INFO: Using rust extraction backend
2:31:48.364226 PROGRESS: Extracting batch of 1001059 precursors
2:31:50.079273 INFO: === Search parameters used ===
2:31:50.079786 INFO: rt_error       : 880.5232746077367
2:31:50.079855 INFO: mobility_error : 0.1
2:31:50.079915 INFO: num_candidates : 3
2:31:50.079967 INFO: ms1_error      : 20
2:31:50.080018 INFO: ms2_error      : 10.0
2:31:50.080077 INFO: fwhm_rt        : 3.0
2:31:50.080131 INFO: quant_window   : 3
2:31:50.080197 INFO: ==============================================
2:32:03.332029 INFO: performing precursor FDR with 40 features
2:32:03.332154 INFO: Decoy channel: -1
2:32:03.332186 INFO: competitive: True
2:32:04.041372 INFO: Setting torch num_threads to 2 for FDR classification task
2:32:05.365378 INFO: Estimating optimal hyperparameters - samples: 2,401,752, batch_size: 4,096, learning_rate: 1.00e-03
2:32:05.370980 INFO: Using random state 512663 for train-test-split
2:32:51.532872 INFO: Test AUC: 0.613
2:32:51.533126 INFO: Train AUC: 0.618
2:32:51.533165 INFO: AUC difference: 0.74%
2:32:52.786812 INFO: Resetting torch num_threads to 32
2:32:52.881810 PROGRESS: === Extracted 3002191 precursors and 18192606 fragments ===
2:32:52.882331 INFO: === FDR correction performed with classifier version 13 ===
2:32:52.883165 PROGRESS: ============================= Precursor FDR =============================
2:32:52.883269 PROGRESS: Total precursors accumulated: 1,934
2:32:52.883343 PROGRESS: Target precursors: 1,915 (99.02%)
2:32:52.883404 PROGRESS: Decoy precursors: 19 (0.98%)
2:32:52.883466 PROGRESS: 
2:32:52.883521 PROGRESS: Precursor Summary:
2:32:52.885006 PROGRESS: Channel   0:	 0.050 FDR: 1,915; 0.010 FDR: 1,915; 0.001 FDR: 1,406
2:32:52.885107 PROGRESS: 
2:32:52.885172 PROGRESS: Protein Summary:
2:32:52.887196 PROGRESS: Channel   0:	 0.050 FDR: 1,502; 0.010 FDR: 1,502; 0.001 FDR: 1,128
2:32:52.887301 PROGRESS: =========================================================================
2:32:52.939346 INFO: Target number of precursors reached.
2:32:54.803392 INFO: fragments_df: keeping 5000 of 18192606 [sum(precursor_idx_mask)=48411 sum(mass_error_mask)=18192606 stop_rank=5000
2:32:55.885971 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:32:56.171808 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:32:56.900732 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:32:56.901219 INFO: Using score_cutoff 5.31712403383255 (fac=0.99, q=1)
2:32:56.901576 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:32:56.901672 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:32:56.901736 INFO: Updating optimization_manager: score_cutoff        : 9.080017197418213 -> 5.31712403383255
2:32:56.901797 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:32:57.511696 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:32:58.864832 INFO: === checking if optimization conditions were reached ===
2:32:58.865124 PROGRESS: === Optimization of rt_error has been performed 18 time(s); minimum number is 5 ===
2:32:58.868443 INFO: Updating optimization_manager: rt_error            : 880.5232746077367 -> 1042.8807511793616
2:32:58.868594 PROGRESS: ❌ rt_error       : optimization incomplete after 18 search(es). Will search with parameter 1042.8808.
2:32:58.868674 INFO: ==============================================
2:32:58.868747 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
2:32:58.868814 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:32:58.868870 PROGRESS: ==============================================
2:32:58.868932 PROGRESS: ms2_error      : 10.0000
2:32:58.868991 PROGRESS: rt_error       : 1042.8808
2:32:58.869045 PROGRESS: ==============================================
2:32:58.870509 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:33:05.406110 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:33:30.595035 INFO: Using rust extraction backend
2:33:30.595584 PROGRESS: Extracting batch of 10770831 precursors
2:33:53.425810 INFO: === Search parameters used ===
2:33:53.426319 INFO: rt_error       : 1042.8807511793616
2:33:53.426420 INFO: mobility_error : 0.1
2:33:53.426481 INFO: num_candidates : 3
2:33:53.426533 INFO: ms1_error      : 20
2:33:53.426582 INFO: ms2_error      : 10.0
2:33:53.426630 INFO: fwhm_rt        : 3.0
2:33:53.426677 INFO: quant_window   : 3
2:33:53.426723 INFO: ==============================================
2:34:57.763762 INFO: Removed 1628914 precursors with score below cutoff 5.31712403383255
2:35:32.512990 INFO: performing precursor FDR with 40 features
2:35:32.513224 INFO: Decoy channel: -1
2:35:32.513256 INFO: competitive: True
2:35:35.727353 INFO: Setting torch num_threads to 2 for FDR classification task
2:35:48.436415 INFO: Estimating optimal hyperparameters - samples: 24,546,858, batch_size: 4,096, learning_rate: 1.00e-03
2:35:48.512892 INFO: Using random state 512663 for train-test-split
2:43:46.391651 INFO: Test AUC: 0.616
2:43:46.391934 INFO: Train AUC: 0.616
2:43:46.391986 INFO: AUC difference: 0.08%
2:43:53.261952 INFO: Resetting torch num_threads to 32
2:43:55.013482 PROGRESS: ============================= Precursor FDR =============================
2:43:55.013743 PROGRESS: Total precursors accumulated: 18,974
2:43:55.013820 PROGRESS: Target precursors: 18,787 (99.01%)
2:43:55.013880 PROGRESS: Decoy precursors: 187 (0.99%)
2:43:55.013933 PROGRESS: 
2:43:55.013988 PROGRESS: Precursor Summary:
2:43:55.018078 PROGRESS: Channel   0:	 0.050 FDR: 18,787; 0.010 FDR: 18,787; 0.001 FDR: 7,187
2:43:55.018192 PROGRESS: 
2:43:55.018256 PROGRESS: Protein Summary:
2:43:55.024663 PROGRESS: Channel   0:	 0.050 FDR: 5,652; 0.010 FDR: 5,652; 0.001 FDR: 2,898
2:43:55.024783 PROGRESS: =========================================================================
2:43:55.210671 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2/psm.parquet
2:43:55.253582 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2/frag.parquet
2:43:55.329353 INFO: Finished workflow for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2
2:43:55.841698 PROGRESS: Loading raw file 6/6: 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3 
2:43:55.841851 INFO: Quantification results path: /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant
2:43:55.841931 INFO: Creating folder /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3/figures
2:43:55.842096 INFO: Initializing TimingManager
2:43:55.842611 INFO: Initializing RawFileManager
2:44:02.315794 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:44:02.316910 INFO: Determining DIA cycle
2:44:02.329396 INFO: Found cycle with start 0.00 min and length 20.
2:44:02.353822 INFO: RT (min)            : 0.0 - 23.9
2:44:02.353977 INFO: RT duration (sec)   : 1433.9
2:44:02.354020 INFO: RT duration (min)   : 23.9
2:44:02.354048 INFO: Cycle len (scans)   : 20
2:44:02.354070 INFO: Cycle len (sec)     : 1.04
2:44:02.354090 INFO: Number of cycles    : 1379
2:44:02.354112 INFO: MS2 range (m/z)     : 400.4 - 800.6
2:44:02.354147 INFO: Creating DIA data object took: 6.511430978775024
2:44:02.940062 INFO: Creating DIA data NG object took: 0.5857818126678467
2:44:04.570467 INFO: Initializing CalibrationManager
2:44:04.570755 INFO: Setting up calibration estimators ..
2:44:04.570829 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:44:04.570925 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'}' ..
2:44:04.571021 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:44:04.571081 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:44:04.571145 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}}' ..
2:44:04.571214 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:44:04.571272 INFO: Done setting up calibration estimators.
2:44:04.571385 INFO: Initializing OptimizationManager
2:44:04.571524 INFO: initial parameter: ms1_error = 20
2:44:04.571589 INFO: initial parameter: ms2_error = 20
2:44:04.571645 INFO: initial parameter: rt_error = 716.9898681640625
2:44:04.571697 INFO: initial parameter: mobility_error = 0.1
2:44:04.571747 INFO: initial parameter: num_candidates = 1
2:44:04.571796 INFO: initial parameter: fwhm_rt = 5
2:44:04.571845 INFO: initial parameter: fwhm_mobility = 0.01
2:44:04.571899 INFO: initial parameter: score_cutoff = 0
2:44:04.571948 INFO: initial parameter: classifier_version = -1
2:44:04.572040 PROGRESS: Initializing workflow 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3
2:44:04.572308 INFO: FDRManager: loading saved state not requested, will be initialized.
2:44:04.572350 INFO: Initializing FDRManager
2:44:04.572390 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2:44:05.783338 PROGRESS: Initializing spectral library: 5,415,345 target precursors potentially observable (2,595,411 removed)
2:44:06.562219 INFO: Updating optimization_manager: ms2_error           : 20 -> 20
2:44:06.562681 INFO: Updating optimization_manager: rt_error            : 716.9898681640625 -> 716.9898681640625
2:44:06.562794 PROGRESS: Starting initial search for precursors.
2:44:06.562886 INFO: Starting optimization step 0.
2:44:06.562956 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:44:06.563028 INFO: Using rust extraction backend
2:44:06.563097 PROGRESS: Extracting batch of 1960 precursors
2:44:06.568514 INFO: === Search parameters used ===
2:44:06.568624 INFO: rt_error       : 716.9898681640625
2:44:06.568683 INFO: mobility_error : 0.1
2:44:06.568735 INFO: num_candidates : 1
2:44:06.568784 INFO: ms1_error      : 20
2:44:06.568835 INFO: ms2_error      : 20
2:44:06.568895 INFO: fwhm_rt        : 5
2:44:06.568942 INFO: quant_window   : 3
2:44:06.569002 INFO: ==============================================
2:44:06.600173 INFO: performing precursor FDR with 40 features
2:44:06.600256 INFO: Decoy channel: -1
2:44:06.600281 INFO: competitive: True
2:44:06.601623 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:06.603573 INFO: Estimating optimal hyperparameters - samples: 1,565, batch_size: 128, learning_rate: 1.77e-04
2:44:06.604508 INFO: Using random state 365155 for train-test-split
2:44:06.757902 INFO: Test AUC: 0.508
2:44:06.757987 INFO: Train AUC: 0.549
2:44:06.758015 INFO: AUC difference: 7.47%
2:44:06.758039 WARNING: AUC difference > 5%. This may indicate overfitting.
2:44:07.009671 INFO: Resetting torch num_threads to 32
2:44:07.011218 PROGRESS: === Extracted 1957 precursors and 10777 fragments ===
2:44:07.011595 INFO: === FDR correction performed with classifier version -1 ===
2:44:07.012078 PROGRESS: ============================= Precursor FDR =============================
2:44:07.012171 PROGRESS: Total precursors accumulated: 5
2:44:07.012235 PROGRESS: Target precursors: 5 (100.00%)
2:44:07.012293 PROGRESS: Decoy precursors: 0 (0.00%)
2:44:07.012341 PROGRESS: 
2:44:07.012387 PROGRESS: Precursor Summary:
2:44:07.013442 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
2:44:07.013531 PROGRESS: 
2:44:07.013590 PROGRESS: Protein Summary:
2:44:07.014760 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
2:44:07.014863 PROGRESS: =========================================================================
2:44:07.015075 INFO: Target number of precursors not reached yet.
2:44:07.091708 INFO: Starting optimization step 1.
2:44:07.091924 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:44:07.092018 INFO: Using rust extraction backend
2:44:07.092086 PROGRESS: Extracting batch of 3921 precursors
2:44:07.100374 INFO: === Search parameters used ===
2:44:07.100505 INFO: rt_error       : 716.9898681640625
2:44:07.100561 INFO: mobility_error : 0.1
2:44:07.100621 INFO: num_candidates : 1
2:44:07.100667 INFO: ms1_error      : 20
2:44:07.100713 INFO: ms2_error      : 20
2:44:07.100758 INFO: fwhm_rt        : 5
2:44:07.100802 INFO: quant_window   : 3
2:44:07.100846 INFO: ==============================================
2:44:07.165938 INFO: performing precursor FDR with 40 features
2:44:07.166033 INFO: Decoy channel: -1
2:44:07.166059 INFO: competitive: True
2:44:07.170494 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:07.173218 INFO: Estimating optimal hyperparameters - samples: 4,699, batch_size: 128, learning_rate: 1.77e-04
2:44:07.173320 INFO: Using random state 376790 for train-test-split
2:44:07.636425 INFO: Test AUC: 0.529
2:44:07.636516 INFO: Train AUC: 0.569
2:44:07.636547 INFO: AUC difference: 7.11%
2:44:07.636570 WARNING: AUC difference > 5%. This may indicate overfitting.
2:44:07.882838 INFO: Resetting torch num_threads to 32
2:44:07.885688 PROGRESS: === Extracted 5874 precursors and 32392 fragments ===
2:44:07.886056 INFO: === FDR correction performed with classifier version -1 ===
2:44:07.886558 PROGRESS: ============================= Precursor FDR =============================
2:44:07.886656 PROGRESS: Total precursors accumulated: 2
2:44:07.886724 PROGRESS: Target precursors: 2 (100.00%)
2:44:07.886780 PROGRESS: Decoy precursors: 0 (0.00%)
2:44:07.886839 PROGRESS: 
2:44:07.886894 PROGRESS: Precursor Summary:
2:44:07.887959 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
2:44:07.888047 PROGRESS: 
2:44:07.888105 PROGRESS: Protein Summary:
2:44:07.889281 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
2:44:07.889368 PROGRESS: =========================================================================
2:44:07.889635 INFO: Target number of precursors not reached yet.
2:44:07.973907 INFO: Starting optimization step 2.
2:44:07.974136 PROGRESS: === Extracting elution groups 3000 to 7000 ===
2:44:07.974224 INFO: Using rust extraction backend
2:44:07.974288 PROGRESS: Extracting batch of 7852 precursors
2:44:07.989317 INFO: === Search parameters used ===
2:44:07.989459 INFO: rt_error       : 716.9898681640625
2:44:07.989516 INFO: mobility_error : 0.1
2:44:07.989565 INFO: num_candidates : 1
2:44:07.989611 INFO: ms1_error      : 20
2:44:07.989655 INFO: ms2_error      : 20
2:44:07.989698 INFO: fwhm_rt        : 5
2:44:07.989743 INFO: quant_window   : 3
2:44:07.989786 INFO: ==============================================
2:44:08.104295 INFO: performing precursor FDR with 40 features
2:44:08.104399 INFO: Decoy channel: -1
2:44:08.104425 INFO: competitive: True
2:44:08.110851 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:08.114404 INFO: Estimating optimal hyperparameters - samples: 10,971, batch_size: 128, learning_rate: 1.77e-04
2:44:08.114522 INFO: Using random state 257250 for train-test-split
2:44:09.213244 INFO: Test AUC: 0.542
2:44:09.213357 INFO: Train AUC: 0.586
2:44:09.213389 INFO: AUC difference: 7.42%
2:44:09.213415 WARNING: AUC difference > 5%. This may indicate overfitting.
2:44:09.470922 INFO: Resetting torch num_threads to 32
2:44:09.474901 PROGRESS: === Extracted 13714 precursors and 75270 fragments ===
2:44:09.475290 INFO: === FDR correction performed with classifier version -1 ===
2:44:09.475806 PROGRESS: ============================= Precursor FDR =============================
2:44:09.475902 PROGRESS: Total precursors accumulated: 13
2:44:09.475970 PROGRESS: Target precursors: 13 (100.00%)
2:44:09.476036 PROGRESS: Decoy precursors: 0 (0.00%)
2:44:09.476089 PROGRESS: 
2:44:09.476139 PROGRESS: Precursor Summary:
2:44:09.477211 PROGRESS: Channel   0:	 0.050 FDR:    13; 0.010 FDR:    13; 0.001 FDR:    13
2:44:09.477305 PROGRESS: 
2:44:09.477370 PROGRESS: Protein Summary:
2:44:09.478586 PROGRESS: Channel   0:	 0.050 FDR:    13; 0.010 FDR:    13; 0.001 FDR:    13
2:44:09.478686 PROGRESS: =========================================================================
2:44:09.479023 INFO: Target number of precursors not reached yet.
2:44:09.570918 INFO: Starting optimization step 3.
2:44:09.571144 PROGRESS: === Extracting elution groups 7000 to 15000 ===
2:44:09.571231 INFO: Using rust extraction backend
2:44:09.571298 PROGRESS: Extracting batch of 15661 precursors
2:44:09.599953 INFO: === Search parameters used ===
2:44:09.600168 INFO: rt_error       : 716.9898681640625
2:44:09.600236 INFO: mobility_error : 0.1
2:44:09.600292 INFO: num_candidates : 1
2:44:09.600355 INFO: ms1_error      : 20
2:44:09.600402 INFO: ms2_error      : 20
2:44:09.600449 INFO: fwhm_rt        : 5
2:44:09.600495 INFO: quant_window   : 3
2:44:09.600538 INFO: ==============================================
2:44:09.767954 INFO: performing precursor FDR with 40 features
2:44:09.768062 INFO: Decoy channel: -1
2:44:09.768090 INFO: competitive: True
2:44:09.779382 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:09.786032 INFO: Estimating optimal hyperparameters - samples: 23,479, batch_size: 128, learning_rate: 1.77e-04
2:44:09.786201 INFO: Using random state 990617 for train-test-split
2:44:12.147832 INFO: Test AUC: 0.552
2:44:12.147934 INFO: Train AUC: 0.602
2:44:12.147965 INFO: AUC difference: 8.39%
2:44:12.147988 WARNING: AUC difference > 5%. This may indicate overfitting.
2:44:12.404178 INFO: Resetting torch num_threads to 32
2:44:12.412256 PROGRESS: === Extracted 29349 precursors and 161204 fragments ===
2:44:12.412813 INFO: === FDR correction performed with classifier version -1 ===
2:44:12.413434 PROGRESS: ============================= Precursor FDR =============================
2:44:12.413538 PROGRESS: Total precursors accumulated: 23
2:44:12.413614 PROGRESS: Target precursors: 23 (100.00%)
2:44:12.413671 PROGRESS: Decoy precursors: 0 (0.00%)
2:44:12.413725 PROGRESS: 
2:44:12.413774 PROGRESS: Precursor Summary:
2:44:12.415130 PROGRESS: Channel   0:	 0.050 FDR:    23; 0.010 FDR:    23; 0.001 FDR:    23
2:44:12.415243 PROGRESS: 
2:44:12.415319 PROGRESS: Protein Summary:
2:44:12.416728 PROGRESS: Channel   0:	 0.050 FDR:    23; 0.010 FDR:    23; 0.001 FDR:    23
2:44:12.416822 PROGRESS: =========================================================================
2:44:12.417434 INFO: Target number of precursors not reached yet.
2:44:12.533844 INFO: Starting optimization step 4.
2:44:12.534086 PROGRESS: === Extracting elution groups 15000 to 31000 ===
2:44:12.534169 INFO: Using rust extraction backend
2:44:12.534234 PROGRESS: Extracting batch of 31339 precursors
2:44:12.590870 INFO: === Search parameters used ===
2:44:12.591139 INFO: rt_error       : 716.9898681640625
2:44:12.591202 INFO: mobility_error : 0.1
2:44:12.591261 INFO: num_candidates : 1
2:44:12.591307 INFO: ms1_error      : 20
2:44:12.591350 INFO: ms2_error      : 20
2:44:12.591393 INFO: fwhm_rt        : 5
2:44:12.591434 INFO: quant_window   : 3
2:44:12.591475 INFO: ==============================================
2:44:12.888881 INFO: performing precursor FDR with 40 features
2:44:12.888992 INFO: Decoy channel: -1
2:44:12.889017 INFO: competitive: True
2:44:12.912242 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:12.926016 INFO: Estimating optimal hyperparameters - samples: 48,511, batch_size: 198, learning_rate: 2.20e-04
2:44:12.926242 INFO: Using random state 350785 for train-test-split
2:44:16.559553 INFO: Test AUC: 0.568
2:44:16.559668 INFO: Train AUC: 0.607
2:44:16.559700 INFO: AUC difference: 6.34%
2:44:16.559723 WARNING: AUC difference > 5%. This may indicate overfitting.
2:44:16.829499 INFO: Resetting torch num_threads to 32
2:44:16.842905 PROGRESS: === Extracted 60639 precursors and 333225 fragments ===
2:44:16.843485 INFO: === FDR correction performed with classifier version -1 ===
2:44:16.844089 PROGRESS: ============================= Precursor FDR =============================
2:44:16.844184 PROGRESS: Total precursors accumulated: 20
2:44:16.844260 PROGRESS: Target precursors: 20 (100.00%)
2:44:16.844320 PROGRESS: Decoy precursors: 0 (0.00%)
2:44:16.844375 PROGRESS: 
2:44:16.844430 PROGRESS: Precursor Summary:
2:44:16.845494 PROGRESS: Channel   0:	 0.050 FDR:    20; 0.010 FDR:    20; 0.001 FDR:    20
2:44:16.845585 PROGRESS: 
2:44:16.845645 PROGRESS: Protein Summary:
2:44:16.846829 PROGRESS: Channel   0:	 0.050 FDR:    20; 0.010 FDR:    20; 0.001 FDR:    20
2:44:16.846936 PROGRESS: =========================================================================
2:44:16.847898 INFO: Target number of precursors not reached yet.
2:44:17.005454 INFO: Starting optimization step 5.
2:44:17.005705 PROGRESS: === Extracting elution groups 31000 to 63000 ===
2:44:17.005791 INFO: Using rust extraction backend
2:44:17.005858 PROGRESS: Extracting batch of 62709 precursors
2:44:17.116637 INFO: === Search parameters used ===
2:44:17.116905 INFO: rt_error       : 716.9898681640625
2:44:17.116968 INFO: mobility_error : 0.1
2:44:17.117031 INFO: num_candidates : 1
2:44:17.117085 INFO: ms1_error      : 20
2:44:17.117136 INFO: ms2_error      : 20
2:44:17.117182 INFO: fwhm_rt        : 5
2:44:17.117228 INFO: quant_window   : 3
2:44:17.117272 INFO: ==============================================
2:44:17.678300 INFO: performing precursor FDR with 40 features
2:44:17.678441 INFO: Decoy channel: -1
2:44:17.678468 INFO: competitive: True
2:44:17.724680 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:17.757448 INFO: Estimating optimal hyperparameters - samples: 98,599, batch_size: 403, learning_rate: 3.14e-04
2:44:17.757818 INFO: Using random state 49354 for train-test-split
2:44:22.409644 INFO: Test AUC: 0.577
2:44:22.409755 INFO: Train AUC: 0.609
2:44:22.409786 INFO: AUC difference: 5.16%
2:44:22.409809 WARNING: AUC difference > 5%. This may indicate overfitting.
2:44:22.697484 INFO: Resetting torch num_threads to 32
2:44:22.718549 PROGRESS: === Extracted 123249 precursors and 677656 fragments ===
2:44:22.719162 INFO: === FDR correction performed with classifier version -1 ===
2:44:22.719729 PROGRESS: ============================= Precursor FDR =============================
2:44:22.719820 PROGRESS: Total precursors accumulated: 103
2:44:22.719884 PROGRESS: Target precursors: 102 (99.03%)
2:44:22.719954 PROGRESS: Decoy precursors: 1 (0.97%)
2:44:22.720003 PROGRESS: 
2:44:22.720055 PROGRESS: Precursor Summary:
2:44:22.721037 PROGRESS: Channel   0:	 0.050 FDR:   102; 0.010 FDR:   102; 0.001 FDR:    94
2:44:22.721131 PROGRESS: 
2:44:22.721189 PROGRESS: Protein Summary:
2:44:22.722296 PROGRESS: Channel   0:	 0.050 FDR:   100; 0.010 FDR:   100; 0.001 FDR:    92
2:44:22.722399 PROGRESS: =========================================================================
2:44:22.724459 INFO: Target number of precursors not reached yet.
2:44:22.957259 INFO: Starting optimization step 6.
2:44:22.957525 PROGRESS: === Extracting elution groups 63000 to 127000 ===
2:44:22.957612 INFO: Using rust extraction backend
2:44:22.957681 PROGRESS: Extracting batch of 125408 precursors
2:44:23.174957 INFO: === Search parameters used ===
2:44:23.175230 INFO: rt_error       : 716.9898681640625
2:44:23.175294 INFO: mobility_error : 0.1
2:44:23.175344 INFO: num_candidates : 1
2:44:23.175396 INFO: ms1_error      : 20
2:44:23.175442 INFO: ms2_error      : 20
2:44:23.175486 INFO: fwhm_rt        : 5
2:44:23.175530 INFO: quant_window   : 3
2:44:23.175575 INFO: ==============================================
2:44:24.205765 INFO: performing precursor FDR with 40 features
2:44:24.205883 INFO: Decoy channel: -1
2:44:24.205910 INFO: competitive: True
2:44:24.304116 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:24.384181 INFO: Estimating optimal hyperparameters - samples: 198,787, batch_size: 814, learning_rate: 4.46e-04
2:44:24.384612 INFO: Using random state 434268 for train-test-split
2:44:30.699977 INFO: Test AUC: 0.584
2:44:30.700135 INFO: Train AUC: 0.605
2:44:30.700170 INFO: AUC difference: 3.42%
2:44:31.023534 INFO: Resetting torch num_threads to 32
2:44:31.066200 PROGRESS: === Extracted 248484 precursors and 1365036 fragments ===
2:44:31.066880 INFO: === FDR correction performed with classifier version -1 ===
2:44:31.067457 PROGRESS: ============================= Precursor FDR =============================
2:44:31.067551 PROGRESS: Total precursors accumulated: 130
2:44:31.067618 PROGRESS: Target precursors: 129 (99.23%)
2:44:31.067677 PROGRESS: Decoy precursors: 1 (0.77%)
2:44:31.067732 PROGRESS: 
2:44:31.067786 PROGRESS: Precursor Summary:
2:44:31.068759 PROGRESS: Channel   0:	 0.050 FDR:   129; 0.010 FDR:   129; 0.001 FDR:     0
2:44:31.068852 PROGRESS: 
2:44:31.068915 PROGRESS: Protein Summary:
2:44:31.070024 PROGRESS: Channel   0:	 0.050 FDR:   124; 0.010 FDR:   124; 0.001 FDR:     0
2:44:31.070117 PROGRESS: =========================================================================
2:44:31.073884 INFO: Target number of precursors not reached yet.
2:44:31.463479 INFO: Starting optimization step 7.
2:44:31.463775 PROGRESS: === Extracting elution groups 127000 to 255000 ===
2:44:31.463870 INFO: Using rust extraction backend
2:44:31.463938 PROGRESS: Extracting batch of 250773 precursors
2:44:31.896381 INFO: === Search parameters used ===
2:44:31.896711 INFO: rt_error       : 716.9898681640625
2:44:31.896776 INFO: mobility_error : 0.1
2:44:31.896831 INFO: num_candidates : 1
2:44:31.896882 INFO: ms1_error      : 20
2:44:31.896940 INFO: ms2_error      : 20
2:44:31.896988 INFO: fwhm_rt        : 5
2:44:31.897034 INFO: quant_window   : 3
2:44:31.897080 INFO: ==============================================
2:44:33.905238 INFO: performing precursor FDR with 40 features
2:44:33.905360 INFO: Decoy channel: -1
2:44:33.905387 INFO: competitive: True
2:44:34.087842 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:34.259778 INFO: Estimating optimal hyperparameters - samples: 399,085, batch_size: 1,634, learning_rate: 6.32e-04
2:44:34.260456 INFO: Using random state 76697 for train-test-split
2:44:44.271348 INFO: Test AUC: 0.587
2:44:44.271496 INFO: Train AUC: 0.605
2:44:44.271534 INFO: AUC difference: 3.05%
2:44:44.675380 INFO: Resetting torch num_threads to 32
2:44:44.767691 PROGRESS: === Extracted 498857 precursors and 2742139 fragments ===
2:44:44.768348 INFO: === FDR correction performed with classifier version -1 ===
2:44:44.769030 PROGRESS: ============================= Precursor FDR =============================
2:44:44.769132 PROGRESS: Total precursors accumulated: 579
2:44:44.769210 PROGRESS: Target precursors: 574 (99.14%)
2:44:44.769274 PROGRESS: Decoy precursors: 5 (0.86%)
2:44:44.769330 PROGRESS: 
2:44:44.769387 PROGRESS: Precursor Summary:
2:44:44.770514 PROGRESS: Channel   0:	 0.050 FDR:   574; 0.010 FDR:   574; 0.001 FDR:   162
2:44:44.770620 PROGRESS: 
2:44:44.770693 PROGRESS: Protein Summary:
2:44:44.772000 PROGRESS: Channel   0:	 0.050 FDR:   500; 0.010 FDR:   500; 0.001 FDR:   144
2:44:44.772098 PROGRESS: =========================================================================
2:44:44.779121 INFO: Target number of precursors not reached yet.
2:44:45.442646 INFO: Starting optimization step 8.
2:44:45.442888 PROGRESS: === Extracting elution groups 255000 to 511000 ===
2:44:45.442990 INFO: Using rust extraction backend
2:44:45.443084 PROGRESS: Extracting batch of 501436 precursors
2:44:46.308514 INFO: === Search parameters used ===
2:44:46.308767 INFO: rt_error       : 716.9898681640625
2:44:46.308840 INFO: mobility_error : 0.1
2:44:46.308897 INFO: num_candidates : 1
2:44:46.308952 INFO: ms1_error      : 20
2:44:46.309008 INFO: ms2_error      : 20
2:44:46.309065 INFO: fwhm_rt        : 5
2:44:46.309130 INFO: quant_window   : 3
2:44:46.309179 INFO: ==============================================
2:44:50.318876 INFO: performing precursor FDR with 40 features
2:44:50.319004 INFO: Decoy channel: -1
2:44:50.319032 INFO: competitive: True
2:44:50.680561 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:51.063221 INFO: Estimating optimal hyperparameters - samples: 799,629, batch_size: 3,275, learning_rate: 8.94e-04
2:44:51.064678 INFO: Using random state 753585 for train-test-split
2:45:08.087869 INFO: Test AUC: 0.589
2:45:08.088004 INFO: Train AUC: 0.602
2:45:08.088040 INFO: AUC difference: 2.14%
2:45:08.656561 INFO: Resetting torch num_threads to 32
2:45:08.807592 PROGRESS: === Extracted 999537 precursors and 5498399 fragments ===
2:45:08.808238 INFO: === FDR correction performed with classifier version -1 ===
2:45:08.809082 PROGRESS: ============================= Precursor FDR =============================
2:45:08.809182 PROGRESS: Total precursors accumulated: 1,325
2:45:08.809252 PROGRESS: Target precursors: 1,312 (99.02%)
2:45:08.809314 PROGRESS: Decoy precursors: 13 (0.98%)
2:45:08.809371 PROGRESS: 
2:45:08.809424 PROGRESS: Precursor Summary:
2:45:08.810755 PROGRESS: Channel   0:	 0.050 FDR: 1,312; 0.010 FDR: 1,312; 0.001 FDR:   583
2:45:08.810863 PROGRESS: 
2:45:08.810933 PROGRESS: Protein Summary:
2:45:08.812622 PROGRESS: Channel   0:	 0.050 FDR: 1,030; 0.010 FDR: 1,030; 0.001 FDR:   479
2:45:08.812752 PROGRESS: =========================================================================
2:45:08.824598 INFO: Target number of precursors reached.
2:45:09.451075 INFO: fragments_df: keeping 5000 of 5498399 [sum(precursor_idx_mask)=14288 sum(mass_error_mask)=5498399 stop_rank=5000
2:45:10.463181 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:45:10.659415 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:45:11.383899 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:45:11.384359 INFO: Using score_cutoff 8.78656800441742 (fac=0.99, q=1)
2:45:11.384686 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:45:11.384769 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:45:11.384831 INFO: Updating optimization_manager: score_cutoff        : 0 -> 8.78656800441742
2:45:11.384891 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:45:11.990324 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:45:13.343438 INFO: Updating optimization_manager: classifier_version  : -1 -> 8
2:45:13.343719 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:45:13.343837 INFO: Starting optimization step 9.
2:45:13.343916 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:45:13.344001 INFO: Using rust extraction backend
2:45:13.344075 PROGRESS: Extracting batch of 1001059 precursors
2:45:15.036245 INFO: === Search parameters used ===
2:45:15.036539 INFO: rt_error       : 716.9898681640625
2:45:15.036609 INFO: mobility_error : 0.1
2:45:15.036665 INFO: num_candidates : 3
2:45:15.036715 INFO: ms1_error      : 20
2:45:15.036761 INFO: ms2_error      : 20
2:45:15.036804 INFO: fwhm_rt        : 3.0
2:45:15.036847 INFO: quant_window   : 3
2:45:15.036892 INFO: ==============================================
2:45:28.411689 INFO: performing precursor FDR with 40 features
2:45:28.411810 INFO: Decoy channel: -1
2:45:28.411839 INFO: competitive: True
2:45:29.131932 INFO: Setting torch num_threads to 2 for FDR classification task
2:45:30.437496 INFO: Estimating optimal hyperparameters - samples: 2,398,925, batch_size: 4,096, learning_rate: 1.00e-03
2:45:30.443055 INFO: Using random state 104357 for train-test-split
2:46:16.722541 INFO: Test AUC: 0.600
2:46:16.722723 INFO: Train AUC: 0.604
2:46:16.722761 INFO: AUC difference: 0.68%
2:46:17.983984 INFO: Resetting torch num_threads to 32
2:46:18.082883 PROGRESS: === Extracted 2998657 precursors and 16325243 fragments ===
2:46:18.083385 INFO: === FDR correction performed with classifier version 8 ===
2:46:18.084077 PROGRESS: ============================= Precursor FDR =============================
2:46:18.084176 PROGRESS: Total precursors accumulated: 1,322
2:46:18.084256 PROGRESS: Target precursors: 1,309 (99.02%)
2:46:18.084330 PROGRESS: Decoy precursors: 13 (0.98%)
2:46:18.084383 PROGRESS: 
2:46:18.084440 PROGRESS: Precursor Summary:
2:46:18.085754 PROGRESS: Channel   0:	 0.050 FDR: 1,309; 0.010 FDR: 1,309; 0.001 FDR:   966
2:46:18.085854 PROGRESS: 
2:46:18.085918 PROGRESS: Protein Summary:
2:46:18.087625 PROGRESS: Channel   0:	 0.050 FDR: 1,062; 0.010 FDR: 1,062; 0.001 FDR:   785
2:46:18.087729 PROGRESS: =========================================================================
2:46:18.150612 INFO: Target number of precursors reached.
2:46:19.849651 INFO: fragments_df: keeping 5000 of 16325243 [sum(precursor_idx_mask)=31959 sum(mass_error_mask)=16325243 stop_rank=5000
2:46:20.932727 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:46:21.158509 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:46:21.885041 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:46:21.885474 INFO: Using score_cutoff 6.818947762870788 (fac=0.99, q=1)
2:46:21.885800 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:46:21.885887 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:46:21.885952 INFO: Updating optimization_manager: score_cutoff        : 8.78656800441742 -> 6.818947762870788
2:46:21.886017 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:22.498029 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:23.874555 INFO: === checking if optimization conditions were reached ===
2:46:23.876771 INFO: Updating optimization_manager: ms2_error           : 20 -> 10.0
2:46:23.876921 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
2:46:23.876999 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:46:23.877074 INFO: ==============================================
2:46:23.877158 INFO: Starting optimization step 10.
2:46:23.877239 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:46:23.877312 INFO: Using rust extraction backend
2:46:23.877384 PROGRESS: Extracting batch of 1001059 precursors
2:46:25.588573 INFO: === Search parameters used ===
2:46:25.589008 INFO: rt_error       : 716.9898681640625
2:46:25.589082 INFO: mobility_error : 0.1
2:46:25.589145 INFO: num_candidates : 3
2:46:25.589206 INFO: ms1_error      : 20
2:46:25.589256 INFO: ms2_error      : 10.0
2:46:25.589313 INFO: fwhm_rt        : 3.0
2:46:25.589360 INFO: quant_window   : 3
2:46:25.589406 INFO: ==============================================
2:46:39.045869 INFO: performing precursor FDR with 40 features
2:46:39.046041 INFO: Decoy channel: -1
2:46:39.046070 INFO: competitive: True
2:46:39.741298 INFO: Setting torch num_threads to 2 for FDR classification task
2:46:41.003777 INFO: Estimating optimal hyperparameters - samples: 2,401,622, batch_size: 4,096, learning_rate: 1.00e-03
2:46:41.008643 INFO: Using random state 669207 for train-test-split
2:47:27.437464 INFO: Test AUC: 0.608
2:47:27.437654 INFO: Train AUC: 0.612
2:47:27.437693 INFO: AUC difference: 0.54%
2:47:28.679036 INFO: Resetting torch num_threads to 32
2:47:28.773400 PROGRESS: === Extracted 3002028 precursors and 17858678 fragments ===
2:47:28.773937 INFO: === FDR correction performed with classifier version 9 ===
2:47:28.774765 PROGRESS: ============================= Precursor FDR =============================
2:47:28.774884 PROGRESS: Total precursors accumulated: 1,741
2:47:28.774956 PROGRESS: Target precursors: 1,724 (99.02%)
2:47:28.775017 PROGRESS: Decoy precursors: 17 (0.98%)
2:47:28.775075 PROGRESS: 
2:47:28.775129 PROGRESS: Precursor Summary:
2:47:28.776567 PROGRESS: Channel   0:	 0.050 FDR: 1,724; 0.010 FDR: 1,724; 0.001 FDR:   642
2:47:28.776668 PROGRESS: 
2:47:28.776732 PROGRESS: Protein Summary:
2:47:28.778516 PROGRESS: Channel   0:	 0.050 FDR: 1,324; 0.010 FDR: 1,324; 0.001 FDR:   537
2:47:28.778629 PROGRESS: =========================================================================
2:47:28.831177 INFO: Target number of precursors reached.
2:47:30.648126 INFO: fragments_df: keeping 5000 of 17858678 [sum(precursor_idx_mask)=44937 sum(mass_error_mask)=17858678 stop_rank=5000
2:47:31.870851 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:47:32.161050 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:47:32.881821 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:47:32.882289 INFO: Using score_cutoff 9.056410066509248 (fac=0.99, q=1)
2:47:32.882630 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:47:32.882717 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:47:32.882784 INFO: Updating optimization_manager: score_cutoff        : 6.818947762870788 -> 9.056410066509248
2:47:32.882847 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:47:33.493878 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:47:34.869872 INFO: === checking if optimization conditions were reached ===
2:47:34.872351 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:47:34.872474 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
2:47:34.872555 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:47:34.872632 INFO: ==============================================
2:47:34.872716 INFO: Starting optimization step 11.
2:47:34.872797 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:47:34.872893 INFO: Using rust extraction backend
2:47:34.872975 PROGRESS: Extracting batch of 1001059 precursors
2:47:36.571013 INFO: === Search parameters used ===
2:47:36.571299 INFO: rt_error       : 716.9898681640625
2:47:36.571369 INFO: mobility_error : 0.1
2:47:36.571434 INFO: num_candidates : 3
2:47:36.571487 INFO: ms1_error      : 20
2:47:36.571537 INFO: ms2_error      : 10.0
2:47:36.571587 INFO: fwhm_rt        : 3.0
2:47:36.571643 INFO: quant_window   : 3
2:47:36.571691 INFO: ==============================================
2:47:49.722193 INFO: performing precursor FDR with 40 features
2:47:49.722386 INFO: Decoy channel: -1
2:47:49.722419 INFO: competitive: True
2:47:50.434998 INFO: Setting torch num_threads to 2 for FDR classification task
2:47:51.763670 INFO: Estimating optimal hyperparameters - samples: 2,401,600, batch_size: 4,096, learning_rate: 1.00e-03
2:47:51.769497 INFO: Using random state 130174 for train-test-split
2:48:38.047872 INFO: Test AUC: 0.609
2:48:38.048036 INFO: Train AUC: 0.613
2:48:38.048071 INFO: AUC difference: 0.71%
2:48:39.315933 INFO: Resetting torch num_threads to 32
2:48:39.420913 PROGRESS: === Extracted 3002001 precursors and 17830908 fragments ===
2:48:39.421436 INFO: === FDR correction performed with classifier version 10 ===
2:48:39.422309 PROGRESS: ============================= Precursor FDR =============================
2:48:39.422415 PROGRESS: Total precursors accumulated: 1,949
2:48:39.422493 PROGRESS: Target precursors: 1,930 (99.03%)
2:48:39.422554 PROGRESS: Decoy precursors: 19 (0.97%)
2:48:39.422613 PROGRESS: 
2:48:39.422672 PROGRESS: Precursor Summary:
2:48:39.424198 PROGRESS: Channel   0:	 0.050 FDR: 1,930; 0.010 FDR: 1,930; 0.001 FDR: 1,081
2:48:39.424298 PROGRESS: 
2:48:39.424371 PROGRESS: Protein Summary:
2:48:39.426305 PROGRESS: Channel   0:	 0.050 FDR: 1,475; 0.010 FDR: 1,475; 0.001 FDR:   883
2:48:39.426419 PROGRESS: =========================================================================
2:48:39.496265 INFO: Target number of precursors reached.
2:48:41.303573 INFO: fragments_df: keeping 5000 of 17830908 [sum(precursor_idx_mask)=49302 sum(mass_error_mask)=17830908 stop_rank=5000
2:48:42.465836 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:48:42.714739 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:48:43.369705 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:48:43.370146 INFO: Using score_cutoff 5.5334147874355315 (fac=0.99, q=1)
2:48:43.370490 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:48:43.370584 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:48:43.370647 INFO: Updating optimization_manager: score_cutoff        : 9.056410066509248 -> 5.5334147874355315
2:48:43.370721 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:48:43.987503 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:48:45.402070 INFO: === checking if optimization conditions were reached ===
2:48:45.404483 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:48:45.404649 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
2:48:45.404733 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:48:45.404808 INFO: ==============================================
2:48:45.404890 INFO: Starting optimization step 12.
2:48:45.404971 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:48:45.405050 INFO: Using rust extraction backend
2:48:45.405124 PROGRESS: Extracting batch of 1001059 precursors
2:48:47.113991 INFO: === Search parameters used ===
2:48:47.114288 INFO: rt_error       : 716.9898681640625
2:48:47.114366 INFO: mobility_error : 0.1
2:48:47.114536 INFO: num_candidates : 3
2:48:47.114591 INFO: ms1_error      : 20
2:48:47.114643 INFO: ms2_error      : 10.0
2:48:47.114692 INFO: fwhm_rt        : 3.0
2:48:47.114752 INFO: quant_window   : 3
2:48:47.114800 INFO: ==============================================
2:49:00.351921 INFO: performing precursor FDR with 40 features
2:49:00.352045 INFO: Decoy channel: -1
2:49:00.352076 INFO: competitive: True
2:49:01.069000 INFO: Setting torch num_threads to 2 for FDR classification task
2:49:02.357412 INFO: Estimating optimal hyperparameters - samples: 2,401,624, batch_size: 4,096, learning_rate: 1.00e-03
2:49:02.362344 INFO: Using random state 621241 for train-test-split
2:49:48.551435 INFO: Test AUC: 0.610
2:49:48.551575 INFO: Train AUC: 0.614
2:49:48.551612 INFO: AUC difference: 0.76%
2:49:49.788531 INFO: Resetting torch num_threads to 32
2:49:49.884685 PROGRESS: === Extracted 3002031 precursors and 17873937 fragments ===
2:49:49.885194 INFO: === FDR correction performed with classifier version 11 ===
2:49:49.885961 PROGRESS: ============================= Precursor FDR =============================
2:49:49.886061 PROGRESS: Total precursors accumulated: 1,837
2:49:49.886133 PROGRESS: Target precursors: 1,819 (99.02%)
2:49:49.886201 PROGRESS: Decoy precursors: 18 (0.98%)
2:49:49.886259 PROGRESS: 
2:49:49.886319 PROGRESS: Precursor Summary:
2:49:49.887748 PROGRESS: Channel   0:	 0.050 FDR: 1,819; 0.010 FDR: 1,819; 0.001 FDR: 1,004
2:49:49.887858 PROGRESS: 
2:49:49.887929 PROGRESS: Protein Summary:
2:49:49.889812 PROGRESS: Channel   0:	 0.050 FDR: 1,394; 0.010 FDR: 1,394; 0.001 FDR:   828
2:49:49.889910 PROGRESS: =========================================================================
2:49:49.941044 INFO: Target number of precursors reached.
2:49:51.817213 INFO: fragments_df: keeping 5000 of 17873937 [sum(precursor_idx_mask)=47147 sum(mass_error_mask)=17873937 stop_rank=5000
2:49:52.877976 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:49:53.156485 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:49:53.878902 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:49:53.879357 INFO: Using score_cutoff 8.408036324501039 (fac=0.99, q=1)
2:49:53.879674 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:49:53.879762 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:49:53.879825 INFO: Updating optimization_manager: score_cutoff        : 5.5334147874355315 -> 8.408036324501039
2:49:53.879894 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:49:54.484149 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:49:55.866762 INFO: === checking if optimization conditions were reached ===
2:49:55.868972 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:49:55.869133 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
2:49:55.869217 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:49:55.869291 INFO: ==============================================
2:49:55.869394 INFO: Starting optimization step 13.
2:49:55.869464 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:49:55.869539 INFO: Using rust extraction backend
2:49:55.869617 PROGRESS: Extracting batch of 1001059 precursors
2:49:57.560943 INFO: === Search parameters used ===
2:49:57.561244 INFO: rt_error       : 716.9898681640625
2:49:57.561310 INFO: mobility_error : 0.1
2:49:57.561374 INFO: num_candidates : 3
2:49:57.561424 INFO: ms1_error      : 20
2:49:57.561470 INFO: ms2_error      : 10.0
2:49:57.561515 INFO: fwhm_rt        : 3.0
2:49:57.561560 INFO: quant_window   : 3
2:49:57.561607 INFO: ==============================================
2:50:10.571799 INFO: performing precursor FDR with 40 features
2:50:10.571926 INFO: Decoy channel: -1
2:50:10.571955 INFO: competitive: True
2:50:11.261331 INFO: Setting torch num_threads to 2 for FDR classification task
2:50:12.489056 INFO: Estimating optimal hyperparameters - samples: 2,401,608, batch_size: 4,096, learning_rate: 1.00e-03
2:50:12.494226 INFO: Using random state 824606 for train-test-split
2:50:57.915494 INFO: Test AUC: 0.612
2:50:57.915631 INFO: Train AUC: 0.616
2:50:57.915666 INFO: AUC difference: 0.56%
2:50:59.143708 INFO: Resetting torch num_threads to 32
2:50:59.237516 PROGRESS: === Extracted 3002010 precursors and 17844082 fragments ===
2:50:59.238014 INFO: === FDR correction performed with classifier version 12 ===
2:50:59.238809 PROGRESS: ============================= Precursor FDR =============================
2:50:59.238911 PROGRESS: Total precursors accumulated: 1,895
2:50:59.238985 PROGRESS: Target precursors: 1,877 (99.05%)
2:50:59.239050 PROGRESS: Decoy precursors: 18 (0.95%)
2:50:59.239111 PROGRESS: 
2:50:59.239164 PROGRESS: Precursor Summary:
2:50:59.240539 PROGRESS: Channel   0:	 0.050 FDR: 1,877; 0.010 FDR: 1,877; 0.001 FDR:   500
2:50:59.240640 PROGRESS: 
2:50:59.240702 PROGRESS: Protein Summary:
2:50:59.242496 PROGRESS: Channel   0:	 0.050 FDR: 1,468; 0.010 FDR: 1,468; 0.001 FDR:   426
2:50:59.242603 PROGRESS: =========================================================================
2:50:59.294475 INFO: Target number of precursors reached.
2:51:01.095262 INFO: fragments_df: keeping 5000 of 17844082 [sum(precursor_idx_mask)=47028 sum(mass_error_mask)=17844082 stop_rank=5000
2:51:02.127895 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:51:02.413252 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:51:03.133019 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:51:03.133467 INFO: Using score_cutoff 5.0282160198211665 (fac=0.99, q=1)
2:51:03.133774 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:51:03.133866 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:51:03.133931 INFO: Updating optimization_manager: score_cutoff        : 8.408036324501039 -> 5.0282160198211665
2:51:03.133997 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:51:03.730755 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:51:05.070944 INFO: === checking if optimization conditions were reached ===
2:51:05.073112 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:51:05.073265 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
2:51:05.073355 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:51:05.073436 INFO: ==============================================
2:51:05.073509 PROGRESS: Optimization finished for ms2_error.
2:51:06.060689 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:51:06.660165 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:51:08.007152 INFO: Starting optimization step 0.
2:51:08.007425 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:51:08.007513 INFO: Using rust extraction backend
2:51:08.007582 PROGRESS: Extracting batch of 1001059 precursors
2:51:09.706882 INFO: === Search parameters used ===
2:51:09.707173 INFO: rt_error       : 716.9898681640625
2:51:09.707242 INFO: mobility_error : 0.1
2:51:09.707303 INFO: num_candidates : 3
2:51:09.707373 INFO: ms1_error      : 20
2:51:09.707423 INFO: ms2_error      : 10.0
2:51:09.707470 INFO: fwhm_rt        : 3.0
2:51:09.707522 INFO: quant_window   : 3
2:51:09.707574 INFO: ==============================================
2:51:22.734108 INFO: performing precursor FDR with 40 features
2:51:22.734233 INFO: Decoy channel: -1
2:51:22.734261 INFO: competitive: True
2:51:23.436239 INFO: Setting torch num_threads to 2 for FDR classification task
2:51:24.739985 INFO: Estimating optimal hyperparameters - samples: 2,401,692, batch_size: 4,096, learning_rate: 1.00e-03
2:51:24.744936 INFO: Using random state 883232 for train-test-split
2:52:10.708114 INFO: Test AUC: 0.612
2:52:10.708305 INFO: Train AUC: 0.617
2:52:10.708341 INFO: AUC difference: 0.67%
2:52:11.951610 INFO: Resetting torch num_threads to 32
2:52:12.048762 PROGRESS: === Extracted 3002115 precursors and 17937634 fragments ===
2:52:12.049278 INFO: === FDR correction performed with classifier version 13 ===
2:52:12.050186 PROGRESS: ============================= Precursor FDR =============================
2:52:12.050311 PROGRESS: Total precursors accumulated: 2,003
2:52:12.050402 PROGRESS: Target precursors: 1,984 (99.05%)
2:52:12.050468 PROGRESS: Decoy precursors: 19 (0.95%)
2:52:12.050528 PROGRESS: 
2:52:12.050587 PROGRESS: Precursor Summary:
2:52:12.052263 PROGRESS: Channel   0:	 0.050 FDR: 1,984; 0.010 FDR: 1,984; 0.001 FDR: 1,115
2:52:12.052378 PROGRESS: 
2:52:12.052445 PROGRESS: Protein Summary:
2:52:12.054486 PROGRESS: Channel   0:	 0.050 FDR: 1,514; 0.010 FDR: 1,514; 0.001 FDR:   911
2:52:12.054596 PROGRESS: =========================================================================
2:52:12.106926 INFO: Target number of precursors reached.
2:52:13.897203 INFO: fragments_df: keeping 5000 of 17937634 [sum(precursor_idx_mask)=50642 sum(mass_error_mask)=17937634 stop_rank=5000
2:52:14.958758 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:52:15.251153 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:52:15.971212 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:52:15.971646 INFO: Using score_cutoff 5.249634804725647 (fac=0.99, q=1)
2:52:15.971985 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:52:15.972071 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:52:15.972136 INFO: Updating optimization_manager: score_cutoff        : 5.0282160198211665 -> 5.249634804725647
2:52:15.972200 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:52:16.565179 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:52:17.865259 INFO: === checking if optimization conditions were reached ===
2:52:17.865520 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:52:17.868442 INFO: Updating optimization_manager: rt_error            : 716.9898681640625 -> 909.0798706149499
2:52:17.868575 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 909.0799.
2:52:17.868649 INFO: ==============================================
2:52:17.868725 INFO: Starting optimization step 1.
2:52:17.868790 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:52:17.868857 INFO: Using rust extraction backend
2:52:17.868923 PROGRESS: Extracting batch of 1001059 precursors
2:52:19.560207 INFO: === Search parameters used ===
2:52:19.560552 INFO: rt_error       : 909.0798706149499
2:52:19.560630 INFO: mobility_error : 0.1
2:52:19.560695 INFO: num_candidates : 3
2:52:19.560749 INFO: ms1_error      : 20
2:52:19.560802 INFO: ms2_error      : 10.0
2:52:19.560853 INFO: fwhm_rt        : 3.0
2:52:19.560911 INFO: quant_window   : 3
2:52:19.560971 INFO: ==============================================
2:52:33.135936 INFO: performing precursor FDR with 40 features
2:52:33.136057 INFO: Decoy channel: -1
2:52:33.136085 INFO: competitive: True
2:52:33.817073 INFO: Setting torch num_threads to 2 for FDR classification task
2:52:35.071677 INFO: Estimating optimal hyperparameters - samples: 2,401,736, batch_size: 4,096, learning_rate: 1.00e-03
2:52:35.077098 INFO: Using random state 883232 for train-test-split
2:53:21.764227 INFO: Test AUC: 0.612
2:53:21.764390 INFO: Train AUC: 0.617
2:53:21.764425 INFO: AUC difference: 0.85%
2:53:23.015857 INFO: Resetting torch num_threads to 32
2:53:23.122324 PROGRESS: === Extracted 3002171 precursors and 18073133 fragments ===
2:53:23.122853 INFO: === FDR correction performed with classifier version 13 ===
2:53:23.123695 PROGRESS: ============================= Precursor FDR =============================
2:53:23.123795 PROGRESS: Total precursors accumulated: 2,062
2:53:23.123863 PROGRESS: Target precursors: 2,042 (99.03%)
2:53:23.123924 PROGRESS: Decoy precursors: 20 (0.97%)
2:53:23.123978 PROGRESS: 
2:53:23.124031 PROGRESS: Precursor Summary:
2:53:23.125533 PROGRESS: Channel   0:	 0.050 FDR: 2,042; 0.010 FDR: 2,042; 0.001 FDR: 1,046
2:53:23.125634 PROGRESS: 
2:53:23.125699 PROGRESS: Protein Summary:
2:53:23.127670 PROGRESS: Channel   0:	 0.050 FDR: 1,555; 0.010 FDR: 1,555; 0.001 FDR:   854
2:53:23.127774 PROGRESS: =========================================================================
2:53:23.180352 INFO: Target number of precursors reached.
2:53:25.027366 INFO: fragments_df: keeping 5000 of 18073133 [sum(precursor_idx_mask)=52146 sum(mass_error_mask)=18073133 stop_rank=5000
2:53:25.807759 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:53:26.113468 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:53:26.832213 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:53:26.832680 INFO: Using score_cutoff 6.719476298332214 (fac=0.99, q=1)
2:53:26.833029 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:53:26.833117 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:53:26.833174 INFO: Updating optimization_manager: score_cutoff        : 5.249634804725647 -> 6.719476298332214
2:53:26.833247 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:53:27.136416 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:53:27.834255 INFO: === checking if optimization conditions were reached ===
2:53:27.834537 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:53:27.837701 INFO: Updating optimization_manager: rt_error            : 909.0798706149499 -> 1194.8493869657102
2:53:27.837838 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 1194.8494.
2:53:27.837913 INFO: ==============================================
2:53:27.837995 INFO: Starting optimization step 2.
2:53:27.838065 PROGRESS: === Extracting elution groups 0 to 255000 ===
2:53:27.838140 INFO: Using rust extraction backend
2:53:27.838210 PROGRESS: Extracting batch of 499623 precursors
2:53:28.692116 INFO: === Search parameters used ===
2:53:28.692395 INFO: rt_error       : 1194.8493869657102
2:53:28.692466 INFO: mobility_error : 0.1
2:53:28.692534 INFO: num_candidates : 3
2:53:28.692596 INFO: ms1_error      : 20
2:53:28.692655 INFO: ms2_error      : 10.0
2:53:28.692706 INFO: fwhm_rt        : 3.0
2:53:28.692756 INFO: quant_window   : 3
2:53:28.692813 INFO: ==============================================
2:53:35.660627 INFO: performing precursor FDR with 40 features
2:53:35.660749 INFO: Decoy channel: -1
2:53:35.660780 INFO: competitive: True
2:53:35.968754 INFO: Setting torch num_threads to 2 for FDR classification task
2:53:36.547877 INFO: Estimating optimal hyperparameters - samples: 1,198,699, batch_size: 4,096, learning_rate: 1.00e-03
2:53:36.550102 INFO: Using random state 883232 for train-test-split
2:53:59.193563 INFO: Test AUC: 0.612
2:53:59.193776 INFO: Train AUC: 0.619
2:53:59.193814 INFO: AUC difference: 1.18%
2:53:59.953933 INFO: Resetting torch num_threads to 32
2:53:59.999362 PROGRESS: === Extracted 1498374 precursors and 9014913 fragments ===
2:53:59.999876 INFO: === FDR correction performed with classifier version 13 ===
2:54:00.000454 PROGRESS: ============================= Precursor FDR =============================
2:54:00.000563 PROGRESS: Total precursors accumulated: 829
2:54:00.000638 PROGRESS: Target precursors: 821 (99.03%)
2:54:00.000709 PROGRESS: Decoy precursors: 8 (0.97%)
2:54:00.000767 PROGRESS: 
2:54:00.000822 PROGRESS: Precursor Summary:
2:54:00.001924 PROGRESS: Channel   0:	 0.050 FDR:   821; 0.010 FDR:   821; 0.001 FDR:     0
2:54:00.002026 PROGRESS: 
2:54:00.002089 PROGRESS: Protein Summary:
2:54:00.003452 PROGRESS: Channel   0:	 0.050 FDR:   700; 0.010 FDR:   700; 0.001 FDR:     0
2:54:00.003553 PROGRESS: =========================================================================
2:54:00.032817 INFO: Target number of precursors not reached yet.
2:54:00.755467 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:54:01.053106 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:54:01.752031 INFO: === skipping optimization until target number of precursors are found ===
2:54:01.752310 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
2:54:01.752433 INFO: Starting optimization step 3.
2:54:01.752513 PROGRESS: === Extracting elution groups 255000 to 511000 ===
2:54:01.752590 INFO: Using rust extraction backend
2:54:01.752678 PROGRESS: Extracting batch of 501436 precursors
2:54:02.615378 INFO: === Search parameters used ===
2:54:02.615655 INFO: rt_error       : 1194.8493869657102
2:54:02.615726 INFO: mobility_error : 0.1
2:54:02.615784 INFO: num_candidates : 3
2:54:02.615836 INFO: ms1_error      : 20
2:54:02.615891 INFO: ms2_error      : 10.0
2:54:02.615952 INFO: fwhm_rt        : 3.0
2:54:02.616003 INFO: quant_window   : 3
2:54:02.616056 INFO: ==============================================
2:54:09.827982 INFO: performing precursor FDR with 40 features
2:54:09.828121 INFO: Decoy channel: -1
2:54:09.828150 INFO: competitive: True
2:54:10.994570 INFO: Setting torch num_threads to 2 for FDR classification task
2:54:12.292511 INFO: Estimating optimal hyperparameters - samples: 2,401,727, batch_size: 4,096, learning_rate: 1.00e-03
2:54:12.299093 INFO: Using random state 883232 for train-test-split
2:54:58.635154 INFO: Test AUC: 0.611
2:54:58.635320 INFO: Train AUC: 0.617
2:54:58.635356 INFO: AUC difference: 0.96%
2:54:59.883879 INFO: Resetting torch num_threads to 32
2:55:00.514603 PROGRESS: === Extracted 3002159 precursors and 18071295 fragments ===
2:55:00.515301 INFO: === FDR correction performed with classifier version 13 ===
2:55:00.516846 PROGRESS: ============================= Precursor FDR =============================
2:55:00.516944 PROGRESS: Total precursors accumulated: 1,923
2:55:00.517013 PROGRESS: Target precursors: 1,904 (99.01%)
2:55:00.517070 PROGRESS: Decoy precursors: 19 (0.99%)
2:55:00.517124 PROGRESS: 
2:55:00.517179 PROGRESS: Precursor Summary:
2:55:00.518699 PROGRESS: Channel   0:	 0.050 FDR: 1,904; 0.010 FDR: 1,904; 0.001 FDR: 1,060
2:55:00.518804 PROGRESS: 
2:55:00.518872 PROGRESS: Protein Summary:
2:55:00.520789 PROGRESS: Channel   0:	 0.050 FDR: 1,452; 0.010 FDR: 1,452; 0.001 FDR:   874
2:55:00.520897 PROGRESS: =========================================================================
2:55:00.593691 INFO: Target number of precursors reached.
2:55:03.284098 INFO: fragments_df: keeping 5000 of 18071295 [sum(precursor_idx_mask)=48812 sum(mass_error_mask)=18071295 stop_rank=5000
2:55:04.368198 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:55:04.650813 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:55:05.369183 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:55:05.369667 INFO: Using score_cutoff 5.734655270576477 (fac=0.99, q=1)
2:55:05.370008 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:55:05.370094 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:55:05.370155 INFO: Updating optimization_manager: score_cutoff        : 6.719476298332214 -> 5.734655270576477
2:55:05.370213 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:55:05.970065 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:55:07.349602 INFO: === checking if optimization conditions were reached ===
2:55:07.349869 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:55:07.352993 INFO: Updating optimization_manager: rt_error            : 1194.8493869657102 -> 1262.856303443667
2:55:07.353131 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 1262.8563.
2:55:07.353208 INFO: ==============================================
2:55:07.353282 INFO: Starting optimization step 4.
2:55:07.353362 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:55:07.353442 INFO: Using rust extraction backend
2:55:07.353508 PROGRESS: Extracting batch of 1001059 precursors
2:55:09.060468 INFO: === Search parameters used ===
2:55:09.060783 INFO: rt_error       : 1262.856303443667
2:55:09.060854 INFO: mobility_error : 0.1
2:55:09.060909 INFO: num_candidates : 3
2:55:09.060956 INFO: ms1_error      : 20
2:55:09.061003 INFO: ms2_error      : 10.0
2:55:09.061052 INFO: fwhm_rt        : 3.0
2:55:09.061099 INFO: quant_window   : 3
2:55:09.061143 INFO: ==============================================
2:55:23.087402 INFO: performing precursor FDR with 40 features
2:55:23.087564 INFO: Decoy channel: -1
2:55:23.087594 INFO: competitive: True
2:55:23.785470 INFO: Setting torch num_threads to 2 for FDR classification task
2:55:25.090231 INFO: Estimating optimal hyperparameters - samples: 2,401,729, batch_size: 4,096, learning_rate: 1.00e-03
2:55:25.095458 INFO: Using random state 883232 for train-test-split
2:56:09.474966 INFO: Test AUC: 0.612
2:56:09.475157 INFO: Train AUC: 0.617
2:56:09.475192 INFO: AUC difference: 0.66%
2:56:10.727269 INFO: Resetting torch num_threads to 32
2:56:10.947580 PROGRESS: === Extracted 3002162 precursors and 18070601 fragments ===
2:56:10.948096 INFO: === FDR correction performed with classifier version 13 ===
2:56:10.948903 PROGRESS: ============================= Precursor FDR =============================
2:56:10.949003 PROGRESS: Total precursors accumulated: 2,003
2:56:10.949073 PROGRESS: Target precursors: 1,984 (99.05%)
2:56:10.949133 PROGRESS: Decoy precursors: 19 (0.95%)
2:56:10.949188 PROGRESS: 
2:56:10.949241 PROGRESS: Precursor Summary:
2:56:10.950784 PROGRESS: Channel   0:	 0.050 FDR: 1,984; 0.010 FDR: 1,984; 0.001 FDR: 1,090
2:56:10.950888 PROGRESS: 
2:56:10.950964 PROGRESS: Protein Summary:
2:56:10.952906 PROGRESS: Channel   0:	 0.050 FDR: 1,518; 0.010 FDR: 1,518; 0.001 FDR:   881
2:56:10.953006 PROGRESS: =========================================================================
2:56:11.005549 INFO: Target number of precursors reached.
2:56:12.844266 INFO: fragments_df: keeping 5000 of 18070601 [sum(precursor_idx_mask)=50189 sum(mass_error_mask)=18070601 stop_rank=5000
2:56:14.022501 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:56:14.315951 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:56:15.034768 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:56:15.035225 INFO: Using score_cutoff 5.22187965259552 (fac=0.99, q=1)
2:56:15.035571 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:56:15.035654 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:56:15.035717 INFO: Updating optimization_manager: score_cutoff        : 5.734655270576477 -> 5.22187965259552
2:56:15.035777 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:56:15.630103 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:56:16.926511 INFO: === checking if optimization conditions were reached ===
2:56:16.926756 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:56:16.929936 INFO: Updating optimization_manager: rt_error            : 1262.856303443667 -> 1157.5776159746192
2:56:16.930066 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 1157.5776.
2:56:16.930152 INFO: ==============================================
2:56:16.930246 INFO: Starting optimization step 5.
2:56:16.930326 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:56:16.930426 INFO: Using rust extraction backend
2:56:16.930514 PROGRESS: Extracting batch of 1001059 precursors
2:56:18.631854 INFO: === Search parameters used ===
2:56:18.632352 INFO: rt_error       : 1157.5776159746192
2:56:18.632420 INFO: mobility_error : 0.1
2:56:18.632477 INFO: num_candidates : 3
2:56:18.632529 INFO: ms1_error      : 20
2:56:18.632579 INFO: ms2_error      : 10.0
2:56:18.632637 INFO: fwhm_rt        : 3.0
2:56:18.632684 INFO: quant_window   : 3
2:56:18.632731 INFO: ==============================================
2:56:32.416944 INFO: performing precursor FDR with 40 features
2:56:32.417073 INFO: Decoy channel: -1
2:56:32.417106 INFO: competitive: True
2:56:33.118103 INFO: Setting torch num_threads to 2 for FDR classification task
2:56:34.414641 INFO: Estimating optimal hyperparameters - samples: 2,401,730, batch_size: 4,096, learning_rate: 1.00e-03
2:56:34.420072 INFO: Using random state 883232 for train-test-split
2:57:20.762644 INFO: Test AUC: 0.612
2:57:20.762891 INFO: Train AUC: 0.617
2:57:20.762930 INFO: AUC difference: 0.79%
2:57:21.965717 INFO: Resetting torch num_threads to 32
2:57:22.064035 PROGRESS: === Extracted 3002163 precursors and 18070226 fragments ===
2:57:22.064591 INFO: === FDR correction performed with classifier version 13 ===
2:57:22.065458 PROGRESS: ============================= Precursor FDR =============================
2:57:22.065564 PROGRESS: Total precursors accumulated: 1,872
2:57:22.065633 PROGRESS: Target precursors: 1,854 (99.04%)
2:57:22.065699 PROGRESS: Decoy precursors: 18 (0.96%)
2:57:22.065757 PROGRESS: 
2:57:22.065809 PROGRESS: Precursor Summary:
2:57:22.067379 PROGRESS: Channel   0:	 0.050 FDR: 1,854; 0.010 FDR: 1,854; 0.001 FDR: 1,054
2:57:22.067482 PROGRESS: 
2:57:22.067545 PROGRESS: Protein Summary:
2:57:22.069527 PROGRESS: Channel   0:	 0.050 FDR: 1,423; 0.010 FDR: 1,423; 0.001 FDR:   865
2:57:22.069630 PROGRESS: =========================================================================
2:57:22.130481 INFO: Target number of precursors reached.
2:57:23.989676 INFO: fragments_df: keeping 5000 of 18070226 [sum(precursor_idx_mask)=47270 sum(mass_error_mask)=18070226 stop_rank=5000
2:57:25.184405 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:57:25.460206 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:57:26.188801 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:57:26.189265 INFO: Using score_cutoff 5.545346458196639 (fac=0.99, q=1)
2:57:26.189610 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:57:26.189697 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:57:26.189761 INFO: Updating optimization_manager: score_cutoff        : 5.22187965259552 -> 5.545346458196639
2:57:26.189829 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:57:26.794632 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:57:28.194242 INFO: === checking if optimization conditions were reached ===
2:57:28.194559 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:57:28.197723 INFO: Updating optimization_manager: rt_error            : 1157.5776159746192 -> 1198.3140703140023
2:57:28.197878 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 1198.3141.
2:57:28.197956 INFO: ==============================================
2:57:28.198048 INFO: Starting optimization step 6.
2:57:28.198130 PROGRESS: === Extracting elution groups 0 to 511000 ===
2:57:28.198220 INFO: Using rust extraction backend
2:57:28.198301 PROGRESS: Extracting batch of 1001059 precursors
2:57:29.893177 INFO: === Search parameters used ===
2:57:29.893472 INFO: rt_error       : 1198.3140703140023
2:57:29.893543 INFO: mobility_error : 0.1
2:57:29.893605 INFO: num_candidates : 3
2:57:29.893664 INFO: ms1_error      : 20
2:57:29.893716 INFO: ms2_error      : 10.0
2:57:29.893765 INFO: fwhm_rt        : 3.0
2:57:29.893821 INFO: quant_window   : 3
2:57:29.893881 INFO: ==============================================
2:57:43.574704 INFO: performing precursor FDR with 40 features
2:57:43.574851 INFO: Decoy channel: -1
2:57:43.574880 INFO: competitive: True
2:57:44.286108 INFO: Setting torch num_threads to 2 for FDR classification task
2:57:45.593577 INFO: Estimating optimal hyperparameters - samples: 2,401,730, batch_size: 4,096, learning_rate: 1.00e-03
2:57:45.598807 INFO: Using random state 883232 for train-test-split
2:58:30.489525 INFO: Test AUC: 0.613
2:58:30.489725 INFO: Train AUC: 0.616
2:58:30.489760 INFO: AUC difference: 0.50%
2:58:31.710665 INFO: Resetting torch num_threads to 32
2:58:31.811141 PROGRESS: === Extracted 3002163 precursors and 18070263 fragments ===
2:58:31.811674 INFO: === FDR correction performed with classifier version 13 ===
2:58:31.812541 PROGRESS: ============================= Precursor FDR =============================
2:58:31.812657 PROGRESS: Total precursors accumulated: 1,980
2:58:31.812734 PROGRESS: Target precursors: 1,961 (99.04%)
2:58:31.812805 PROGRESS: Decoy precursors: 19 (0.96%)
2:58:31.812865 PROGRESS: 
2:58:31.812916 PROGRESS: Precursor Summary:
2:58:31.814457 PROGRESS: Channel   0:	 0.050 FDR: 1,961; 0.010 FDR: 1,961; 0.001 FDR:   978
2:58:31.814562 PROGRESS: 
2:58:31.814626 PROGRESS: Protein Summary:
2:58:31.816548 PROGRESS: Channel   0:	 0.050 FDR: 1,505; 0.010 FDR: 1,505; 0.001 FDR:   807
2:58:31.816647 PROGRESS: =========================================================================
2:58:31.868899 INFO: Target number of precursors reached.
2:58:33.743331 INFO: fragments_df: keeping 5000 of 18070263 [sum(precursor_idx_mask)=49888 sum(mass_error_mask)=18070263 stop_rank=5000
2:58:34.966313 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:58:35.258323 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:58:35.981354 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:58:35.981797 INFO: Using score_cutoff 4.927909163475037 (fac=0.99, q=1)
2:58:35.982120 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:58:35.982208 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:58:35.982273 INFO: Updating optimization_manager: score_cutoff        : 5.545346458196639 -> 4.927909163475037
2:58:35.982339 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:58:36.599828 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:58:37.992563 INFO: === checking if optimization conditions were reached ===
2:58:37.992903 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:58:37.994057 INFO: Updating optimization_manager: rt_error            : 1198.3140703140023 -> 909.0798706149499
2:58:37.994220 INFO: Updating optimization_manager: classifier_version  : 13 -> 15
2:58:37.994330 INFO: Updating optimization_manager: score_cutoff        : 4.927909163475037 -> 6.719476298332214
2:58:37.994681 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:58:37.994790 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:58:37.994894 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 909.0799 found after 6 searches.
2:58:37.994967 INFO: ==============================================
2:58:37.995059 PROGRESS: Optimization finished for rt_error.
2:58:38.795254 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:58:39.091727 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:58:39.793851 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:58:39.794089 PROGRESS: ==============================================
2:58:39.794176 PROGRESS: ms2_error      : 10.0000
2:58:39.794243 PROGRESS: rt_error       : 909.0799
2:58:39.794299 PROGRESS: ==============================================
2:58:39.795108 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:58:46.367581 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:59:11.687310 INFO: Using rust extraction backend
2:59:11.688035 PROGRESS: Extracting batch of 10770831 precursors
2:59:34.784737 INFO: === Search parameters used ===
2:59:34.785248 INFO: rt_error       : 909.0798706149499
2:59:34.785329 INFO: mobility_error : 0.1
2:59:34.785397 INFO: num_candidates : 3
2:59:34.785457 INFO: ms1_error      : 20
2:59:34.785508 INFO: ms2_error      : 10.0
2:59:34.785566 INFO: fwhm_rt        : 3.0
2:59:34.785622 INFO: quant_window   : 3
2:59:34.785672 INFO: ==============================================
3:00:35.236473 INFO: Removed 4584756 precursors with score below cutoff 6.719476298332214
3:01:05.584603 INFO: performing precursor FDR with 40 features
3:01:05.584824 INFO: Decoy channel: -1
3:01:05.584855 INFO: competitive: True
3:01:08.459735 INFO: Setting torch num_threads to 2 for FDR classification task
3:01:19.728444 INFO: Estimating optimal hyperparameters - samples: 22,182,184, batch_size: 4,096, learning_rate: 1.00e-03
3:01:19.796527 INFO: Using random state 485117 for train-test-split
3:08:23.294497 INFO: Test AUC: 0.616
3:08:23.294768 INFO: Train AUC: 0.616
3:08:23.294814 INFO: AUC difference: 0.05%
3:08:29.789785 INFO: Resetting torch num_threads to 32
3:08:31.522990 PROGRESS: ============================= Precursor FDR =============================
3:08:31.523259 PROGRESS: Total precursors accumulated: 20,359
3:08:31.523342 PROGRESS: Target precursors: 20,158 (99.01%)
3:08:31.523408 PROGRESS: Decoy precursors: 201 (0.99%)
3:08:31.523464 PROGRESS: 
3:08:31.523527 PROGRESS: Precursor Summary:
3:08:31.528243 PROGRESS: Channel   0:	 0.050 FDR: 20,158; 0.010 FDR: 20,158; 0.001 FDR: 12,107
3:08:31.528368 PROGRESS: 
3:08:31.528435 PROGRESS: Protein Summary:
3:08:31.535636 PROGRESS: Channel   0:	 0.050 FDR: 6,084; 0.010 FDR: 6,084; 0.001 FDR: 4,230
3:08:31.535759 PROGRESS: =========================================================================
3:08:31.690586 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3/psm.parquet
3:08:31.733195 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3/frag.parquet
3:08:31.809604 INFO: Finished workflow for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3
3:09:07.007978 PROGRESS: Processing search outputs
3:09:07.008216 PROGRESS: Performing protein grouping and FDR
3:09:07.008274 INFO: Building output for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1
3:09:07.056308 INFO: Building output for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2
3:09:07.073168 INFO: Building output for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3
3:09:07.091707 INFO: Building output for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1
3:09:07.108201 INFO: Building output for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2
3:09:07.127579 INFO: Building output for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3
3:09:07.148533 INFO: Building combined output
3:09:07.162900 INFO: Performing protein inference
3:09:07.350714 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
3:09:18.496486 INFO: Performing protein FDR
3:09:21.626710 INFO: Normalizing q-values using 9,260 targets and 937 decoys
3:09:21.629602 INFO: Test AUC: 0.866
3:09:21.629660 INFO: Train AUC: 0.860
3:09:21.629697 INFO: AUC difference: 0.68%
3:09:21.993965 INFO: ================ Protein FDR =================
3:09:21.994118 INFO: Unique protein groups in output
3:09:21.994159 INFO:   1% protein FDR: 4,545
3:09:21.994183 INFO: 
3:09:21.994204 INFO: Unique precursor in output
3:09:21.994225 INFO:   1% protein FDR: 28,122
3:09:21.994246 INFO: ================================================
3:09:22.006532 PROGRESS: Building search statistics
3:09:22.028458 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1/optimization_manager.pkl
3:09:22.028649 INFO: Initializing OptimizationManager
3:09:22.028898 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1/calibration_manager.pkl
3:09:22.028979 INFO: Initializing CalibrationManager
3:09:22.029229 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1/raw_file_manager.pkl
3:09:22.029309 INFO: Initializing RawFileManager
3:09:22.037359 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2/optimization_manager.pkl
3:09:22.037481 INFO: Initializing OptimizationManager
3:09:22.037685 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2/calibration_manager.pkl
3:09:22.037773 INFO: Initializing CalibrationManager
3:09:22.037998 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2/raw_file_manager.pkl
3:09:22.038082 INFO: Initializing RawFileManager
3:09:22.045683 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3/optimization_manager.pkl
3:09:22.045801 INFO: Initializing OptimizationManager
3:09:22.045998 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3/calibration_manager.pkl
3:09:22.046078 INFO: Initializing CalibrationManager
3:09:22.046280 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3/raw_file_manager.pkl
3:09:22.046374 INFO: Initializing RawFileManager
3:09:22.053963 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1/optimization_manager.pkl
3:09:22.054080 INFO: Initializing OptimizationManager
3:09:22.054272 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1/calibration_manager.pkl
3:09:22.054349 INFO: Initializing CalibrationManager
3:09:22.054621 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1/raw_file_manager.pkl
3:09:22.054707 INFO: Initializing RawFileManager
3:09:22.062382 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2/optimization_manager.pkl
3:09:22.062508 INFO: Initializing OptimizationManager
3:09:22.062703 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2/calibration_manager.pkl
3:09:22.062789 INFO: Initializing CalibrationManager
3:09:22.062988 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2/raw_file_manager.pkl
3:09:22.063068 INFO: Initializing RawFileManager
3:09:22.070517 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3/optimization_manager.pkl
3:09:22.070641 INFO: Initializing OptimizationManager
3:09:22.070837 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3/calibration_manager.pkl
3:09:22.070915 INFO: Initializing CalibrationManager
3:09:22.071106 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3/raw_file_manager.pkl
3:09:22.071187 INFO: Initializing RawFileManager
3:09:22.072688 INFO: Writing stat output to disk
3:09:22.072749 INFO: Saving /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/stat.tsv to disk
3:09:22.076109 PROGRESS: Building internal statistics
3:09:22.076282 INFO: Loaded TimingManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1/timing_manager.pkl
3:09:22.076322 INFO: Initializing TimingManager
3:09:22.076583 INFO: Loaded TimingManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2/timing_manager.pkl
3:09:22.076627 INFO: Initializing TimingManager
3:09:22.076830 INFO: Loaded TimingManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3/timing_manager.pkl
3:09:22.076870 INFO: Initializing TimingManager
3:09:22.077061 INFO: Loaded TimingManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1/timing_manager.pkl
3:09:22.077099 INFO: Initializing TimingManager
3:09:22.077290 INFO: Loaded TimingManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2/timing_manager.pkl
3:09:22.077330 INFO: Initializing TimingManager
3:09:22.077515 INFO: Loaded TimingManager from /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/quant/20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3/timing_manager.pkl
3:09:22.077553 INFO: Initializing TimingManager
3:09:22.077936 INFO: Writing internal output to disk
3:09:22.077980 INFO: Saving /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/internal.tsv to disk
3:09:22.092793 INFO: Performing label free quantification
3:09:22.092924 INFO: Accumulating fragment data
3:09:22.092981 INFO: reading frag file for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r1
3:09:22.275686 INFO: reading frag file for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r2
3:09:22.531935 INFO: reading frag file for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_200pg_50pg_H_Y_r3
3:09:22.793717 INFO: reading frag file for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r1
3:09:23.071098 INFO: reading frag file for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r2
3:09:23.357200 INFO: reading frag file for 20231123_DIA_240k_20Th_40ms_FAIMSCV-48_gas3p8_240pg_10pg_H_Y_r3
3:09:23.714464 INFO: Performing label free quantification on the precursor level
3:09:23.714595 INFO: Filtering fragments by quality
3:09:23.785688 INFO: Performing label-free quantification with directlfq normalization
3:09:23.886166 INFO: Applying directLFQ normalization
3:09:24.620370 INFO: 28122 lfq-groups total
3:09:42.075220 INFO: using 32 processes
3:09:42.198731 INFO: lfq-object 0
3:09:42.324371 INFO: lfq-object 100
3:09:42.370172 INFO: lfq-object 300
3:09:42.407068 INFO: lfq-object 500
3:09:42.445475 INFO: lfq-object 700
3:09:42.449661 INFO: lfq-object 200
3:09:42.488759 INFO: lfq-object 900
3:09:42.489151 INFO: lfq-object 400
3:09:42.529458 INFO: lfq-object 600
3:09:42.557254 INFO: lfq-object 1100
3:09:42.575091 INFO: lfq-object 800
3:09:42.614202 INFO: lfq-object 1000
3:09:42.688798 INFO: lfq-object 1200
3:09:42.707696 INFO: lfq-object 1400
3:09:42.777394 INFO: lfq-object 1600
3:09:42.821570 INFO: lfq-object 1300
3:09:42.827257 INFO: lfq-object 1800
3:09:42.830959 INFO: lfq-object 1500
3:09:42.896455 INFO: lfq-object 2000
3:09:42.917697 INFO: lfq-object 1700
3:09:42.949768 INFO: lfq-object 1900
3:09:42.949720 INFO: lfq-object 2200
3:09:43.015413 INFO: lfq-object 2100
3:09:43.064010 INFO: lfq-object 2300
3:09:43.155635 INFO: lfq-object 2500
3:09:43.185088 INFO: lfq-object 2400
3:09:43.230584 INFO: lfq-object 2700
3:09:43.276144 INFO: lfq-object 2600
3:09:43.305954 INFO: lfq-object 2900
3:09:43.356035 INFO: lfq-object 2800
3:09:43.385061 INFO: lfq-object 3100
3:09:43.423955 INFO: lfq-object 3000
3:09:43.438508 INFO: lfq-object 3300
3:09:43.503773 INFO: lfq-object 3200
3:09:43.584814 INFO: lfq-object 3400
3:09:43.646148 INFO: lfq-object 3600
3:09:43.699160 INFO: lfq-object 3500
3:09:43.731594 INFO: lfq-object 3800
3:09:43.797910 INFO: lfq-object 3700
3:09:43.828770 INFO: lfq-object 4000
3:09:43.860395 INFO: lfq-object 3900
3:09:43.920149 INFO: lfq-object 4200
3:09:43.962446 INFO: lfq-object 4100
3:09:43.999626 INFO: lfq-object 4400
3:09:44.044648 INFO: lfq-object 4300
3:09:44.126730 INFO: lfq-object 4500
3:09:44.178318 INFO: lfq-object 4700
3:09:44.229914 INFO: lfq-object 4900
3:09:44.255160 INFO: lfq-object 4600
3:09:44.284708 INFO: lfq-object 5100
3:09:44.300820 INFO: lfq-object 4800
3:09:44.340461 INFO: lfq-object 5300
3:09:44.351833 INFO: lfq-object 5000
3:09:44.396432 INFO: lfq-object 5500
3:09:44.406191 INFO: lfq-object 5200
3:09:44.459367 INFO: lfq-object 5400
3:09:44.516652 INFO: lfq-object 5600
3:09:44.574929 INFO: lfq-object 5800
3:09:44.638454 INFO: lfq-object 5700
3:09:44.650154 INFO: lfq-object 6000
3:09:44.699724 INFO: lfq-object 5900
3:09:44.773084 INFO: lfq-object 6100
3:09:46.978101 INFO: lfq-object 6200
3:09:47.063021 INFO: lfq-object 6400
3:09:47.098041 INFO: lfq-object 6300
3:09:47.178045 INFO: lfq-object 6600
3:09:47.184613 INFO: lfq-object 6500
3:09:47.301784 INFO: lfq-object 6700
3:09:47.386792 INFO: lfq-object 6900
3:09:47.424564 INFO: lfq-object 6800
3:09:47.486940 INFO: lfq-object 7100
3:09:47.505020 INFO: lfq-object 7000
3:09:47.554099 INFO: lfq-object 7300
3:09:47.602964 INFO: lfq-object 7200
3:09:47.619680 INFO: lfq-object 7500
3:09:47.676774 INFO: lfq-object 7700
3:09:47.699518 INFO: lfq-object 7400
3:09:47.733952 INFO: lfq-object 7600
3:09:47.814514 INFO: lfq-object 7800
3:09:47.861697 INFO: lfq-object 8000
3:09:47.928023 INFO: lfq-object 8200
3:09:47.957888 INFO: lfq-object 7900
3:09:47.993349 INFO: lfq-object 8400
3:09:47.998127 INFO: lfq-object 8100
3:09:48.040396 INFO: lfq-object 8300
3:09:48.088130 INFO: lfq-object 8600
3:09:48.103222 INFO: lfq-object 8500
3:09:48.129342 INFO: lfq-object 8800
3:09:48.206928 INFO: lfq-object 8700
3:09:48.267549 INFO: lfq-object 8900
3:09:48.338509 INFO: lfq-object 9100
3:09:48.381503 INFO: lfq-object 9000
3:09:48.453310 INFO: lfq-object 9300
3:09:48.454531 INFO: lfq-object 9200
3:09:48.503564 INFO: lfq-object 9500
3:09:48.555839 INFO: lfq-object 9700
3:09:48.566785 INFO: lfq-object 9400
3:09:48.594699 INFO: lfq-object 9900
3:09:48.625601 INFO: lfq-object 9600
3:09:48.677061 INFO: lfq-object 9800
3:09:48.712055 INFO: lfq-object 10000
3:09:48.790291 INFO: lfq-object 10200
3:09:48.829910 INFO: lfq-object 10100
3:09:48.842849 INFO: lfq-object 10400
3:09:48.906198 INFO: lfq-object 10300
3:09:48.955373 INFO: lfq-object 10600
3:09:48.965424 INFO: lfq-object 10500
3:09:49.053824 INFO: lfq-object 10800
3:09:49.090739 INFO: lfq-object 10700
3:09:49.096159 INFO: lfq-object 11000
3:09:49.180843 INFO: lfq-object 10900
3:09:49.213026 INFO: lfq-object 11100
3:09:49.288754 INFO: lfq-object 11300
3:09:49.336632 INFO: lfq-object 11200
3:09:49.370774 INFO: lfq-object 11500
3:09:49.407817 INFO: lfq-object 11400
3:09:49.464577 INFO: lfq-object 11700
3:09:49.488450 INFO: lfq-object 11600
3:09:49.567603 INFO: lfq-object 11900
3:09:49.582726 INFO: lfq-object 11800
3:09:49.609376 INFO: lfq-object 12100
3:09:49.680422 INFO: lfq-object 12000
3:09:49.743549 INFO: lfq-object 12200
3:09:49.828619 INFO: lfq-object 12400
3:09:49.856546 INFO: lfq-object 12300
3:09:49.946269 INFO: lfq-object 12500
3:09:49.946516 INFO: lfq-object 12600
3:09:50.100237 INFO: lfq-object 12700
3:09:50.125217 INFO: lfq-object 12800
3:09:50.214634 INFO: lfq-object 13000
3:09:50.248476 INFO: lfq-object 12900
3:09:50.256115 INFO: lfq-object 13200
3:09:50.334271 INFO: lfq-object 13100
3:09:50.370552 INFO: lfq-object 13300
3:09:50.483737 INFO: lfq-object 13500
3:09:50.490402 INFO: lfq-object 13400
3:09:50.586858 INFO: lfq-object 13700
3:09:50.600774 INFO: lfq-object 13600
3:09:50.673782 INFO: lfq-object 13900
3:09:50.700895 INFO: lfq-object 13800
3:09:50.769627 INFO: lfq-object 14100
3:09:50.800249 INFO: lfq-object 14000
3:09:50.817243 INFO: lfq-object 14300
3:09:50.881774 INFO: lfq-object 14200
3:09:50.936695 INFO: lfq-object 14400
3:09:51.007922 INFO: lfq-object 14600
3:09:51.057568 INFO: lfq-object 14500
3:09:51.087448 INFO: lfq-object 14800
3:09:51.146284 INFO: lfq-object 14700
3:09:51.163744 INFO: lfq-object 15000
3:09:51.207123 INFO: lfq-object 15200
3:09:51.210962 INFO: lfq-object 14900
3:09:51.267709 INFO: lfq-object 15400
3:09:51.280597 INFO: lfq-object 15100
3:09:51.324958 INFO: lfq-object 15300
3:09:51.394657 INFO: lfq-object 15500
3:09:51.467452 INFO: lfq-object 15700
3:09:51.514637 INFO: lfq-object 15600
3:09:51.572011 INFO: lfq-object 15900
3:09:51.609364 INFO: lfq-object 16100
3:09:51.613885 INFO: lfq-object 15800
3:09:51.688832 INFO: lfq-object 16000
3:09:51.714184 INFO: lfq-object 16300
3:09:51.725386 INFO: lfq-object 16200
3:09:51.829638 INFO: lfq-object 16400
3:09:53.989319 INFO: lfq-object 16500
3:09:54.115423 INFO: lfq-object 16600
3:09:54.222833 INFO: lfq-object 16800
3:09:54.237029 INFO: lfq-object 16700
3:09:54.257177 INFO: lfq-object 17000
3:09:54.313912 INFO: lfq-object 17200
3:09:54.339002 INFO: lfq-object 16900
3:09:54.358085 INFO: lfq-object 17400
3:09:54.364340 INFO: lfq-object 17600
3:09:54.371693 INFO: lfq-object 17100
3:09:54.430691 INFO: lfq-object 17300
3:09:54.474853 INFO: lfq-object 17500
3:09:54.497289 INFO: lfq-object 17700
3:09:54.591634 INFO: lfq-object 17900
3:09:54.615621 INFO: lfq-object 17800
3:09:54.653486 INFO: lfq-object 18100
3:09:54.712483 INFO: lfq-object 18000
3:09:54.774092 INFO: lfq-object 18200
3:09:54.831234 INFO: lfq-object 18300
3:09:54.929321 INFO: lfq-object 18500
3:09:54.952636 INFO: lfq-object 18400
3:09:55.038514 INFO: lfq-object 18700
3:09:55.041399 INFO: lfq-object 18600
3:09:55.176136 INFO: lfq-object 18800
3:09:55.246375 INFO: lfq-object 19000
3:09:55.250777 INFO: lfq-object 19200
3:09:55.291603 INFO: lfq-object 19400
3:09:55.297174 INFO: lfq-object 18900
3:09:55.343610 INFO: lfq-object 19600
3:09:55.371552 INFO: lfq-object 19300
3:09:55.392316 INFO: lfq-object 19100
3:09:55.392528 INFO: lfq-object 19800
3:09:55.408767 INFO: lfq-object 19500
3:09:55.465844 INFO: lfq-object 19700
3:09:55.508569 INFO: lfq-object 19900
3:09:55.548066 INFO: lfq-object 20100
3:09:55.626235 INFO: lfq-object 20300
3:09:55.628623 INFO: lfq-object 20000
3:09:55.666834 INFO: lfq-object 20200
3:09:55.718570 INFO: lfq-object 20500
3:09:55.740620 INFO: lfq-object 20400
3:09:55.817400 INFO: lfq-object 20700
3:09:55.835290 INFO: lfq-object 20600
3:09:55.924037 INFO: lfq-object 20900
3:09:55.933392 INFO: lfq-object 20800
3:09:56.061109 INFO: lfq-object 21000
3:09:56.127384 INFO: lfq-object 21200
3:09:56.184557 INFO: lfq-object 21100
3:09:56.201377 INFO: lfq-object 21400
3:09:56.244671 INFO: lfq-object 21300
3:09:56.259344 INFO: lfq-object 21600
3:09:56.324265 INFO: lfq-object 21500
3:09:56.330925 INFO: lfq-object 21800
3:09:56.370966 INFO: lfq-object 22000
3:09:56.380698 INFO: lfq-object 21700
3:09:56.450996 INFO: lfq-object 21900
3:09:56.491748 INFO: lfq-object 22100
3:09:56.611449 INFO: lfq-object 22200
3:09:56.614826 INFO: lfq-object 22300
3:09:56.689841 INFO: lfq-object 22500
3:09:56.739604 INFO: lfq-object 22400
3:09:56.783633 INFO: lfq-object 22700
3:09:56.818320 INFO: lfq-object 22600
3:09:56.875633 INFO: lfq-object 22900
3:09:56.906216 INFO: lfq-object 22800
3:09:56.981277 INFO: lfq-object 23100
3:09:57.009667 INFO: lfq-object 23000
3:09:57.114550 INFO: lfq-object 23200
3:09:57.155785 INFO: lfq-object 23400
3:09:57.234207 INFO: lfq-object 23300
3:09:57.239830 INFO: lfq-object 23600
3:09:57.272102 INFO: lfq-object 23500
3:09:57.309155 INFO: lfq-object 23800
3:09:57.354580 INFO: lfq-object 23700
3:09:57.378610 INFO: lfq-object 24000
3:09:57.426098 INFO: lfq-object 24200
3:09:57.427254 INFO: lfq-object 23900
3:09:57.498769 INFO: lfq-object 24100
3:09:57.550779 INFO: lfq-object 24300
3:09:57.628940 INFO: lfq-object 24500
3:09:57.672538 INFO: lfq-object 24400
3:09:57.748871 INFO: lfq-object 24600
3:09:57.755173 INFO: lfq-object 24700
3:09:57.822095 INFO: lfq-object 24900
3:09:57.871598 INFO: lfq-object 24800
3:09:57.933766 INFO: lfq-object 25000
3:09:57.947848 INFO: lfq-object 25100
3:09:58.024571 INFO: lfq-object 25300
3:09:58.066621 INFO: lfq-object 25200
3:09:58.140924 INFO: lfq-object 25400
3:09:58.193099 INFO: lfq-object 25600
3:09:58.252042 INFO: lfq-object 25500
3:09:58.306313 INFO: lfq-object 25800
3:09:58.310639 INFO: lfq-object 25700
3:09:58.349377 INFO: lfq-object 26000
3:09:58.401627 INFO: lfq-object 26200
3:09:58.420383 INFO: lfq-object 25900
3:09:58.479921 INFO: lfq-object 26100
3:09:58.494426 INFO: lfq-object 26400
3:09:58.538814 INFO: lfq-object 26300
3:09:58.618768 INFO: lfq-object 26500
3:09:58.722564 INFO: lfq-object 26700
3:09:58.737279 INFO: lfq-object 26600
3:09:58.760573 INFO: lfq-object 26900
3:09:58.821429 INFO: lfq-object 27100
3:09:58.843037 INFO: lfq-object 26800
3:09:58.875752 INFO: lfq-object 27000
3:09:58.909875 INFO: lfq-object 27300
3:09:58.940264 INFO: lfq-object 27200
3:09:58.967314 INFO: lfq-object 27500
3:09:59.032163 INFO: lfq-object 27400
3:09:59.089059 INFO: lfq-object 27600
3:09:59.125131 INFO: lfq-object 27800
3:09:59.210607 INFO: lfq-object 27700
3:09:59.263292 INFO: lfq-object 27900
3:10:01.514416 INFO: lfq-object 28000
3:10:01.631432 INFO: lfq-object 28100
3:10:03.578547 INFO: Performing label free quantification on the peptide level
3:10:03.578675 INFO: Filtering fragments by quality
3:10:03.659620 INFO: Performing label-free quantification with directlfq normalization
3:10:03.764269 INFO: Applying directLFQ normalization
3:10:03.892626 INFO: 27616 lfq-groups total
3:10:19.570031 INFO: using 32 processes
3:10:21.852575 INFO: lfq-object 0
3:10:21.977852 INFO: lfq-object 100
3:10:22.031645 INFO: lfq-object 300
3:10:22.081682 INFO: lfq-object 500
3:10:22.105152 INFO: lfq-object 200
3:10:22.137139 INFO: lfq-object 700
3:10:22.155193 INFO: lfq-object 400
3:10:22.184942 INFO: lfq-object 900
3:10:22.204015 INFO: lfq-object 600
3:10:22.237612 INFO: lfq-object 1100
3:10:22.259714 INFO: lfq-object 800
3:10:22.277004 INFO: lfq-object 1300
3:10:22.306660 INFO: lfq-object 1000
3:10:22.355991 INFO: lfq-object 1200
3:10:22.391889 INFO: lfq-object 1400
3:10:22.444221 INFO: lfq-object 1600
3:10:22.512794 INFO: lfq-object 1800
3:10:22.514723 INFO: lfq-object 1500
3:10:22.566716 INFO: lfq-object 1700
3:10:22.573067 INFO: lfq-object 2000
3:10:22.606772 INFO: lfq-object 2200
3:10:22.634668 INFO: lfq-object 1900
3:10:22.659233 INFO: lfq-object 2400
3:10:22.692273 INFO: lfq-object 2100
3:10:22.702337 INFO: lfq-object 2600
3:10:22.730936 INFO: lfq-object 2300
3:10:22.785121 INFO: lfq-object 2500
3:10:22.849412 INFO: lfq-object 2700
3:10:22.889029 INFO: lfq-object 2900
3:10:22.904574 INFO: lfq-object 3100
3:10:22.955795 INFO: lfq-object 3300
3:10:22.982787 INFO: lfq-object 2800
3:10:23.013306 INFO: lfq-object 3000
3:10:23.036434 INFO: lfq-object 3500
3:10:23.072214 INFO: lfq-object 3200
3:10:23.080208 INFO: lfq-object 3700
3:10:23.103993 INFO: lfq-object 3900
3:10:23.139312 INFO: lfq-object 3400
3:10:23.227590 INFO: lfq-object 3600
3:10:23.256527 INFO: lfq-object 4200
3:10:23.258703 INFO: lfq-object 3800
3:10:23.262946 INFO: lfq-object 4000
3:10:23.299345 INFO: lfq-object 4400
3:10:23.366877 INFO: lfq-object 4600
3:10:23.382570 INFO: lfq-object 4100
3:10:23.383347 INFO: lfq-object 4300
3:10:23.390461 INFO: lfq-object 4800
3:10:23.416757 INFO: lfq-object 4500
3:10:23.430970 INFO: lfq-object 5000
3:10:23.472710 INFO: lfq-object 5200
3:10:23.491875 INFO: lfq-object 4700
3:10:23.509908 INFO: lfq-object 4900
3:10:23.529793 INFO: lfq-object 5400
3:10:23.591456 INFO: lfq-object 5300
3:10:23.595585 INFO: lfq-object 5100
3:10:23.739589 INFO: lfq-object 5500
3:10:23.752111 INFO: lfq-object 5900
3:10:23.753731 INFO: lfq-object 5700
3:10:23.848651 INFO: lfq-object 6300
3:10:23.860191 INFO: lfq-object 6100
3:10:23.861414 INFO: lfq-object 5600
3:10:23.875191 INFO: lfq-object 6000
3:10:23.884987 INFO: lfq-object 6500
3:10:23.926685 INFO: lfq-object 6700
3:10:23.948597 INFO: lfq-object 5800
3:10:23.985219 INFO: lfq-object 6400
3:10:24.011954 INFO: lfq-object 6600
3:10:24.029773 INFO: lfq-object 6200
3:10:24.050150 INFO: lfq-object 6800
3:10:24.165457 INFO: lfq-object 6900
3:10:24.884487 INFO: lfq-object 7000
3:10:25.022280 INFO: lfq-object 7100
3:10:25.022700 INFO: lfq-object 7200
3:10:25.068449 INFO: lfq-object 7400
3:10:25.143450 INFO: lfq-object 7600
3:10:25.145686 INFO: lfq-object 7300
3:10:25.172334 INFO: lfq-object 7800
3:10:25.179887 INFO: lfq-object 7500
3:10:25.267504 INFO: lfq-object 7700
3:10:25.268484 INFO: lfq-object 8000
3:10:25.301239 INFO: lfq-object 7900
3:10:25.405214 INFO: lfq-object 8100
3:10:25.509499 INFO: lfq-object 8300
3:10:25.553777 INFO: lfq-object 8200
3:10:25.610697 INFO: lfq-object 8500
3:10:25.629277 INFO: lfq-object 8400
3:10:25.725637 INFO: lfq-object 8700
3:10:25.764122 INFO: lfq-object 8600
3:10:25.773738 INFO: lfq-object 8900
3:10:25.841036 INFO: lfq-object 8800
3:10:25.841364 INFO: lfq-object 9100
3:10:25.915344 INFO: lfq-object 9000
3:10:25.955692 INFO: lfq-object 9300
3:10:25.959693 INFO: lfq-object 9200
3:10:26.077283 INFO: lfq-object 9400
3:10:26.177998 INFO: lfq-object 9600
3:10:26.221129 INFO: lfq-object 9500
3:10:26.332569 INFO: lfq-object 9800
3:10:26.334993 INFO: lfq-object 9700
3:10:26.413140 INFO: lfq-object 10000
3:10:26.452990 INFO: lfq-object 9900
3:10:26.545513 INFO: lfq-object 10100
3:10:26.553784 INFO: lfq-object 10200
3:10:26.621674 INFO: lfq-object 10400
3:10:26.680763 INFO: lfq-object 10300
3:10:26.708291 INFO: lfq-object 10600
3:10:26.743984 INFO: lfq-object 10500
3:10:26.821897 INFO: lfq-object 10800
3:10:26.825325 INFO: lfq-object 10700
3:10:26.964438 INFO: lfq-object 10900
3:10:27.086839 INFO: lfq-object 11000
3:10:27.101058 INFO: lfq-object 11100
3:10:27.223244 INFO: lfq-object 11200
3:10:27.283325 INFO: lfq-object 11300
3:10:27.399693 INFO: lfq-object 11400
3:10:29.384002 INFO: lfq-object 11500
3:10:29.542082 INFO: lfq-object 11600
3:10:29.596078 INFO: lfq-object 11700
3:10:29.685284 INFO: lfq-object 11900
3:10:29.712607 INFO: lfq-object 11800
3:10:29.756994 INFO: lfq-object 12100
3:10:29.805429 INFO: lfq-object 12000
3:10:29.884670 INFO: lfq-object 12200
3:10:29.989825 INFO: lfq-object 12400
3:10:30.010276 INFO: lfq-object 12300
3:10:30.090000 INFO: lfq-object 12600
3:10:30.106513 INFO: lfq-object 12500
3:10:30.164431 INFO: lfq-object 12800
3:10:30.223923 INFO: lfq-object 13000
3:10:30.230264 INFO: lfq-object 12700
3:10:30.287890 INFO: lfq-object 12900
3:10:30.316295 INFO: lfq-object 13200
3:10:30.349078 INFO: lfq-object 13100
3:10:30.432246 INFO: lfq-object 13300
3:10:30.453990 INFO: lfq-object 13400
3:10:30.579735 INFO: lfq-object 13500
3:10:30.661402 INFO: lfq-object 13700
3:10:30.700670 INFO: lfq-object 13600
3:10:30.746054 INFO: lfq-object 13900
3:10:30.808997 INFO: lfq-object 14100
3:10:30.812643 INFO: lfq-object 13800
3:10:30.855498 INFO: lfq-object 14300
3:10:30.884638 INFO: lfq-object 14000
3:10:30.929715 INFO: lfq-object 14200
3:10:30.933717 INFO: lfq-object 14500
3:10:30.983297 INFO: lfq-object 14400
3:10:31.029180 INFO: lfq-object 14700
3:10:31.060938 INFO: lfq-object 14600
3:10:31.149631 INFO: lfq-object 14800
3:10:31.215205 INFO: lfq-object 15000
3:10:31.269865 INFO: lfq-object 14900
3:10:31.288083 INFO: lfq-object 15200
3:10:31.333673 INFO: lfq-object 15100
3:10:31.386243 INFO: lfq-object 15400
3:10:31.404915 INFO: lfq-object 15300
3:10:31.477440 INFO: lfq-object 15600
3:10:31.508906 INFO: lfq-object 15500
3:10:31.525382 INFO: lfq-object 15800
3:10:31.594246 INFO: lfq-object 15700
3:10:31.628125 INFO: lfq-object 16000
3:10:31.641438 INFO: lfq-object 15900
3:10:31.715888 INFO: lfq-object 16200
3:10:31.744797 INFO: lfq-object 16100
3:10:31.844802 INFO: lfq-object 16300
3:10:31.876494 INFO: lfq-object 16500
3:10:31.961787 INFO: lfq-object 16400
3:10:31.977484 INFO: lfq-object 16700
3:10:31.991739 INFO: lfq-object 16600
3:10:32.064075 INFO: lfq-object 16900
3:10:32.083695 INFO: lfq-object 17100
3:10:32.094162 INFO: lfq-object 16800
3:10:32.174680 INFO: lfq-object 17300
3:10:32.178499 INFO: lfq-object 17000
3:10:32.216561 INFO: lfq-object 17200
3:10:32.230623 INFO: lfq-object 17500
3:10:32.291265 INFO: lfq-object 17400
3:10:32.373810 INFO: lfq-object 17600
3:10:32.436275 INFO: lfq-object 17800
3:10:32.491245 INFO: lfq-object 17700
3:10:32.546832 INFO: lfq-object 18000
3:10:32.557061 INFO: lfq-object 17900
3:10:32.613745 INFO: lfq-object 18200
3:10:32.668667 INFO: lfq-object 18100
3:10:32.730950 INFO: lfq-object 18300
3:10:32.743648 INFO: lfq-object 18400
3:10:32.772342 INFO: lfq-object 18600
3:10:32.825603 INFO: lfq-object 18800
3:10:32.869235 INFO: lfq-object 18500
3:10:32.889301 INFO: lfq-object 18700
3:10:32.965896 INFO: lfq-object 18900
3:10:33.034230 INFO: lfq-object 19100
3:10:33.087133 INFO: lfq-object 19000
3:10:33.101167 INFO: lfq-object 19300
3:10:33.128338 INFO: lfq-object 19500
3:10:33.150666 INFO: lfq-object 19200
3:10:33.186641 INFO: lfq-object 19700
3:10:33.222317 INFO: lfq-object 19400
3:10:33.246240 INFO: lfq-object 19900
3:10:33.246491 INFO: lfq-object 19600
3:10:33.311182 INFO: lfq-object 19800
3:10:33.352988 INFO: lfq-object 20100
3:10:33.367088 INFO: lfq-object 20000
3:10:33.476466 INFO: lfq-object 20200
3:10:33.570302 INFO: lfq-object 20400
3:10:33.593531 INFO: lfq-object 20300
3:10:33.685312 INFO: lfq-object 20500
3:10:33.701303 INFO: lfq-object 20600
3:10:33.775424 INFO: lfq-object 20800
3:10:33.823247 INFO: lfq-object 20700
3:10:33.862700 INFO: lfq-object 21000
3:10:33.900276 INFO: lfq-object 20900
3:10:33.983687 INFO: lfq-object 21100
3:10:36.128594 INFO: lfq-object 21200
3:10:36.184889 INFO: lfq-object 21400
3:10:36.245121 INFO: lfq-object 21300
3:10:36.271638 INFO: lfq-object 21600
3:10:36.304783 INFO: lfq-object 21500
3:10:36.388394 INFO: lfq-object 21700
3:10:36.477925 INFO: lfq-object 21900
3:10:36.511267 INFO: lfq-object 21800
3:10:36.536574 INFO: lfq-object 22100
3:10:36.585304 INFO: lfq-object 22300
3:10:36.597482 INFO: lfq-object 22000
3:10:36.655573 INFO: lfq-object 22200
3:10:36.693791 INFO: lfq-object 22500
3:10:36.706780 INFO: lfq-object 22400
3:10:36.761118 INFO: lfq-object 22700
3:10:36.790826 INFO: lfq-object 22900
3:10:36.818949 INFO: lfq-object 22600
3:10:36.879930 INFO: lfq-object 22800
3:10:36.909680 INFO: lfq-object 23000
3:10:36.967168 INFO: lfq-object 23200
3:10:37.022761 INFO: lfq-object 23100
3:10:37.083553 INFO: lfq-object 23300
3:10:37.090769 INFO: lfq-object 23400
3:10:37.127316 INFO: lfq-object 23600
3:10:37.206068 INFO: lfq-object 23800
3:10:37.211680 INFO: lfq-object 23500
3:10:37.245689 INFO: lfq-object 23700
3:10:37.284344 INFO: lfq-object 24000
3:10:37.329124 INFO: lfq-object 23900
3:10:37.341759 INFO: lfq-object 24200
3:10:37.410089 INFO: lfq-object 24100
3:10:37.465936 INFO: lfq-object 24300
3:10:37.509266 INFO: lfq-object 24500
3:10:37.572583 INFO: lfq-object 24700
3:10:37.584889 INFO: lfq-object 24400
3:10:37.625023 INFO: lfq-object 24600
3:10:37.632215 INFO: lfq-object 24900
3:10:37.696502 INFO: lfq-object 24800
3:10:37.730790 INFO: lfq-object 25100
3:10:37.750680 INFO: lfq-object 25000
3:10:37.871191 INFO: lfq-object 25200
3:10:37.884045 INFO: lfq-object 25300
3:10:37.964849 INFO: lfq-object 25500
3:10:38.002567 INFO: lfq-object 25400
3:10:38.090214 INFO: lfq-object 25600
3:10:38.161426 INFO: lfq-object 25800
3:10:38.209783 INFO: lfq-object 25700
3:10:38.247362 INFO: lfq-object 26000
3:10:38.282812 INFO: lfq-object 25900
3:10:38.325751 INFO: lfq-object 26200
3:10:38.363451 INFO: lfq-object 26100
3:10:38.428624 INFO: lfq-object 26400
3:10:38.442480 INFO: lfq-object 26300
3:10:38.543652 INFO: lfq-object 26500
3:10:38.566514 INFO: lfq-object 26600
3:10:38.640198 INFO: lfq-object 26800
3:10:38.685289 INFO: lfq-object 26700
3:10:38.690484 INFO: lfq-object 27000
3:10:38.759731 INFO: lfq-object 26900
3:10:38.812854 INFO: lfq-object 27100
3:10:38.900931 INFO: lfq-object 27300
3:10:38.937314 INFO: lfq-object 27200
3:10:38.975500 INFO: lfq-object 27500
3:10:39.019727 INFO: lfq-object 27400
3:10:39.094714 INFO: lfq-object 27600
3:10:41.280990 INFO: Performing label free quantification on the pg level
3:10:41.281206 INFO: Filtering fragments by quality
3:10:41.365426 INFO: Performing label-free quantification with directlfq normalization
3:10:41.423408 INFO: Applying directLFQ normalization
3:10:41.490911 INFO: 4545 lfq-groups total
3:10:53.847222 INFO: using 32 processes
3:10:53.884706 INFO: lfq-object 0
3:10:54.148925 INFO: lfq-object 600
3:10:54.178350 INFO: lfq-object 800
3:10:54.191722 INFO: lfq-object 400
3:10:54.197727 INFO: lfq-object 900
3:10:54.205733 INFO: lfq-object 300
3:10:54.290061 INFO: lfq-object 200
3:10:54.331814 INFO: lfq-object 1200
3:10:54.340858 INFO: lfq-object 1000
3:10:54.345270 INFO: lfq-object 500
3:10:54.376292 INFO: lfq-object 1300
3:10:54.378507 INFO: lfq-object 700
3:10:54.480815 INFO: lfq-object 100
3:10:54.559591 INFO: lfq-object 1100
3:10:54.574140 INFO: lfq-object 1400
3:10:54.618816 INFO: lfq-object 1600
3:10:54.625328 INFO: lfq-object 1500
3:10:54.655605 INFO: lfq-object 1700
3:10:54.698641 INFO: lfq-object 1800
3:10:54.841941 INFO: lfq-object 2000
3:10:54.852976 INFO: lfq-object 2100
3:10:54.865185 INFO: lfq-object 1900
3:10:54.872306 INFO: lfq-object 2200
3:10:54.981316 INFO: lfq-object 2300
3:10:55.033187 INFO: lfq-object 2400
3:10:55.041160 INFO: lfq-object 2500
3:10:55.086958 INFO: lfq-object 2700
3:10:55.089356 INFO: lfq-object 2600
3:10:55.218762 INFO: lfq-object 2800
3:10:55.282434 INFO: lfq-object 3100
3:10:55.319966 INFO: lfq-object 2900
3:10:55.386103 INFO: lfq-object 3200
3:10:55.417432 INFO: lfq-object 3000
3:10:55.418022 INFO: lfq-object 3300
3:10:57.140110 INFO: lfq-object 3400
3:10:57.151977 INFO: lfq-object 3500
3:10:57.185636 INFO: lfq-object 3600
3:10:57.270059 INFO: lfq-object 3700
3:10:57.383521 INFO: lfq-object 3800
3:10:57.402712 INFO: lfq-object 3900
3:10:57.422154 INFO: lfq-object 4000
3:10:57.504927 INFO: lfq-object 4100
3:10:57.536146 INFO: lfq-object 4200
3:10:57.549852 INFO: lfq-object 4300
3:10:57.603569 INFO: lfq-object 4500
3:10:57.647540 INFO: lfq-object 4400
3:10:59.103284 INFO: Writing psm output to disk
3:10:59.121243 INFO: Saving /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/precursors.parquet to disk
3:10:59.284320 INFO: Writing precursor output to disk
3:10:59.285491 INFO: Saving /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/precursor.matrix.parquet to disk
3:10:59.305784 INFO: Writing peptide output to disk
3:10:59.308124 INFO: Saving /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/peptide.matrix.parquet to disk
3:10:59.326938 INFO: Writing pg output to disk
3:10:59.328758 INFO: Saving /home/robbe/PB_output/results/test_run/HYE_Astral_Single_Cell/alphadia_v2.1.1/pg.matrix.parquet to disk
3:10:59.345714 PROGRESS: Building MBR spectral library
3:10:59.345864 INFO: Running MbrLibraryBuilder
3:11:01.440516 INFO: MBR spectral library contains 28,122 precursors, 4,545 proteins
3:11:01.440629 INFO: Writing MBR spectral library to disk
3:11:01.684545 PROGRESS: =================== Search step 'library' finished ===================
3:11:03.307602 INFO: =================== Search Finished ===================
