0:00:00.000042 INFO: Moved old log file /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/log.txt to /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/log.1.bkp.txt
0:00:00.000218 INFO: Output directory: /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1, cwd: /home/robbe/PB_output.
0:00:00.000275 INFO: User provided config file: /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/alphadia_config.yaml.
0:00:00.018037 PROGRESS:           _      _         ___ ___   _   
0:00:00.018126 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.018156 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.018179 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.018206 PROGRESS:            |_|                           
0:00:00.018232 PROGRESS: 
0:00:00.018253 PROGRESS: version: 2.1.0
0:00:00.018273 PROGRESS: Please cite: Wallmann, et al., Nature Biotechnology (2025), https://doi.org/10.1038/s41587-025-02791-w
0:00:00.018299 INFO: hostname: thestral
0:00:00.018326 PROGRESS: os: Linux 6.12.48+deb13-amd64 (x86_64)
0:00:00.018352 PROGRESS: python: 3.11.11 (CPython)
0:00:00.018407 INFO: date: 2026-04-19 11:42:34
0:00:00.018429 INFO: ================ AlphaX Environment ===============
0:00:00.018451 INFO: alphabase       : 1.7.4
0:00:00.018472 INFO: alpharaw        : 0.4.8
0:00:00.018491 INFO: alphatims       : 1.0.9
0:00:00.018511 INFO: alphapeptdeep   : 1.4.1
0:00:00.018529 INFO: directlfq       : 0.3.3
0:00:00.018545 INFO: ===================================================
0:00:00.018564 INFO: ================= Pip Environment =================
0:00:00.107940 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
0:00:00.108047 INFO: ===================================================
0:00:00.108094 INFO: =================== Running step 'library' ===================
0:00:00.108188 INFO: loading default config from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/default.yaml
0:00:00.129301 INFO: loading additional config provided via CLI
0:00:00.129410 INFO: loading additional config provided via CLI parameters
0:00:00.129935 INFO: Updating config with 'user defined'
0:00:00.130033 INFO: Updating config with 'user defined (cli)'
0:00:00.130121 INFO: updating config with user defined values: [{'raw_paths': ['/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw'], 'fasta_paths': ['/public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta'], 'output_directory': '/home/robbe/PB_output/results/test_run/HYE_Astral/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/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw', '/public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw']}]
0:00:00.130439 INFO: Updating config with 'user defined'
0:00:00.130515 INFO: Updating config with 'user defined (cli)'
0:00:00.130564 INFO: ├──version: None
0:00:00.130601 INFO: ├──workflow_name: None
0:00:00.130635 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1 [user defined, default: None][0m
0:00:00.130671 INFO: ├──library_path: None
0:00:00.130703 INFO: ├──raw_paths:
0:00:00.130734 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:00:00.130766 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:00:00.130795 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:00:00.130829 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:00:00.130859 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:00:00.130887 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:00:00.130916 INFO: ├──fasta_paths:
0:00:00.130947 INFO: │   [32;20m- /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta [user defined, default: None][0m
0:00:00.130977 INFO: ├──quant_directory: None
0:00:00.131006 INFO: ├──general
0:00:00.131037 INFO: │   [32;20m├──thread_count: 32 [user defined, default: 10][0m
0:00:00.131069 INFO: │   ├──transfer_step_enabled: False
0:00:00.131099 INFO: │   ├──mbr_step_enabled: False
0:00:00.131129 INFO: │   ├──reuse_calibration: False
0:00:00.131160 INFO: │   ├──reuse_quant: False
0:00:00.131190 INFO: │   ├──log_level: INFO
0:00:00.131218 INFO: │   ├──use_gpu: True
0:00:00.131248 INFO: │   ├──save_figures: True
0:00:00.131278 INFO: │   ├──save_library: True
0:00:00.131313 INFO: │   ├──save_flat_library: False
0:00:00.131342 INFO: │   ├──input_library_type: base
0:00:00.131375 INFO: │   ├──save_mbr_library: True
0:00:00.131405 INFO: │   └──random_state: None
0:00:00.131433 INFO: ├──library_loading
0:00:00.131464 INFO: │   └──drop_decoys: False
0:00:00.131493 INFO: ├──library_prediction
0:00:00.131524 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.131555 INFO: │   ├──enzyme: trypsin
0:00:00.131582 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.131613 INFO: │   [32;20m├──variable_modifications: Oxidation@M [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
0:00:00.131644 INFO: │   [32;20m├──max_var_mod_num: 3 [user defined, default: 2][0m
0:00:00.131674 INFO: │   [32;20m├──missed_cleavages: 2 [user defined, default: 1][0m
0:00:00.131704 INFO: │   ├──precursor_len:
0:00:00.131733 INFO: │   │   - 7
0:00:00.131766 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.131795 INFO: │   ├──precursor_charge:
0:00:00.131823 INFO: │   │   - 2
0:00:00.131850 INFO: │   │   - 4
0:00:00.131878 INFO: │   ├──precursor_mz:
0:00:00.131907 INFO: │   │   - 400.0
0:00:00.131936 INFO: │   │   - 1200.0
0:00:00.131963 INFO: │   ├──fragment_mz:
0:00:00.131992 INFO: │   │   - 200.0
0:00:00.132020 INFO: │   │   - 2000.0
0:00:00.132050 INFO: │   ├──nce: 25.0
0:00:00.132079 INFO: │   ├──fragment_types:
0:00:00.132107 INFO: │   │   - b
0:00:00.132135 INFO: │   │   - y
0:00:00.132165 INFO: │   ├──max_fragment_charge: 2
0:00:00.132193 INFO: │   ├──instrument: Lumos
0:00:00.132223 INFO: │   ├──peptdeep_model_path: None
0:00:00.132252 INFO: │   ├──peptdeep_model_type: generic
0:00:00.132281 INFO: │   ├──predict_charge: False
0:00:00.132312 INFO: │   └──min_charge_probability: 0.1
0:00:00.132341 INFO: ├──custom_modifications:
0:00:00.132371 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.132400 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.132429 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.132457 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.132487 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.132514 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.132544 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.132571 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.132600 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.132644 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.132673 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.132703 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.132731 INFO: │   ├──name: Label:13C(12)@K
0:00:00.132758 INFO: │   └──composition: C(12)
0:00:00.132786 INFO: ├──search
0:00:00.132815 INFO: │   ├──extraction_backend: rust
0:00:00.132846 INFO: │   ├──target_ms1_tolerance: 5
0:00:00.132876 INFO: │   ├──target_ms2_tolerance: 10
0:00:00.132905 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.132935 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.132964 INFO: │   ├──quant_window: 3
0:00:00.132995 INFO: │   ├──target_num_candidates: 3
0:00:00.133024 INFO: │   ├──channel_filter: 
0:00:00.133051 INFO: │   ├──compete_for_fragments: True
0:00:00.133080 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.133108 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.133137 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.133166 INFO: │   ├──optimized_peak_group_score: False
0:00:00.133193 INFO: │   ├──exclude_shared_ions: True
0:00:00.133221 INFO: │   ├──quant_all: True
0:00:00.133248 INFO: │   └──experimental_xic: True
0:00:00.133275 INFO: ├──calibration
0:00:00.133306 INFO: │   ├──batch_size: 1000
0:00:00.133341 INFO: │   ├──optimization_lock_target: 1000
0:00:00.133370 INFO: │   ├──max_steps: 20
0:00:00.133404 INFO: │   ├──min_steps: 5
0:00:00.133433 INFO: │   ├──max_skips: 1
0:00:00.133462 INFO: │   ├──max_fragments: 5000
0:00:00.133496 INFO: │   └──min_correlation: 0.7
0:00:00.133525 INFO: ├──search_initial
0:00:00.133555 INFO: │   ├──num_candidates: 1
0:00:00.133585 INFO: │   [32;20m├──ms1_tolerance: 20 [user defined, default: 30][0m
0:00:00.133614 INFO: │   [32;20m├──ms2_tolerance: 20 [user defined, default: 30][0m
0:00:00.133643 INFO: │   ├──mobility_tolerance: 0.1
0:00:00.133673 INFO: │   └──rt_tolerance: 0.5
0:00:00.133699 INFO: ├──library_multiplexing
0:00:00.133727 INFO: │   ├──enabled: False
0:00:00.133754 INFO: │   ├──input_channel: 0
0:00:00.133780 INFO: │   └──multiplex_mapping:
0:00:00.133805 INFO: ├──multiplexing
0:00:00.133832 INFO: │   ├──enabled: False
0:00:00.133858 INFO: │   ├──target_channels: 4,8
0:00:00.133883 INFO: │   ├──decoy_channel: 12
0:00:00.133909 INFO: │   ├──reference_channel: 0
0:00:00.133933 INFO: │   └──competitive_scoring: True
0:00:00.133957 INFO: ├──fdr
0:00:00.133984 INFO: │   ├──fdr: 0.01
0:00:00.134009 INFO: │   ├──group_level: proteins
0:00:00.134034 INFO: │   ├──inference_strategy: heuristic
0:00:00.134058 INFO: │   ├──competitive_scoring: True
0:00:00.134083 INFO: │   ├──keep_decoys: False
0:00:00.134108 INFO: │   ├──keep_decoys_in_mbr_library: False
0:00:00.134133 INFO: │   ├──channel_wise_fdr: False
0:00:00.134159 INFO: │   └──enable_nn_hyperparameter_tuning: True
0:00:00.134183 INFO: ├──search_output
0:00:00.134209 INFO: │   ├──file_format: parquet
0:00:00.134233 INFO: │   ├──precursor_level_lfq: True
0:00:00.134259 INFO: │   ├──peptide_level_lfq: True
0:00:00.134285 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.134310 INFO: │   ├──min_k_fragments: 12
0:00:00.134336 INFO: │   ├──min_correlation: 0.9
0:00:00.134363 INFO: │   ├──num_samples_quadratic: 50
0:00:00.134391 INFO: │   ├──min_nonnan: 3
0:00:00.134417 INFO: │   ├──normalization_method: directlfq
0:00:00.134443 INFO: │   └──normalize_directlfq: True
0:00:00.134469 INFO: ├──optimization
0:00:00.134495 INFO: │   ├──order_of_optimization: None
0:00:00.134521 INFO: │   ├──ms2_error
0:00:00.134548 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.134576 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.134602 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.134630 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.134656 INFO: │   │   ├──try_narrower_values: True
0:00:00.134685 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.134710 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.134738 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.134764 INFO: │   ├──ms1_error
0:00:00.134791 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.134818 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.134845 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.134873 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.134897 INFO: │   │   ├──try_narrower_values: False
0:00:00.134924 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.134949 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.134974 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.135000 INFO: │   ├──mobility_error
0:00:00.135027 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.135054 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.135080 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.135115 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.135135 INFO: │   │   ├──try_narrower_values: False
0:00:00.135159 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.135180 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.135201 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.135220 INFO: │   └──rt_error
0:00:00.135241 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.135260 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.135280 INFO: │       ├──automatic_update_percentile_range: 0.999
0:00:00.135300 INFO: │       ├──automatic_update_factor: 1.5
0:00:00.135319 INFO: │       ├──try_narrower_values: True
0:00:00.135338 INFO: │       ├──maximal_decrease: 0.1
0:00:00.135358 INFO: │       ├──favour_narrower_optimum: False
0:00:00.135376 INFO: │       └──maximum_decrease_from_maximum: 0.5
0:00:00.135395 INFO: ├──optimization_manager
0:00:00.135415 INFO: │   ├──fwhm_rt: 5
0:00:00.135434 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.135455 INFO: │   └──score_cutoff: 0
0:00:00.135473 INFO: ├──transfer_library
0:00:00.135492 INFO: │   ├──enabled: False
0:00:00.135510 INFO: │   ├──fragment_types:
0:00:00.135529 INFO: │   │   - b
0:00:00.135547 INFO: │   │   - y
0:00:00.135566 INFO: │   ├──max_charge: 2
0:00:00.135584 INFO: │   ├──top_k_samples: 3
0:00:00.135603 INFO: │   ├──norm_delta_max: True
0:00:00.135623 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.135642 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.135661 INFO: └──transfer_learning
0:00:00.135680 INFO:     ├──enabled: False
0:00:00.135699 INFO:     ├──batch_size: 2000
0:00:00.135718 INFO:     ├──max_lr: 0.0001
0:00:00.135737 INFO:     ├──train_fraction: 0.7
0:00:00.135756 INFO:     ├──validation_fraction: 0.2
0:00:00.135775 INFO:     ├──test_fraction: 0.1
0:00:00.135793 INFO:     ├──test_interval: 1
0:00:00.135813 INFO:     ├──lr_patience: 3
0:00:00.135832 INFO:     ├──epochs: 51
0:00:00.135850 INFO:     ├──warmup_epochs: 5
0:00:00.135869 INFO:     ├──nce: 25
0:00:00.135887 INFO:     └──instrument: Lumos
0:00:00.140885 INFO: Moved existing config file /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/frozen_config.yaml to /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/frozen_config.0.bkp.yaml
0:00:00.141119 INFO: Registering 7 custom modifications
0:00:00.173311 INFO: Searching 6 files:
0:00:00.173414 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:00:00.173441 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:00:00.173462 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:00:00.173481 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:00:00.173500 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:00:00.173518 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:00:00.173536 INFO: Using 1 fasta files:
0:00:00.173555 INFO:   /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
0:00:00.173575 INFO: Using library: None
0:00:00.173593 INFO: Saving output to: /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1
0:00:00.173619 PROGRESS: Loading spectral library
0:00:00.173644 PROGRESS: No library provided. Building library from fasta files.
0:00:00.173675 INFO: Running FastaDigest
0:00:00.174853 INFO: Digesting fasta file
0:00:11.394504 INFO: Adding modifications
0:02:44.137084 INFO: Removing non-canonical amino acids
0:02:54.705526 INFO: Fasta library contains 8,767,137 precursors
0:02:54.705728 PROGRESS: Predicting library properties.
0:02:54.705809 INFO: Running PeptDeepPrediction
0:02:54.707112 INFO: Device set to cpu
0:02:56.010594 INFO: Loading PeptDeep models of type generic
0:02:57.021476 INFO: Predicting RT, MS2 and mobility
0:02:57.021775 INFO: Using multiprocessing with 32 processes ...
0:02:57.559154 INFO: Predicting rt,ms2,mobility ...
0:28:44.494224 INFO: Adding fragment mz information
0:28:45.097224 INFO: Adding fragment intensity information
0:28:45.656208 INFO: Adding precursor information
0:28:46.191151 INFO: Running PrecursorInitializer
0:28:46.248589 INFO: Running AnnotateFasta
0:29:24.947686 INFO: Running IsotopeGenerator
0:29:24.948916 WARNING: Multiprocessing not compatible with custom modifications yet, falling back to single process.
0:36:02.440144 INFO: Running RTNormalization
0:36:02.440693 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:36:02.440825 INFO: Saving library to /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/speclib.hdf
0:36:56.031878 INFO: Running DecoyGenerator
0:40:08.386213 INFO: Running FlattenLibrary
0:40:49.845880 INFO: Running InitFlatColumns
0:40:50.344624 INFO: Running LogFlatLibraryStats
0:40:50.344804 INFO: ============ Library Stats ============
0:40:50.344863 INFO: Number of precursors: 17,532,137
0:40:53.373672 INFO: 	thereof targets:8,767,137
0:40:53.373842 INFO: 	thereof decoys: 8,765,000
0:40:53.547851 INFO: Number of elution groups: 8,767,137
0:40:53.548012 INFO: 	average size: 2.00
0:40:53.945365 INFO: Number of proteins: 52,753
0:40:53.992463 INFO: Number of channels: 1 ([0])
0:40:53.992704 INFO: Isotopes Distribution for 4 isotopes
0:40:53.992744 INFO: =======================================
0:40:53.992812 PROGRESS: =================== Starting Search Workflows for step library ===================
0:40:53.992938 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 
0:40:53.993024 INFO: Quantification results path: /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant
0:40:53.993102 INFO: Creating folder /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/figures
0:40:53.993347 INFO: Initializing TimingManager
0:40:53.993891 INFO: Initializing RawFileManager
0:41:48.908048 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.
0:41:48.916377 INFO: Determining DIA cycle
0:41:49.238254 INFO: Found cycle with start 0.00 min and length 300.
0:41:49.415278 INFO: RT (min)            : 0.0 - 26.9
0:41:49.415376 INFO: RT duration (sec)   : 1611.2
0:41:49.415407 INFO: RT duration (min)   : 26.9
0:41:49.415431 INFO: Cycle len (scans)   : 300
0:41:49.415452 INFO: Cycle len (sec)     : 1.65
0:41:49.415473 INFO: Number of cycles    : 977
0:41:49.415494 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:41:49.415529 INFO: Creating DIA data object took: 55.42153549194336
0:41:50.918462 INFO: Creating DIA data NG object took: 1.5027880668640137
0:41:53.033072 INFO: Initializing CalibrationManager
0:41:53.033388 INFO: Setting up calibration estimators ..
0:41:53.033462 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:41:53.033547 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'}' ..
0:41:53.033649 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:41:53.033711 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:41:53.033774 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}}' ..
0:41:53.033831 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:41:53.033880 INFO: Done setting up calibration estimators.
0:41:53.034076 INFO: Initializing OptimizationManager
0:41:53.034231 INFO: initial parameter: ms1_error = 20
0:41:53.034293 INFO: initial parameter: ms2_error = 20
0:41:53.034345 INFO: initial parameter: rt_error = 805.5992431640625
0:41:53.034394 INFO: initial parameter: mobility_error = 0.1
0:41:53.034446 INFO: initial parameter: num_candidates = 1
0:41:53.034490 INFO: initial parameter: fwhm_rt = 5
0:41:53.034534 INFO: initial parameter: fwhm_mobility = 0.01
0:41:53.034579 INFO: initial parameter: score_cutoff = 0
0:41:53.034625 INFO: initial parameter: classifier_version = -1
0:41:53.034699 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:41:53.035058 INFO: FDRManager: loading saved state not requested, will be initialized.
0:41:53.035105 INFO: Initializing FDRManager
0:41:53.035160 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
0:41:55.443212 PROGRESS: Initializing spectral library: 7,536,970 target precursors potentially observable (1,230,167 removed)
0:41:58.214336 INFO: Updating optimization_manager: ms2_error           : 20 -> 20
0:41:58.214827 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
0:41:58.214970 PROGRESS: Starting initial search for precursors.
0:41:58.215073 INFO: Starting optimization step 0.
0:41:58.215150 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:41:58.215218 INFO: Using rust extraction backend
0:41:58.215289 PROGRESS: Extracting batch of 1988 precursors
0:41:58.221041 INFO: === Search parameters used ===
0:41:58.221191 INFO: rt_error       : 805.5992431640625
0:41:58.221254 INFO: mobility_error : 0.1
0:41:58.221308 INFO: num_candidates : 1
0:41:58.221359 INFO: ms1_error      : 20
0:41:58.221406 INFO: ms2_error      : 20
0:41:58.221454 INFO: fwhm_rt        : 5
0:41:58.221501 INFO: quant_window   : 3
0:41:58.221550 INFO: ==============================================
0:41:58.259082 INFO: performing precursor FDR with 40 features
0:41:58.259202 INFO: Decoy channel: -1
0:41:58.259230 INFO: competitive: True
0:41:58.260567 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:58.262573 INFO: Estimating optimal hyperparameters - samples: 1,582, batch_size: 128, learning_rate: 1.77e-04
0:41:58.263518 INFO: Using random state 521800 for train-test-split
0:41:58.408553 INFO: Test AUC: 0.505
0:41:58.408698 INFO: Train AUC: 0.598
0:41:58.408736 INFO: AUC difference: 15.61%
0:41:58.408766 WARNING: AUC difference > 5%. This may indicate overfitting.
0:41:58.722532 INFO: Resetting torch num_threads to 32
0:41:58.724068 PROGRESS: === Extracted 1978 precursors and 9370 fragments ===
0:41:58.724434 INFO: === FDR correction performed with classifier version -1 ===
0:41:58.724950 PROGRESS: ============================= Precursor FDR =============================
0:41:58.725047 PROGRESS: Total precursors accumulated: 3
0:41:58.725108 PROGRESS: Target precursors: 3 (100.00%)
0:41:58.725161 PROGRESS: Decoy precursors: 0 (0.00%)
0:41:58.725210 PROGRESS: 
0:41:58.725256 PROGRESS: Precursor Summary:
0:41:58.726323 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
0:41:58.726410 PROGRESS: 
0:41:58.726465 PROGRESS: Protein Summary:
0:41:58.727690 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
0:41:58.727781 PROGRESS: =========================================================================
0:41:58.727969 INFO: Target number of precursors not reached yet.
0:41:58.832234 INFO: Starting optimization step 1.
0:41:58.832521 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:41:58.832648 INFO: Using rust extraction backend
0:41:58.832744 PROGRESS: Extracting batch of 3976 precursors
0:41:58.841417 INFO: === Search parameters used ===
0:41:58.841606 INFO: rt_error       : 805.5992431640625
0:41:58.841686 INFO: mobility_error : 0.1
0:41:58.841753 INFO: num_candidates : 1
0:41:58.841818 INFO: ms1_error      : 20
0:41:58.841879 INFO: ms2_error      : 20
0:41:58.841942 INFO: fwhm_rt        : 5
0:41:58.842002 INFO: quant_window   : 3
0:41:58.842062 INFO: ==============================================
0:41:58.906565 INFO: performing precursor FDR with 40 features
0:41:58.906709 INFO: Decoy channel: -1
0:41:58.906741 INFO: competitive: True
0:41:58.912576 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:58.916093 INFO: Estimating optimal hyperparameters - samples: 4,742, batch_size: 128, learning_rate: 1.77e-04
0:41:58.916208 INFO: Using random state 334822 for train-test-split
0:41:59.451886 INFO: Test AUC: 0.532
0:41:59.452007 INFO: Train AUC: 0.586
0:41:59.452037 INFO: AUC difference: 9.31%
0:41:59.452060 WARNING: AUC difference > 5%. This may indicate overfitting.
0:41:59.709830 INFO: Resetting torch num_threads to 32
0:41:59.713443 PROGRESS: === Extracted 5928 precursors and 28282 fragments ===
0:41:59.713887 INFO: === FDR correction performed with classifier version -1 ===
0:41:59.714505 PROGRESS: ============================= Precursor FDR =============================
0:41:59.714608 PROGRESS: Total precursors accumulated: 84
0:41:59.714681 PROGRESS: Target precursors: 84 (100.00%)
0:41:59.714748 PROGRESS: Decoy precursors: 0 (0.00%)
0:41:59.714807 PROGRESS: 
0:41:59.714865 PROGRESS: Precursor Summary:
0:41:59.716347 PROGRESS: Channel   0:	 0.050 FDR:    84; 0.010 FDR:    84; 0.001 FDR:    84
0:41:59.716454 PROGRESS: 
0:41:59.716523 PROGRESS: Protein Summary:
0:41:59.718212 PROGRESS: Channel   0:	 0.050 FDR:    84; 0.010 FDR:    84; 0.001 FDR:    84
0:41:59.718326 PROGRESS: =========================================================================
0:41:59.718659 INFO: Target number of precursors not reached yet.
0:41:59.849249 INFO: Starting optimization step 2.
0:41:59.849561 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:41:59.849673 INFO: Using rust extraction backend
0:41:59.849755 PROGRESS: Extracting batch of 7946 precursors
0:41:59.868318 INFO: === Search parameters used ===
0:41:59.868597 INFO: rt_error       : 805.5992431640625
0:41:59.868680 INFO: mobility_error : 0.1
0:41:59.868736 INFO: num_candidates : 1
0:41:59.868788 INFO: ms1_error      : 20
0:41:59.868839 INFO: ms2_error      : 20
0:41:59.868891 INFO: fwhm_rt        : 5
0:41:59.868944 INFO: quant_window   : 3
0:41:59.868994 INFO: ==============================================
0:41:59.968623 INFO: performing precursor FDR with 40 features
0:41:59.968751 INFO: Decoy channel: -1
0:41:59.968786 INFO: competitive: True
0:41:59.975031 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:59.978715 INFO: Estimating optimal hyperparameters - samples: 11,046, batch_size: 128, learning_rate: 1.77e-04
0:41:59.978851 INFO: Using random state 962894 for train-test-split
0:42:00.882068 INFO: Test AUC: 0.529
0:42:00.882212 INFO: Train AUC: 0.594
0:42:00.882246 INFO: AUC difference: 10.84%
0:42:00.882271 WARNING: AUC difference > 5%. This may indicate overfitting.
0:42:01.137423 INFO: Resetting torch num_threads to 32
0:42:01.142587 PROGRESS: === Extracted 13808 precursors and 65473 fragments ===
0:42:01.143111 INFO: === FDR correction performed with classifier version -1 ===
0:42:01.143705 PROGRESS: ============================= Precursor FDR =============================
0:42:01.143800 PROGRESS: Total precursors accumulated: 37
0:42:01.143865 PROGRESS: Target precursors: 37 (100.00%)
0:42:01.143921 PROGRESS: Decoy precursors: 0 (0.00%)
0:42:01.143972 PROGRESS: 
0:42:01.144022 PROGRESS: Precursor Summary:
0:42:01.145145 PROGRESS: Channel   0:	 0.050 FDR:    37; 0.010 FDR:    37; 0.001 FDR:    37
0:42:01.145245 PROGRESS: 
0:42:01.145308 PROGRESS: Protein Summary:
0:42:01.146524 PROGRESS: Channel   0:	 0.050 FDR:    37; 0.010 FDR:    37; 0.001 FDR:    37
0:42:01.146620 PROGRESS: =========================================================================
0:42:01.146973 INFO: Target number of precursors not reached yet.
0:42:01.268397 INFO: Starting optimization step 3.
0:42:01.268688 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:42:01.268817 INFO: Using rust extraction backend
0:42:01.268902 PROGRESS: Extracting batch of 15879 precursors
0:42:01.299145 INFO: === Search parameters used ===
0:42:01.299378 INFO: rt_error       : 805.5992431640625
0:42:01.299440 INFO: mobility_error : 0.1
0:42:01.299492 INFO: num_candidates : 1
0:42:01.299556 INFO: ms1_error      : 20
0:42:01.299600 INFO: ms2_error      : 20
0:42:01.299658 INFO: fwhm_rt        : 5
0:42:01.299703 INFO: quant_window   : 3
0:42:01.299745 INFO: ==============================================
0:42:01.467997 INFO: performing precursor FDR with 40 features
0:42:01.468151 INFO: Decoy channel: -1
0:42:01.468182 INFO: competitive: True
0:42:01.488557 INFO: Setting torch num_threads to 2 for FDR classification task
0:42:01.500962 INFO: Estimating optimal hyperparameters - samples: 23,642, batch_size: 128, learning_rate: 1.77e-04
0:42:01.501192 INFO: Using random state 434968 for train-test-split
0:42:03.589041 INFO: Test AUC: 0.551
0:42:03.589167 INFO: Train AUC: 0.599
0:42:03.589197 INFO: AUC difference: 8.03%
0:42:03.589220 WARNING: AUC difference > 5%. This may indicate overfitting.
0:42:03.848213 INFO: Resetting torch num_threads to 32
0:42:03.856185 PROGRESS: === Extracted 29553 precursors and 139734 fragments ===
0:42:03.856775 INFO: === FDR correction performed with classifier version -1 ===
0:42:03.857362 PROGRESS: ============================= Precursor FDR =============================
0:42:03.857450 PROGRESS: Total precursors accumulated: 19
0:42:03.857508 PROGRESS: Target precursors: 19 (100.00%)
0:42:03.857559 PROGRESS: Decoy precursors: 0 (0.00%)
0:42:03.857607 PROGRESS: 
0:42:03.857653 PROGRESS: Precursor Summary:
0:42:03.858702 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
0:42:03.858787 PROGRESS: 
0:42:03.858842 PROGRESS: Protein Summary:
0:42:03.859997 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
0:42:03.860084 PROGRESS: =========================================================================
0:42:03.860548 INFO: Target number of precursors not reached yet.
0:42:04.005498 INFO: Starting optimization step 4.
0:42:04.005767 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:42:04.005858 INFO: Using rust extraction backend
0:42:04.005927 PROGRESS: Extracting batch of 31750 precursors
0:42:04.064263 INFO: === Search parameters used ===
0:42:04.064554 INFO: rt_error       : 805.5992431640625
0:42:04.064630 INFO: mobility_error : 0.1
0:42:04.064689 INFO: num_candidates : 1
0:42:04.064734 INFO: ms1_error      : 20
0:42:04.064778 INFO: ms2_error      : 20
0:42:04.064820 INFO: fwhm_rt        : 5
0:42:04.064862 INFO: quant_window   : 3
0:42:04.064903 INFO: ==============================================
0:42:04.338167 INFO: performing precursor FDR with 40 features
0:42:04.338309 INFO: Decoy channel: -1
0:42:04.338335 INFO: competitive: True
0:42:04.362906 INFO: Setting torch num_threads to 2 for FDR classification task
0:42:04.379885 INFO: Estimating optimal hyperparameters - samples: 48,839, batch_size: 200, learning_rate: 2.21e-04
0:42:04.380110 INFO: Using random state 738154 for train-test-split
0:42:08.092050 INFO: Test AUC: 0.566
0:42:08.092171 INFO: Train AUC: 0.609
0:42:08.092205 INFO: AUC difference: 7.16%
0:42:08.092231 WARNING: AUC difference > 5%. This may indicate overfitting.
0:42:08.364912 INFO: Resetting torch num_threads to 32
0:42:08.376504 PROGRESS: === Extracted 61049 precursors and 289390 fragments ===
0:42:08.377137 INFO: === FDR correction performed with classifier version -1 ===
0:42:08.377709 PROGRESS: ============================= Precursor FDR =============================
0:42:08.377818 PROGRESS: Total precursors accumulated: 158
0:42:08.377886 PROGRESS: Target precursors: 157 (99.37%)
0:42:08.377945 PROGRESS: Decoy precursors: 1 (0.63%)
0:42:08.377997 PROGRESS: 
0:42:08.378046 PROGRESS: Precursor Summary:
0:42:08.379054 PROGRESS: Channel   0:	 0.050 FDR:   157; 0.010 FDR:   157; 0.001 FDR:   152
0:42:08.379156 PROGRESS: 
0:42:08.379220 PROGRESS: Protein Summary:
0:42:08.380354 PROGRESS: Channel   0:	 0.050 FDR:   152; 0.010 FDR:   152; 0.001 FDR:   147
0:42:08.380448 PROGRESS: =========================================================================
0:42:08.381402 INFO: Target number of precursors not reached yet.
0:42:08.571506 INFO: Starting optimization step 5.
0:42:08.571789 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:42:08.571883 INFO: Using rust extraction backend
0:42:08.571951 PROGRESS: Extracting batch of 63536 precursors
0:42:08.686574 INFO: === Search parameters used ===
0:42:08.686836 INFO: rt_error       : 805.5992431640625
0:42:08.686898 INFO: mobility_error : 0.1
0:42:08.686948 INFO: num_candidates : 1
0:42:08.686994 INFO: ms1_error      : 20
0:42:08.687039 INFO: ms2_error      : 20
0:42:08.687081 INFO: fwhm_rt        : 5
0:42:08.687122 INFO: quant_window   : 3
0:42:08.687162 INFO: ==============================================
0:42:09.222622 INFO: performing precursor FDR with 40 features
0:42:09.222750 INFO: Decoy channel: -1
0:42:09.222777 INFO: competitive: True
0:42:09.276284 INFO: Setting torch num_threads to 2 for FDR classification task
0:42:09.313401 INFO: Estimating optimal hyperparameters - samples: 99,280, batch_size: 406, learning_rate: 3.15e-04
0:42:09.313698 INFO: Using random state 752949 for train-test-split
0:42:13.674229 INFO: Test AUC: 0.579
0:42:13.674402 INFO: Train AUC: 0.608
0:42:13.674445 INFO: AUC difference: 4.76%
0:42:13.961120 INFO: Resetting torch num_threads to 32
0:42:13.984023 PROGRESS: === Extracted 124100 precursors and 588205 fragments ===
0:42:13.984770 INFO: === FDR correction performed with classifier version -1 ===
0:42:13.985443 PROGRESS: ============================= Precursor FDR =============================
0:42:13.985564 PROGRESS: Total precursors accumulated: 328
0:42:13.985656 PROGRESS: Target precursors: 325 (99.09%)
0:42:13.985736 PROGRESS: Decoy precursors: 3 (0.91%)
0:42:13.985807 PROGRESS: 
0:42:13.985874 PROGRESS: Precursor Summary:
0:42:13.986985 PROGRESS: Channel   0:	 0.050 FDR:   325; 0.010 FDR:   325; 0.001 FDR:     0
0:42:13.987098 PROGRESS: 
0:42:13.987180 PROGRESS: Protein Summary:
0:42:13.988427 PROGRESS: Channel   0:	 0.050 FDR:   311; 0.010 FDR:   311; 0.001 FDR:     0
0:42:13.988535 PROGRESS: =========================================================================
0:42:13.990458 INFO: Target number of precursors not reached yet.
0:42:14.267781 INFO: Starting optimization step 6.
0:42:14.268087 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:42:14.268199 INFO: Using rust extraction backend
0:42:14.268300 PROGRESS: Extracting batch of 127107 precursors
0:42:14.496049 INFO: === Search parameters used ===
0:42:14.496329 INFO: rt_error       : 805.5992431640625
0:42:14.496411 INFO: mobility_error : 0.1
0:42:14.496482 INFO: num_candidates : 1
0:42:14.496548 INFO: ms1_error      : 20
0:42:14.496642 INFO: ms2_error      : 20
0:42:14.496712 INFO: fwhm_rt        : 5
0:42:14.496773 INFO: quant_window   : 3
0:42:14.496833 INFO: ==============================================
0:42:15.535028 INFO: performing precursor FDR with 40 features
0:42:15.535181 INFO: Decoy channel: -1
0:42:15.535208 INFO: competitive: True
0:42:15.642209 INFO: Setting torch num_threads to 2 for FDR classification task
0:42:15.725744 INFO: Estimating optimal hyperparameters - samples: 200,189, batch_size: 819, learning_rate: 4.47e-04
0:42:15.726238 INFO: Using random state 622129 for train-test-split
0:42:22.126038 INFO: Test AUC: 0.584
0:42:22.126184 INFO: Train AUC: 0.605
0:42:22.126220 INFO: AUC difference: 3.55%
0:42:22.451352 INFO: Resetting torch num_threads to 32
0:42:22.499659 PROGRESS: === Extracted 250237 precursors and 1182593 fragments ===
0:42:22.500371 INFO: === FDR correction performed with classifier version -1 ===
0:42:22.501137 PROGRESS: ============================= Precursor FDR =============================
0:42:22.501234 PROGRESS: Total precursors accumulated: 779
0:42:22.501296 PROGRESS: Target precursors: 772 (99.10%)
0:42:22.501350 PROGRESS: Decoy precursors: 7 (0.90%)
0:42:22.501399 PROGRESS: 
0:42:22.501446 PROGRESS: Precursor Summary:
0:42:22.502636 PROGRESS: Channel   0:	 0.050 FDR:   772; 0.010 FDR:   772; 0.001 FDR:   417
0:42:22.502733 PROGRESS: 
0:42:22.502791 PROGRESS: Protein Summary:
0:42:22.504209 PROGRESS: Channel   0:	 0.050 FDR:   696; 0.010 FDR:   696; 0.001 FDR:   385
0:42:22.504310 PROGRESS: =========================================================================
0:42:22.508197 INFO: Target number of precursors not reached yet.
0:42:22.949616 INFO: Starting optimization step 7.
0:42:22.949896 PROGRESS: === Extracting elution groups 127000 to 255000 ===
0:42:22.949999 INFO: Using rust extraction backend
0:42:22.950084 PROGRESS: Extracting batch of 254254 precursors
0:42:23.404139 INFO: === Search parameters used ===
0:42:23.404420 INFO: rt_error       : 805.5992431640625
0:42:23.404486 INFO: mobility_error : 0.1
0:42:23.404540 INFO: num_candidates : 1
0:42:23.404588 INFO: ms1_error      : 20
0:42:23.404673 INFO: ms2_error      : 20
0:42:23.404738 INFO: fwhm_rt        : 5
0:42:23.404793 INFO: quant_window   : 3
0:42:23.404839 INFO: ==============================================
0:42:25.431999 INFO: performing precursor FDR with 40 features
0:42:25.432123 INFO: Decoy channel: -1
0:42:25.432150 INFO: competitive: True
0:42:25.659584 INFO: Setting torch num_threads to 2 for FDR classification task
0:42:25.882474 INFO: Estimating optimal hyperparameters - samples: 402,024, batch_size: 1,646, learning_rate: 6.34e-04
0:42:25.883186 INFO: Using random state 606650 for train-test-split
0:42:36.228564 INFO: Test AUC: 0.586
0:42:36.228767 INFO: Train AUC: 0.603
0:42:36.228814 INFO: AUC difference: 2.78%
0:42:36.673785 INFO: Resetting torch num_threads to 32
0:42:36.779876 PROGRESS: === Extracted 502530 precursors and 2374719 fragments ===
0:42:36.780642 INFO: === FDR correction performed with classifier version -1 ===
0:42:36.781603 PROGRESS: ============================= Precursor FDR =============================
0:42:36.781699 PROGRESS: Total precursors accumulated: 1,757
0:42:36.781775 PROGRESS: Target precursors: 1,740 (99.03%)
0:42:36.781831 PROGRESS: Decoy precursors: 17 (0.97%)
0:42:36.781882 PROGRESS: 
0:42:36.781931 PROGRESS: Precursor Summary:
0:42:36.783299 PROGRESS: Channel   0:	 0.050 FDR: 1,740; 0.010 FDR: 1,740; 0.001 FDR:     0
0:42:36.783393 PROGRESS: 
0:42:36.783453 PROGRESS: Protein Summary:
0:42:36.785175 PROGRESS: Channel   0:	 0.050 FDR: 1,443; 0.010 FDR: 1,443; 0.001 FDR:     0
0:42:36.785275 PROGRESS: =========================================================================
0:42:36.793687 INFO: Target number of precursors reached.
0:42:37.138642 INFO: fragments_df: keeping 5000 of 2374719 [sum(precursor_idx_mask)=18529 sum(mass_error_mask)=2374719 stop_rank=5000
0:42:38.160555 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:42:38.443514 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:42:39.217885 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:42:39.218649 INFO: Using score_cutoff 12.8558999001503 (fac=0.99, q=1)
0:42:39.219151 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:42:39.219251 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:42:39.219321 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.8558999001503
0:42:39.219407 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:42:39.534531 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:42:40.296696 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
0:42:40.296936 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:42:40.297060 INFO: Starting optimization step 8.
0:42:40.297140 PROGRESS: === Extracting elution groups 0 to 255000 ===
0:42:40.297228 INFO: Using rust extraction backend
0:42:40.297304 PROGRESS: Extracting batch of 506436 precursors
0:42:41.197494 INFO: === Search parameters used ===
0:42:41.197806 INFO: rt_error       : 805.5992431640625
0:42:41.197881 INFO: mobility_error : 0.1
0:42:41.197943 INFO: num_candidates : 3
0:42:41.197995 INFO: ms1_error      : 20
0:42:41.198043 INFO: ms2_error      : 20
0:42:41.198092 INFO: fwhm_rt        : 3.0
0:42:41.198157 INFO: quant_window   : 3
0:42:41.198209 INFO: ==============================================
0:42:48.387754 INFO: performing precursor FDR with 40 features
0:42:48.387957 INFO: Decoy channel: -1
0:42:48.387989 INFO: competitive: True
0:42:48.841220 INFO: Setting torch num_threads to 2 for FDR classification task
0:42:49.521504 INFO: Estimating optimal hyperparameters - samples: 1,204,568, batch_size: 4,096, learning_rate: 1.00e-03
0:42:49.523668 INFO: Using random state 190806 for train-test-split
0:43:14.790734 INFO: Test AUC: 0.595
0:43:14.790961 INFO: Train AUC: 0.602
0:43:14.790999 INFO: AUC difference: 1.27%
0:43:15.968363 INFO: Resetting torch num_threads to 32
0:43:16.024820 PROGRESS: === Extracted 1505710 precursors and 6888398 fragments ===
0:43:16.025407 INFO: === FDR correction performed with classifier version 7 ===
0:43:16.026499 PROGRESS: ============================= Precursor FDR =============================
0:43:16.026640 PROGRESS: Total precursors accumulated: 1,989
0:43:16.026709 PROGRESS: Target precursors: 1,970 (99.04%)
0:43:16.026767 PROGRESS: Decoy precursors: 19 (0.96%)
0:43:16.026819 PROGRESS: 
0:43:16.026870 PROGRESS: Precursor Summary:
0:43:16.028637 PROGRESS: Channel   0:	 0.050 FDR: 1,970; 0.010 FDR: 1,970; 0.001 FDR: 1,340
0:43:16.028768 PROGRESS: 
0:43:16.028832 PROGRESS: Protein Summary:
0:43:16.030992 PROGRESS: Channel   0:	 0.050 FDR: 1,594; 0.010 FDR: 1,594; 0.001 FDR: 1,111
0:43:16.031116 PROGRESS: =========================================================================
0:43:16.063315 INFO: Target number of precursors reached.
0:43:16.790009 INFO: fragments_df: keeping 5000 of 6888398 [sum(precursor_idx_mask)=45321 sum(mass_error_mask)=6888398 stop_rank=5000
0:43:17.666587 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:43:18.003776 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:43:18.727943 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:43:18.728466 INFO: Using score_cutoff 12.630478340148926 (fac=0.99, q=1)
0:43:18.728825 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:43:18.728915 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:43:18.728973 INFO: Updating optimization_manager: score_cutoff        : 12.8558999001503 -> 12.630478340148926
0:43:18.729037 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:43:19.041717 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:43:19.872629 INFO: === checking if optimization conditions were reached ===
0:43:19.875214 INFO: Updating optimization_manager: ms2_error           : 20 -> 10.0
0:43:19.875351 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:43:19.875431 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:43:19.875501 INFO: ==============================================
0:43:19.875608 INFO: Starting optimization step 9.
0:43:19.875692 PROGRESS: === Extracting elution groups 0 to 255000 ===
0:43:19.875774 INFO: Using rust extraction backend
0:43:19.875848 PROGRESS: Extracting batch of 506436 precursors
0:43:20.978971 INFO: === Search parameters used ===
0:43:20.979405 INFO: rt_error       : 805.5992431640625
0:43:20.979536 INFO: mobility_error : 0.1
0:43:20.979630 INFO: num_candidates : 3
0:43:20.979724 INFO: ms1_error      : 20
0:43:20.979834 INFO: ms2_error      : 10.0
0:43:20.979925 INFO: fwhm_rt        : 3.0
0:43:20.980002 INFO: quant_window   : 3
0:43:20.980077 INFO: ==============================================
0:43:27.930533 INFO: performing precursor FDR with 40 features
0:43:27.930718 INFO: Decoy channel: -1
0:43:27.930747 INFO: competitive: True
0:43:28.404937 INFO: Setting torch num_threads to 2 for FDR classification task
0:43:29.081969 INFO: Estimating optimal hyperparameters - samples: 1,211,811, batch_size: 4,096, learning_rate: 1.00e-03
0:43:29.084143 INFO: Using random state 49516 for train-test-split
0:43:52.202054 INFO: Test AUC: 0.600
0:43:52.202258 INFO: Train AUC: 0.607
0:43:52.202295 INFO: AUC difference: 1.13%
0:43:52.975794 INFO: Resetting torch num_threads to 32
0:43:53.098951 PROGRESS: === Extracted 1514764 precursors and 7657401 fragments ===
0:43:53.099539 INFO: === FDR correction performed with classifier version 8 ===
0:43:53.100500 PROGRESS: ============================= Precursor FDR =============================
0:43:53.100620 PROGRESS: Total precursors accumulated: 2,353
0:43:53.100692 PROGRESS: Target precursors: 2,330 (99.02%)
0:43:53.100749 PROGRESS: Decoy precursors: 23 (0.98%)
0:43:53.100799 PROGRESS: 
0:43:53.100846 PROGRESS: Precursor Summary:
0:43:53.102658 PROGRESS: Channel   0:	 0.050 FDR: 2,330; 0.010 FDR: 2,330; 0.001 FDR: 1,705
0:43:53.102764 PROGRESS: 
0:43:53.102822 PROGRESS: Protein Summary:
0:43:53.105017 PROGRESS: Channel   0:	 0.050 FDR: 1,851; 0.010 FDR: 1,851; 0.001 FDR: 1,401
0:43:53.105119 PROGRESS: =========================================================================
0:43:53.135120 INFO: Target number of precursors reached.
0:43:53.948512 INFO: fragments_df: keeping 5000 of 7657401 [sum(precursor_idx_mask)=55926 sum(mass_error_mask)=7657401 stop_rank=5000
0:43:54.458492 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:43:54.803216 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:43:55.534517 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:43:55.535024 INFO: Using score_cutoff 12.288440740299226 (fac=0.99, q=1)
0:43:55.535378 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:43:55.535460 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:43:55.535517 INFO: Updating optimization_manager: score_cutoff        : 12.630478340148926 -> 12.288440740299226
0:43:55.535581 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:43:55.690996 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:43:56.087937 INFO: === checking if optimization conditions were reached ===
0:43:56.090729 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:43:56.090927 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:43:56.091015 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:43:56.091097 INFO: ==============================================
0:43:56.091191 INFO: Starting optimization step 10.
0:43:56.091282 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:43:56.091407 INFO: Using rust extraction backend
0:43:56.091506 PROGRESS: Extracting batch of 252182 precursors
0:43:56.552357 INFO: === Search parameters used ===
0:43:56.552713 INFO: rt_error       : 805.5992431640625
0:43:56.552783 INFO: mobility_error : 0.1
0:43:56.552842 INFO: num_candidates : 3
0:43:56.552893 INFO: ms1_error      : 20
0:43:56.552959 INFO: ms2_error      : 10.0
0:43:56.553012 INFO: fwhm_rt        : 3.0
0:43:56.553062 INFO: quant_window   : 3
0:43:56.553109 INFO: ==============================================
0:44:00.019110 INFO: performing precursor FDR with 40 features
0:44:00.019257 INFO: Decoy channel: -1
0:44:00.019284 INFO: competitive: True
0:44:00.222118 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:00.533326 INFO: Estimating optimal hyperparameters - samples: 603,453, batch_size: 2,471, learning_rate: 7.77e-04
0:44:00.534238 INFO: Using random state 210665 for train-test-split
0:44:14.384048 INFO: Test AUC: 0.601
0:44:14.384259 INFO: Train AUC: 0.614
0:44:14.384296 INFO: AUC difference: 1.99%
0:44:14.861787 INFO: Resetting torch num_threads to 32
0:44:14.898527 PROGRESS: === Extracted 754317 precursors and 3814486 fragments ===
0:44:14.899069 INFO: === FDR correction performed with classifier version 9 ===
0:44:14.899757 PROGRESS: ============================= Precursor FDR =============================
0:44:14.899853 PROGRESS: Total precursors accumulated: 1,354
0:44:14.899920 PROGRESS: Target precursors: 1,341 (99.04%)
0:44:14.899976 PROGRESS: Decoy precursors: 13 (0.96%)
0:44:14.900027 PROGRESS: 
0:44:14.900074 PROGRESS: Precursor Summary:
0:44:14.901334 PROGRESS: Channel   0:	 0.050 FDR: 1,341; 0.010 FDR: 1,341; 0.001 FDR:     1
0:44:14.901438 PROGRESS: 
0:44:14.901498 PROGRESS: Protein Summary:
0:44:14.903059 PROGRESS: Channel   0:	 0.050 FDR: 1,171; 0.010 FDR: 1,171; 0.001 FDR:     1
0:44:14.903165 PROGRESS: =========================================================================
0:44:14.917366 INFO: Target number of precursors reached.
0:44:15.337030 INFO: fragments_df: keeping 5000 of 3814486 [sum(precursor_idx_mask)=31683 sum(mass_error_mask)=3814486 stop_rank=5000
0:44:15.809826 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:16.037625 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:16.941826 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:44:16.942694 INFO: Using score_cutoff 11.317833297729491 (fac=0.99, q=1)
0:44:16.943310 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:44:16.943449 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:44:16.943524 INFO: Updating optimization_manager: score_cutoff        : 12.288440740299226 -> 11.317833297729491
0:44:16.943617 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:17.115762 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:17.630456 INFO: === checking if optimization conditions were reached ===
0:44:17.633924 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:44:17.634106 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:44:17.634200 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:44:17.634313 INFO: ==============================================
0:44:17.634418 INFO: Starting optimization step 11.
0:44:17.634508 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:44:17.634620 INFO: Using rust extraction backend
0:44:17.634725 PROGRESS: Extracting batch of 252182 precursors
0:44:18.183263 INFO: === Search parameters used ===
0:44:18.183674 INFO: rt_error       : 805.5992431640625
0:44:18.183808 INFO: mobility_error : 0.1
0:44:18.183927 INFO: num_candidates : 3
0:44:18.184008 INFO: ms1_error      : 20
0:44:18.184073 INFO: ms2_error      : 10.0
0:44:18.184136 INFO: fwhm_rt        : 3.0
0:44:18.184202 INFO: quant_window   : 3
0:44:18.184276 INFO: ==============================================
0:44:22.841712 INFO: performing precursor FDR with 40 features
0:44:22.841893 INFO: Decoy channel: -1
0:44:22.841930 INFO: competitive: True
0:44:23.146004 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:23.659583 INFO: Estimating optimal hyperparameters - samples: 603,454, batch_size: 2,471, learning_rate: 7.77e-04
0:44:23.661268 INFO: Using random state 804993 for train-test-split
0:44:41.060760 INFO: Test AUC: 0.605
0:44:41.061029 INFO: Train AUC: 0.616
0:44:41.061077 INFO: AUC difference: 1.77%
0:44:41.699366 INFO: Resetting torch num_threads to 32
0:44:41.769576 PROGRESS: === Extracted 754318 precursors and 3814258 fragments ===
0:44:41.770193 INFO: === FDR correction performed with classifier version 10 ===
0:44:41.771001 PROGRESS: ============================= Precursor FDR =============================
0:44:41.771102 PROGRESS: Total precursors accumulated: 1,429
0:44:41.771185 PROGRESS: Target precursors: 1,415 (99.02%)
0:44:41.771260 PROGRESS: Decoy precursors: 14 (0.98%)
0:44:41.771315 PROGRESS: 
0:44:41.771364 PROGRESS: Precursor Summary:
0:44:41.772806 PROGRESS: Channel   0:	 0.050 FDR: 1,415; 0.010 FDR: 1,415; 0.001 FDR: 1,062
0:44:41.772912 PROGRESS: 
0:44:41.772972 PROGRESS: Protein Summary:
0:44:41.774796 PROGRESS: Channel   0:	 0.050 FDR: 1,240; 0.010 FDR: 1,240; 0.001 FDR:   944
0:44:41.774896 PROGRESS: =========================================================================
0:44:41.796441 INFO: Target number of precursors reached.
0:44:42.246314 INFO: fragments_df: keeping 5000 of 3814258 [sum(precursor_idx_mask)=33135 sum(mass_error_mask)=3814258 stop_rank=5000
0:44:42.897239 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:44:43.268027 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:44:44.336200 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:44:44.337054 INFO: Using score_cutoff 10.163426165771485 (fac=0.99, q=1)
0:44:44.337608 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:44:44.337728 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:44:44.337800 INFO: Updating optimization_manager: score_cutoff        : 11.317833297729491 -> 10.163426165771485
0:44:44.337887 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:44:44.512319 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:44.973677 INFO: === checking if optimization conditions were reached ===
0:44:44.976789 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:44:44.977003 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:44:44.977090 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:44:44.977166 INFO: ==============================================
0:44:44.977256 INFO: Starting optimization step 12.
0:44:44.977334 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:44:44.977428 INFO: Using rust extraction backend
0:44:44.977516 PROGRESS: Extracting batch of 252182 precursors
0:44:45.488997 INFO: === Search parameters used ===
0:44:45.489390 INFO: rt_error       : 805.5992431640625
0:44:45.489500 INFO: mobility_error : 0.1
0:44:45.489569 INFO: num_candidates : 3
0:44:45.489629 INFO: ms1_error      : 20
0:44:45.489688 INFO: ms2_error      : 10.0
0:44:45.489744 INFO: fwhm_rt        : 3.0
0:44:45.489801 INFO: quant_window   : 3
0:44:45.489856 INFO: ==============================================
0:44:50.912264 INFO: performing precursor FDR with 40 features
0:44:50.912459 INFO: Decoy channel: -1
0:44:50.912495 INFO: competitive: True
0:44:51.286277 INFO: Setting torch num_threads to 2 for FDR classification task
0:44:51.916001 INFO: Estimating optimal hyperparameters - samples: 603,444, batch_size: 2,471, learning_rate: 7.77e-04
0:44:51.920088 INFO: Using random state 583343 for train-test-split
0:45:08.493986 INFO: Test AUC: 0.605
0:45:08.494198 INFO: Train AUC: 0.620
0:45:08.494234 INFO: AUC difference: 2.44%
0:45:09.047633 INFO: Resetting torch num_threads to 32
0:45:09.162754 PROGRESS: === Extracted 754305 precursors and 3814336 fragments ===
0:45:09.163498 INFO: === FDR correction performed with classifier version 11 ===
0:45:09.164608 PROGRESS: ============================= Precursor FDR =============================
0:45:09.164779 PROGRESS: Total precursors accumulated: 1,070
0:45:09.164862 PROGRESS: Target precursors: 1,060 (99.07%)
0:45:09.164935 PROGRESS: Decoy precursors: 10 (0.93%)
0:45:09.164998 PROGRESS: 
0:45:09.165058 PROGRESS: Precursor Summary:
0:45:09.166891 PROGRESS: Channel   0:	 0.050 FDR: 1,060; 0.010 FDR: 1,060; 0.001 FDR:     0
0:45:09.167034 PROGRESS: 
0:45:09.167106 PROGRESS: Protein Summary:
0:45:09.169278 PROGRESS: Channel   0:	 0.050 FDR:   950; 0.010 FDR:   950; 0.001 FDR:     0
0:45:09.169409 PROGRESS: =========================================================================
0:45:09.206865 INFO: Target number of precursors reached.
0:45:09.681935 INFO: fragments_df: keeping 5000 of 3814336 [sum(precursor_idx_mask)=25509 sum(mass_error_mask)=3814336 stop_rank=5000
0:45:10.301514 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:10.573814 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:11.345811 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:11.346575 INFO: Using score_cutoff 11.55432133026123 (fac=0.99, q=1)
0:45:11.347394 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:11.347519 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:11.347580 INFO: Updating optimization_manager: score_cutoff        : 10.163426165771485 -> 11.55432133026123
0:45:11.347651 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:11.527390 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:11.975498 INFO: === checking if optimization conditions were reached ===
0:45:11.979057 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:45:11.979281 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
0:45:11.979418 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:45:11.979514 INFO: ==============================================
0:45:11.979640 PROGRESS: Optimization finished for ms2_error.
0:45:12.768163 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:12.945741 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:13.405916 INFO: Starting optimization step 0.
0:45:13.406357 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:45:13.406538 INFO: Using rust extraction backend
0:45:13.406666 PROGRESS: Extracting batch of 252182 precursors
0:45:13.951272 INFO: === Search parameters used ===
0:45:13.951988 INFO: rt_error       : 805.5992431640625
0:45:13.952123 INFO: mobility_error : 0.1
0:45:13.952191 INFO: num_candidates : 3
0:45:13.952255 INFO: ms1_error      : 20
0:45:13.952309 INFO: ms2_error      : 10.0
0:45:13.952366 INFO: fwhm_rt        : 3.0
0:45:13.952415 INFO: quant_window   : 3
0:45:13.952466 INFO: ==============================================
0:45:18.873277 INFO: performing precursor FDR with 40 features
0:45:18.873508 INFO: Decoy channel: -1
0:45:18.873538 INFO: competitive: True
0:45:19.202840 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:19.671273 INFO: Estimating optimal hyperparameters - samples: 603,445, batch_size: 2,471, learning_rate: 7.77e-04
0:45:19.672940 INFO: Using random state 408365 for train-test-split
0:45:34.657765 INFO: Test AUC: 0.609
0:45:34.658018 INFO: Train AUC: 0.621
0:45:34.658061 INFO: AUC difference: 1.94%
0:45:35.267147 INFO: Resetting torch num_threads to 32
0:45:35.355547 PROGRESS: === Extracted 754307 precursors and 3814627 fragments ===
0:45:35.356374 INFO: === FDR correction performed with classifier version 12 ===
0:45:35.357796 PROGRESS: ============================= Precursor FDR =============================
0:45:35.357977 PROGRESS: Total precursors accumulated: 1,241
0:45:35.358065 PROGRESS: Target precursors: 1,229 (99.03%)
0:45:35.358140 PROGRESS: Decoy precursors: 12 (0.97%)
0:45:35.358206 PROGRESS: 
0:45:35.358286 PROGRESS: Precursor Summary:
0:45:35.360768 PROGRESS: Channel   0:	 0.050 FDR: 1,229; 0.010 FDR: 1,229; 0.001 FDR: 1,048
0:45:35.361039 PROGRESS: 
0:45:35.361154 PROGRESS: Protein Summary:
0:45:35.364325 PROGRESS: Channel   0:	 0.050 FDR: 1,089; 0.010 FDR: 1,089; 0.001 FDR:   937
0:45:35.364563 PROGRESS: =========================================================================
0:45:35.401590 INFO: Target number of precursors reached.
0:45:35.851979 INFO: fragments_df: keeping 5000 of 3814627 [sum(precursor_idx_mask)=28445 sum(mass_error_mask)=3814627 stop_rank=5000
0:45:36.472018 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:45:36.864150 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:45:37.929298 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:45:37.930041 INFO: Using score_cutoff 7.761738278388977 (fac=0.99, q=1)
0:45:37.930491 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:45:37.930593 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:45:37.930671 INFO: Updating optimization_manager: score_cutoff        : 11.55432133026123 -> 7.761738278388977
0:45:37.930761 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:45:38.108913 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:45:38.560571 INFO: === checking if optimization conditions were reached ===
0:45:38.561071 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:45:38.564813 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 627.5844030410176
0:45:38.564962 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 627.5844.
0:45:38.565068 INFO: ==============================================
0:45:38.565171 INFO: Starting optimization step 1.
0:45:38.565255 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:45:38.565371 INFO: Using rust extraction backend
0:45:38.565470 PROGRESS: Extracting batch of 252182 precursors
0:45:39.085997 INFO: === Search parameters used ===
0:45:39.086399 INFO: rt_error       : 627.5844030410176
0:45:39.086484 INFO: mobility_error : 0.1
0:45:39.086538 INFO: num_candidates : 3
0:45:39.086587 INFO: ms1_error      : 20
0:45:39.086637 INFO: ms2_error      : 10.0
0:45:39.086682 INFO: fwhm_rt        : 3.0
0:45:39.086727 INFO: quant_window   : 3
0:45:39.086771 INFO: ==============================================
0:45:43.595064 INFO: performing precursor FDR with 40 features
0:45:43.595230 INFO: Decoy channel: -1
0:45:43.595260 INFO: competitive: True
0:45:43.895935 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:44.331206 INFO: Estimating optimal hyperparameters - samples: 603,535, batch_size: 2,472, learning_rate: 7.77e-04
0:45:44.332939 INFO: Using random state 408365 for train-test-split
0:45:58.651762 INFO: Test AUC: 0.606
0:45:58.651991 INFO: Train AUC: 0.622
0:45:58.652029 INFO: AUC difference: 2.50%
0:45:59.199332 INFO: Resetting torch num_threads to 32
0:45:59.237377 PROGRESS: === Extracted 754419 precursors and 3815370 fragments ===
0:45:59.237970 INFO: === FDR correction performed with classifier version 12 ===
0:45:59.238794 PROGRESS: ============================= Precursor FDR =============================
0:45:59.238895 PROGRESS: Total precursors accumulated: 1,479
0:45:59.238966 PROGRESS: Target precursors: 1,465 (99.05%)
0:45:59.239026 PROGRESS: Decoy precursors: 14 (0.95%)
0:45:59.239079 PROGRESS: 
0:45:59.239128 PROGRESS: Precursor Summary:
0:45:59.240604 PROGRESS: Channel   0:	 0.050 FDR: 1,465; 0.010 FDR: 1,465; 0.001 FDR: 1,148
0:45:59.240734 PROGRESS: 
0:45:59.240794 PROGRESS: Protein Summary:
0:45:59.242692 PROGRESS: Channel   0:	 0.050 FDR: 1,282; 0.010 FDR: 1,282; 0.001 FDR: 1,012
0:45:59.242793 PROGRESS: =========================================================================
0:45:59.263954 INFO: Target number of precursors reached.
0:45:59.726289 INFO: fragments_df: keeping 5000 of 3815370 [sum(precursor_idx_mask)=34287 sum(mass_error_mask)=3815370 stop_rank=5000
0:46:00.365262 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:00.649367 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:02.322001 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:02.322543 INFO: Using score_cutoff 10.805512376403808 (fac=0.99, q=1)
0:46:02.322896 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:02.322985 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:02.323049 INFO: Updating optimization_manager: score_cutoff        : 7.761738278388977 -> 10.805512376403808
0:46:02.323116 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:02.500587 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:02.930985 INFO: === checking if optimization conditions were reached ===
0:46:02.931321 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:46:02.935139 INFO: Updating optimization_manager: rt_error            : 627.5844030410176 -> 707.9275098201135
0:46:02.935339 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 707.9275.
0:46:02.935425 INFO: ==============================================
0:46:02.935523 INFO: Starting optimization step 2.
0:46:02.935606 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:46:02.935699 INFO: Using rust extraction backend
0:46:02.935778 PROGRESS: Extracting batch of 252182 precursors
0:46:03.470158 INFO: === Search parameters used ===
0:46:03.470565 INFO: rt_error       : 707.9275098201135
0:46:03.470669 INFO: mobility_error : 0.1
0:46:03.470727 INFO: num_candidates : 3
0:46:03.470779 INFO: ms1_error      : 20
0:46:03.470827 INFO: ms2_error      : 10.0
0:46:03.470877 INFO: fwhm_rt        : 3.0
0:46:03.470924 INFO: quant_window   : 3
0:46:03.470971 INFO: ==============================================
0:46:08.266602 INFO: performing precursor FDR with 40 features
0:46:08.266856 INFO: Decoy channel: -1
0:46:08.266890 INFO: competitive: True
0:46:08.576409 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:09.101004 INFO: Estimating optimal hyperparameters - samples: 603,472, batch_size: 2,471, learning_rate: 7.77e-04
0:46:09.102978 INFO: Using random state 408365 for train-test-split
0:46:25.891649 INFO: Test AUC: 0.606
0:46:25.891865 INFO: Train AUC: 0.620
0:46:25.891902 INFO: AUC difference: 2.23%
0:46:26.429033 INFO: Resetting torch num_threads to 32
0:46:26.468498 PROGRESS: === Extracted 754340 precursors and 3813337 fragments ===
0:46:26.469140 INFO: === FDR correction performed with classifier version 12 ===
0:46:26.470113 PROGRESS: ============================= Precursor FDR =============================
0:46:26.470240 PROGRESS: Total precursors accumulated: 1,515
0:46:26.470309 PROGRESS: Target precursors: 1,500 (99.01%)
0:46:26.470366 PROGRESS: Decoy precursors: 15 (0.99%)
0:46:26.470425 PROGRESS: 
0:46:26.470477 PROGRESS: Precursor Summary:
0:46:26.472010 PROGRESS: Channel   0:	 0.050 FDR: 1,500; 0.010 FDR: 1,500; 0.001 FDR: 1,192
0:46:26.472113 PROGRESS: 
0:46:26.472176 PROGRESS: Protein Summary:
0:46:26.474201 PROGRESS: Channel   0:	 0.050 FDR: 1,320; 0.010 FDR: 1,320; 0.001 FDR: 1,050
0:46:26.474311 PROGRESS: =========================================================================
0:46:26.519669 INFO: Target number of precursors reached.
0:46:26.966578 INFO: fragments_df: keeping 5000 of 3813337 [sum(precursor_idx_mask)=33409 sum(mass_error_mask)=3813337 stop_rank=5000
0:46:27.574378 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:27.937875 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:28.754039 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:28.754734 INFO: Using score_cutoff 7.2091971294879915 (fac=0.99, q=1)
0:46:28.755142 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:28.755232 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:28.755306 INFO: Updating optimization_manager: score_cutoff        : 10.805512376403808 -> 7.2091971294879915
0:46:28.755386 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:28.920092 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:29.339638 INFO: === checking if optimization conditions were reached ===
0:46:29.340088 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:46:29.344135 INFO: Updating optimization_manager: rt_error            : 707.9275098201135 -> 729.4581311646555
0:46:29.344326 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 729.4581.
0:46:29.344433 INFO: ==============================================
0:46:29.344543 INFO: Starting optimization step 3.
0:46:29.344647 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:46:29.344775 INFO: Using rust extraction backend
0:46:29.344880 PROGRESS: Extracting batch of 252182 precursors
0:46:29.897306 INFO: === Search parameters used ===
0:46:29.897676 INFO: rt_error       : 729.4581311646555
0:46:29.897758 INFO: mobility_error : 0.1
0:46:29.897815 INFO: num_candidates : 3
0:46:29.897868 INFO: ms1_error      : 20
0:46:29.897919 INFO: ms2_error      : 10.0
0:46:29.897969 INFO: fwhm_rt        : 3.0
0:46:29.898019 INFO: quant_window   : 3
0:46:29.898069 INFO: ==============================================
0:46:34.794097 INFO: performing precursor FDR with 40 features
0:46:34.794315 INFO: Decoy channel: -1
0:46:34.794348 INFO: competitive: True
0:46:35.120064 INFO: Setting torch num_threads to 2 for FDR classification task
0:46:35.600966 INFO: Estimating optimal hyperparameters - samples: 603,474, batch_size: 2,471, learning_rate: 7.77e-04
0:46:35.602488 INFO: Using random state 408365 for train-test-split
0:46:54.556560 INFO: Test AUC: 0.610
0:46:54.556858 INFO: Train AUC: 0.622
0:46:54.556934 INFO: AUC difference: 1.94%
0:46:55.302602 INFO: Resetting torch num_threads to 32
0:46:55.367263 PROGRESS: === Extracted 754343 precursors and 3815725 fragments ===
0:46:55.367877 INFO: === FDR correction performed with classifier version 12 ===
0:46:55.368769 PROGRESS: ============================= Precursor FDR =============================
0:46:55.368881 PROGRESS: Total precursors accumulated: 1,493
0:46:55.368965 PROGRESS: Target precursors: 1,479 (99.06%)
0:46:55.369023 PROGRESS: Decoy precursors: 14 (0.94%)
0:46:55.369073 PROGRESS: 
0:46:55.369121 PROGRESS: Precursor Summary:
0:46:55.370596 PROGRESS: Channel   0:	 0.050 FDR: 1,479; 0.010 FDR: 1,479; 0.001 FDR: 1,125
0:46:55.370690 PROGRESS: 
0:46:55.370751 PROGRESS: Protein Summary:
0:46:55.372637 PROGRESS: Channel   0:	 0.050 FDR: 1,305; 0.010 FDR: 1,305; 0.001 FDR:   995
0:46:55.372747 PROGRESS: =========================================================================
0:46:55.394966 INFO: Target number of precursors reached.
0:46:55.854123 INFO: fragments_df: keeping 5000 of 3815725 [sum(precursor_idx_mask)=33857 sum(mass_error_mask)=3815725 stop_rank=5000
0:46:56.579731 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:46:56.850384 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:46:57.839234 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:46:57.840263 INFO: Using score_cutoff 7.844055055904389 (fac=0.99, q=1)
0:46:57.840983 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:46:57.841099 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:46:57.841174 INFO: Updating optimization_manager: score_cutoff        : 7.2091971294879915 -> 7.844055055904389
0:46:57.841260 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:46:58.051479 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:46:58.473576 INFO: === checking if optimization conditions were reached ===
0:46:58.474102 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:46:58.478385 INFO: Updating optimization_manager: rt_error            : 729.4581311646555 -> 710.5064589326232
0:46:58.478595 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 710.5065.
0:46:58.478691 INFO: ==============================================
0:46:58.478790 INFO: Starting optimization step 4.
0:46:58.478873 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:46:58.478979 INFO: Using rust extraction backend
0:46:58.479072 PROGRESS: Extracting batch of 252182 precursors
0:46:59.146410 INFO: === Search parameters used ===
0:46:59.146854 INFO: rt_error       : 710.5064589326232
0:46:59.146970 INFO: mobility_error : 0.1
0:46:59.147053 INFO: num_candidates : 3
0:46:59.147129 INFO: ms1_error      : 20
0:46:59.147198 INFO: ms2_error      : 10.0
0:46:59.147267 INFO: fwhm_rt        : 3.0
0:46:59.147336 INFO: quant_window   : 3
0:46:59.147408 INFO: ==============================================
0:47:04.289771 INFO: performing precursor FDR with 40 features
0:47:04.289971 INFO: Decoy channel: -1
0:47:04.290011 INFO: competitive: True
0:47:04.711604 INFO: Setting torch num_threads to 2 for FDR classification task
0:47:05.372576 INFO: Estimating optimal hyperparameters - samples: 603,492, batch_size: 2,471, learning_rate: 7.77e-04
0:47:05.374263 INFO: Using random state 408365 for train-test-split
0:47:21.743814 INFO: Test AUC: 0.607
0:47:21.744041 INFO: Train AUC: 0.622
0:47:21.744082 INFO: AUC difference: 2.44%
0:47:22.238147 INFO: Resetting torch num_threads to 32
0:47:22.282820 PROGRESS: === Extracted 754365 precursors and 3815495 fragments ===
0:47:22.283376 INFO: === FDR correction performed with classifier version 12 ===
0:47:22.284141 PROGRESS: ============================= Precursor FDR =============================
0:47:22.284258 PROGRESS: Total precursors accumulated: 1,416
0:47:22.284330 PROGRESS: Target precursors: 1,402 (99.01%)
0:47:22.284388 PROGRESS: Decoy precursors: 14 (0.99%)
0:47:22.284439 PROGRESS: 
0:47:22.284487 PROGRESS: Precursor Summary:
0:47:22.285961 PROGRESS: Channel   0:	 0.050 FDR: 1,402; 0.010 FDR: 1,402; 0.001 FDR: 1,141
0:47:22.286061 PROGRESS: 
0:47:22.286122 PROGRESS: Protein Summary:
0:47:22.287948 PROGRESS: Channel   0:	 0.050 FDR: 1,233; 0.010 FDR: 1,233; 0.001 FDR: 1,011
0:47:22.288048 PROGRESS: =========================================================================
0:47:22.305689 INFO: Target number of precursors reached.
0:47:22.735679 INFO: fragments_df: keeping 5000 of 3815495 [sum(precursor_idx_mask)=32523 sum(mass_error_mask)=3815495 stop_rank=5000
0:47:23.277211 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:47:23.630738 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:47:24.404422 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:47:24.404949 INFO: Using score_cutoff 9.333157371425628 (fac=0.99, q=1)
0:47:24.405322 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:24.405409 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:24.405465 INFO: Updating optimization_manager: score_cutoff        : 7.844055055904389 -> 9.333157371425628
0:47:24.405529 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:24.559047 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:24.929729 INFO: === checking if optimization conditions were reached ===
0:47:24.930098 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:47:24.931331 INFO: Updating optimization_manager: rt_error            : 710.5064589326232 -> 707.9275098201135
0:47:24.931493 INFO: Updating optimization_manager: classifier_version  : 12 -> 15
0:47:24.931626 INFO: Updating optimization_manager: score_cutoff        : 9.333157371425628 -> 7.2091971294879915
0:47:24.931754 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:47:24.931876 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:47:24.932001 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 707.9275 found after 5 searches.
0:47:24.932091 INFO: ==============================================
0:47:24.932202 PROGRESS: Optimization finished for rt_error.
0:47:25.380558 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:25.530918 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:47:25.910943 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:47:25.911270 PROGRESS: ==============================================
0:47:25.911386 PROGRESS: ms2_error      : 10.0000
0:47:25.911462 PROGRESS: rt_error       : 707.9275
0:47:25.911526 PROGRESS: ==============================================
0:47:25.912443 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:47:35.396128 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:48:01.538068 INFO: Using rust extraction backend
0:48:01.538682 PROGRESS: Extracting batch of 15081856 precursors
0:48:26.979920 INFO: === Search parameters used ===
0:48:26.980379 INFO: rt_error       : 707.9275098201135
0:48:26.980465 INFO: mobility_error : 0.1
0:48:26.980528 INFO: num_candidates : 3
0:48:26.980584 INFO: ms1_error      : 20
0:48:26.980659 INFO: ms2_error      : 10.0
0:48:26.980718 INFO: fwhm_rt        : 3.0
0:48:26.980766 INFO: quant_window   : 3
0:48:26.980813 INFO: ==============================================
0:49:38.623500 INFO: Removed 3400572 precursors with score below cutoff 7.2091971294879915
0:50:19.816822 INFO: performing precursor FDR with 40 features
0:50:19.817071 INFO: Decoy channel: -1
0:50:19.817104 INFO: competitive: True
0:50:24.411077 INFO: Setting torch num_threads to 2 for FDR classification task
0:50:42.466039 INFO: Estimating optimal hyperparameters - samples: 33,475,632, batch_size: 4,096, learning_rate: 1.00e-03
0:50:42.565919 INFO: Using random state 717924 for train-test-split
1:07:33.924206 INFO: Test AUC: 0.615
1:07:33.924507 INFO: Train AUC: 0.616
1:07:33.924557 INFO: AUC difference: 0.06%
1:07:42.217591 INFO: Resetting torch num_threads to 32
1:07:45.661072 PROGRESS: ============================= Precursor FDR =============================
1:07:45.661433 PROGRESS: Total precursors accumulated: 82,558
1:07:45.661515 PROGRESS: Target precursors: 81,741 (99.01%)
1:07:45.661578 PROGRESS: Decoy precursors: 817 (0.99%)
1:07:45.661634 PROGRESS: 
1:07:45.661686 PROGRESS: Precursor Summary:
1:07:45.682837 PROGRESS: Channel   0:	 0.050 FDR: 81,741; 0.010 FDR: 81,741; 0.001 FDR:     3
1:07:45.683045 PROGRESS: 
1:07:45.683128 PROGRESS: Protein Summary:
1:07:45.712909 PROGRESS: Channel   0:	 0.050 FDR: 11,856; 0.010 FDR: 11,856; 0.001 FDR:     3
1:07:45.713114 PROGRESS: =========================================================================
1:07:46.009778 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/psm.parquet
1:07:46.186721 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.parquet
1:07:46.467099 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:07:47.303514 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 
1:07:47.303884 INFO: Quantification results path: /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant
1:07:47.304001 INFO: Creating folder /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/figures
1:07:47.304618 INFO: Initializing TimingManager
1:07:47.305429 INFO: Initializing RawFileManager
1:08:39.523536 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.
1:08:39.531771 INFO: Determining DIA cycle
1:08:39.549436 INFO: Found cycle with start 0.00 min and length 300.
1:08:39.751501 INFO: RT (min)            : 0.0 - 26.9
1:08:39.751615 INFO: RT duration (sec)   : 1611.2
1:08:39.751654 INFO: RT duration (min)   : 26.9
1:08:39.751691 INFO: Cycle len (scans)   : 300
1:08:39.751722 INFO: Cycle len (sec)     : 1.65
1:08:39.751752 INFO: Number of cycles    : 978
1:08:39.751782 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:08:39.751826 INFO: Creating DIA data object took: 52.446216344833374
1:08:41.383478 INFO: Creating DIA data NG object took: 1.6314797401428223
1:08:43.669292 INFO: Initializing CalibrationManager
1:08:43.669624 INFO: Setting up calibration estimators ..
1:08:43.669728 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:08:43.669878 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'}' ..
1:08:43.670069 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:08:43.670182 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:08:43.670285 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}}' ..
1:08:43.670387 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:08:43.670480 INFO: Done setting up calibration estimators.
1:08:43.670776 INFO: Initializing OptimizationManager
1:08:43.671044 INFO: initial parameter: ms1_error = 20
1:08:43.671151 INFO: initial parameter: ms2_error = 20
1:08:43.671249 INFO: initial parameter: rt_error = 805.6019897460938
1:08:43.671337 INFO: initial parameter: mobility_error = 0.1
1:08:43.671420 INFO: initial parameter: num_candidates = 1
1:08:43.671497 INFO: initial parameter: fwhm_rt = 5
1:08:43.671584 INFO: initial parameter: fwhm_mobility = 0.01
1:08:43.671670 INFO: initial parameter: score_cutoff = 0
1:08:43.671756 INFO: initial parameter: classifier_version = -1
1:08:43.671909 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:08:43.672356 INFO: FDRManager: loading saved state not requested, will be initialized.
1:08:43.672413 INFO: Initializing FDRManager
1:08:43.672480 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
1:08:46.024664 PROGRESS: Initializing spectral library: 7,536,970 target precursors potentially observable (1,230,167 removed)
1:08:47.526117 INFO: Updating optimization_manager: ms2_error           : 20 -> 20
1:08:47.526557 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
1:08:47.526679 PROGRESS: Starting initial search for precursors.
1:08:47.526778 INFO: Starting optimization step 0.
1:08:47.526849 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:08:47.526921 INFO: Using rust extraction backend
1:08:47.526989 PROGRESS: Extracting batch of 1988 precursors
1:08:47.532287 INFO: === Search parameters used ===
1:08:47.532411 INFO: rt_error       : 805.6019897460938
1:08:47.532471 INFO: mobility_error : 0.1
1:08:47.532522 INFO: num_candidates : 1
1:08:47.532569 INFO: ms1_error      : 20
1:08:47.532629 INFO: ms2_error      : 20
1:08:47.532680 INFO: fwhm_rt        : 5
1:08:47.532729 INFO: quant_window   : 3
1:08:47.532772 INFO: ==============================================
1:08:47.581381 INFO: performing precursor FDR with 40 features
1:08:47.581519 INFO: Decoy channel: -1
1:08:47.581568 INFO: competitive: True
1:08:47.583661 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:47.587127 INFO: Estimating optimal hyperparameters - samples: 1,580, batch_size: 128, learning_rate: 1.77e-04
1:08:47.588493 INFO: Using random state 467647 for train-test-split
1:08:47.737204 INFO: Test AUC: 0.500
1:08:47.737316 INFO: Train AUC: 0.588
1:08:47.737349 INFO: AUC difference: 14.94%
1:08:47.737375 WARNING: AUC difference > 5%. This may indicate overfitting.
1:08:48.078026 INFO: Resetting torch num_threads to 32
1:08:48.079675 PROGRESS: === Extracted 1975 precursors and 9226 fragments ===
1:08:48.080054 INFO: === FDR correction performed with classifier version -1 ===
1:08:48.080563 PROGRESS: ============================= Precursor FDR =============================
1:08:48.080682 PROGRESS: Total precursors accumulated: 1
1:08:48.080752 PROGRESS: Target precursors: 1 (100.00%)
1:08:48.080809 PROGRESS: Decoy precursors: 0 (0.00%)
1:08:48.080867 PROGRESS: 
1:08:48.080918 PROGRESS: Precursor Summary:
1:08:48.082009 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:08:48.082104 PROGRESS: 
1:08:48.082167 PROGRESS: Protein Summary:
1:08:48.083354 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
1:08:48.083454 PROGRESS: =========================================================================
1:08:48.083696 INFO: Target number of precursors not reached yet.
1:08:48.191286 INFO: Starting optimization step 1.
1:08:48.191494 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:08:48.191581 INFO: Using rust extraction backend
1:08:48.191648 PROGRESS: Extracting batch of 3976 precursors
1:08:48.200799 INFO: === Search parameters used ===
1:08:48.200961 INFO: rt_error       : 805.6019897460938
1:08:48.201024 INFO: mobility_error : 0.1
1:08:48.201080 INFO: num_candidates : 1
1:08:48.201136 INFO: ms1_error      : 20
1:08:48.201191 INFO: ms2_error      : 20
1:08:48.201241 INFO: fwhm_rt        : 5
1:08:48.201288 INFO: quant_window   : 3
1:08:48.201334 INFO: ==============================================
1:08:48.276464 INFO: performing precursor FDR with 40 features
1:08:48.276609 INFO: Decoy channel: -1
1:08:48.276678 INFO: competitive: True
1:08:48.284380 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:48.288111 INFO: Estimating optimal hyperparameters - samples: 4,734, batch_size: 128, learning_rate: 1.77e-04
1:08:48.288260 INFO: Using random state 361110 for train-test-split
1:08:48.765331 INFO: Test AUC: 0.520
1:08:48.765454 INFO: Train AUC: 0.568
1:08:48.765486 INFO: AUC difference: 8.40%
1:08:48.765509 WARNING: AUC difference > 5%. This may indicate overfitting.
1:08:49.039451 INFO: Resetting torch num_threads to 32
1:08:49.043321 PROGRESS: === Extracted 5918 precursors and 27943 fragments ===
1:08:49.043840 INFO: === FDR correction performed with classifier version -1 ===
1:08:49.044497 PROGRESS: ============================= Precursor FDR =============================
1:08:49.044603 PROGRESS: Total precursors accumulated: 14
1:08:49.044703 PROGRESS: Target precursors: 14 (100.00%)
1:08:49.044775 PROGRESS: Decoy precursors: 0 (0.00%)
1:08:49.044857 PROGRESS: 
1:08:49.044926 PROGRESS: Precursor Summary:
1:08:49.046233 PROGRESS: Channel   0:	 0.050 FDR:    14; 0.010 FDR:    14; 0.001 FDR:    14
1:08:49.046354 PROGRESS: 
1:08:49.046431 PROGRESS: Protein Summary:
1:08:49.047860 PROGRESS: Channel   0:	 0.050 FDR:    14; 0.010 FDR:    14; 0.001 FDR:    14
1:08:49.047993 PROGRESS: =========================================================================
1:08:49.048340 INFO: Target number of precursors not reached yet.
1:08:49.178204 INFO: Starting optimization step 2.
1:08:49.178463 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:08:49.178565 INFO: Using rust extraction backend
1:08:49.178640 PROGRESS: Extracting batch of 7946 precursors
1:08:49.197301 INFO: === Search parameters used ===
1:08:49.197539 INFO: rt_error       : 805.6019897460938
1:08:49.197605 INFO: mobility_error : 0.1
1:08:49.197666 INFO: num_candidates : 1
1:08:49.197723 INFO: ms1_error      : 20
1:08:49.197778 INFO: ms2_error      : 20
1:08:49.197835 INFO: fwhm_rt        : 5
1:08:49.197889 INFO: quant_window   : 3
1:08:49.197943 INFO: ==============================================
1:08:49.310329 INFO: performing precursor FDR with 40 features
1:08:49.310467 INFO: Decoy channel: -1
1:08:49.310504 INFO: competitive: True
1:08:49.322513 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:49.328722 INFO: Estimating optimal hyperparameters - samples: 11,031, batch_size: 128, learning_rate: 1.77e-04
1:08:49.328926 INFO: Using random state 228923 for train-test-split
1:08:50.389168 INFO: Test AUC: 0.539
1:08:50.389286 INFO: Train AUC: 0.581
1:08:50.389321 INFO: AUC difference: 7.14%
1:08:50.389348 WARNING: AUC difference > 5%. This may indicate overfitting.
1:08:50.652542 INFO: Resetting torch num_threads to 32
1:08:50.658587 PROGRESS: === Extracted 13789 precursors and 64595 fragments ===
1:08:50.659175 INFO: === FDR correction performed with classifier version -1 ===
1:08:50.659852 PROGRESS: ============================= Precursor FDR =============================
1:08:50.659966 PROGRESS: Total precursors accumulated: 22
1:08:50.660041 PROGRESS: Target precursors: 22 (100.00%)
1:08:50.660107 PROGRESS: Decoy precursors: 0 (0.00%)
1:08:50.660179 PROGRESS: 
1:08:50.660239 PROGRESS: Precursor Summary:
1:08:50.661578 PROGRESS: Channel   0:	 0.050 FDR:    22; 0.010 FDR:    22; 0.001 FDR:    22
1:08:50.661690 PROGRESS: 
1:08:50.661758 PROGRESS: Protein Summary:
1:08:50.663214 PROGRESS: Channel   0:	 0.050 FDR:    22; 0.010 FDR:    22; 0.001 FDR:    22
1:08:50.663320 PROGRESS: =========================================================================
1:08:50.663938 INFO: Target number of precursors not reached yet.
1:08:50.808294 INFO: Starting optimization step 3.
1:08:50.808570 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:08:50.808701 INFO: Using rust extraction backend
1:08:50.808785 PROGRESS: Extracting batch of 15879 precursors
1:08:50.840848 INFO: === Search parameters used ===
1:08:50.841138 INFO: rt_error       : 805.6019897460938
1:08:50.841207 INFO: mobility_error : 0.1
1:08:50.841266 INFO: num_candidates : 1
1:08:50.841323 INFO: ms1_error      : 20
1:08:50.841380 INFO: ms2_error      : 20
1:08:50.841450 INFO: fwhm_rt        : 5
1:08:50.841506 INFO: quant_window   : 3
1:08:50.841563 INFO: ==============================================
1:08:51.034623 INFO: performing precursor FDR with 40 features
1:08:51.034748 INFO: Decoy channel: -1
1:08:51.034776 INFO: competitive: True
1:08:51.048934 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:51.057068 INFO: Estimating optimal hyperparameters - samples: 23,638, batch_size: 128, learning_rate: 1.77e-04
1:08:51.057263 INFO: Using random state 649629 for train-test-split
1:08:53.247875 INFO: Test AUC: 0.572
1:08:53.248008 INFO: Train AUC: 0.595
1:08:53.248040 INFO: AUC difference: 3.85%
1:08:53.542051 INFO: Resetting torch num_threads to 32
1:08:53.557360 PROGRESS: === Extracted 29548 precursors and 138544 fragments ===
1:08:53.558001 INFO: === FDR correction performed with classifier version -1 ===
1:08:53.558743 PROGRESS: ============================= Precursor FDR =============================
1:08:53.558860 PROGRESS: Total precursors accumulated: 39
1:08:53.558932 PROGRESS: Target precursors: 39 (100.00%)
1:08:53.558993 PROGRESS: Decoy precursors: 0 (0.00%)
1:08:53.559052 PROGRESS: 
1:08:53.559109 PROGRESS: Precursor Summary:
1:08:53.560498 PROGRESS: Channel   0:	 0.050 FDR:    39; 0.010 FDR:    39; 0.001 FDR:    39
1:08:53.560607 PROGRESS: 
1:08:53.560702 PROGRESS: Protein Summary:
1:08:53.562220 PROGRESS: Channel   0:	 0.050 FDR:    39; 0.010 FDR:    39; 0.001 FDR:    39
1:08:53.562326 PROGRESS: =========================================================================
1:08:53.563533 INFO: Target number of precursors not reached yet.
1:08:53.741947 INFO: Starting optimization step 4.
1:08:53.742221 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:08:53.742330 INFO: Using rust extraction backend
1:08:53.742409 PROGRESS: Extracting batch of 31750 precursors
1:08:53.805490 INFO: === Search parameters used ===
1:08:53.805772 INFO: rt_error       : 805.6019897460938
1:08:53.805844 INFO: mobility_error : 0.1
1:08:53.805903 INFO: num_candidates : 1
1:08:53.805956 INFO: ms1_error      : 20
1:08:53.806023 INFO: ms2_error      : 20
1:08:53.806076 INFO: fwhm_rt        : 5
1:08:53.806126 INFO: quant_window   : 3
1:08:53.806181 INFO: ==============================================
1:08:54.137627 INFO: performing precursor FDR with 40 features
1:08:54.137743 INFO: Decoy channel: -1
1:08:54.137770 INFO: competitive: True
1:08:54.178728 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:54.207461 INFO: Estimating optimal hyperparameters - samples: 48,833, batch_size: 200, learning_rate: 2.21e-04
1:08:54.207754 INFO: Using random state 593235 for train-test-split
1:08:57.539702 INFO: Test AUC: 0.582
1:08:57.539824 INFO: Train AUC: 0.603
1:08:57.539858 INFO: AUC difference: 3.52%
1:08:57.854637 INFO: Resetting torch num_threads to 32
1:08:57.879344 PROGRESS: === Extracted 61042 precursors and 286608 fragments ===
1:08:57.880116 INFO: === FDR correction performed with classifier version -1 ===
1:08:57.881034 PROGRESS: ============================= Precursor FDR =============================
1:08:57.881193 PROGRESS: Total precursors accumulated: 2
1:08:57.881276 PROGRESS: Target precursors: 2 (100.00%)
1:08:57.881345 PROGRESS: Decoy precursors: 0 (0.00%)
1:08:57.881410 PROGRESS: 
1:08:57.881471 PROGRESS: Precursor Summary:
1:08:57.882925 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:08:57.883053 PROGRESS: 
1:08:57.883127 PROGRESS: Protein Summary:
1:08:57.884653 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
1:08:57.884780 PROGRESS: =========================================================================
1:08:57.887085 INFO: Target number of precursors not reached yet.
1:08:58.128404 INFO: Starting optimization step 5.
1:08:58.128676 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:08:58.128776 INFO: Using rust extraction backend
1:08:58.128848 PROGRESS: Extracting batch of 63536 precursors
1:08:58.246611 INFO: === Search parameters used ===
1:08:58.246879 INFO: rt_error       : 805.6019897460938
1:08:58.246947 INFO: mobility_error : 0.1
1:08:58.247002 INFO: num_candidates : 1
1:08:58.247052 INFO: ms1_error      : 20
1:08:58.247102 INFO: ms2_error      : 20
1:08:58.247150 INFO: fwhm_rt        : 5
1:08:58.247212 INFO: quant_window   : 3
1:08:58.247260 INFO: ==============================================
1:08:58.962944 INFO: performing precursor FDR with 40 features
1:08:58.963058 INFO: Decoy channel: -1
1:08:58.963086 INFO: competitive: True
1:08:59.045016 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:59.084251 INFO: Estimating optimal hyperparameters - samples: 99,252, batch_size: 406, learning_rate: 3.15e-04
1:08:59.084703 INFO: Using random state 979832 for train-test-split
1:09:04.569423 INFO: Test AUC: 0.585
1:09:04.569571 INFO: Train AUC: 0.603
1:09:04.569614 INFO: AUC difference: 2.90%
1:09:04.937835 INFO: Resetting torch num_threads to 32
1:09:04.977489 PROGRESS: === Extracted 124066 precursors and 582615 fragments ===
1:09:04.978148 INFO: === FDR correction performed with classifier version -1 ===
1:09:04.978804 PROGRESS: ============================= Precursor FDR =============================
1:09:04.978901 PROGRESS: Total precursors accumulated: 354
1:09:04.978967 PROGRESS: Target precursors: 351 (99.15%)
1:09:04.979027 PROGRESS: Decoy precursors: 3 (0.85%)
1:09:04.979079 PROGRESS: 
1:09:04.979146 PROGRESS: Precursor Summary:
1:09:04.980242 PROGRESS: Channel   0:	 0.050 FDR:   351; 0.010 FDR:   351; 0.001 FDR:   271
1:09:04.980341 PROGRESS: 
1:09:04.980403 PROGRESS: Protein Summary:
1:09:04.981677 PROGRESS: Channel   0:	 0.050 FDR:   335; 0.010 FDR:   335; 0.001 FDR:   261
1:09:04.981780 PROGRESS: =========================================================================
1:09:04.984481 INFO: Target number of precursors not reached yet.
1:09:05.319112 INFO: Starting optimization step 6.
1:09:05.319391 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:09:05.319494 INFO: Using rust extraction backend
1:09:05.319569 PROGRESS: Extracting batch of 127107 precursors
1:09:05.552195 INFO: === Search parameters used ===
1:09:05.552453 INFO: rt_error       : 805.6019897460938
1:09:05.552520 INFO: mobility_error : 0.1
1:09:05.552573 INFO: num_candidates : 1
1:09:05.552645 INFO: ms1_error      : 20
1:09:05.552704 INFO: ms2_error      : 20
1:09:05.552754 INFO: fwhm_rt        : 5
1:09:05.552804 INFO: quant_window   : 3
1:09:05.552851 INFO: ==============================================
1:09:06.907310 INFO: performing precursor FDR with 40 features
1:09:06.907439 INFO: Decoy channel: -1
1:09:06.907468 INFO: competitive: True
1:09:07.029829 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:07.152752 INFO: Estimating optimal hyperparameters - samples: 200,166, batch_size: 819, learning_rate: 4.47e-04
1:09:07.153307 INFO: Using random state 75656 for train-test-split
1:09:14.388370 INFO: Test AUC: 0.583
1:09:14.388500 INFO: Train AUC: 0.602
1:09:14.388536 INFO: AUC difference: 3.21%
1:09:14.764489 INFO: Resetting torch num_threads to 32
1:09:14.847982 PROGRESS: === Extracted 250208 precursors and 1172124 fragments ===
1:09:14.848837 INFO: === FDR correction performed with classifier version -1 ===
1:09:14.849763 PROGRESS: ============================= Precursor FDR =============================
1:09:14.849873 PROGRESS: Total precursors accumulated: 722
1:09:14.849944 PROGRESS: Target precursors: 715 (99.03%)
1:09:14.850011 PROGRESS: Decoy precursors: 7 (0.97%)
1:09:14.850071 PROGRESS: 
1:09:14.850133 PROGRESS: Precursor Summary:
1:09:14.851630 PROGRESS: Channel   0:	 0.050 FDR:   715; 0.010 FDR:   715; 0.001 FDR:   559
1:09:14.851751 PROGRESS: 
1:09:14.851820 PROGRESS: Protein Summary:
1:09:14.853649 PROGRESS: Channel   0:	 0.050 FDR:   653; 0.010 FDR:   653; 0.001 FDR:   516
1:09:14.853761 PROGRESS: =========================================================================
1:09:14.861303 INFO: Target number of precursors not reached yet.
1:09:15.402767 INFO: Starting optimization step 7.
1:09:15.403031 PROGRESS: === Extracting elution groups 127000 to 255000 ===
1:09:15.403142 INFO: Using rust extraction backend
1:09:15.403217 PROGRESS: Extracting batch of 254254 precursors
1:09:15.904217 INFO: === Search parameters used ===
1:09:15.904483 INFO: rt_error       : 805.6019897460938
1:09:15.904575 INFO: mobility_error : 0.1
1:09:15.904652 INFO: num_candidates : 1
1:09:15.904710 INFO: ms1_error      : 20
1:09:15.904759 INFO: ms2_error      : 20
1:09:15.904811 INFO: fwhm_rt        : 5
1:09:15.904858 INFO: quant_window   : 3
1:09:15.904902 INFO: ==============================================
1:09:18.581490 INFO: performing precursor FDR with 40 features
1:09:18.581626 INFO: Decoy channel: -1
1:09:18.581656 INFO: competitive: True
1:09:18.862533 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:19.121923 INFO: Estimating optimal hyperparameters - samples: 401,935, batch_size: 1,646, learning_rate: 6.34e-04
1:09:19.122846 INFO: Using random state 48163 for train-test-split
1:09:30.946684 INFO: Test AUC: 0.588
1:09:30.946866 INFO: Train AUC: 0.602
1:09:30.946921 INFO: AUC difference: 2.21%
1:09:32.118199 INFO: Resetting torch num_threads to 32
1:09:32.233677 PROGRESS: === Extracted 502419 precursors and 2353892 fragments ===
1:09:32.234460 INFO: === FDR correction performed with classifier version -1 ===
1:09:32.235674 PROGRESS: ============================= Precursor FDR =============================
1:09:32.235790 PROGRESS: Total precursors accumulated: 1,522
1:09:32.235869 PROGRESS: Target precursors: 1,507 (99.01%)
1:09:32.235938 PROGRESS: Decoy precursors: 15 (0.99%)
1:09:32.236003 PROGRESS: 
1:09:32.236065 PROGRESS: Precursor Summary:
1:09:32.237915 PROGRESS: Channel   0:	 0.050 FDR: 1,507; 0.010 FDR: 1,507; 0.001 FDR:     0
1:09:32.238370 PROGRESS: 
1:09:32.238472 PROGRESS: Protein Summary:
1:09:32.240931 PROGRESS: Channel   0:	 0.050 FDR: 1,254; 0.010 FDR: 1,254; 0.001 FDR:     0
1:09:32.241052 PROGRESS: =========================================================================
1:09:32.254887 INFO: Target number of precursors reached.
1:09:32.601264 INFO: fragments_df: keeping 5000 of 2353892 [sum(precursor_idx_mask)=16146 sum(mass_error_mask)=2353892 stop_rank=5000
1:09:33.768873 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:09:34.121882 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:09:34.884013 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:09:34.884504 INFO: Using score_cutoff 12.30712002067566 (fac=0.99, q=1)
1:09:34.884895 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:09:34.884997 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:09:34.885072 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.30712002067566
1:09:34.885148 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:09:35.209611 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:09:35.981706 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
1:09:35.981934 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:09:35.982038 INFO: Starting optimization step 8.
1:09:35.982109 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:09:35.982188 INFO: Using rust extraction backend
1:09:35.982261 PROGRESS: Extracting batch of 506436 precursors
1:09:36.940456 INFO: === Search parameters used ===
1:09:36.940738 INFO: rt_error       : 805.6019897460938
1:09:36.940819 INFO: mobility_error : 0.1
1:09:36.940878 INFO: num_candidates : 3
1:09:36.940932 INFO: ms1_error      : 20
1:09:36.940985 INFO: ms2_error      : 20
1:09:36.941056 INFO: fwhm_rt        : 3.0
1:09:36.941114 INFO: quant_window   : 3
1:09:36.941176 INFO: ==============================================
1:09:45.117250 INFO: performing precursor FDR with 40 features
1:09:45.117373 INFO: Decoy channel: -1
1:09:45.117402 INFO: competitive: True
1:09:45.640145 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:46.458691 INFO: Estimating optimal hyperparameters - samples: 1,204,221, batch_size: 4,096, learning_rate: 1.00e-03
1:09:46.461006 INFO: Using random state 887589 for train-test-split
1:10:12.111219 INFO: Test AUC: 0.596
1:10:12.111411 INFO: Train AUC: 0.601
1:10:12.111449 INFO: AUC difference: 0.88%
1:10:12.836525 INFO: Resetting torch num_threads to 32
1:10:12.893545 PROGRESS: === Extracted 1505277 precursors and 6840306 fragments ===
1:10:12.894108 INFO: === FDR correction performed with classifier version 7 ===
1:10:12.895021 PROGRESS: ============================= Precursor FDR =============================
1:10:12.895134 PROGRESS: Total precursors accumulated: 1,824
1:10:12.895219 PROGRESS: Target precursors: 1,806 (99.01%)
1:10:12.895293 PROGRESS: Decoy precursors: 18 (0.99%)
1:10:12.895360 PROGRESS: 
1:10:12.895428 PROGRESS: Precursor Summary:
1:10:12.897063 PROGRESS: Channel   0:	 0.050 FDR: 1,806; 0.010 FDR: 1,806; 0.001 FDR: 1,140
1:10:12.897183 PROGRESS: 
1:10:12.897264 PROGRESS: Protein Summary:
1:10:12.899285 PROGRESS: Channel   0:	 0.050 FDR: 1,470; 0.010 FDR: 1,470; 0.001 FDR:   955
1:10:12.899402 PROGRESS: =========================================================================
1:10:12.935061 INFO: Target number of precursors reached.
1:10:13.867803 INFO: fragments_df: keeping 5000 of 6840306 [sum(precursor_idx_mask)=41912 sum(mass_error_mask)=6840306 stop_rank=5000
1:10:14.997218 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:10:15.326785 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:10:16.155850 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:10:16.156362 INFO: Using score_cutoff 12.876795382976532 (fac=0.99, q=1)
1:10:16.156760 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:10:16.156857 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:10:16.156918 INFO: Updating optimization_manager: score_cutoff        : 12.30712002067566 -> 12.876795382976532
1:10:16.156982 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:10:16.483118 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:10:17.422484 INFO: === checking if optimization conditions were reached ===
1:10:17.426077 INFO: Updating optimization_manager: ms2_error           : 20 -> 10.0
1:10:17.426391 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:10:17.426511 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:10:17.426615 INFO: ==============================================
1:10:17.426737 INFO: Starting optimization step 9.
1:10:17.426838 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:10:17.426959 INFO: Using rust extraction backend
1:10:17.427064 PROGRESS: Extracting batch of 506436 precursors
1:10:18.399279 INFO: === Search parameters used ===
1:10:18.399636 INFO: rt_error       : 805.6019897460938
1:10:18.399710 INFO: mobility_error : 0.1
1:10:18.399766 INFO: num_candidates : 3
1:10:18.399819 INFO: ms1_error      : 20
1:10:18.399874 INFO: ms2_error      : 10.0
1:10:18.399938 INFO: fwhm_rt        : 3.0
1:10:18.399989 INFO: quant_window   : 3
1:10:18.400038 INFO: ==============================================
1:10:26.841120 INFO: performing precursor FDR with 40 features
1:10:26.841305 INFO: Decoy channel: -1
1:10:26.841338 INFO: competitive: True
1:10:27.437086 INFO: Setting torch num_threads to 2 for FDR classification task
1:10:28.297882 INFO: Estimating optimal hyperparameters - samples: 1,211,750, batch_size: 4,096, learning_rate: 1.00e-03
1:10:28.301305 INFO: Using random state 226602 for train-test-split
1:10:48.746651 INFO: Test AUC: 0.600
1:10:48.746849 INFO: Train AUC: 0.606
1:10:48.746887 INFO: AUC difference: 1.05%
1:10:49.585546 INFO: Resetting torch num_threads to 32
1:10:49.682304 PROGRESS: === Extracted 1514688 precursors and 7617375 fragments ===
1:10:49.682987 INFO: === FDR correction performed with classifier version 8 ===
1:10:49.684534 PROGRESS: ============================= Precursor FDR =============================
1:10:49.684692 PROGRESS: Total precursors accumulated: 2,598
1:10:49.684773 PROGRESS: Target precursors: 2,573 (99.04%)
1:10:49.684840 PROGRESS: Decoy precursors: 25 (0.96%)
1:10:49.684901 PROGRESS: 
1:10:49.684964 PROGRESS: Precursor Summary:
1:10:49.687620 PROGRESS: Channel   0:	 0.050 FDR: 2,573; 0.010 FDR: 2,573; 0.001 FDR: 1,340
1:10:49.687788 PROGRESS: 
1:10:49.687861 PROGRESS: Protein Summary:
1:10:49.691074 PROGRESS: Channel   0:	 0.050 FDR: 2,031; 0.010 FDR: 2,031; 0.001 FDR: 1,121
1:10:49.691206 PROGRESS: =========================================================================
1:10:49.749844 INFO: Target number of precursors reached.
1:10:50.807071 INFO: fragments_df: keeping 5000 of 7617375 [sum(precursor_idx_mask)=60916 sum(mass_error_mask)=7617375 stop_rank=5000
1:10:51.400519 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:10:51.916772 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:10:52.782041 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:10:52.782552 INFO: Using score_cutoff 10.55648007888794 (fac=0.99, q=1)
1:10:52.782942 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:10:52.783036 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:10:52.783098 INFO: Updating optimization_manager: score_cutoff        : 12.876795382976532 -> 10.55648007888794
1:10:52.783160 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:10:52.936905 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:10:53.388716 INFO: === checking if optimization conditions were reached ===
1:10:53.390930 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:10:53.391050 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:10:53.391123 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:10:53.391184 INFO: ==============================================
1:10:53.391255 INFO: Starting optimization step 10.
1:10:53.391318 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:10:53.391391 INFO: Using rust extraction backend
1:10:53.391454 PROGRESS: Extracting batch of 252182 precursors
1:10:53.869262 INFO: === Search parameters used ===
1:10:53.869536 INFO: rt_error       : 805.6019897460938
1:10:53.869602 INFO: mobility_error : 0.1
1:10:53.869655 INFO: num_candidates : 3
1:10:53.869718 INFO: ms1_error      : 20
1:10:53.869819 INFO: ms2_error      : 10.0
1:10:53.869921 INFO: fwhm_rt        : 3.0
1:10:53.870009 INFO: quant_window   : 3
1:10:53.870078 INFO: ==============================================
1:10:58.289180 INFO: performing precursor FDR with 40 features
1:10:58.289357 INFO: Decoy channel: -1
1:10:58.289388 INFO: competitive: True
1:10:58.535641 INFO: Setting torch num_threads to 2 for FDR classification task
1:10:58.900958 INFO: Estimating optimal hyperparameters - samples: 603,387, batch_size: 2,471, learning_rate: 7.77e-04
1:10:58.902210 INFO: Using random state 43575 for train-test-split
1:11:13.515989 INFO: Test AUC: 0.602
1:11:13.516173 INFO: Train AUC: 0.612
1:11:13.516220 INFO: AUC difference: 1.70%
1:11:14.094421 INFO: Resetting torch num_threads to 32
1:11:14.142998 PROGRESS: === Extracted 754234 precursors and 3793276 fragments ===
1:11:14.143699 INFO: === FDR correction performed with classifier version 9 ===
1:11:14.144843 PROGRESS: ============================= Precursor FDR =============================
1:11:14.144985 PROGRESS: Total precursors accumulated: 1,319
1:11:14.145087 PROGRESS: Target precursors: 1,306 (99.01%)
1:11:14.145175 PROGRESS: Decoy precursors: 13 (0.99%)
1:11:14.145256 PROGRESS: 
1:11:14.145332 PROGRESS: Precursor Summary:
1:11:14.147194 PROGRESS: Channel   0:	 0.050 FDR: 1,306; 0.010 FDR: 1,306; 0.001 FDR:   757
1:11:14.147315 PROGRESS: 
1:11:14.147384 PROGRESS: Protein Summary:
1:11:14.149129 PROGRESS: Channel   0:	 0.050 FDR: 1,157; 0.010 FDR: 1,157; 0.001 FDR:   689
1:11:14.149238 PROGRESS: =========================================================================
1:11:14.180709 INFO: Target number of precursors reached.
1:11:14.666206 INFO: fragments_df: keeping 5000 of 3793276 [sum(precursor_idx_mask)=30525 sum(mass_error_mask)=3793276 stop_rank=5000
1:11:15.178499 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:11:15.572114 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:11:16.544094 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:11:16.544591 INFO: Using score_cutoff 9.37412948656082 (fac=0.99, q=1)
1:11:16.544968 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:11:16.545056 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:11:16.545115 INFO: Updating optimization_manager: score_cutoff        : 10.55648007888794 -> 9.37412948656082
1:11:16.545179 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:11:16.703915 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:11:17.090661 INFO: === checking if optimization conditions were reached ===
1:11:17.093494 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:11:17.093634 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:11:17.093716 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:11:17.093788 INFO: ==============================================
1:11:17.093873 INFO: Starting optimization step 11.
1:11:17.093945 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:11:17.094037 INFO: Using rust extraction backend
1:11:17.094125 PROGRESS: Extracting batch of 252182 precursors
1:11:17.592003 INFO: === Search parameters used ===
1:11:17.592352 INFO: rt_error       : 805.6019897460938
1:11:17.592437 INFO: mobility_error : 0.1
1:11:17.592514 INFO: num_candidates : 3
1:11:17.592576 INFO: ms1_error      : 20
1:11:17.592646 INFO: ms2_error      : 10.0
1:11:17.592707 INFO: fwhm_rt        : 3.0
1:11:17.592760 INFO: quant_window   : 3
1:11:17.592815 INFO: ==============================================
1:11:21.974357 INFO: performing precursor FDR with 40 features
1:11:21.974493 INFO: Decoy channel: -1
1:11:21.974522 INFO: competitive: True
1:11:22.216022 INFO: Setting torch num_threads to 2 for FDR classification task
1:11:22.618034 INFO: Estimating optimal hyperparameters - samples: 603,378, batch_size: 2,471, learning_rate: 7.77e-04
1:11:22.619736 INFO: Using random state 431851 for train-test-split
1:11:33.839387 INFO: Test AUC: 0.606
1:11:33.839605 INFO: Train AUC: 0.615
1:11:33.839651 INFO: AUC difference: 1.42%
1:11:34.432139 INFO: Resetting torch num_threads to 32
1:11:34.466530 PROGRESS: === Extracted 754223 precursors and 3793370 fragments ===
1:11:34.467050 INFO: === FDR correction performed with classifier version 10 ===
1:11:34.467849 PROGRESS: ============================= Precursor FDR =============================
1:11:34.467954 PROGRESS: Total precursors accumulated: 1,471
1:11:34.468024 PROGRESS: Target precursors: 1,457 (99.05%)
1:11:34.468081 PROGRESS: Decoy precursors: 14 (0.95%)
1:11:34.468132 PROGRESS: 
1:11:34.468186 PROGRESS: Precursor Summary:
1:11:34.469562 PROGRESS: Channel   0:	 0.050 FDR: 1,457; 0.010 FDR: 1,457; 0.001 FDR:   387
1:11:34.469675 PROGRESS: 
1:11:34.469739 PROGRESS: Protein Summary:
1:11:34.471481 PROGRESS: Channel   0:	 0.050 FDR: 1,276; 0.010 FDR: 1,276; 0.001 FDR:   367
1:11:34.471584 PROGRESS: =========================================================================
1:11:34.490427 INFO: Target number of precursors reached.
1:11:35.197238 INFO: fragments_df: keeping 5000 of 3793370 [sum(precursor_idx_mask)=34283 sum(mass_error_mask)=3793370 stop_rank=5000
1:11:35.820838 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:11:36.176630 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:11:37.052951 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:11:37.053435 INFO: Using score_cutoff 10.646214237213135 (fac=0.99, q=1)
1:11:37.053815 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:11:37.053914 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:11:37.053976 INFO: Updating optimization_manager: score_cutoff        : 9.37412948656082 -> 10.646214237213135
1:11:37.054041 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:11:37.219507 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:11:37.612134 INFO: === checking if optimization conditions were reached ===
1:11:37.615096 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:11:37.615228 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:11:37.615311 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:11:37.615385 INFO: ==============================================
1:11:37.615474 INFO: Starting optimization step 12.
1:11:37.615578 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:11:37.615680 INFO: Using rust extraction backend
1:11:37.615770 PROGRESS: Extracting batch of 252182 precursors
1:11:38.090851 INFO: === Search parameters used ===
1:11:38.091171 INFO: rt_error       : 805.6019897460938
1:11:38.091273 INFO: mobility_error : 0.1
1:11:38.091339 INFO: num_candidates : 3
1:11:38.091396 INFO: ms1_error      : 20
1:11:38.091451 INFO: ms2_error      : 10.0
1:11:38.091512 INFO: fwhm_rt        : 3.0
1:11:38.091565 INFO: quant_window   : 3
1:11:38.091620 INFO: ==============================================
1:11:42.538261 INFO: performing precursor FDR with 40 features
1:11:42.538425 INFO: Decoy channel: -1
1:11:42.538458 INFO: competitive: True
1:11:42.805036 INFO: Setting torch num_threads to 2 for FDR classification task
1:11:43.197209 INFO: Estimating optimal hyperparameters - samples: 603,372, batch_size: 2,471, learning_rate: 7.77e-04
1:11:43.198471 INFO: Using random state 342867 for train-test-split
1:11:58.593429 INFO: Test AUC: 0.607
1:11:58.593618 INFO: Train AUC: 0.618
1:11:58.593666 INFO: AUC difference: 1.77%
1:11:59.147599 INFO: Resetting torch num_threads to 32
1:11:59.194623 PROGRESS: === Extracted 754215 precursors and 3792945 fragments ===
1:11:59.195132 INFO: === FDR correction performed with classifier version 11 ===
1:11:59.195894 PROGRESS: ============================= Precursor FDR =============================
1:11:59.195991 PROGRESS: Total precursors accumulated: 1,574
1:11:59.196056 PROGRESS: Target precursors: 1,559 (99.05%)
1:11:59.196115 PROGRESS: Decoy precursors: 15 (0.95%)
1:11:59.196181 PROGRESS: 
1:11:59.196232 PROGRESS: Precursor Summary:
1:11:59.197646 PROGRESS: Channel   0:	 0.050 FDR: 1,559; 0.010 FDR: 1,559; 0.001 FDR: 1,178
1:11:59.197750 PROGRESS: 
1:11:59.197815 PROGRESS: Protein Summary:
1:11:59.199649 PROGRESS: Channel   0:	 0.050 FDR: 1,364; 0.010 FDR: 1,364; 0.001 FDR: 1,041
1:11:59.199752 PROGRESS: =========================================================================
1:11:59.226995 INFO: Target number of precursors reached.
1:11:59.727645 INFO: fragments_df: keeping 5000 of 3792945 [sum(precursor_idx_mask)=36299 sum(mass_error_mask)=3792945 stop_rank=5000
1:12:00.328557 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:12:00.605428 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:12:01.382473 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:12:01.382958 INFO: Using score_cutoff 10.12500146598816 (fac=0.99, q=1)
1:12:01.383313 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:12:01.383406 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:12:01.383470 INFO: Updating optimization_manager: score_cutoff        : 10.646214237213135 -> 10.12500146598816
1:12:01.383535 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:12:01.538971 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:12:01.947241 INFO: === checking if optimization conditions were reached ===
1:12:01.949914 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:12:01.950051 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
1:12:01.950149 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:12:01.950227 INFO: ==============================================
1:12:01.950318 PROGRESS: Optimization finished for ms2_error.
1:12:02.483148 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:12:02.639669 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:12:03.090580 INFO: Starting optimization step 0.
1:12:03.090940 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:12:03.091051 INFO: Using rust extraction backend
1:12:03.091145 PROGRESS: Extracting batch of 252182 precursors
1:12:03.565408 INFO: === Search parameters used ===
1:12:03.565691 INFO: rt_error       : 805.6019897460938
1:12:03.565763 INFO: mobility_error : 0.1
1:12:03.565820 INFO: num_candidates : 3
1:12:03.565870 INFO: ms1_error      : 20
1:12:03.565918 INFO: ms2_error      : 10.0
1:12:03.565964 INFO: fwhm_rt        : 3.0
1:12:03.566010 INFO: quant_window   : 3
1:12:03.566055 INFO: ==============================================
1:12:08.095859 INFO: performing precursor FDR with 40 features
1:12:08.095993 INFO: Decoy channel: -1
1:12:08.096022 INFO: competitive: True
1:12:08.359756 INFO: Setting torch num_threads to 2 for FDR classification task
1:12:08.759536 INFO: Estimating optimal hyperparameters - samples: 603,372, batch_size: 2,471, learning_rate: 7.77e-04
1:12:08.760852 INFO: Using random state 861664 for train-test-split
1:12:24.472288 INFO: Test AUC: 0.608
1:12:24.472484 INFO: Train AUC: 0.618
1:12:24.472521 INFO: AUC difference: 1.62%
1:12:25.038114 INFO: Resetting torch num_threads to 32
1:12:25.073108 PROGRESS: === Extracted 754215 precursors and 3792574 fragments ===
1:12:25.073612 INFO: === FDR correction performed with classifier version 12 ===
1:12:25.074401 PROGRESS: ============================= Precursor FDR =============================
1:12:25.074502 PROGRESS: Total precursors accumulated: 1,571
1:12:25.074569 PROGRESS: Target precursors: 1,556 (99.05%)
1:12:25.074625 PROGRESS: Decoy precursors: 15 (0.95%)
1:12:25.074677 PROGRESS: 
1:12:25.074727 PROGRESS: Precursor Summary:
1:12:25.076083 PROGRESS: Channel   0:	 0.050 FDR: 1,556; 0.010 FDR: 1,556; 0.001 FDR:   652
1:12:25.076182 PROGRESS: 
1:12:25.076257 PROGRESS: Protein Summary:
1:12:25.078039 PROGRESS: Channel   0:	 0.050 FDR: 1,381; 0.010 FDR: 1,381; 0.001 FDR:   601
1:12:25.078141 PROGRESS: =========================================================================
1:12:25.096815 INFO: Target number of precursors reached.
1:12:25.589073 INFO: fragments_df: keeping 5000 of 3792574 [sum(precursor_idx_mask)=34671 sum(mass_error_mask)=3792574 stop_rank=5000
1:12:26.155240 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:12:26.474772 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:12:27.445570 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:12:27.446067 INFO: Using score_cutoff 6.6938331913948055 (fac=0.99, q=1)
1:12:27.446456 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:12:27.446553 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:12:27.446615 INFO: Updating optimization_manager: score_cutoff        : 10.12500146598816 -> 6.6938331913948055
1:12:27.446682 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:12:27.605556 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:12:28.010997 INFO: === checking if optimization conditions were reached ===
1:12:28.011455 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:12:28.014985 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 897.8865871725855
1:12:28.015119 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 897.8866.
1:12:28.015225 INFO: ==============================================
1:12:28.015320 INFO: Starting optimization step 1.
1:12:28.015399 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:12:28.015505 INFO: Using rust extraction backend
1:12:28.015597 PROGRESS: Extracting batch of 252182 precursors
1:12:28.497666 INFO: === Search parameters used ===
1:12:28.497944 INFO: rt_error       : 897.8865871725855
1:12:28.498021 INFO: mobility_error : 0.1
1:12:28.498079 INFO: num_candidates : 3
1:12:28.498129 INFO: ms1_error      : 20
1:12:28.498179 INFO: ms2_error      : 10.0
1:12:28.498227 INFO: fwhm_rt        : 3.0
1:12:28.498274 INFO: quant_window   : 3
1:12:28.498335 INFO: ==============================================
1:12:32.959028 INFO: performing precursor FDR with 40 features
1:12:32.959173 INFO: Decoy channel: -1
1:12:32.959219 INFO: competitive: True
1:12:33.216434 INFO: Setting torch num_threads to 2 for FDR classification task
1:12:33.619223 INFO: Estimating optimal hyperparameters - samples: 603,340, batch_size: 2,471, learning_rate: 7.77e-04
1:12:33.620754 INFO: Using random state 861664 for train-test-split
1:12:49.396290 INFO: Test AUC: 0.607
1:12:49.396490 INFO: Train AUC: 0.618
1:12:49.396541 INFO: AUC difference: 1.75%
1:12:49.967141 INFO: Resetting torch num_threads to 32
1:12:50.017048 PROGRESS: === Extracted 754176 precursors and 3792293 fragments ===
1:12:50.017668 INFO: === FDR correction performed with classifier version 12 ===
1:12:50.018698 PROGRESS: ============================= Precursor FDR =============================
1:12:50.018838 PROGRESS: Total precursors accumulated: 1,439
1:12:50.018921 PROGRESS: Target precursors: 1,425 (99.03%)
1:12:50.018989 PROGRESS: Decoy precursors: 14 (0.97%)
1:12:50.019053 PROGRESS: 
1:12:50.019115 PROGRESS: Precursor Summary:
1:12:50.020943 PROGRESS: Channel   0:	 0.050 FDR: 1,425; 0.010 FDR: 1,425; 0.001 FDR:    86
1:12:50.021073 PROGRESS: 
1:12:50.021145 PROGRESS: Protein Summary:
1:12:50.023324 PROGRESS: Channel   0:	 0.050 FDR: 1,252; 0.010 FDR: 1,252; 0.001 FDR:    85
1:12:50.023446 PROGRESS: =========================================================================
1:12:50.052804 INFO: Target number of precursors reached.
1:12:50.549041 INFO: fragments_df: keeping 5000 of 3792293 [sum(precursor_idx_mask)=32931 sum(mass_error_mask)=3792293 stop_rank=5000
1:12:51.087455 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:12:51.370921 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:12:52.289065 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:12:52.289779 INFO: Using score_cutoff 7.799527667999267 (fac=0.99, q=1)
1:12:52.290427 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:12:52.290566 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:12:52.290657 INFO: Updating optimization_manager: score_cutoff        : 6.6938331913948055 -> 7.799527667999267
1:12:52.290750 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:12:52.451638 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:12:52.884588 INFO: === checking if optimization conditions were reached ===
1:12:52.884928 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:12:52.888196 INFO: Updating optimization_manager: rt_error            : 897.8865871725855 -> 782.3669644863444
1:12:52.888343 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 782.3670.
1:12:52.888429 INFO: ==============================================
1:12:52.888523 INFO: Starting optimization step 2.
1:12:52.888599 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:12:52.888718 INFO: Using rust extraction backend
1:12:52.888807 PROGRESS: Extracting batch of 252182 precursors
1:12:53.366546 INFO: === Search parameters used ===
1:12:53.366873 INFO: rt_error       : 782.3669644863444
1:12:53.366982 INFO: mobility_error : 0.1
1:12:53.367069 INFO: num_candidates : 3
1:12:53.367143 INFO: ms1_error      : 20
1:12:53.367214 INFO: ms2_error      : 10.0
1:12:53.367285 INFO: fwhm_rt        : 3.0
1:12:53.367357 INFO: quant_window   : 3
1:12:53.367429 INFO: ==============================================
1:12:57.771819 INFO: performing precursor FDR with 40 features
1:12:57.771979 INFO: Decoy channel: -1
1:12:57.772011 INFO: competitive: True
1:12:58.049358 INFO: Setting torch num_threads to 2 for FDR classification task
1:12:58.514454 INFO: Estimating optimal hyperparameters - samples: 603,390, batch_size: 2,471, learning_rate: 7.77e-04
1:12:58.515746 INFO: Using random state 861664 for train-test-split
1:13:13.781746 INFO: Test AUC: 0.609
1:13:13.781981 INFO: Train AUC: 0.619
1:13:13.782049 INFO: AUC difference: 1.65%
1:13:14.328312 INFO: Resetting torch num_threads to 32
1:13:14.370500 PROGRESS: === Extracted 754238 precursors and 3793639 fragments ===
1:13:14.371186 INFO: === FDR correction performed with classifier version 12 ===
1:13:14.372347 PROGRESS: ============================= Precursor FDR =============================
1:13:14.372491 PROGRESS: Total precursors accumulated: 1,636
1:13:14.372592 PROGRESS: Target precursors: 1,620 (99.02%)
1:13:14.372701 PROGRESS: Decoy precursors: 16 (0.98%)
1:13:14.372811 PROGRESS: 
1:13:14.372901 PROGRESS: Precursor Summary:
1:13:14.375256 PROGRESS: Channel   0:	 0.050 FDR: 1,620; 0.010 FDR: 1,620; 0.001 FDR: 1,193
1:13:14.375385 PROGRESS: 
1:13:14.375477 PROGRESS: Protein Summary:
1:13:14.378477 PROGRESS: Channel   0:	 0.050 FDR: 1,417; 0.010 FDR: 1,417; 0.001 FDR: 1,060
1:13:14.378613 PROGRESS: =========================================================================
1:13:14.406432 INFO: Target number of precursors reached.
1:13:14.917553 INFO: fragments_df: keeping 5000 of 3793639 [sum(precursor_idx_mask)=37065 sum(mass_error_mask)=3793639 stop_rank=5000
1:13:15.491712 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:13:15.820394 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:13:16.730348 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:13:16.730983 INFO: Using score_cutoff 9.134335027599334 (fac=0.99, q=1)
1:13:16.731421 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:13:16.731519 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:13:16.731578 INFO: Updating optimization_manager: score_cutoff        : 7.799527667999267 -> 9.134335027599334
1:13:16.731644 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:13:16.937114 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:13:17.440006 INFO: === checking if optimization conditions were reached ===
1:13:17.440353 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:13:17.444189 INFO: Updating optimization_manager: rt_error            : 782.3669644863444 -> 721.4461016313361
1:13:17.444334 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 721.4461.
1:13:17.444412 INFO: ==============================================
1:13:17.444501 INFO: Starting optimization step 3.
1:13:17.444577 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:13:17.444688 INFO: Using rust extraction backend
1:13:17.444779 PROGRESS: Extracting batch of 252182 precursors
1:13:17.912276 INFO: === Search parameters used ===
1:13:17.912596 INFO: rt_error       : 721.4461016313361
1:13:17.912726 INFO: mobility_error : 0.1
1:13:17.912813 INFO: num_candidates : 3
1:13:17.912888 INFO: ms1_error      : 20
1:13:17.912963 INFO: ms2_error      : 10.0
1:13:17.913033 INFO: fwhm_rt        : 3.0
1:13:17.913102 INFO: quant_window   : 3
1:13:17.913171 INFO: ==============================================
1:13:22.156578 INFO: performing precursor FDR with 40 features
1:13:22.156748 INFO: Decoy channel: -1
1:13:22.156784 INFO: competitive: True
1:13:22.404495 INFO: Setting torch num_threads to 2 for FDR classification task
1:13:22.787783 INFO: Estimating optimal hyperparameters - samples: 603,424, batch_size: 2,471, learning_rate: 7.77e-04
1:13:22.789005 INFO: Using random state 861664 for train-test-split
1:13:33.617453 INFO: Test AUC: 0.610
1:13:33.617664 INFO: Train AUC: 0.620
1:13:33.617720 INFO: AUC difference: 1.52%
1:13:34.204862 INFO: Resetting torch num_threads to 32
1:13:34.238265 PROGRESS: === Extracted 754281 precursors and 3793637 fragments ===
1:13:34.238754 INFO: === FDR correction performed with classifier version 12 ===
1:13:34.239475 PROGRESS: ============================= Precursor FDR =============================
1:13:34.239575 PROGRESS: Total precursors accumulated: 1,487
1:13:34.239654 PROGRESS: Target precursors: 1,473 (99.06%)
1:13:34.239713 PROGRESS: Decoy precursors: 14 (0.94%)
1:13:34.239765 PROGRESS: 
1:13:34.239820 PROGRESS: Precursor Summary:
1:13:34.241196 PROGRESS: Channel   0:	 0.050 FDR: 1,473; 0.010 FDR: 1,473; 0.001 FDR:   956
1:13:34.241297 PROGRESS: 
1:13:34.241360 PROGRESS: Protein Summary:
1:13:34.243113 PROGRESS: Channel   0:	 0.050 FDR: 1,293; 0.010 FDR: 1,293; 0.001 FDR:   857
1:13:34.243211 PROGRESS: =========================================================================
1:13:34.261241 INFO: Target number of precursors reached.
1:13:34.836934 INFO: fragments_df: keeping 5000 of 3793637 [sum(precursor_idx_mask)=33891 sum(mass_error_mask)=3793637 stop_rank=5000
1:13:35.401791 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:13:35.742718 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:13:36.631624 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:13:36.632107 INFO: Using score_cutoff 8.590093032073975 (fac=0.99, q=1)
1:13:36.632472 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:13:36.632563 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:13:36.632644 INFO: Updating optimization_manager: score_cutoff        : 9.134335027599334 -> 8.590093032073975
1:13:36.632718 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:13:36.791201 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:13:37.180111 INFO: === checking if optimization conditions were reached ===
1:13:37.180504 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:13:37.184120 INFO: Updating optimization_manager: rt_error            : 721.4461016313361 -> 929.9511924711305
1:13:37.184292 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 929.9512.
1:13:37.184379 INFO: ==============================================
1:13:37.184470 INFO: Starting optimization step 4.
1:13:37.184551 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:13:37.184651 INFO: Using rust extraction backend
1:13:37.184732 PROGRESS: Extracting batch of 252182 precursors
1:13:37.648775 INFO: === Search parameters used ===
1:13:37.649073 INFO: rt_error       : 929.9511924711305
1:13:37.649151 INFO: mobility_error : 0.1
1:13:37.649207 INFO: num_candidates : 3
1:13:37.649260 INFO: ms1_error      : 20
1:13:37.649311 INFO: ms2_error      : 10.0
1:13:37.649358 INFO: fwhm_rt        : 3.0
1:13:37.649403 INFO: quant_window   : 3
1:13:37.649464 INFO: ==============================================
1:13:42.226773 INFO: performing precursor FDR with 40 features
1:13:42.226931 INFO: Decoy channel: -1
1:13:42.226963 INFO: competitive: True
1:13:42.477553 INFO: Setting torch num_threads to 2 for FDR classification task
1:13:42.897076 INFO: Estimating optimal hyperparameters - samples: 603,341, batch_size: 2,471, learning_rate: 7.77e-04
1:13:42.898649 INFO: Using random state 861664 for train-test-split
1:13:53.882168 INFO: Test AUC: 0.609
1:13:53.882361 INFO: Train AUC: 0.620
1:13:53.882403 INFO: AUC difference: 1.69%
1:13:55.341231 INFO: Resetting torch num_threads to 32
1:13:55.388474 PROGRESS: === Extracted 754177 precursors and 3792527 fragments ===
1:13:55.389149 INFO: === FDR correction performed with classifier version 12 ===
1:13:55.390432 PROGRESS: ============================= Precursor FDR =============================
1:13:55.390595 PROGRESS: Total precursors accumulated: 1,589
1:13:55.390673 PROGRESS: Target precursors: 1,574 (99.06%)
1:13:55.390739 PROGRESS: Decoy precursors: 15 (0.94%)
1:13:55.390802 PROGRESS: 
1:13:55.390863 PROGRESS: Precursor Summary:
1:13:55.392910 PROGRESS: Channel   0:	 0.050 FDR: 1,574; 0.010 FDR: 1,574; 0.001 FDR:   366
1:13:55.393041 PROGRESS: 
1:13:55.393113 PROGRESS: Protein Summary:
1:13:55.395529 PROGRESS: Channel   0:	 0.050 FDR: 1,379; 0.010 FDR: 1,379; 0.001 FDR:   344
1:13:55.395649 PROGRESS: =========================================================================
1:13:55.427028 INFO: Target number of precursors reached.
1:13:55.950969 INFO: fragments_df: keeping 5000 of 3792527 [sum(precursor_idx_mask)=36143 sum(mass_error_mask)=3792527 stop_rank=5000
1:13:56.536073 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:13:56.881646 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:13:57.648259 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:13:57.648754 INFO: Using score_cutoff 8.720931909656525 (fac=0.99, q=1)
1:13:57.649128 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:13:57.649220 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:13:57.649279 INFO: Updating optimization_manager: score_cutoff        : 8.590093032073975 -> 8.720931909656525
1:13:57.649346 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:13:57.805547 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:13:58.203810 INFO: === checking if optimization conditions were reached ===
1:13:58.204402 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:13:58.209014 INFO: Updating optimization_manager: rt_error            : 929.9511924711305 -> 800.2106613078922
1:13:58.209208 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 800.2107.
1:13:58.209321 INFO: ==============================================
1:13:58.209444 INFO: Starting optimization step 5.
1:13:58.209552 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:13:58.209670 INFO: Using rust extraction backend
1:13:58.209773 PROGRESS: Extracting batch of 252182 precursors
1:13:58.678577 INFO: === Search parameters used ===
1:13:58.678857 INFO: rt_error       : 800.2106613078922
1:13:58.678929 INFO: mobility_error : 0.1
1:13:58.678985 INFO: num_candidates : 3
1:13:58.679034 INFO: ms1_error      : 20
1:13:58.679080 INFO: ms2_error      : 10.0
1:13:58.679124 INFO: fwhm_rt        : 3.0
1:13:58.679167 INFO: quant_window   : 3
1:13:58.679210 INFO: ==============================================
1:14:03.006185 INFO: performing precursor FDR with 40 features
1:14:03.006308 INFO: Decoy channel: -1
1:14:03.006338 INFO: competitive: True
1:14:03.249580 INFO: Setting torch num_threads to 2 for FDR classification task
1:14:03.622886 INFO: Estimating optimal hyperparameters - samples: 603,374, batch_size: 2,471, learning_rate: 7.77e-04
1:14:03.624163 INFO: Using random state 861664 for train-test-split
1:14:14.171186 INFO: Test AUC: 0.613
1:14:14.171367 INFO: Train AUC: 0.619
1:14:14.171408 INFO: AUC difference: 1.01%
1:14:14.695076 INFO: Resetting torch num_threads to 32
1:14:14.732124 PROGRESS: === Extracted 754218 precursors and 3793422 fragments ===
1:14:14.732685 INFO: === FDR correction performed with classifier version 12 ===
1:14:14.733491 PROGRESS: ============================= Precursor FDR =============================
1:14:14.733589 PROGRESS: Total precursors accumulated: 1,559
1:14:14.733673 PROGRESS: Target precursors: 1,544 (99.04%)
1:14:14.733736 PROGRESS: Decoy precursors: 15 (0.96%)
1:14:14.733791 PROGRESS: 
1:14:14.733840 PROGRESS: Precursor Summary:
1:14:14.735262 PROGRESS: Channel   0:	 0.050 FDR: 1,544; 0.010 FDR: 1,544; 0.001 FDR: 1,055
1:14:14.735364 PROGRESS: 
1:14:14.735428 PROGRESS: Protein Summary:
1:14:14.737302 PROGRESS: Channel   0:	 0.050 FDR: 1,356; 0.010 FDR: 1,356; 0.001 FDR:   935
1:14:14.737408 PROGRESS: =========================================================================
1:14:14.756886 INFO: Target number of precursors reached.
1:14:15.321525 INFO: fragments_df: keeping 5000 of 3793422 [sum(precursor_idx_mask)=35312 sum(mass_error_mask)=3793422 stop_rank=5000
1:14:15.869451 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:14:16.237005 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:14:17.049939 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:14:17.050446 INFO: Using score_cutoff 7.50987580575943 (fac=0.99, q=1)
1:14:17.050780 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:14:17.050864 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:14:17.050934 INFO: Updating optimization_manager: score_cutoff        : 8.720931909656525 -> 7.50987580575943
1:14:17.050995 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:14:17.209969 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:14:17.587672 INFO: === checking if optimization conditions were reached ===
1:14:17.588018 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
1:14:17.591085 INFO: Updating optimization_manager: rt_error            : 800.2106613078922 -> 906.7222650731378
1:14:17.591215 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 906.7223.
1:14:17.591302 INFO: ==============================================
1:14:17.591419 INFO: Starting optimization step 6.
1:14:17.591497 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:14:17.591592 INFO: Using rust extraction backend
1:14:17.591682 PROGRESS: Extracting batch of 252182 precursors
1:14:18.062622 INFO: === Search parameters used ===
1:14:18.063007 INFO: rt_error       : 906.7222650731378
1:14:18.063113 INFO: mobility_error : 0.1
1:14:18.063184 INFO: num_candidates : 3
1:14:18.063246 INFO: ms1_error      : 20
1:14:18.063306 INFO: ms2_error      : 10.0
1:14:18.063365 INFO: fwhm_rt        : 3.0
1:14:18.063422 INFO: quant_window   : 3
1:14:18.063502 INFO: ==============================================
1:14:22.318912 INFO: performing precursor FDR with 40 features
1:14:22.319037 INFO: Decoy channel: -1
1:14:22.319067 INFO: competitive: True
1:14:22.582552 INFO: Setting torch num_threads to 2 for FDR classification task
1:14:23.067172 INFO: Estimating optimal hyperparameters - samples: 603,324, batch_size: 2,471, learning_rate: 7.77e-04
1:14:23.068605 INFO: Using random state 861664 for train-test-split
1:14:34.156116 INFO: Test AUC: 0.608
1:14:34.156286 INFO: Train AUC: 0.619
1:14:34.156336 INFO: AUC difference: 1.72%
1:14:34.745642 INFO: Resetting torch num_threads to 32
1:14:34.780229 PROGRESS: === Extracted 754156 precursors and 3792757 fragments ===
1:14:34.780759 INFO: === FDR correction performed with classifier version 12 ===
1:14:34.781540 PROGRESS: ============================= Precursor FDR =============================
1:14:34.781634 PROGRESS: Total precursors accumulated: 1,561
1:14:34.781700 PROGRESS: Target precursors: 1,546 (99.04%)
1:14:34.781755 PROGRESS: Decoy precursors: 15 (0.96%)
1:14:34.781806 PROGRESS: 
1:14:34.781855 PROGRESS: Precursor Summary:
1:14:34.783160 PROGRESS: Channel   0:	 0.050 FDR: 1,546; 0.010 FDR: 1,546; 0.001 FDR:    44
1:14:34.783253 PROGRESS: 
1:14:34.783313 PROGRESS: Protein Summary:
1:14:34.785002 PROGRESS: Channel   0:	 0.050 FDR: 1,364; 0.010 FDR: 1,364; 0.001 FDR:    44
1:14:34.785103 PROGRESS: =========================================================================
1:14:34.803789 INFO: Target number of precursors reached.
1:14:35.224125 INFO: fragments_df: keeping 5000 of 3792757 [sum(precursor_idx_mask)=35758 sum(mass_error_mask)=3792757 stop_rank=5000
1:14:35.776269 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:14:36.096040 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:14:36.951561 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:14:36.952137 INFO: Using score_cutoff 8.749253119468689 (fac=0.99, q=1)
1:14:36.952576 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:14:36.952699 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:14:36.952767 INFO: Updating optimization_manager: score_cutoff        : 7.50987580575943 -> 8.749253119468689
1:14:36.952839 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:14:37.114333 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:14:37.525259 INFO: === checking if optimization conditions were reached ===
1:14:37.525743 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
1:14:37.530506 INFO: Updating optimization_manager: rt_error            : 906.7222650731378 -> 875.234897805595
1:14:37.530891 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 875.2349.
1:14:37.531001 INFO: ==============================================
1:14:37.531743 INFO: Starting optimization step 7.
1:14:37.532766 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:14:37.533015 INFO: Using rust extraction backend
1:14:37.533111 PROGRESS: Extracting batch of 252182 precursors
1:14:38.005220 INFO: === Search parameters used ===
1:14:38.005517 INFO: rt_error       : 875.234897805595
1:14:38.005594 INFO: mobility_error : 0.1
1:14:38.005656 INFO: num_candidates : 3
1:14:38.005714 INFO: ms1_error      : 20
1:14:38.005768 INFO: ms2_error      : 10.0
1:14:38.005836 INFO: fwhm_rt        : 3.0
1:14:38.005890 INFO: quant_window   : 3
1:14:38.005941 INFO: ==============================================
1:14:42.189793 INFO: performing precursor FDR with 40 features
1:14:42.189920 INFO: Decoy channel: -1
1:14:42.189952 INFO: competitive: True
1:14:42.414983 INFO: Setting torch num_threads to 2 for FDR classification task
1:14:42.773697 INFO: Estimating optimal hyperparameters - samples: 603,348, batch_size: 2,471, learning_rate: 7.77e-04
1:14:42.775179 INFO: Using random state 861664 for train-test-split
1:14:58.395137 INFO: Test AUC: 0.606
1:14:58.395301 INFO: Train AUC: 0.619
1:14:58.395353 INFO: AUC difference: 2.03%
1:14:58.955897 INFO: Resetting torch num_threads to 32
1:14:59.002734 PROGRESS: === Extracted 754186 precursors and 3792763 fragments ===
1:14:59.003323 INFO: === FDR correction performed with classifier version 12 ===
1:14:59.004397 PROGRESS: ============================= Precursor FDR =============================
1:14:59.004526 PROGRESS: Total precursors accumulated: 1,672
1:14:59.004600 PROGRESS: Target precursors: 1,656 (99.04%)
1:14:59.004685 PROGRESS: Decoy precursors: 16 (0.96%)
1:14:59.004745 PROGRESS: 
1:14:59.004807 PROGRESS: Precursor Summary:
1:14:59.006842 PROGRESS: Channel   0:	 0.050 FDR: 1,656; 0.010 FDR: 1,656; 0.001 FDR: 1,029
1:14:59.006968 PROGRESS: 
1:14:59.007043 PROGRESS: Protein Summary:
1:14:59.009618 PROGRESS: Channel   0:	 0.050 FDR: 1,452; 0.010 FDR: 1,452; 0.001 FDR:   922
1:14:59.009741 PROGRESS: =========================================================================
1:14:59.039533 INFO: Target number of precursors reached.
1:14:59.548131 INFO: fragments_df: keeping 5000 of 3792763 [sum(precursor_idx_mask)=37848 sum(mass_error_mask)=3792763 stop_rank=5000
1:15:00.106003 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:15:00.498257 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:15:01.353972 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:15:01.354550 INFO: Using score_cutoff 9.045718407154084 (fac=0.99, q=1)
1:15:01.354970 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:15:01.355074 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:15:01.355144 INFO: Updating optimization_manager: score_cutoff        : 8.749253119468689 -> 9.045718407154084
1:15:01.355226 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:15:01.514674 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:15:01.897405 INFO: === checking if optimization conditions were reached ===
1:15:01.897706 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
1:15:01.899009 INFO: Updating optimization_manager: rt_error            : 875.234897805595 -> 875.234897805595
1:15:01.899228 INFO: Updating optimization_manager: classifier_version  : 12 -> 20
1:15:01.899406 INFO: Updating optimization_manager: score_cutoff        : 9.045718407154084 -> 9.045718407154084
1:15:01.899559 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:15:01.899719 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:15:01.899886 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 875.2349 found after 8 searches.
1:15:01.899996 INFO: ==============================================
1:15:01.900135 PROGRESS: Optimization finished for rt_error.
1:15:02.443674 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:15:02.599020 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:15:02.989471 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:15:02.989766 PROGRESS: ==============================================
1:15:02.989849 PROGRESS: ms2_error      : 10.0000
1:15:02.989918 PROGRESS: rt_error       : 875.2349
1:15:02.989977 PROGRESS: ==============================================
1:15:02.990855 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:15:12.638614 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:15:41.103336 INFO: Using rust extraction backend
1:15:41.103707 PROGRESS: Extracting batch of 15081856 precursors
1:16:08.486173 INFO: === Search parameters used ===
1:16:08.486428 INFO: rt_error       : 875.234897805595
1:16:08.486506 INFO: mobility_error : 0.1
1:16:08.486571 INFO: num_candidates : 3
1:16:08.486626 INFO: ms1_error      : 20
1:16:08.486679 INFO: ms2_error      : 10.0
1:16:08.486731 INFO: fwhm_rt        : 3.0
1:16:08.486783 INFO: quant_window   : 3
1:16:08.486833 INFO: ==============================================
1:17:49.090291 INFO: Removed 7719188 precursors with score below cutoff 9.045718407154084
1:18:30.967806 INFO: performing precursor FDR with 40 features
1:18:30.967934 INFO: Decoy channel: -1
1:18:30.967964 INFO: competitive: True
1:18:35.635649 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:56.398583 INFO: Estimating optimal hyperparameters - samples: 30,020,780, batch_size: 4,096, learning_rate: 1.00e-03
1:18:56.498250 INFO: Using random state 28875 for train-test-split
1:32:04.753199 INFO: Test AUC: 0.616
1:32:04.753458 INFO: Train AUC: 0.616
1:32:04.753539 INFO: AUC difference: 0.07%
1:32:13.027547 INFO: Resetting torch num_threads to 32
1:32:16.068164 PROGRESS: ============================= Precursor FDR =============================
1:32:16.068422 PROGRESS: Total precursors accumulated: 88,703
1:32:16.068507 PROGRESS: Target precursors: 87,825 (99.01%)
1:32:16.068568 PROGRESS: Decoy precursors: 878 (0.99%)
1:32:16.068642 PROGRESS: 
1:32:16.068699 PROGRESS: Precursor Summary:
1:32:16.114689 PROGRESS: Channel   0:	 0.050 FDR: 87,825; 0.010 FDR: 87,825; 0.001 FDR: 50,562
1:32:16.114939 PROGRESS: 
1:32:16.115005 PROGRESS: Protein Summary:
1:32:16.173752 PROGRESS: Channel   0:	 0.050 FDR: 12,994; 0.010 FDR: 12,994; 0.001 FDR: 8,742
1:32:16.173973 PROGRESS: =========================================================================
1:32:16.478442 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/psm.parquet
1:32:16.651409 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.parquet
1:32:16.890506 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:32:17.827372 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 
1:32:17.827557 INFO: Quantification results path: /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant
1:32:17.827650 INFO: Creating folder /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/figures
1:32:17.827874 INFO: Initializing TimingManager
1:32:17.828511 INFO: Initializing RawFileManager
1:33:09.581266 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.
1:33:09.589010 INFO: Determining DIA cycle
1:33:09.606797 INFO: Found cycle with start 0.00 min and length 300.
1:33:09.800414 INFO: RT (min)            : 0.0 - 26.9
1:33:09.800531 INFO: RT duration (sec)   : 1611.2
1:33:09.800570 INFO: RT duration (min)   : 26.9
1:33:09.800647 INFO: Cycle len (scans)   : 300
1:33:09.800682 INFO: Cycle len (sec)     : 1.65
1:33:09.800709 INFO: Number of cycles    : 977
1:33:09.800738 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:33:09.800793 INFO: Creating DIA data object took: 51.972132205963135
1:33:11.351012 INFO: Creating DIA data NG object took: 1.5500481128692627
1:33:13.366961 INFO: Initializing CalibrationManager
1:33:13.367306 INFO: Setting up calibration estimators ..
1:33:13.367375 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:33:13.367478 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'}' ..
1:33:13.367618 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:33:13.367690 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:33:13.367754 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}}' ..
1:33:13.367832 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:33:13.367887 INFO: Done setting up calibration estimators.
1:33:13.368096 INFO: Initializing OptimizationManager
1:33:13.368283 INFO: initial parameter: ms1_error = 20
1:33:13.368340 INFO: initial parameter: ms2_error = 20
1:33:13.368389 INFO: initial parameter: rt_error = 805.6004638671875
1:33:13.368435 INFO: initial parameter: mobility_error = 0.1
1:33:13.368478 INFO: initial parameter: num_candidates = 1
1:33:13.368520 INFO: initial parameter: fwhm_rt = 5
1:33:13.368565 INFO: initial parameter: fwhm_mobility = 0.01
1:33:13.368622 INFO: initial parameter: score_cutoff = 0
1:33:13.368678 INFO: initial parameter: classifier_version = -1
1:33:13.368756 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:33:13.369075 INFO: FDRManager: loading saved state not requested, will be initialized.
1:33:13.369109 INFO: Initializing FDRManager
1:33:13.369149 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
1:33:15.899810 PROGRESS: Initializing spectral library: 7,536,970 target precursors potentially observable (1,230,167 removed)
1:33:17.338801 INFO: Updating optimization_manager: ms2_error           : 20 -> 20
1:33:17.339309 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
1:33:17.339440 PROGRESS: Starting initial search for precursors.
1:33:17.339548 INFO: Starting optimization step 0.
1:33:17.339619 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:33:17.339696 INFO: Using rust extraction backend
1:33:17.339780 PROGRESS: Extracting batch of 1988 precursors
1:33:17.345314 INFO: === Search parameters used ===
1:33:17.345466 INFO: rt_error       : 805.6004638671875
1:33:17.345528 INFO: mobility_error : 0.1
1:33:17.345581 INFO: num_candidates : 1
1:33:17.345630 INFO: ms1_error      : 20
1:33:17.345677 INFO: ms2_error      : 20
1:33:17.345723 INFO: fwhm_rt        : 5
1:33:17.345770 INFO: quant_window   : 3
1:33:17.345818 INFO: ==============================================
1:33:17.383280 INFO: performing precursor FDR with 40 features
1:33:17.383388 INFO: Decoy channel: -1
1:33:17.383416 INFO: competitive: True
1:33:17.384919 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:17.387177 INFO: Estimating optimal hyperparameters - samples: 1,576, batch_size: 128, learning_rate: 1.77e-04
1:33:17.388388 INFO: Using random state 344169 for train-test-split
1:33:17.565537 INFO: Test AUC: 0.477
1:33:17.565640 INFO: Train AUC: 0.552
1:33:17.565671 INFO: AUC difference: 13.52%
1:33:17.565696 WARNING: AUC difference > 5%. This may indicate overfitting.
1:33:17.830309 INFO: Resetting torch num_threads to 32
1:33:17.832588 PROGRESS: === Extracted 1970 precursors and 9289 fragments ===
1:33:17.833149 INFO: === FDR correction performed with classifier version -1 ===
1:33:17.833840 PROGRESS: ============================= Precursor FDR =============================
1:33:17.833954 PROGRESS: Total precursors accumulated: 13
1:33:17.834024 PROGRESS: Target precursors: 13 (100.00%)
1:33:17.834086 PROGRESS: Decoy precursors: 0 (0.00%)
1:33:17.834145 PROGRESS: 
1:33:17.834200 PROGRESS: Precursor Summary:
1:33:17.835585 PROGRESS: Channel   0:	 0.050 FDR:    13; 0.010 FDR:    13; 0.001 FDR:    13
1:33:17.835693 PROGRESS: 
1:33:17.835758 PROGRESS: Protein Summary:
1:33:17.837265 PROGRESS: Channel   0:	 0.050 FDR:    13; 0.010 FDR:    13; 0.001 FDR:    13
1:33:17.837383 PROGRESS: =========================================================================
1:33:17.837792 INFO: Target number of precursors not reached yet.
1:33:17.957517 INFO: Starting optimization step 1.
1:33:17.957754 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:33:17.957860 INFO: Using rust extraction backend
1:33:17.957943 PROGRESS: Extracting batch of 3976 precursors
1:33:17.969133 INFO: === Search parameters used ===
1:33:17.969330 INFO: rt_error       : 805.6004638671875
1:33:17.969395 INFO: mobility_error : 0.1
1:33:17.969453 INFO: num_candidates : 1
1:33:17.969508 INFO: ms1_error      : 20
1:33:17.969563 INFO: ms2_error      : 20
1:33:17.969616 INFO: fwhm_rt        : 5
1:33:17.969670 INFO: quant_window   : 3
1:33:17.969721 INFO: ==============================================
1:33:18.039640 INFO: performing precursor FDR with 40 features
1:33:18.039777 INFO: Decoy channel: -1
1:33:18.039817 INFO: competitive: True
1:33:18.047295 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:18.051409 INFO: Estimating optimal hyperparameters - samples: 4,732, batch_size: 128, learning_rate: 1.77e-04
1:33:18.051563 INFO: Using random state 224976 for train-test-split
1:33:18.547547 INFO: Test AUC: 0.508
1:33:18.547697 INFO: Train AUC: 0.562
1:33:18.547733 INFO: AUC difference: 9.69%
1:33:18.547760 WARNING: AUC difference > 5%. This may indicate overfitting.
1:33:18.862084 INFO: Resetting torch num_threads to 32
1:33:18.865286 PROGRESS: === Extracted 5915 precursors and 27897 fragments ===
1:33:18.865683 INFO: === FDR correction performed with classifier version -1 ===
1:33:18.866194 PROGRESS: ============================= Precursor FDR =============================
1:33:18.866281 PROGRESS: Total precursors accumulated: 14
1:33:18.866342 PROGRESS: Target precursors: 14 (100.00%)
1:33:18.866395 PROGRESS: Decoy precursors: 0 (0.00%)
1:33:18.866443 PROGRESS: 
1:33:18.866489 PROGRESS: Precursor Summary:
1:33:18.867562 PROGRESS: Channel   0:	 0.050 FDR:    14; 0.010 FDR:    14; 0.001 FDR:    14
1:33:18.867650 PROGRESS: 
1:33:18.867707 PROGRESS: Protein Summary:
1:33:18.868890 PROGRESS: Channel   0:	 0.050 FDR:    14; 0.010 FDR:    14; 0.001 FDR:    14
1:33:18.868981 PROGRESS: =========================================================================
1:33:18.869270 INFO: Target number of precursors not reached yet.
1:33:18.979687 INFO: Starting optimization step 2.
1:33:18.979912 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:33:18.980002 INFO: Using rust extraction backend
1:33:18.980067 PROGRESS: Extracting batch of 7946 precursors
1:33:18.997145 INFO: === Search parameters used ===
1:33:18.997408 INFO: rt_error       : 805.6004638671875
1:33:18.997485 INFO: mobility_error : 0.1
1:33:18.997552 INFO: num_candidates : 1
1:33:18.997617 INFO: ms1_error      : 20
1:33:18.997663 INFO: ms2_error      : 20
1:33:18.997708 INFO: fwhm_rt        : 5
1:33:18.997752 INFO: quant_window   : 3
1:33:18.997797 INFO: ==============================================
1:33:19.097438 INFO: performing precursor FDR with 40 features
1:33:19.097552 INFO: Decoy channel: -1
1:33:19.097577 INFO: competitive: True
1:33:19.105069 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:19.109422 INFO: Estimating optimal hyperparameters - samples: 11,042, batch_size: 128, learning_rate: 1.77e-04
1:33:19.109583 INFO: Using random state 317272 for train-test-split
1:33:20.376299 INFO: Test AUC: 0.546
1:33:20.376406 INFO: Train AUC: 0.578
1:33:20.376439 INFO: AUC difference: 5.53%
1:33:20.376463 WARNING: AUC difference > 5%. This may indicate overfitting.
1:33:20.687133 INFO: Resetting torch num_threads to 32
1:33:20.693860 PROGRESS: === Extracted 13803 precursors and 64889 fragments ===
1:33:20.694540 INFO: === FDR correction performed with classifier version -1 ===
1:33:20.695381 PROGRESS: ============================= Precursor FDR =============================
1:33:20.695509 PROGRESS: Total precursors accumulated: 31
1:33:20.695607 PROGRESS: Target precursors: 31 (100.00%)
1:33:20.695703 PROGRESS: Decoy precursors: 0 (0.00%)
1:33:20.695794 PROGRESS: 
1:33:20.695885 PROGRESS: Precursor Summary:
1:33:20.697708 PROGRESS: Channel   0:	 0.050 FDR:    31; 0.010 FDR:    31; 0.001 FDR:    31
1:33:20.697844 PROGRESS: 
1:33:20.697941 PROGRESS: Protein Summary:
1:33:20.699980 PROGRESS: Channel   0:	 0.050 FDR:    31; 0.010 FDR:    31; 0.001 FDR:    31
1:33:20.700113 PROGRESS: =========================================================================
1:33:20.700714 INFO: Target number of precursors not reached yet.
1:33:20.852750 INFO: Starting optimization step 3.
1:33:20.852970 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:33:20.853060 INFO: Using rust extraction backend
1:33:20.853128 PROGRESS: Extracting batch of 15879 precursors
1:33:20.883221 INFO: === Search parameters used ===
1:33:20.883460 INFO: rt_error       : 805.6004638671875
1:33:20.883521 INFO: mobility_error : 0.1
1:33:20.883572 INFO: num_candidates : 1
1:33:20.883620 INFO: ms1_error      : 20
1:33:20.883667 INFO: ms2_error      : 20
1:33:20.883723 INFO: fwhm_rt        : 5
1:33:20.883772 INFO: quant_window   : 3
1:33:20.883817 INFO: ==============================================
1:33:21.070103 INFO: performing precursor FDR with 40 features
1:33:21.070222 INFO: Decoy channel: -1
1:33:21.070250 INFO: competitive: True
1:33:21.085202 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:21.093221 INFO: Estimating optimal hyperparameters - samples: 23,642, batch_size: 128, learning_rate: 1.77e-04
1:33:21.093420 INFO: Using random state 620450 for train-test-split
1:33:23.186576 INFO: Test AUC: 0.567
1:33:23.186755 INFO: Train AUC: 0.589
1:33:23.186805 INFO: AUC difference: 3.69%
1:33:23.455692 INFO: Resetting torch num_threads to 32
1:33:23.463907 PROGRESS: === Extracted 29553 precursors and 139299 fragments ===
1:33:23.464482 INFO: === FDR correction performed with classifier version -1 ===
1:33:23.465112 PROGRESS: ============================= Precursor FDR =============================
1:33:23.465211 PROGRESS: Total precursors accumulated: 57
1:33:23.465276 PROGRESS: Target precursors: 57 (100.00%)
1:33:23.465332 PROGRESS: Decoy precursors: 0 (0.00%)
1:33:23.465380 PROGRESS: 
1:33:23.465430 PROGRESS: Precursor Summary:
1:33:23.466527 PROGRESS: Channel   0:	 0.050 FDR:    57; 0.010 FDR:    57; 0.001 FDR:    57
1:33:23.466620 PROGRESS: 
1:33:23.466681 PROGRESS: Protein Summary:
1:33:23.467881 PROGRESS: Channel   0:	 0.050 FDR:    57; 0.010 FDR:    57; 0.001 FDR:    57
1:33:23.467974 PROGRESS: =========================================================================
1:33:23.468580 INFO: Target number of precursors not reached yet.
1:33:23.617195 INFO: Starting optimization step 4.
1:33:23.617428 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:33:23.617530 INFO: Using rust extraction backend
1:33:23.617603 PROGRESS: Extracting batch of 31750 precursors
1:33:23.678902 INFO: === Search parameters used ===
1:33:23.679199 INFO: rt_error       : 805.6004638671875
1:33:23.679280 INFO: mobility_error : 0.1
1:33:23.679347 INFO: num_candidates : 1
1:33:23.679410 INFO: ms1_error      : 20
1:33:23.679471 INFO: ms2_error      : 20
1:33:23.679530 INFO: fwhm_rt        : 5
1:33:23.679589 INFO: quant_window   : 3
1:33:23.679647 INFO: ==============================================
1:33:24.042096 INFO: performing precursor FDR with 40 features
1:33:24.042242 INFO: Decoy channel: -1
1:33:24.042280 INFO: competitive: True
1:33:24.085714 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:24.105214 INFO: Estimating optimal hyperparameters - samples: 48,854, batch_size: 200, learning_rate: 2.21e-04
1:33:24.105445 INFO: Using random state 962444 for train-test-split
1:33:27.018393 INFO: Test AUC: 0.578
1:33:27.018521 INFO: Train AUC: 0.599
1:33:27.018554 INFO: AUC difference: 3.38%
1:33:27.357419 INFO: Resetting torch num_threads to 32
1:33:27.371056 PROGRESS: === Extracted 61068 precursors and 289248 fragments ===
1:33:27.371668 INFO: === FDR correction performed with classifier version -1 ===
1:33:27.372250 PROGRESS: ============================= Precursor FDR =============================
1:33:27.372346 PROGRESS: Total precursors accumulated: 155
1:33:27.372411 PROGRESS: Target precursors: 154 (99.35%)
1:33:27.372474 PROGRESS: Decoy precursors: 1 (0.65%)
1:33:27.372529 PROGRESS: 
1:33:27.372579 PROGRESS: Precursor Summary:
1:33:27.373634 PROGRESS: Channel   0:	 0.050 FDR:   154; 0.010 FDR:   154; 0.001 FDR:   138
1:33:27.373732 PROGRESS: 
1:33:27.373794 PROGRESS: Protein Summary:
1:33:27.374919 PROGRESS: Channel   0:	 0.050 FDR:   152; 0.010 FDR:   152; 0.001 FDR:   136
1:33:27.375012 PROGRESS: =========================================================================
1:33:27.376329 INFO: Target number of precursors not reached yet.
1:33:27.574133 INFO: Starting optimization step 5.
1:33:27.574378 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:33:27.574466 INFO: Using rust extraction backend
1:33:27.574537 PROGRESS: Extracting batch of 63536 precursors
1:33:27.695931 INFO: === Search parameters used ===
1:33:27.696248 INFO: rt_error       : 805.6004638671875
1:33:27.696326 INFO: mobility_error : 0.1
1:33:27.696394 INFO: num_candidates : 1
1:33:27.696455 INFO: ms1_error      : 20
1:33:27.696515 INFO: ms2_error      : 20
1:33:27.696571 INFO: fwhm_rt        : 5
1:33:27.696644 INFO: quant_window   : 3
1:33:27.696709 INFO: ==============================================
1:33:28.321973 INFO: performing precursor FDR with 40 features
1:33:28.322096 INFO: Decoy channel: -1
1:33:28.322132 INFO: competitive: True
1:33:28.380820 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:28.426052 INFO: Estimating optimal hyperparameters - samples: 99,305, batch_size: 406, learning_rate: 3.15e-04
1:33:28.426465 INFO: Using random state 479729 for train-test-split
1:33:33.006446 INFO: Test AUC: 0.577
1:33:33.006566 INFO: Train AUC: 0.603
1:33:33.006599 INFO: AUC difference: 4.31%
1:33:33.297714 INFO: Resetting torch num_threads to 32
1:33:33.326615 PROGRESS: === Extracted 124132 precursors and 587239 fragments ===
1:33:33.327452 INFO: === FDR correction performed with classifier version -1 ===
1:33:33.328412 PROGRESS: ============================= Precursor FDR =============================
1:33:33.328534 PROGRESS: Total precursors accumulated: 336
1:33:33.328636 PROGRESS: Target precursors: 333 (99.11%)
1:33:33.328717 PROGRESS: Decoy precursors: 3 (0.89%)
1:33:33.328785 PROGRESS: 
1:33:33.328866 PROGRESS: Precursor Summary:
1:33:33.330344 PROGRESS: Channel   0:	 0.050 FDR:   333; 0.010 FDR:   333; 0.001 FDR:   137
1:33:33.330461 PROGRESS: 
1:33:33.330539 PROGRESS: Protein Summary:
1:33:33.332209 PROGRESS: Channel   0:	 0.050 FDR:   320; 0.010 FDR:   320; 0.001 FDR:   133
1:33:33.332327 PROGRESS: =========================================================================
1:33:33.336446 INFO: Target number of precursors not reached yet.
1:33:33.771720 INFO: Starting optimization step 6.
1:33:33.771993 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:33:33.772083 INFO: Using rust extraction backend
1:33:33.772154 PROGRESS: Extracting batch of 127107 precursors
1:33:34.006761 INFO: === Search parameters used ===
1:33:34.007101 INFO: rt_error       : 805.6004638671875
1:33:34.007225 INFO: mobility_error : 0.1
1:33:34.007323 INFO: num_candidates : 1
1:33:34.007419 INFO: ms1_error      : 20
1:33:34.007514 INFO: ms2_error      : 20
1:33:34.007626 INFO: fwhm_rt        : 5
1:33:34.007712 INFO: quant_window   : 3
1:33:34.007813 INFO: ==============================================
1:33:35.274232 INFO: performing precursor FDR with 40 features
1:33:35.274371 INFO: Decoy channel: -1
1:33:35.274410 INFO: competitive: True
1:33:35.412858 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:35.518920 INFO: Estimating optimal hyperparameters - samples: 200,177, batch_size: 819, learning_rate: 4.47e-04
1:33:35.519379 INFO: Using random state 456714 for train-test-split
1:33:40.953264 INFO: Test AUC: 0.585
1:33:40.953393 INFO: Train AUC: 0.601
1:33:40.953428 INFO: AUC difference: 2.66%
1:33:41.354776 INFO: Resetting torch num_threads to 32
1:33:41.434635 PROGRESS: === Extracted 250222 precursors and 1180010 fragments ===
1:33:41.435478 INFO: === FDR correction performed with classifier version -1 ===
1:33:41.436519 PROGRESS: ============================= Precursor FDR =============================
1:33:41.436662 PROGRESS: Total precursors accumulated: 839
1:33:41.436765 PROGRESS: Target precursors: 831 (99.05%)
1:33:41.436861 PROGRESS: Decoy precursors: 8 (0.95%)
1:33:41.436951 PROGRESS: 
1:33:41.437037 PROGRESS: Precursor Summary:
1:33:41.438996 PROGRESS: Channel   0:	 0.050 FDR:   831; 0.010 FDR:   831; 0.001 FDR:   459
1:33:41.439120 PROGRESS: 
1:33:41.439209 PROGRESS: Protein Summary:
1:33:41.441518 PROGRESS: Channel   0:	 0.050 FDR:   748; 0.010 FDR:   748; 0.001 FDR:   422
1:33:41.441652 PROGRESS: =========================================================================
1:33:41.448111 INFO: Target number of precursors not reached yet.
1:33:41.965363 INFO: Starting optimization step 7.
1:33:41.965621 PROGRESS: === Extracting elution groups 127000 to 255000 ===
1:33:41.965723 INFO: Using rust extraction backend
1:33:41.965800 PROGRESS: Extracting batch of 254254 precursors
1:33:42.459043 INFO: === Search parameters used ===
1:33:42.459347 INFO: rt_error       : 805.6004638671875
1:33:42.459427 INFO: mobility_error : 0.1
1:33:42.459485 INFO: num_candidates : 1
1:33:42.459540 INFO: ms1_error      : 20
1:33:42.459599 INFO: ms2_error      : 20
1:33:42.459649 INFO: fwhm_rt        : 5
1:33:42.459702 INFO: quant_window   : 3
1:33:42.459750 INFO: ==============================================
1:33:44.972155 INFO: performing precursor FDR with 40 features
1:33:44.972276 INFO: Decoy channel: -1
1:33:44.972306 INFO: competitive: True
1:33:45.220117 INFO: Setting torch num_threads to 2 for FDR classification task
1:33:45.474015 INFO: Estimating optimal hyperparameters - samples: 401,993, batch_size: 1,646, learning_rate: 6.34e-04
1:33:45.474830 INFO: Using random state 238654 for train-test-split
1:33:53.436352 INFO: Test AUC: 0.587
1:33:53.436481 INFO: Train AUC: 0.600
1:33:53.436515 INFO: AUC difference: 2.21%
1:33:53.843274 INFO: Resetting torch num_threads to 32
1:33:53.942301 PROGRESS: === Extracted 502492 precursors and 2368647 fragments ===
1:33:53.942960 INFO: === FDR correction performed with classifier version -1 ===
1:33:53.943847 PROGRESS: ============================= Precursor FDR =============================
1:33:53.943945 PROGRESS: Total precursors accumulated: 1,666
1:33:53.944013 PROGRESS: Target precursors: 1,650 (99.04%)
1:33:53.944072 PROGRESS: Decoy precursors: 16 (0.96%)
1:33:53.944126 PROGRESS: 
1:33:53.944178 PROGRESS: Precursor Summary:
1:33:53.945613 PROGRESS: Channel   0:	 0.050 FDR: 1,650; 0.010 FDR: 1,650; 0.001 FDR: 1,049
1:33:53.945718 PROGRESS: 
1:33:53.945781 PROGRESS: Protein Summary:
1:33:53.947591 PROGRESS: Channel   0:	 0.050 FDR: 1,352; 0.010 FDR: 1,352; 0.001 FDR:   900
1:33:53.947689 PROGRESS: =========================================================================
1:33:53.955672 INFO: Target number of precursors reached.
1:33:54.226894 INFO: fragments_df: keeping 5000 of 2368647 [sum(precursor_idx_mask)=17804 sum(mass_error_mask)=2368647 stop_rank=5000
1:33:55.158998 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:33:55.478147 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:33:56.300042 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:33:56.300651 INFO: Using score_cutoff 12.919026354503632 (fac=0.99, q=1)
1:33:56.301146 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:33:56.301257 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:33:56.301335 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.919026354503632
1:33:56.301418 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:33:56.616589 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:33:57.449415 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
1:33:57.449651 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:33:57.449765 INFO: Starting optimization step 8.
1:33:57.449839 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:33:57.449918 INFO: Using rust extraction backend
1:33:57.449988 PROGRESS: Extracting batch of 506436 precursors
1:33:58.397621 INFO: === Search parameters used ===
1:33:58.398044 INFO: rt_error       : 805.6004638671875
1:33:58.398124 INFO: mobility_error : 0.1
1:33:58.398185 INFO: num_candidates : 3
1:33:58.398236 INFO: ms1_error      : 20
1:33:58.398291 INFO: ms2_error      : 20
1:33:58.398340 INFO: fwhm_rt        : 3.0
1:33:58.398389 INFO: quant_window   : 3
1:33:58.398449 INFO: ==============================================
1:34:06.275679 INFO: performing precursor FDR with 40 features
1:34:06.275835 INFO: Decoy channel: -1
1:34:06.275863 INFO: competitive: True
1:34:06.817376 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:07.648753 INFO: Estimating optimal hyperparameters - samples: 1,204,382, batch_size: 4,096, learning_rate: 1.00e-03
1:34:07.652083 INFO: Using random state 628090 for train-test-split
1:34:35.203562 INFO: Test AUC: 0.594
1:34:35.203826 INFO: Train AUC: 0.601
1:34:35.203884 INFO: AUC difference: 1.15%
1:34:36.073124 INFO: Resetting torch num_threads to 32
1:34:36.140823 PROGRESS: === Extracted 1505478 precursors and 6871679 fragments ===
1:34:36.141346 INFO: === FDR correction performed with classifier version 7 ===
1:34:36.142201 PROGRESS: ============================= Precursor FDR =============================
1:34:36.142295 PROGRESS: Total precursors accumulated: 1,962
1:34:36.142360 PROGRESS: Target precursors: 1,943 (99.03%)
1:34:36.142416 PROGRESS: Decoy precursors: 19 (0.97%)
1:34:36.142466 PROGRESS: 
1:34:36.142514 PROGRESS: Precursor Summary:
1:34:36.143986 PROGRESS: Channel   0:	 0.050 FDR: 1,943; 0.010 FDR: 1,943; 0.001 FDR: 1,212
1:34:36.144082 PROGRESS: 
1:34:36.144141 PROGRESS: Protein Summary:
1:34:36.146098 PROGRESS: Channel   0:	 0.050 FDR: 1,579; 0.010 FDR: 1,579; 0.001 FDR: 1,029
1:34:36.146197 PROGRESS: =========================================================================
1:34:36.180037 INFO: Target number of precursors reached.
1:34:37.016491 INFO: fragments_df: keeping 5000 of 6871679 [sum(precursor_idx_mask)=44697 sum(mass_error_mask)=6871679 stop_rank=5000
1:34:38.099861 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:34:38.457648 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:34:40.325889 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:34:40.326378 INFO: Using score_cutoff 12.452949961853028 (fac=0.99, q=1)
1:34:40.326779 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:34:40.326883 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:34:40.326956 INFO: Updating optimization_manager: score_cutoff        : 12.919026354503632 -> 12.452949961853028
1:34:40.327032 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:34:40.659895 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:34:41.498808 INFO: === checking if optimization conditions were reached ===
1:34:41.501308 INFO: Updating optimization_manager: ms2_error           : 20 -> 10.0
1:34:41.501485 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:34:41.501576 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:34:41.501641 INFO: ==============================================
1:34:41.501714 INFO: Starting optimization step 9.
1:34:41.501783 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:34:41.501850 INFO: Using rust extraction backend
1:34:41.501913 PROGRESS: Extracting batch of 506436 precursors
1:34:42.455676 INFO: === Search parameters used ===
1:34:42.456178 INFO: rt_error       : 805.6004638671875
1:34:42.456267 INFO: mobility_error : 0.1
1:34:42.456331 INFO: num_candidates : 3
1:34:42.456390 INFO: ms1_error      : 20
1:34:42.456444 INFO: ms2_error      : 10.0
1:34:42.456511 INFO: fwhm_rt        : 3.0
1:34:42.456566 INFO: quant_window   : 3
1:34:42.456635 INFO: ==============================================
1:34:51.176222 INFO: performing precursor FDR with 40 features
1:34:51.176401 INFO: Decoy channel: -1
1:34:51.176442 INFO: competitive: True
1:34:51.744483 INFO: Setting torch num_threads to 2 for FDR classification task
1:34:52.562179 INFO: Estimating optimal hyperparameters - samples: 1,211,696, batch_size: 4,096, learning_rate: 1.00e-03
1:34:52.565238 INFO: Using random state 710838 for train-test-split
1:35:22.019527 INFO: Test AUC: 0.600
1:35:22.019720 INFO: Train AUC: 0.606
1:35:22.019758 INFO: AUC difference: 0.90%
1:35:22.901706 INFO: Resetting torch num_threads to 32
1:35:23.038595 PROGRESS: === Extracted 1514621 precursors and 7644935 fragments ===
1:35:23.039133 INFO: === FDR correction performed with classifier version 8 ===
1:35:23.040109 PROGRESS: ============================= Precursor FDR =============================
1:35:23.040208 PROGRESS: Total precursors accumulated: 2,229
1:35:23.040279 PROGRESS: Target precursors: 2,207 (99.01%)
1:35:23.040338 PROGRESS: Decoy precursors: 22 (0.99%)
1:35:23.040393 PROGRESS: 
1:35:23.040443 PROGRESS: Precursor Summary:
1:35:23.042084 PROGRESS: Channel   0:	 0.050 FDR: 2,207; 0.010 FDR: 2,207; 0.001 FDR: 1,298
1:35:23.042206 PROGRESS: 
1:35:23.042289 PROGRESS: Protein Summary:
1:35:23.044588 PROGRESS: Channel   0:	 0.050 FDR: 1,786; 0.010 FDR: 1,786; 0.001 FDR: 1,095
1:35:23.044725 PROGRESS: =========================================================================
1:35:23.084146 INFO: Target number of precursors reached.
1:35:24.053156 INFO: fragments_df: keeping 5000 of 7644935 [sum(precursor_idx_mask)=52221 sum(mass_error_mask)=7644935 stop_rank=5000
1:35:24.668771 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:35:25.092962 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:35:26.008999 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:35:26.009498 INFO: Using score_cutoff 9.559116731071471 (fac=0.99, q=1)
1:35:26.009849 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:35:26.009938 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:35:26.010000 INFO: Updating optimization_manager: score_cutoff        : 12.452949961853028 -> 9.559116731071471
1:35:26.010065 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:35:26.163989 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:35:26.583883 INFO: === checking if optimization conditions were reached ===
1:35:26.586340 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:35:26.586501 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:35:26.586579 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:35:26.586649 INFO: ==============================================
1:35:26.586731 INFO: Starting optimization step 10.
1:35:26.586809 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:35:26.586900 INFO: Using rust extraction backend
1:35:26.586979 PROGRESS: Extracting batch of 252182 precursors
1:35:27.080287 INFO: === Search parameters used ===
1:35:27.080555 INFO: rt_error       : 805.6004638671875
1:35:27.080639 INFO: mobility_error : 0.1
1:35:27.080701 INFO: num_candidates : 3
1:35:27.080752 INFO: ms1_error      : 20
1:35:27.080823 INFO: ms2_error      : 10.0
1:35:27.080872 INFO: fwhm_rt        : 3.0
1:35:27.080917 INFO: quant_window   : 3
1:35:27.080963 INFO: ==============================================
1:35:31.332653 INFO: performing precursor FDR with 40 features
1:35:31.332797 INFO: Decoy channel: -1
1:35:31.332825 INFO: competitive: True
1:35:31.565797 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:31.968993 INFO: Estimating optimal hyperparameters - samples: 603,344, batch_size: 2,471, learning_rate: 7.77e-04
1:35:31.970455 INFO: Using random state 105413 for train-test-split
1:35:46.103414 INFO: Test AUC: 0.602
1:35:46.103590 INFO: Train AUC: 0.612
1:35:46.103630 INFO: AUC difference: 1.71%
1:35:46.608349 INFO: Resetting torch num_threads to 32
1:35:46.649723 PROGRESS: === Extracted 754181 precursors and 3807472 fragments ===
1:35:46.650440 INFO: === FDR correction performed with classifier version 9 ===
1:35:46.651605 PROGRESS: ============================= Precursor FDR =============================
1:35:46.651731 PROGRESS: Total precursors accumulated: 1,249
1:35:46.651834 PROGRESS: Target precursors: 1,237 (99.04%)
1:35:46.651932 PROGRESS: Decoy precursors: 12 (0.96%)
1:35:46.652025 PROGRESS: 
1:35:46.652117 PROGRESS: Precursor Summary:
1:35:46.654276 PROGRESS: Channel   0:	 0.050 FDR: 1,237; 0.010 FDR: 1,237; 0.001 FDR:   423
1:35:46.654408 PROGRESS: 
1:35:46.654505 PROGRESS: Protein Summary:
1:35:46.657261 PROGRESS: Channel   0:	 0.050 FDR: 1,102; 0.010 FDR: 1,102; 0.001 FDR:   399
1:35:46.657396 PROGRESS: =========================================================================
1:35:46.680540 INFO: Target number of precursors reached.
1:35:47.149323 INFO: fragments_df: keeping 5000 of 3807472 [sum(precursor_idx_mask)=29034 sum(mass_error_mask)=3807472 stop_rank=5000
1:35:47.675864 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:35:47.909005 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:35:48.723278 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:35:48.723909 INFO: Using score_cutoff 10.69764956817627 (fac=0.99, q=1)
1:35:48.724396 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:35:48.724519 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:35:48.724607 INFO: Updating optimization_manager: score_cutoff        : 9.559116731071471 -> 10.69764956817627
1:35:48.724716 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:35:48.885556 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:35:49.271900 INFO: === checking if optimization conditions were reached ===
1:35:49.274675 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:35:49.274818 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:35:49.274905 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:35:49.274984 INFO: ==============================================
1:35:49.275074 INFO: Starting optimization step 11.
1:35:49.275150 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:35:49.275243 INFO: Using rust extraction backend
1:35:49.275326 PROGRESS: Extracting batch of 252182 precursors
1:35:49.761530 INFO: === Search parameters used ===
1:35:49.761816 INFO: rt_error       : 805.6004638671875
1:35:49.761896 INFO: mobility_error : 0.1
1:35:49.761969 INFO: num_candidates : 3
1:35:49.762029 INFO: ms1_error      : 20
1:35:49.762081 INFO: ms2_error      : 10.0
1:35:49.762130 INFO: fwhm_rt        : 3.0
1:35:49.762177 INFO: quant_window   : 3
1:35:49.762222 INFO: ==============================================
1:35:54.031558 INFO: performing precursor FDR with 40 features
1:35:54.031712 INFO: Decoy channel: -1
1:35:54.031753 INFO: competitive: True
1:35:54.300993 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:54.712467 INFO: Estimating optimal hyperparameters - samples: 603,332, batch_size: 2,471, learning_rate: 7.77e-04
1:35:54.713653 INFO: Using random state 163565 for train-test-split
1:36:10.415681 INFO: Test AUC: 0.605
1:36:10.415897 INFO: Train AUC: 0.615
1:36:10.415932 INFO: AUC difference: 1.56%
1:36:11.046371 INFO: Resetting torch num_threads to 32
1:36:11.093269 PROGRESS: === Extracted 754165 precursors and 3806762 fragments ===
1:36:11.093781 INFO: === FDR correction performed with classifier version 10 ===
1:36:11.094509 PROGRESS: ============================= Precursor FDR =============================
1:36:11.094609 PROGRESS: Total precursors accumulated: 1,194
1:36:11.094676 PROGRESS: Target precursors: 1,183 (99.08%)
1:36:11.094734 PROGRESS: Decoy precursors: 11 (0.92%)
1:36:11.094783 PROGRESS: 
1:36:11.094833 PROGRESS: Precursor Summary:
1:36:11.096108 PROGRESS: Channel   0:	 0.050 FDR: 1,183; 0.010 FDR: 1,183; 0.001 FDR:   522
1:36:11.096207 PROGRESS: 
1:36:11.096266 PROGRESS: Protein Summary:
1:36:11.098086 PROGRESS: Channel   0:	 0.050 FDR: 1,054; 0.010 FDR: 1,054; 0.001 FDR:   480
1:36:11.098206 PROGRESS: =========================================================================
1:36:11.117402 INFO: Target number of precursors reached.
1:36:11.609154 INFO: fragments_df: keeping 5000 of 3806762 [sum(precursor_idx_mask)=28275 sum(mass_error_mask)=3806762 stop_rank=5000
1:36:12.159795 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:12.411633 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:13.270202 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:13.270825 INFO: Using score_cutoff 11.905488693237306 (fac=0.99, q=1)
1:36:13.271295 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:13.271413 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:13.271506 INFO: Updating optimization_manager: score_cutoff        : 10.69764956817627 -> 11.905488693237306
1:36:13.271598 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:13.440735 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:13.834712 INFO: === checking if optimization conditions were reached ===
1:36:13.837535 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:36:13.837683 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:36:13.837779 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:36:13.837862 INFO: ==============================================
1:36:13.837962 INFO: Starting optimization step 12.
1:36:13.838044 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:36:13.838152 INFO: Using rust extraction backend
1:36:13.838256 PROGRESS: Extracting batch of 252182 precursors
1:36:14.306723 INFO: === Search parameters used ===
1:36:14.307035 INFO: rt_error       : 805.6004638671875
1:36:14.307111 INFO: mobility_error : 0.1
1:36:14.307173 INFO: num_candidates : 3
1:36:14.307227 INFO: ms1_error      : 20
1:36:14.307276 INFO: ms2_error      : 10.0
1:36:14.307323 INFO: fwhm_rt        : 3.0
1:36:14.307368 INFO: quant_window   : 3
1:36:14.307412 INFO: ==============================================
1:36:18.826774 INFO: performing precursor FDR with 40 features
1:36:18.826957 INFO: Decoy channel: -1
1:36:18.826986 INFO: competitive: True
1:36:19.076825 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:19.501029 INFO: Estimating optimal hyperparameters - samples: 603,338, batch_size: 2,471, learning_rate: 7.77e-04
1:36:19.502084 INFO: Using random state 508179 for train-test-split
1:36:35.035195 INFO: Test AUC: 0.605
1:36:35.035383 INFO: Train AUC: 0.617
1:36:35.035419 INFO: AUC difference: 2.00%
1:36:35.645160 INFO: Resetting torch num_threads to 32
1:36:35.695587 PROGRESS: === Extracted 754173 precursors and 3807097 fragments ===
1:36:35.696241 INFO: === FDR correction performed with classifier version 11 ===
1:36:35.697315 PROGRESS: ============================= Precursor FDR =============================
1:36:35.697469 PROGRESS: Total precursors accumulated: 1,141
1:36:35.697554 PROGRESS: Target precursors: 1,130 (99.04%)
1:36:35.697624 PROGRESS: Decoy precursors: 11 (0.96%)
1:36:35.697690 PROGRESS: 
1:36:35.697754 PROGRESS: Precursor Summary:
1:36:35.699485 PROGRESS: Channel   0:	 0.050 FDR: 1,130; 0.010 FDR: 1,130; 0.001 FDR:     0
1:36:35.699615 PROGRESS: 
1:36:35.699691 PROGRESS: Protein Summary:
1:36:35.701723 PROGRESS: Channel   0:	 0.050 FDR: 1,012; 0.010 FDR: 1,012; 0.001 FDR:     0
1:36:35.701857 PROGRESS: =========================================================================
1:36:35.733858 INFO: Target number of precursors reached.
1:36:36.254329 INFO: fragments_df: keeping 5000 of 3807097 [sum(precursor_idx_mask)=26864 sum(mass_error_mask)=3807097 stop_rank=5000
1:36:36.848126 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:37.122571 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:38.007174 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:38.007648 INFO: Using score_cutoff 11.461072194957733 (fac=0.99, q=1)
1:36:38.007989 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:38.008077 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:38.008138 INFO: Updating optimization_manager: score_cutoff        : 11.905488693237306 -> 11.461072194957733
1:36:38.008201 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:38.171959 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:38.550727 INFO: === checking if optimization conditions were reached ===
1:36:38.553448 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:36:38.553589 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
1:36:38.553681 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:36:38.553759 INFO: ==============================================
1:36:38.553860 PROGRESS: Optimization finished for ms2_error.
1:36:39.129076 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:39.287064 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:39.738837 INFO: Starting optimization step 0.
1:36:39.739108 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:36:39.739212 INFO: Using rust extraction backend
1:36:39.739290 PROGRESS: Extracting batch of 252182 precursors
1:36:40.211495 INFO: === Search parameters used ===
1:36:40.211810 INFO: rt_error       : 805.6004638671875
1:36:40.211894 INFO: mobility_error : 0.1
1:36:40.211961 INFO: num_candidates : 3
1:36:40.212025 INFO: ms1_error      : 20
1:36:40.212091 INFO: ms2_error      : 10.0
1:36:40.212149 INFO: fwhm_rt        : 3.0
1:36:40.212208 INFO: quant_window   : 3
1:36:40.212262 INFO: ==============================================
1:36:44.602752 INFO: performing precursor FDR with 40 features
1:36:44.602946 INFO: Decoy channel: -1
1:36:44.602979 INFO: competitive: True
1:36:44.867368 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:45.321642 INFO: Estimating optimal hyperparameters - samples: 603,331, batch_size: 2,471, learning_rate: 7.77e-04
1:36:45.322871 INFO: Using random state 573826 for train-test-split
1:36:56.239390 INFO: Test AUC: 0.607
1:36:56.239579 INFO: Train AUC: 0.619
1:36:56.239638 INFO: AUC difference: 2.06%
1:36:56.870345 INFO: Resetting torch num_threads to 32
1:36:56.952911 PROGRESS: === Extracted 754164 precursors and 3807331 fragments ===
1:36:56.953586 INFO: === FDR correction performed with classifier version 12 ===
1:36:56.954819 PROGRESS: ============================= Precursor FDR =============================
1:36:56.954972 PROGRESS: Total precursors accumulated: 1,425
1:36:56.955048 PROGRESS: Target precursors: 1,411 (99.02%)
1:36:56.955113 PROGRESS: Decoy precursors: 14 (0.98%)
1:36:56.955172 PROGRESS: 
1:36:56.955229 PROGRESS: Precursor Summary:
1:36:56.957199 PROGRESS: Channel   0:	 0.050 FDR: 1,411; 0.010 FDR: 1,411; 0.001 FDR:   524
1:36:56.957336 PROGRESS: 
1:36:56.957418 PROGRESS: Protein Summary:
1:36:56.959727 PROGRESS: Channel   0:	 0.050 FDR: 1,240; 0.010 FDR: 1,240; 0.001 FDR:   480
1:36:56.959856 PROGRESS: =========================================================================
1:36:56.989913 INFO: Target number of precursors reached.
1:36:57.518092 INFO: fragments_df: keeping 5000 of 3807331 [sum(precursor_idx_mask)=32983 sum(mass_error_mask)=3807331 stop_rank=5000
1:36:58.145952 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:58.399254 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:59.220183 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:59.220731 INFO: Using score_cutoff 10.907373264312744 (fac=0.99, q=1)
1:36:59.221097 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:59.221187 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:59.221249 INFO: Updating optimization_manager: score_cutoff        : 11.461072194957733 -> 10.907373264312744
1:36:59.221320 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:59.380954 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:59.759441 INFO: === checking if optimization conditions were reached ===
1:36:59.760907 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:36:59.765823 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 368.72612005438106
1:36:59.766063 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 368.7261.
1:36:59.766202 INFO: ==============================================
1:36:59.766361 INFO: Starting optimization step 1.
1:36:59.766478 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:36:59.766630 INFO: Using rust extraction backend
1:36:59.766768 PROGRESS: Extracting batch of 252182 precursors
1:37:00.323796 INFO: === Search parameters used ===
1:37:00.324083 INFO: rt_error       : 368.72612005438106
1:37:00.324156 INFO: mobility_error : 0.1
1:37:00.324210 INFO: num_candidates : 3
1:37:00.324261 INFO: ms1_error      : 20
1:37:00.324310 INFO: ms2_error      : 10.0
1:37:00.324356 INFO: fwhm_rt        : 3.0
1:37:00.324400 INFO: quant_window   : 3
1:37:00.324445 INFO: ==============================================
1:37:04.067709 INFO: performing precursor FDR with 40 features
1:37:04.067864 INFO: Decoy channel: -1
1:37:04.067899 INFO: competitive: True
1:37:04.319081 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:04.745567 INFO: Estimating optimal hyperparameters - samples: 602,477, batch_size: 2,467, learning_rate: 7.76e-04
1:37:04.746978 INFO: Using random state 573826 for train-test-split
1:37:15.844038 INFO: Test AUC: 0.603
1:37:15.844218 INFO: Train AUC: 0.616
1:37:15.844254 INFO: AUC difference: 2.10%
1:37:16.440487 INFO: Resetting torch num_threads to 32
1:37:16.473437 PROGRESS: === Extracted 753097 precursors and 3674782 fragments ===
1:37:16.473961 INFO: === FDR correction performed with classifier version 12 ===
1:37:16.474714 PROGRESS: ============================= Precursor FDR =============================
1:37:16.474822 PROGRESS: Total precursors accumulated: 1,337
1:37:16.474893 PROGRESS: Target precursors: 1,324 (99.03%)
1:37:16.474954 PROGRESS: Decoy precursors: 13 (0.97%)
1:37:16.475008 PROGRESS: 
1:37:16.475060 PROGRESS: Precursor Summary:
1:37:16.476407 PROGRESS: Channel   0:	 0.050 FDR: 1,324; 0.010 FDR: 1,324; 0.001 FDR:   107
1:37:16.476511 PROGRESS: 
1:37:16.476580 PROGRESS: Protein Summary:
1:37:16.478229 PROGRESS: Channel   0:	 0.050 FDR: 1,177; 0.010 FDR: 1,177; 0.001 FDR:   106
1:37:16.478335 PROGRESS: =========================================================================
1:37:16.496740 INFO: Target number of precursors reached.
1:37:17.037644 INFO: fragments_df: keeping 5000 of 3674782 [sum(precursor_idx_mask)=30796 sum(mass_error_mask)=3674782 stop_rank=5000
1:37:17.599379 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:37:17.979068 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:37:18.823890 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:37:18.824368 INFO: Using score_cutoff 10.2576774559021 (fac=0.99, q=1)
1:37:18.824737 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:37:18.824834 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:37:18.824907 INFO: Updating optimization_manager: score_cutoff        : 10.907373264312744 -> 10.2576774559021
1:37:18.824984 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:37:18.979134 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:37:19.407002 INFO: === checking if optimization conditions were reached ===
1:37:19.407348 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:37:19.411229 INFO: Updating optimization_manager: rt_error            : 368.72612005438106 -> 386.902558835061
1:37:19.411460 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 386.9026.
1:37:19.411577 INFO: ==============================================
1:37:19.411702 INFO: Starting optimization step 2.
1:37:19.411790 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:37:19.411897 INFO: Using rust extraction backend
1:37:19.411988 PROGRESS: Extracting batch of 252182 precursors
1:37:19.889590 INFO: === Search parameters used ===
1:37:19.889897 INFO: rt_error       : 386.902558835061
1:37:19.889977 INFO: mobility_error : 0.1
1:37:19.890042 INFO: num_candidates : 3
1:37:19.890101 INFO: ms1_error      : 20
1:37:19.890159 INFO: ms2_error      : 10.0
1:37:19.890215 INFO: fwhm_rt        : 3.0
1:37:19.890269 INFO: quant_window   : 3
1:37:19.890327 INFO: ==============================================
1:37:23.587213 INFO: performing precursor FDR with 40 features
1:37:23.587380 INFO: Decoy channel: -1
1:37:23.587429 INFO: competitive: True
1:37:23.861093 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:24.235180 INFO: Estimating optimal hyperparameters - samples: 602,636, batch_size: 2,468, learning_rate: 7.76e-04
1:37:24.236799 INFO: Using random state 573826 for train-test-split
1:37:39.090824 INFO: Test AUC: 0.605
1:37:39.090994 INFO: Train AUC: 0.617
1:37:39.091030 INFO: AUC difference: 1.99%
1:37:39.649292 INFO: Resetting torch num_threads to 32
1:37:39.682390 PROGRESS: === Extracted 753295 precursors and 3696095 fragments ===
1:37:39.682909 INFO: === FDR correction performed with classifier version 12 ===
1:37:39.683673 PROGRESS: ============================= Precursor FDR =============================
1:37:39.683775 PROGRESS: Total precursors accumulated: 1,447
1:37:39.683844 PROGRESS: Target precursors: 1,433 (99.03%)
1:37:39.683903 PROGRESS: Decoy precursors: 14 (0.97%)
1:37:39.683974 PROGRESS: 
1:37:39.684027 PROGRESS: Precursor Summary:
1:37:39.685569 PROGRESS: Channel   0:	 0.050 FDR: 1,433; 0.010 FDR: 1,433; 0.001 FDR:   660
1:37:39.685686 PROGRESS: 
1:37:39.685753 PROGRESS: Protein Summary:
1:37:39.687489 PROGRESS: Channel   0:	 0.050 FDR: 1,260; 0.010 FDR: 1,260; 0.001 FDR:   602
1:37:39.687596 PROGRESS: =========================================================================
1:37:39.705564 INFO: Target number of precursors reached.
1:37:40.228407 INFO: fragments_df: keeping 5000 of 3696095 [sum(precursor_idx_mask)=33320 sum(mass_error_mask)=3696095 stop_rank=5000
1:37:40.750080 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:37:41.076217 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:37:41.890191 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:37:41.890802 INFO: Using score_cutoff 10.620839520263672 (fac=0.99, q=1)
1:37:41.891246 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:37:41.891356 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:37:41.891439 INFO: Updating optimization_manager: score_cutoff        : 10.2576774559021 -> 10.620839520263672
1:37:41.891528 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:37:42.051276 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:37:42.440538 INFO: === checking if optimization conditions were reached ===
1:37:42.440957 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:37:42.444340 INFO: Updating optimization_manager: rt_error            : 386.902558835061 -> 392.7709468319048
1:37:42.444494 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 392.7709.
1:37:42.444581 INFO: ==============================================
1:37:42.444697 INFO: Starting optimization step 3.
1:37:42.444779 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:37:42.444868 INFO: Using rust extraction backend
1:37:42.444946 PROGRESS: Extracting batch of 252182 precursors
1:37:42.931867 INFO: === Search parameters used ===
1:37:42.932140 INFO: rt_error       : 392.7709468319048
1:37:42.932211 INFO: mobility_error : 0.1
1:37:42.932269 INFO: num_candidates : 3
1:37:42.932319 INFO: ms1_error      : 20
1:37:42.932368 INFO: ms2_error      : 10.0
1:37:42.932414 INFO: fwhm_rt        : 3.0
1:37:42.932458 INFO: quant_window   : 3
1:37:42.932505 INFO: ==============================================
1:37:46.616549 INFO: performing precursor FDR with 40 features
1:37:46.616697 INFO: Decoy channel: -1
1:37:46.616728 INFO: competitive: True
1:37:46.870609 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:47.244122 INFO: Estimating optimal hyperparameters - samples: 602,688, batch_size: 2,468, learning_rate: 7.76e-04
1:37:47.245220 INFO: Using random state 573826 for train-test-split
1:38:02.434397 INFO: Test AUC: 0.605
1:38:02.434561 INFO: Train AUC: 0.618
1:38:02.434608 INFO: AUC difference: 2.15%
1:38:03.000569 INFO: Resetting torch num_threads to 32
1:38:03.037931 PROGRESS: === Extracted 753361 precursors and 3702979 fragments ===
1:38:03.038607 INFO: === FDR correction performed with classifier version 12 ===
1:38:03.039825 PROGRESS: ============================= Precursor FDR =============================
1:38:03.039958 PROGRESS: Total precursors accumulated: 1,423
1:38:03.040071 PROGRESS: Target precursors: 1,409 (99.02%)
1:38:03.040163 PROGRESS: Decoy precursors: 14 (0.98%)
1:38:03.040252 PROGRESS: 
1:38:03.040342 PROGRESS: Precursor Summary:
1:38:03.042702 PROGRESS: Channel   0:	 0.050 FDR: 1,409; 0.010 FDR: 1,409; 0.001 FDR:   591
1:38:03.042838 PROGRESS: 
1:38:03.042942 PROGRESS: Protein Summary:
1:38:03.045886 PROGRESS: Channel   0:	 0.050 FDR: 1,244; 0.010 FDR: 1,244; 0.001 FDR:   545
1:38:03.046045 PROGRESS: =========================================================================
1:38:03.073289 INFO: Target number of precursors reached.
1:38:03.572944 INFO: fragments_df: keeping 5000 of 3702979 [sum(precursor_idx_mask)=32497 sum(mass_error_mask)=3702979 stop_rank=5000
1:38:04.125475 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:38:04.414222 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:38:05.240417 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:38:05.240897 INFO: Using score_cutoff 10.26407470550537 (fac=0.99, q=1)
1:38:05.241242 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:38:05.241335 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:38:05.241396 INFO: Updating optimization_manager: score_cutoff        : 10.620839520263672 -> 10.26407470550537
1:38:05.241455 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:38:05.399098 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:38:05.808952 INFO: === checking if optimization conditions were reached ===
1:38:05.809292 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:38:05.812736 INFO: Updating optimization_manager: rt_error            : 392.7709468319048 -> 400.89677613076765
1:38:05.812881 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 400.8968.
1:38:05.812971 INFO: ==============================================
1:38:05.813070 INFO: Starting optimization step 4.
1:38:05.813155 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:38:05.813243 INFO: Using rust extraction backend
1:38:05.813325 PROGRESS: Extracting batch of 252182 precursors
1:38:06.277642 INFO: === Search parameters used ===
1:38:06.277970 INFO: rt_error       : 400.89677613076765
1:38:06.278050 INFO: mobility_error : 0.1
1:38:06.278111 INFO: num_candidates : 3
1:38:06.278172 INFO: ms1_error      : 20
1:38:06.278230 INFO: ms2_error      : 10.0
1:38:06.278284 INFO: fwhm_rt        : 3.0
1:38:06.278340 INFO: quant_window   : 3
1:38:06.278397 INFO: ==============================================
1:38:09.830980 INFO: performing precursor FDR with 40 features
1:38:09.831154 INFO: Decoy channel: -1
1:38:09.831208 INFO: competitive: True
1:38:10.067191 INFO: Setting torch num_threads to 2 for FDR classification task
1:38:10.437876 INFO: Estimating optimal hyperparameters - samples: 602,712, batch_size: 2,468, learning_rate: 7.76e-04
1:38:10.439126 INFO: Using random state 573826 for train-test-split
1:38:24.979731 INFO: Test AUC: 0.607
1:38:24.979873 INFO: Train AUC: 0.617
1:38:24.979909 INFO: AUC difference: 1.51%
1:38:25.494618 INFO: Resetting torch num_threads to 32
1:38:25.564047 PROGRESS: === Extracted 753390 precursors and 3708161 fragments ===
1:38:25.564627 INFO: === FDR correction performed with classifier version 12 ===
1:38:25.565570 PROGRESS: ============================= Precursor FDR =============================
1:38:25.565704 PROGRESS: Total precursors accumulated: 1,366
1:38:25.565790 PROGRESS: Target precursors: 1,353 (99.05%)
1:38:25.565866 PROGRESS: Decoy precursors: 13 (0.95%)
1:38:25.565932 PROGRESS: 
1:38:25.565994 PROGRESS: Precursor Summary:
1:38:25.567672 PROGRESS: Channel   0:	 0.050 FDR: 1,353; 0.010 FDR: 1,353; 0.001 FDR:   691
1:38:25.567792 PROGRESS: 
1:38:25.567864 PROGRESS: Protein Summary:
1:38:25.570036 PROGRESS: Channel   0:	 0.050 FDR: 1,188; 0.010 FDR: 1,188; 0.001 FDR:   629
1:38:25.570156 PROGRESS: =========================================================================
1:38:25.599255 INFO: Target number of precursors reached.
1:38:26.091159 INFO: fragments_df: keeping 5000 of 3708161 [sum(precursor_idx_mask)=31615 sum(mass_error_mask)=3708161 stop_rank=5000
1:38:26.702169 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:38:26.999444 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:38:27.847892 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:38:27.848381 INFO: Using score_cutoff 11.366227674865723 (fac=0.99, q=1)
1:38:27.848735 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:38:27.848837 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:38:27.848902 INFO: Updating optimization_manager: score_cutoff        : 10.26407470550537 -> 11.366227674865723
1:38:27.848968 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:38:28.008590 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:38:28.427621 INFO: === checking if optimization conditions were reached ===
1:38:28.427975 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:38:28.429173 INFO: Updating optimization_manager: rt_error            : 400.89677613076765 -> 386.902558835061
1:38:28.429355 INFO: Updating optimization_manager: classifier_version  : 12 -> 15
1:38:28.429494 INFO: Updating optimization_manager: score_cutoff        : 11.366227674865723 -> 10.620839520263672
1:38:28.429618 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:38:28.429739 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:38:28.429867 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 386.9026 found after 5 searches.
1:38:28.429954 INFO: ==============================================
1:38:28.430053 PROGRESS: Optimization finished for rt_error.
1:38:28.944883 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:38:29.109316 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:38:29.519904 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:38:29.520190 PROGRESS: ==============================================
1:38:29.520294 PROGRESS: ms2_error      : 10.0000
1:38:29.520389 PROGRESS: rt_error       : 386.9026
1:38:29.520458 PROGRESS: ==============================================
1:38:29.522190 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:38:39.462522 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:39:07.579630 INFO: Using rust extraction backend
1:39:07.580046 PROGRESS: Extracting batch of 15081856 precursors
1:39:35.306247 INFO: === Search parameters used ===
1:39:35.306704 INFO: rt_error       : 386.902558835061
1:39:35.306792 INFO: mobility_error : 0.1
1:39:35.306861 INFO: num_candidates : 3
1:39:35.306918 INFO: ms1_error      : 20
1:39:35.306976 INFO: ms2_error      : 10.0
1:39:35.307031 INFO: fwhm_rt        : 3.0
1:39:35.307085 INFO: quant_window   : 3
1:39:35.307133 INFO: ==============================================
1:40:36.887073 INFO: Removed 14518388 precursors with score below cutoff 10.620839520263672
1:41:12.888270 INFO: performing precursor FDR with 40 features
1:41:12.888481 INFO: Decoy channel: -1
1:41:12.888520 INFO: competitive: True
1:41:16.830254 INFO: Setting torch num_threads to 2 for FDR classification task
1:41:33.743698 INFO: Estimating optimal hyperparameters - samples: 24,578,097, batch_size: 4,096, learning_rate: 1.00e-03
1:41:33.834013 INFO: Using random state 376193 for train-test-split
1:50:44.273390 INFO: Test AUC: 0.614
1:50:44.273690 INFO: Train AUC: 0.614
1:50:44.273747 INFO: AUC difference: 0.01%
1:50:51.778089 INFO: Resetting torch num_threads to 32
1:50:55.065453 PROGRESS: ============================= Precursor FDR =============================
1:50:55.065760 PROGRESS: Total precursors accumulated: 80,216
1:50:55.065849 PROGRESS: Target precursors: 79,422 (99.01%)
1:50:55.065918 PROGRESS: Decoy precursors: 794 (0.99%)
1:50:55.065982 PROGRESS: 
1:50:55.066043 PROGRESS: Precursor Summary:
1:50:55.096166 PROGRESS: Channel   0:	 0.050 FDR: 79,422; 0.010 FDR: 79,422; 0.001 FDR:     2
1:50:55.096417 PROGRESS: 
1:50:55.096517 PROGRESS: Protein Summary:
1:50:55.141370 PROGRESS: Channel   0:	 0.050 FDR: 12,793; 0.010 FDR: 12,793; 0.001 FDR:     2
1:50:55.141611 PROGRESS: =========================================================================
1:50:55.384128 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/psm.parquet
1:50:55.556484 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.parquet
1:50:55.786697 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:50:56.761026 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 
1:50:56.761186 INFO: Quantification results path: /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant
1:50:56.761265 INFO: Creating folder /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/figures
1:50:56.761460 INFO: Initializing TimingManager
1:50:56.761958 INFO: Initializing RawFileManager
1:51:51.308565 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.
1:51:51.321922 INFO: Determining DIA cycle
1:51:51.343232 INFO: Found cycle with start 0.00 min and length 300.
1:51:51.559585 INFO: RT (min)            : 0.0 - 26.9
1:51:51.559707 INFO: RT duration (sec)   : 1611.2
1:51:51.559767 INFO: RT duration (min)   : 26.9
1:51:51.559814 INFO: Cycle len (scans)   : 300
1:51:51.559856 INFO: Cycle len (sec)     : 1.65
1:51:51.559898 INFO: Number of cycles    : 977
1:51:51.559938 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:51:51.559999 INFO: Creating DIA data object took: 54.797927141189575
1:51:53.278515 INFO: Creating DIA data NG object took: 1.7183337211608887
1:51:55.513008 INFO: Initializing CalibrationManager
1:51:55.513399 INFO: Setting up calibration estimators ..
1:51:55.513525 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:51:55.513683 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'}' ..
1:51:55.513908 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:51:55.514025 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:51:55.514133 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}}' ..
1:51:55.514238 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:51:55.514331 INFO: Done setting up calibration estimators.
1:51:55.514633 INFO: Initializing OptimizationManager
1:51:55.514884 INFO: initial parameter: ms1_error = 20
1:51:55.514988 INFO: initial parameter: ms2_error = 20
1:51:55.515085 INFO: initial parameter: rt_error = 805.5982666015625
1:51:55.515177 INFO: initial parameter: mobility_error = 0.1
1:51:55.515259 INFO: initial parameter: num_candidates = 1
1:51:55.515335 INFO: initial parameter: fwhm_rt = 5
1:51:55.515421 INFO: initial parameter: fwhm_mobility = 0.01
1:51:55.515503 INFO: initial parameter: score_cutoff = 0
1:51:55.515579 INFO: initial parameter: classifier_version = -1
1:51:55.515715 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:51:55.516118 INFO: FDRManager: loading saved state not requested, will be initialized.
1:51:55.516176 INFO: Initializing FDRManager
1:51:55.516241 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
1:51:58.074633 PROGRESS: Initializing spectral library: 7,536,970 target precursors potentially observable (1,230,167 removed)
1:51:59.612863 INFO: Updating optimization_manager: ms2_error           : 20 -> 20
1:51:59.613291 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
1:51:59.613411 PROGRESS: Starting initial search for precursors.
1:51:59.613508 INFO: Starting optimization step 0.
1:51:59.613581 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:51:59.613654 INFO: Using rust extraction backend
1:51:59.613720 PROGRESS: Extracting batch of 1988 precursors
1:51:59.619177 INFO: === Search parameters used ===
1:51:59.619319 INFO: rt_error       : 805.5982666015625
1:51:59.619380 INFO: mobility_error : 0.1
1:51:59.619435 INFO: num_candidates : 1
1:51:59.619485 INFO: ms1_error      : 20
1:51:59.619532 INFO: ms2_error      : 20
1:51:59.619577 INFO: fwhm_rt        : 5
1:51:59.619621 INFO: quant_window   : 3
1:51:59.619664 INFO: ==============================================
1:51:59.666945 INFO: performing precursor FDR with 40 features
1:51:59.667076 INFO: Decoy channel: -1
1:51:59.667119 INFO: competitive: True
1:51:59.669013 INFO: Setting torch num_threads to 2 for FDR classification task
1:51:59.671988 INFO: Estimating optimal hyperparameters - samples: 1,581, batch_size: 128, learning_rate: 1.77e-04
1:51:59.673356 INFO: Using random state 433278 for train-test-split
1:51:59.818780 INFO: Test AUC: 0.498
1:51:59.818919 INFO: Train AUC: 0.526
1:51:59.818975 INFO: AUC difference: 5.18%
1:51:59.819019 WARNING: AUC difference > 5%. This may indicate overfitting.
1:52:00.220329 INFO: Resetting torch num_threads to 32
1:52:00.222088 PROGRESS: === Extracted 1977 precursors and 9354 fragments ===
1:52:00.222473 INFO: === FDR correction performed with classifier version -1 ===
1:52:00.222976 PROGRESS: ============================= Precursor FDR =============================
1:52:00.223071 PROGRESS: Total precursors accumulated: 3
1:52:00.223137 PROGRESS: Target precursors: 3 (100.00%)
1:52:00.223192 PROGRESS: Decoy precursors: 0 (0.00%)
1:52:00.223242 PROGRESS: 
1:52:00.223294 PROGRESS: Precursor Summary:
1:52:00.224380 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
1:52:00.224468 PROGRESS: 
1:52:00.224526 PROGRESS: Protein Summary:
1:52:00.225729 PROGRESS: Channel   0:	 0.050 FDR:     3; 0.010 FDR:     3; 0.001 FDR:     3
1:52:00.225826 PROGRESS: =========================================================================
1:52:00.226077 INFO: Target number of precursors not reached yet.
1:52:00.349881 INFO: Starting optimization step 1.
1:52:00.350131 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:52:00.350250 INFO: Using rust extraction backend
1:52:00.350343 PROGRESS: Extracting batch of 3976 precursors
1:52:00.359677 INFO: === Search parameters used ===
1:52:00.359864 INFO: rt_error       : 805.5982666015625
1:52:00.359927 INFO: mobility_error : 0.1
1:52:00.359980 INFO: num_candidates : 1
1:52:00.360027 INFO: ms1_error      : 20
1:52:00.360073 INFO: ms2_error      : 20
1:52:00.360118 INFO: fwhm_rt        : 5
1:52:00.360161 INFO: quant_window   : 3
1:52:00.360204 INFO: ==============================================
1:52:00.422400 INFO: performing precursor FDR with 40 features
1:52:00.422516 INFO: Decoy channel: -1
1:52:00.422541 INFO: competitive: True
1:52:00.427485 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:00.430144 INFO: Estimating optimal hyperparameters - samples: 4,744, batch_size: 128, learning_rate: 1.77e-04
1:52:00.430266 INFO: Using random state 676186 for train-test-split
1:52:01.022999 INFO: Test AUC: 0.527
1:52:01.023138 INFO: Train AUC: 0.564
1:52:01.023189 INFO: AUC difference: 6.55%
1:52:01.023227 WARNING: AUC difference > 5%. This may indicate overfitting.
1:52:01.282619 INFO: Resetting torch num_threads to 32
1:52:01.286297 PROGRESS: === Extracted 5931 precursors and 28193 fragments ===
1:52:01.286716 INFO: === FDR correction performed with classifier version -1 ===
1:52:01.287230 PROGRESS: ============================= Precursor FDR =============================
1:52:01.287327 PROGRESS: Total precursors accumulated: 22
1:52:01.287394 PROGRESS: Target precursors: 22 (100.00%)
1:52:01.287454 PROGRESS: Decoy precursors: 0 (0.00%)
1:52:01.287506 PROGRESS: 
1:52:01.287559 PROGRESS: Precursor Summary:
1:52:01.288646 PROGRESS: Channel   0:	 0.050 FDR:    22; 0.010 FDR:    22; 0.001 FDR:    22
1:52:01.288749 PROGRESS: 
1:52:01.288812 PROGRESS: Protein Summary:
1:52:01.289995 PROGRESS: Channel   0:	 0.050 FDR:    22; 0.010 FDR:    22; 0.001 FDR:    22
1:52:01.290089 PROGRESS: =========================================================================
1:52:01.290435 INFO: Target number of precursors not reached yet.
1:52:01.408843 INFO: Starting optimization step 2.
1:52:01.409123 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:52:01.409233 INFO: Using rust extraction backend
1:52:01.409309 PROGRESS: Extracting batch of 7946 precursors
1:52:01.425824 INFO: === Search parameters used ===
1:52:01.426072 INFO: rt_error       : 805.5982666015625
1:52:01.426134 INFO: mobility_error : 0.1
1:52:01.426187 INFO: num_candidates : 1
1:52:01.426236 INFO: ms1_error      : 20
1:52:01.426286 INFO: ms2_error      : 20
1:52:01.426333 INFO: fwhm_rt        : 5
1:52:01.426381 INFO: quant_window   : 3
1:52:01.426429 INFO: ==============================================
1:52:01.531940 INFO: performing precursor FDR with 40 features
1:52:01.532073 INFO: Decoy channel: -1
1:52:01.532110 INFO: competitive: True
1:52:01.541897 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:01.547529 INFO: Estimating optimal hyperparameters - samples: 11,067, batch_size: 128, learning_rate: 1.77e-04
1:52:01.547730 INFO: Using random state 506027 for train-test-split
1:52:02.592428 INFO: Test AUC: 0.550
1:52:02.592587 INFO: Train AUC: 0.580
1:52:02.592641 INFO: AUC difference: 5.07%
1:52:02.592670 WARNING: AUC difference > 5%. This may indicate overfitting.
1:52:02.876893 INFO: Resetting torch num_threads to 32
1:52:02.881771 PROGRESS: === Extracted 13834 precursors and 65844 fragments ===
1:52:02.882245 INFO: === FDR correction performed with classifier version -1 ===
1:52:02.882813 PROGRESS: ============================= Precursor FDR =============================
1:52:02.882906 PROGRESS: Total precursors accumulated: 35
1:52:02.882970 PROGRESS: Target precursors: 35 (100.00%)
1:52:02.883027 PROGRESS: Decoy precursors: 0 (0.00%)
1:52:02.883075 PROGRESS: 
1:52:02.883122 PROGRESS: Precursor Summary:
1:52:02.884212 PROGRESS: Channel   0:	 0.050 FDR:    35; 0.010 FDR:    35; 0.001 FDR:    35
1:52:02.884301 PROGRESS: 
1:52:02.884358 PROGRESS: Protein Summary:
1:52:02.885565 PROGRESS: Channel   0:	 0.050 FDR:    35; 0.010 FDR:    35; 0.001 FDR:    35
1:52:02.885664 PROGRESS: =========================================================================
1:52:02.886063 INFO: Target number of precursors not reached yet.
1:52:03.031124 INFO: Starting optimization step 3.
1:52:03.031352 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:52:03.031450 INFO: Using rust extraction backend
1:52:03.031519 PROGRESS: Extracting batch of 15879 precursors
1:52:03.064424 INFO: === Search parameters used ===
1:52:03.064766 INFO: rt_error       : 805.5982666015625
1:52:03.064849 INFO: mobility_error : 0.1
1:52:03.064915 INFO: num_candidates : 1
1:52:03.064980 INFO: ms1_error      : 20
1:52:03.065041 INFO: ms2_error      : 20
1:52:03.065114 INFO: fwhm_rt        : 5
1:52:03.065177 INFO: quant_window   : 3
1:52:03.065235 INFO: ==============================================
1:52:03.259421 INFO: performing precursor FDR with 40 features
1:52:03.259549 INFO: Decoy channel: -1
1:52:03.259580 INFO: competitive: True
1:52:03.276946 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:03.286849 INFO: Estimating optimal hyperparameters - samples: 23,664, batch_size: 128, learning_rate: 1.77e-04
1:52:03.287055 INFO: Using random state 890435 for train-test-split
1:52:05.447799 INFO: Test AUC: 0.572
1:52:05.447947 INFO: Train AUC: 0.586
1:52:05.447990 INFO: AUC difference: 2.42%
1:52:05.786034 INFO: Resetting torch num_threads to 32
1:52:05.800105 PROGRESS: === Extracted 29581 precursors and 140793 fragments ===
1:52:05.800761 INFO: === FDR correction performed with classifier version -1 ===
1:52:05.801486 PROGRESS: ============================= Precursor FDR =============================
1:52:05.801605 PROGRESS: Total precursors accumulated: 52
1:52:05.801675 PROGRESS: Target precursors: 52 (100.00%)
1:52:05.801742 PROGRESS: Decoy precursors: 0 (0.00%)
1:52:05.801801 PROGRESS: 
1:52:05.801858 PROGRESS: Precursor Summary:
1:52:05.803181 PROGRESS: Channel   0:	 0.050 FDR:    52; 0.010 FDR:    52; 0.001 FDR:    52
1:52:05.803278 PROGRESS: 
1:52:05.803344 PROGRESS: Protein Summary:
1:52:05.804821 PROGRESS: Channel   0:	 0.050 FDR:    52; 0.010 FDR:    52; 0.001 FDR:    52
1:52:05.804932 PROGRESS: =========================================================================
1:52:05.806085 INFO: Target number of precursors not reached yet.
1:52:05.962602 INFO: Starting optimization step 4.
1:52:05.962830 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:52:05.962914 INFO: Using rust extraction backend
1:52:05.962980 PROGRESS: Extracting batch of 31750 precursors
1:52:06.022613 INFO: === Search parameters used ===
1:52:06.022942 INFO: rt_error       : 805.5982666015625
1:52:06.023044 INFO: mobility_error : 0.1
1:52:06.023128 INFO: num_candidates : 1
1:52:06.023207 INFO: ms1_error      : 20
1:52:06.023283 INFO: ms2_error      : 20
1:52:06.023369 INFO: fwhm_rt        : 5
1:52:06.023456 INFO: quant_window   : 3
1:52:06.023534 INFO: ==============================================
1:52:06.364202 INFO: performing precursor FDR with 40 features
1:52:06.364329 INFO: Decoy channel: -1
1:52:06.364358 INFO: competitive: True
1:52:06.390821 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:06.407539 INFO: Estimating optimal hyperparameters - samples: 48,886, batch_size: 200, learning_rate: 2.21e-04
1:52:06.407961 INFO: Using random state 900571 for train-test-split
1:52:09.600105 INFO: Test AUC: 0.570
1:52:09.600257 INFO: Train AUC: 0.598
1:52:09.600297 INFO: AUC difference: 4.78%
1:52:09.905986 INFO: Resetting torch num_threads to 32
1:52:09.921590 PROGRESS: === Extracted 61108 precursors and 291977 fragments ===
1:52:09.922352 INFO: === FDR correction performed with classifier version -1 ===
1:52:09.923111 PROGRESS: ============================= Precursor FDR =============================
1:52:09.923226 PROGRESS: Total precursors accumulated: 169
1:52:09.923306 PROGRESS: Target precursors: 168 (99.41%)
1:52:09.923377 PROGRESS: Decoy precursors: 1 (0.59%)
1:52:09.923443 PROGRESS: 
1:52:09.923507 PROGRESS: Precursor Summary:
1:52:09.924935 PROGRESS: Channel   0:	 0.050 FDR:   168; 0.010 FDR:   168; 0.001 FDR:   119
1:52:09.925043 PROGRESS: 
1:52:09.925110 PROGRESS: Protein Summary:
1:52:09.926280 PROGRESS: Channel   0:	 0.050 FDR:   166; 0.010 FDR:   166; 0.001 FDR:   117
1:52:09.926375 PROGRESS: =========================================================================
1:52:09.927954 INFO: Target number of precursors not reached yet.
1:52:10.216889 INFO: Starting optimization step 5.
1:52:10.217194 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:52:10.217300 INFO: Using rust extraction backend
1:52:10.217384 PROGRESS: Extracting batch of 63536 precursors
1:52:10.338681 INFO: === Search parameters used ===
1:52:10.338995 INFO: rt_error       : 805.5982666015625
1:52:10.339078 INFO: mobility_error : 0.1
1:52:10.339137 INFO: num_candidates : 1
1:52:10.339193 INFO: ms1_error      : 20
1:52:10.339246 INFO: ms2_error      : 20
1:52:10.339300 INFO: fwhm_rt        : 5
1:52:10.339355 INFO: quant_window   : 3
1:52:10.339406 INFO: ==============================================
1:52:10.988439 INFO: performing precursor FDR with 40 features
1:52:10.988564 INFO: Decoy channel: -1
1:52:10.988591 INFO: competitive: True
1:52:11.064030 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:11.105145 INFO: Estimating optimal hyperparameters - samples: 99,397, batch_size: 407, learning_rate: 3.15e-04
1:52:11.105812 INFO: Using random state 868342 for train-test-split
1:52:15.052999 INFO: Test AUC: 0.573
1:52:15.053146 INFO: Train AUC: 0.606
1:52:15.053184 INFO: AUC difference: 5.45%
1:52:15.053219 WARNING: AUC difference > 5%. This may indicate overfitting.
1:52:15.370536 INFO: Resetting torch num_threads to 32
1:52:15.403880 PROGRESS: === Extracted 124247 precursors and 593643 fragments ===
1:52:15.404733 INFO: === FDR correction performed with classifier version -1 ===
1:52:15.405722 PROGRESS: ============================= Precursor FDR =============================
1:52:15.405859 PROGRESS: Total precursors accumulated: 310
1:52:15.405967 PROGRESS: Target precursors: 307 (99.03%)
1:52:15.406062 PROGRESS: Decoy precursors: 3 (0.97%)
1:52:15.406153 PROGRESS: 
1:52:15.406248 PROGRESS: Precursor Summary:
1:52:15.407993 PROGRESS: Channel   0:	 0.050 FDR:   307; 0.010 FDR:   307; 0.001 FDR:   210
1:52:15.408121 PROGRESS: 
1:52:15.408210 PROGRESS: Protein Summary:
1:52:15.410308 PROGRESS: Channel   0:	 0.050 FDR:   295; 0.010 FDR:   295; 0.001 FDR:   202
1:52:15.410449 PROGRESS: =========================================================================
1:52:15.414545 INFO: Target number of precursors not reached yet.
1:52:15.788974 INFO: Starting optimization step 6.
1:52:15.789278 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:52:15.789391 INFO: Using rust extraction backend
1:52:15.789478 PROGRESS: Extracting batch of 127107 precursors
1:52:16.029088 INFO: === Search parameters used ===
1:52:16.029368 INFO: rt_error       : 805.5982666015625
1:52:16.029432 INFO: mobility_error : 0.1
1:52:16.029486 INFO: num_candidates : 1
1:52:16.029537 INFO: ms1_error      : 20
1:52:16.029586 INFO: ms2_error      : 20
1:52:16.029635 INFO: fwhm_rt        : 5
1:52:16.029682 INFO: quant_window   : 3
1:52:16.029729 INFO: ==============================================
1:52:17.374871 INFO: performing precursor FDR with 40 features
1:52:17.374989 INFO: Decoy channel: -1
1:52:17.375017 INFO: competitive: True
1:52:17.491757 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:17.616636 INFO: Estimating optimal hyperparameters - samples: 200,458, batch_size: 821, learning_rate: 4.48e-04
1:52:17.617118 INFO: Using random state 164196 for train-test-split
1:52:24.047538 INFO: Test AUC: 0.581
1:52:24.047676 INFO: Train AUC: 0.603
1:52:24.047710 INFO: AUC difference: 3.59%
1:52:25.674875 INFO: Resetting torch num_threads to 32
1:52:25.733026 PROGRESS: === Extracted 250573 precursors and 1194546 fragments ===
1:52:25.733705 INFO: === FDR correction performed with classifier version -1 ===
1:52:25.734493 PROGRESS: ============================= Precursor FDR =============================
1:52:25.734590 PROGRESS: Total precursors accumulated: 810
1:52:25.734656 PROGRESS: Target precursors: 802 (99.01%)
1:52:25.734711 PROGRESS: Decoy precursors: 8 (0.99%)
1:52:25.734762 PROGRESS: 
1:52:25.734810 PROGRESS: Precursor Summary:
1:52:25.736028 PROGRESS: Channel   0:	 0.050 FDR:   802; 0.010 FDR:   802; 0.001 FDR:   510
1:52:25.736129 PROGRESS: 
1:52:25.736189 PROGRESS: Protein Summary:
1:52:25.737689 PROGRESS: Channel   0:	 0.050 FDR:   714; 0.010 FDR:   714; 0.001 FDR:   461
1:52:25.737789 PROGRESS: =========================================================================
1:52:25.742179 INFO: Target number of precursors not reached yet.
1:52:26.373668 INFO: Starting optimization step 7.
1:52:26.373930 PROGRESS: === Extracting elution groups 127000 to 255000 ===
1:52:26.374025 INFO: Using rust extraction backend
1:52:26.374097 PROGRESS: Extracting batch of 254254 precursors
1:52:26.846676 INFO: === Search parameters used ===
1:52:26.846985 INFO: rt_error       : 805.5982666015625
1:52:26.847080 INFO: mobility_error : 0.1
1:52:26.847157 INFO: num_candidates : 1
1:52:26.847227 INFO: ms1_error      : 20
1:52:26.847293 INFO: ms2_error      : 20
1:52:26.847370 INFO: fwhm_rt        : 5
1:52:26.847435 INFO: quant_window   : 3
1:52:26.847497 INFO: ==============================================
1:52:29.379278 INFO: performing precursor FDR with 40 features
1:52:29.379410 INFO: Decoy channel: -1
1:52:29.379440 INFO: competitive: True
1:52:29.621570 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:29.880394 INFO: Estimating optimal hyperparameters - samples: 402,588, batch_size: 1,649, learning_rate: 6.34e-04
1:52:29.881569 INFO: Using random state 709839 for train-test-split
1:52:42.096217 INFO: Test AUC: 0.590
1:52:42.096357 INFO: Train AUC: 0.603
1:52:42.096391 INFO: AUC difference: 2.23%
1:52:42.665035 INFO: Resetting torch num_threads to 32
1:52:42.784602 PROGRESS: === Extracted 503235 precursors and 2399742 fragments ===
1:52:42.785398 INFO: === FDR correction performed with classifier version -1 ===
1:52:42.786329 PROGRESS: ============================= Precursor FDR =============================
1:52:42.786430 PROGRESS: Total precursors accumulated: 1,617
1:52:42.786496 PROGRESS: Target precursors: 1,601 (99.01%)
1:52:42.786571 PROGRESS: Decoy precursors: 16 (0.99%)
1:52:42.786623 PROGRESS: 
1:52:42.786672 PROGRESS: Precursor Summary:
1:52:42.788155 PROGRESS: Channel   0:	 0.050 FDR: 1,601; 0.010 FDR: 1,601; 0.001 FDR: 1,040
1:52:42.788267 PROGRESS: 
1:52:42.788330 PROGRESS: Protein Summary:
1:52:42.790546 PROGRESS: Channel   0:	 0.050 FDR: 1,309; 0.010 FDR: 1,309; 0.001 FDR:   877
1:52:42.790678 PROGRESS: =========================================================================
1:52:42.803596 INFO: Target number of precursors reached.
1:52:43.171627 INFO: fragments_df: keeping 5000 of 2399742 [sum(precursor_idx_mask)=17204 sum(mass_error_mask)=2399742 stop_rank=5000
1:52:44.060773 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:52:44.378558 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:52:45.287177 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:52:45.287699 INFO: Using score_cutoff 12.570672512054443 (fac=0.99, q=1)
1:52:45.288059 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:52:45.288149 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:52:45.288208 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.570672512054443
1:52:45.288277 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:52:45.605887 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:52:46.423966 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
1:52:46.424231 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:52:46.424358 INFO: Starting optimization step 8.
1:52:46.424435 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:52:46.424524 INFO: Using rust extraction backend
1:52:46.424605 PROGRESS: Extracting batch of 506436 precursors
1:52:47.374286 INFO: === Search parameters used ===
1:52:47.374657 INFO: rt_error       : 805.5982666015625
1:52:47.374745 INFO: mobility_error : 0.1
1:52:47.374810 INFO: num_candidates : 3
1:52:47.374876 INFO: ms1_error      : 20
1:52:47.374938 INFO: ms2_error      : 20
1:52:47.374998 INFO: fwhm_rt        : 3.0
1:52:47.375054 INFO: quant_window   : 3
1:52:47.375123 INFO: ==============================================
1:52:55.957419 INFO: performing precursor FDR with 40 features
1:52:55.957602 INFO: Decoy channel: -1
1:52:55.957644 INFO: competitive: True
1:52:56.503579 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:57.383870 INFO: Estimating optimal hyperparameters - samples: 1,206,505, batch_size: 4,096, learning_rate: 1.00e-03
1:52:57.386941 INFO: Using random state 711110 for train-test-split
1:53:24.729741 INFO: Test AUC: 0.596
1:53:24.729942 INFO: Train AUC: 0.602
1:53:24.729980 INFO: AUC difference: 0.99%
1:53:25.593257 INFO: Resetting torch num_threads to 32
1:53:25.676699 PROGRESS: === Extracted 1508132 precursors and 6968047 fragments ===
1:53:25.677223 INFO: === FDR correction performed with classifier version 7 ===
1:53:25.678175 PROGRESS: ============================= Precursor FDR =============================
1:53:25.678279 PROGRESS: Total precursors accumulated: 1,994
1:53:25.678351 PROGRESS: Target precursors: 1,975 (99.05%)
1:53:25.678425 PROGRESS: Decoy precursors: 19 (0.95%)
1:53:25.678477 PROGRESS: 
1:53:25.678527 PROGRESS: Precursor Summary:
1:53:25.680053 PROGRESS: Channel   0:	 0.050 FDR: 1,975; 0.010 FDR: 1,975; 0.001 FDR: 1,074
1:53:25.680155 PROGRESS: 
1:53:25.680224 PROGRESS: Protein Summary:
1:53:25.682247 PROGRESS: Channel   0:	 0.050 FDR: 1,579; 0.010 FDR: 1,579; 0.001 FDR:   903
1:53:25.682358 PROGRESS: =========================================================================
1:53:25.718919 INFO: Target number of precursors reached.
1:53:26.599333 INFO: fragments_df: keeping 5000 of 6968047 [sum(precursor_idx_mask)=45486 sum(mass_error_mask)=6968047 stop_rank=5000
1:53:27.547643 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:53:27.953736 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:53:28.783188 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:53:28.783688 INFO: Using score_cutoff 12.230346907424927 (fac=0.99, q=1)
1:53:28.784057 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:53:28.784147 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:53:28.784209 INFO: Updating optimization_manager: score_cutoff        : 12.570672512054443 -> 12.230346907424927
1:53:28.784276 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:53:29.113001 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:53:29.957216 INFO: === checking if optimization conditions were reached ===
1:53:29.959662 INFO: Updating optimization_manager: ms2_error           : 20 -> 10.0
1:53:29.959780 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:53:29.959854 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:53:29.959924 INFO: ==============================================
1:53:29.960002 INFO: Starting optimization step 9.
1:53:29.960070 PROGRESS: === Extracting elution groups 0 to 255000 ===
1:53:29.960158 INFO: Using rust extraction backend
1:53:29.960236 PROGRESS: Extracting batch of 506436 precursors
1:53:30.933241 INFO: === Search parameters used ===
1:53:30.933555 INFO: rt_error       : 805.5982666015625
1:53:30.933637 INFO: mobility_error : 0.1
1:53:30.933700 INFO: num_candidates : 3
1:53:30.933760 INFO: ms1_error      : 20
1:53:30.933818 INFO: ms2_error      : 10.0
1:53:30.933885 INFO: fwhm_rt        : 3.0
1:53:30.933947 INFO: quant_window   : 3
1:53:30.934003 INFO: ==============================================
1:53:39.342887 INFO: performing precursor FDR with 40 features
1:53:39.343020 INFO: Decoy channel: -1
1:53:39.343049 INFO: competitive: True
1:53:39.873740 INFO: Setting torch num_threads to 2 for FDR classification task
1:53:40.771867 INFO: Estimating optimal hyperparameters - samples: 1,212,569, batch_size: 4,096, learning_rate: 1.00e-03
1:53:40.774848 INFO: Using random state 273231 for train-test-split
1:54:00.858549 INFO: Test AUC: 0.601
1:54:00.858792 INFO: Train AUC: 0.607
1:54:00.858856 INFO: AUC difference: 1.01%
1:54:01.664223 INFO: Resetting torch num_threads to 32
1:54:01.722419 PROGRESS: === Extracted 1515712 precursors and 7753258 fragments ===
1:54:01.722943 INFO: === FDR correction performed with classifier version 8 ===
1:54:01.723912 PROGRESS: ============================= Precursor FDR =============================
1:54:01.724012 PROGRESS: Total precursors accumulated: 2,335
1:54:01.724080 PROGRESS: Target precursors: 2,312 (99.01%)
1:54:01.724137 PROGRESS: Decoy precursors: 23 (0.99%)
1:54:01.724190 PROGRESS: 
1:54:01.724241 PROGRESS: Precursor Summary:
1:54:01.725888 PROGRESS: Channel   0:	 0.050 FDR: 2,312; 0.010 FDR: 2,312; 0.001 FDR: 1,234
1:54:01.725993 PROGRESS: 
1:54:01.726055 PROGRESS: Protein Summary:
1:54:01.728189 PROGRESS: Channel   0:	 0.050 FDR: 1,800; 0.010 FDR: 1,800; 0.001 FDR: 1,022
1:54:01.728293 PROGRESS: =========================================================================
1:54:01.760995 INFO: Target number of precursors reached.
1:54:02.619719 INFO: fragments_df: keeping 5000 of 7753258 [sum(precursor_idx_mask)=55481 sum(mass_error_mask)=7753258 stop_rank=5000
1:54:03.171340 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:54:03.500522 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:54:04.269302 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:54:04.269795 INFO: Using score_cutoff 11.863619260311127 (fac=0.99, q=1)
1:54:04.270153 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:54:04.270241 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:54:04.270305 INFO: Updating optimization_manager: score_cutoff        : 12.230346907424927 -> 11.863619260311127
1:54:04.270371 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:54:04.423802 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:54:04.804445 INFO: === checking if optimization conditions were reached ===
1:54:04.807113 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:54:04.807266 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:54:04.807359 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:54:04.807445 INFO: ==============================================
1:54:04.807549 INFO: Starting optimization step 10.
1:54:04.807640 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:54:04.807756 INFO: Using rust extraction backend
1:54:04.807854 PROGRESS: Extracting batch of 252182 precursors
1:54:05.278622 INFO: === Search parameters used ===
1:54:05.278934 INFO: rt_error       : 805.5982666015625
1:54:05.279008 INFO: mobility_error : 0.1
1:54:05.279067 INFO: num_candidates : 3
1:54:05.279121 INFO: ms1_error      : 20
1:54:05.279179 INFO: ms2_error      : 10.0
1:54:05.279230 INFO: fwhm_rt        : 3.0
1:54:05.279278 INFO: quant_window   : 3
1:54:05.279328 INFO: ==============================================
1:54:09.338253 INFO: performing precursor FDR with 40 features
1:54:09.338380 INFO: Decoy channel: -1
1:54:09.338409 INFO: competitive: True
1:54:09.557057 INFO: Setting torch num_threads to 2 for FDR classification task
1:54:09.907822 INFO: Estimating optimal hyperparameters - samples: 603,813, batch_size: 2,473, learning_rate: 7.77e-04
1:54:09.909130 INFO: Using random state 516113 for train-test-split
1:54:20.655780 INFO: Test AUC: 0.602
1:54:20.655941 INFO: Train AUC: 0.614
1:54:20.655987 INFO: AUC difference: 1.85%
1:54:21.135333 INFO: Resetting torch num_threads to 32
1:54:21.166179 PROGRESS: === Extracted 754767 precursors and 3861076 fragments ===
1:54:21.166653 INFO: === FDR correction performed with classifier version 9 ===
1:54:21.167341 PROGRESS: ============================= Precursor FDR =============================
1:54:21.167441 PROGRESS: Total precursors accumulated: 1,267
1:54:21.167509 PROGRESS: Target precursors: 1,255 (99.05%)
1:54:21.167568 PROGRESS: Decoy precursors: 12 (0.95%)
1:54:21.167620 PROGRESS: 
1:54:21.167670 PROGRESS: Precursor Summary:
1:54:21.169014 PROGRESS: Channel   0:	 0.050 FDR: 1,255; 0.010 FDR: 1,255; 0.001 FDR: 1,144
1:54:21.169118 PROGRESS: 
1:54:21.169180 PROGRESS: Protein Summary:
1:54:21.170889 PROGRESS: Channel   0:	 0.050 FDR: 1,096; 0.010 FDR: 1,096; 0.001 FDR: 1,005
1:54:21.170989 PROGRESS: =========================================================================
1:54:21.188199 INFO: Target number of precursors reached.
1:54:21.618392 INFO: fragments_df: keeping 5000 of 3861076 [sum(precursor_idx_mask)=29770 sum(mass_error_mask)=3861076 stop_rank=5000
1:54:22.105496 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:54:22.337480 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:54:23.062068 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:54:23.062524 INFO: Using score_cutoff 9.906539776611329 (fac=0.99, q=1)
1:54:23.062861 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:54:23.062956 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:54:23.063014 INFO: Updating optimization_manager: score_cutoff        : 11.863619260311127 -> 9.906539776611329
1:54:23.063074 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:54:23.215153 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:54:23.598384 INFO: === checking if optimization conditions were reached ===
1:54:23.601253 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:54:23.601396 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:54:23.601478 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:54:23.601552 INFO: ==============================================
1:54:23.601642 INFO: Starting optimization step 11.
1:54:23.601719 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:54:23.601818 INFO: Using rust extraction backend
1:54:23.601906 PROGRESS: Extracting batch of 252182 precursors
1:54:24.069228 INFO: === Search parameters used ===
1:54:24.069501 INFO: rt_error       : 805.5982666015625
1:54:24.069572 INFO: mobility_error : 0.1
1:54:24.069639 INFO: num_candidates : 3
1:54:24.069694 INFO: ms1_error      : 20
1:54:24.069744 INFO: ms2_error      : 10.0
1:54:24.069798 INFO: fwhm_rt        : 3.0
1:54:24.069848 INFO: quant_window   : 3
1:54:24.069896 INFO: ==============================================
1:54:27.929217 INFO: performing precursor FDR with 40 features
1:54:27.929345 INFO: Decoy channel: -1
1:54:27.929377 INFO: competitive: True
1:54:28.144336 INFO: Setting torch num_threads to 2 for FDR classification task
1:54:28.477144 INFO: Estimating optimal hyperparameters - samples: 603,832, batch_size: 2,473, learning_rate: 7.77e-04
1:54:28.478361 INFO: Using random state 999660 for train-test-split
1:54:38.187736 INFO: Test AUC: 0.606
1:54:38.187925 INFO: Train AUC: 0.614
1:54:38.187980 INFO: AUC difference: 1.37%
1:54:38.745910 INFO: Resetting torch num_threads to 32
1:54:38.781819 PROGRESS: === Extracted 754791 precursors and 3861352 fragments ===
1:54:38.782311 INFO: === FDR correction performed with classifier version 10 ===
1:54:38.783010 PROGRESS: ============================= Precursor FDR =============================
1:54:38.783118 PROGRESS: Total precursors accumulated: 1,240
1:54:38.783184 PROGRESS: Target precursors: 1,228 (99.03%)
1:54:38.783242 PROGRESS: Decoy precursors: 12 (0.97%)
1:54:38.783294 PROGRESS: 
1:54:38.783344 PROGRESS: Precursor Summary:
1:54:38.784658 PROGRESS: Channel   0:	 0.050 FDR: 1,228; 0.010 FDR: 1,228; 0.001 FDR:   912
1:54:38.784762 PROGRESS: 
1:54:38.784826 PROGRESS: Protein Summary:
1:54:38.786479 PROGRESS: Channel   0:	 0.050 FDR: 1,072; 0.010 FDR: 1,072; 0.001 FDR:   811
1:54:38.786580 PROGRESS: =========================================================================
1:54:38.804093 INFO: Target number of precursors reached.
1:54:39.248581 INFO: fragments_df: keeping 5000 of 3861352 [sum(precursor_idx_mask)=29446 sum(mass_error_mask)=3861352 stop_rank=5000
1:54:39.768382 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:54:40.025337 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:54:40.760080 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:54:40.760548 INFO: Using score_cutoff 12.158764558696747 (fac=0.99, q=1)
1:54:40.760900 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:54:40.760985 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:54:40.761045 INFO: Updating optimization_manager: score_cutoff        : 9.906539776611329 -> 12.158764558696747
1:54:40.761105 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:54:40.919424 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:54:41.313621 INFO: === checking if optimization conditions were reached ===
1:54:41.341810 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:54:41.341928 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:54:41.342000 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:54:41.342062 INFO: ==============================================
1:54:41.342144 INFO: Starting optimization step 12.
1:54:41.342207 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:54:41.342279 INFO: Using rust extraction backend
1:54:41.342343 PROGRESS: Extracting batch of 252182 precursors
1:54:41.824477 INFO: === Search parameters used ===
1:54:41.824755 INFO: rt_error       : 805.5982666015625
1:54:41.824855 INFO: mobility_error : 0.1
1:54:41.824914 INFO: num_candidates : 3
1:54:41.824970 INFO: ms1_error      : 20
1:54:41.825019 INFO: ms2_error      : 10.0
1:54:41.825066 INFO: fwhm_rt        : 3.0
1:54:41.825112 INFO: quant_window   : 3
1:54:41.825161 INFO: ==============================================
1:54:45.976701 INFO: performing precursor FDR with 40 features
1:54:45.976838 INFO: Decoy channel: -1
1:54:45.976870 INFO: competitive: True
1:54:46.210183 INFO: Setting torch num_threads to 2 for FDR classification task
1:54:46.601151 INFO: Estimating optimal hyperparameters - samples: 603,819, batch_size: 2,473, learning_rate: 7.77e-04
1:54:46.602703 INFO: Using random state 28772 for train-test-split
1:54:56.645355 INFO: Test AUC: 0.607
1:54:56.645515 INFO: Train AUC: 0.619
1:54:56.645550 INFO: AUC difference: 1.82%
1:54:57.121685 INFO: Resetting torch num_threads to 32
1:54:57.153417 PROGRESS: === Extracted 754774 precursors and 3860592 fragments ===
1:54:57.153893 INFO: === FDR correction performed with classifier version 11 ===
1:54:57.154580 PROGRESS: ============================= Precursor FDR =============================
1:54:57.154676 PROGRESS: Total precursors accumulated: 1,370
1:54:57.154743 PROGRESS: Target precursors: 1,357 (99.05%)
1:54:57.154801 PROGRESS: Decoy precursors: 13 (0.95%)
1:54:57.154855 PROGRESS: 
1:54:57.154909 PROGRESS: Precursor Summary:
1:54:57.156197 PROGRESS: Channel   0:	 0.050 FDR: 1,357; 0.010 FDR: 1,357; 0.001 FDR:   818
1:54:57.156296 PROGRESS: 
1:54:57.156362 PROGRESS: Protein Summary:
1:54:57.158057 PROGRESS: Channel   0:	 0.050 FDR: 1,183; 0.010 FDR: 1,183; 0.001 FDR:   730
1:54:57.158161 PROGRESS: =========================================================================
1:54:57.175613 INFO: Target number of precursors reached.
1:54:57.609885 INFO: fragments_df: keeping 5000 of 3860592 [sum(precursor_idx_mask)=32027 sum(mass_error_mask)=3860592 stop_rank=5000
1:54:58.094470 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:54:58.416578 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:54:59.277427 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:54:59.277887 INFO: Using score_cutoff 9.273965600967406 (fac=0.99, q=1)
1:54:59.278211 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:54:59.278295 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:54:59.278355 INFO: Updating optimization_manager: score_cutoff        : 12.158764558696747 -> 9.273965600967406
1:54:59.278414 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:54:59.427098 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:54:59.866936 INFO: === checking if optimization conditions were reached ===
1:54:59.869625 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:54:59.869751 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
1:54:59.869835 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:54:59.869912 INFO: ==============================================
1:54:59.870003 PROGRESS: Optimization finished for ms2_error.
1:55:00.425527 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:55:00.583132 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:55:00.981920 INFO: Starting optimization step 0.
1:55:00.982279 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:55:00.982386 INFO: Using rust extraction backend
1:55:00.982471 PROGRESS: Extracting batch of 252182 precursors
1:55:01.467620 INFO: === Search parameters used ===
1:55:01.467979 INFO: rt_error       : 805.5982666015625
1:55:01.468106 INFO: mobility_error : 0.1
1:55:01.468208 INFO: num_candidates : 3
1:55:01.468300 INFO: ms1_error      : 20
1:55:01.468381 INFO: ms2_error      : 10.0
1:55:01.468468 INFO: fwhm_rt        : 3.0
1:55:01.468559 INFO: quant_window   : 3
1:55:01.468689 INFO: ==============================================
1:55:05.610469 INFO: performing precursor FDR with 40 features
1:55:05.610625 INFO: Decoy channel: -1
1:55:05.610669 INFO: competitive: True
1:55:05.868274 INFO: Setting torch num_threads to 2 for FDR classification task
1:55:06.259891 INFO: Estimating optimal hyperparameters - samples: 603,832, batch_size: 2,473, learning_rate: 7.77e-04
1:55:06.261037 INFO: Using random state 743242 for train-test-split
1:55:16.632173 INFO: Test AUC: 0.610
1:55:16.632328 INFO: Train AUC: 0.621
1:55:16.632370 INFO: AUC difference: 1.66%
1:55:17.210249 INFO: Resetting torch num_threads to 32
1:55:17.260972 PROGRESS: === Extracted 754790 precursors and 3861109 fragments ===
1:55:17.261604 INFO: === FDR correction performed with classifier version 12 ===
1:55:17.262745 PROGRESS: ============================= Precursor FDR =============================
1:55:17.262897 PROGRESS: Total precursors accumulated: 1,381
1:55:17.262982 PROGRESS: Target precursors: 1,368 (99.06%)
1:55:17.263054 PROGRESS: Decoy precursors: 13 (0.94%)
1:55:17.263120 PROGRESS: 
1:55:17.263181 PROGRESS: Precursor Summary:
1:55:17.265139 PROGRESS: Channel   0:	 0.050 FDR: 1,368; 0.010 FDR: 1,368; 0.001 FDR:   884
1:55:17.265285 PROGRESS: 
1:55:17.265372 PROGRESS: Protein Summary:
1:55:17.267765 PROGRESS: Channel   0:	 0.050 FDR: 1,194; 0.010 FDR: 1,194; 0.001 FDR:   783
1:55:17.267897 PROGRESS: =========================================================================
1:55:17.299603 INFO: Target number of precursors reached.
1:55:17.790815 INFO: fragments_df: keeping 5000 of 3861109 [sum(precursor_idx_mask)=32136 sum(mass_error_mask)=3861109 stop_rank=5000
1:55:18.328477 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:55:18.593291 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:55:19.385293 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:55:19.385901 INFO: Using score_cutoff 8.42051700181961 (fac=0.99, q=1)
1:55:19.386339 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:55:19.386442 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:55:19.386511 INFO: Updating optimization_manager: score_cutoff        : 9.273965600967406 -> 8.42051700181961
1:55:19.386586 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:55:19.543290 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:55:19.950458 INFO: === checking if optimization conditions were reached ===
1:55:19.950774 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:55:19.954241 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 612.51119506129
1:55:19.954407 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 612.5112.
1:55:19.954528 INFO: ==============================================
1:55:19.954653 INFO: Starting optimization step 1.
1:55:19.954755 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:55:19.954878 INFO: Using rust extraction backend
1:55:19.954990 PROGRESS: Extracting batch of 252182 precursors
1:55:20.419415 INFO: === Search parameters used ===
1:55:20.419686 INFO: rt_error       : 612.51119506129
1:55:20.419756 INFO: mobility_error : 0.1
1:55:20.419810 INFO: num_candidates : 3
1:55:20.419860 INFO: ms1_error      : 20
1:55:20.419908 INFO: ms2_error      : 10.0
1:55:20.419955 INFO: fwhm_rt        : 3.0
1:55:20.420003 INFO: quant_window   : 3
1:55:20.420062 INFO: ==============================================
1:55:24.255735 INFO: performing precursor FDR with 40 features
1:55:24.255866 INFO: Decoy channel: -1
1:55:24.255893 INFO: competitive: True
1:55:24.492962 INFO: Setting torch num_threads to 2 for FDR classification task
1:55:24.894402 INFO: Estimating optimal hyperparameters - samples: 603,889, batch_size: 2,473, learning_rate: 7.77e-04
1:55:24.895747 INFO: Using random state 743242 for train-test-split
1:55:39.964891 INFO: Test AUC: 0.610
1:55:39.965059 INFO: Train AUC: 0.621
1:55:39.965096 INFO: AUC difference: 1.77%
1:55:40.523980 INFO: Resetting torch num_threads to 32
1:55:40.570434 PROGRESS: === Extracted 754862 precursors and 3859641 fragments ===
1:55:40.571128 INFO: === FDR correction performed with classifier version 12 ===
1:55:40.572233 PROGRESS: ============================= Precursor FDR =============================
1:55:40.572367 PROGRESS: Total precursors accumulated: 1,303
1:55:40.572464 PROGRESS: Target precursors: 1,291 (99.08%)
1:55:40.572546 PROGRESS: Decoy precursors: 12 (0.92%)
1:55:40.572674 PROGRESS: 
1:55:40.572764 PROGRESS: Precursor Summary:
1:55:40.575010 PROGRESS: Channel   0:	 0.050 FDR: 1,291; 0.010 FDR: 1,291; 0.001 FDR:   827
1:55:40.575137 PROGRESS: 
1:55:40.575222 PROGRESS: Protein Summary:
1:55:40.577905 PROGRESS: Channel   0:	 0.050 FDR: 1,131; 0.010 FDR: 1,131; 0.001 FDR:   739
1:55:40.578040 PROGRESS: =========================================================================
1:55:40.603107 INFO: Target number of precursors reached.
1:55:41.076580 INFO: fragments_df: keeping 5000 of 3859641 [sum(precursor_idx_mask)=30490 sum(mass_error_mask)=3859641 stop_rank=5000
1:55:41.603493 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:55:41.838150 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:55:42.635244 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:55:42.635725 INFO: Using score_cutoff 9.247483297348023 (fac=0.99, q=1)
1:55:42.636063 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:55:42.636151 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:55:42.636213 INFO: Updating optimization_manager: score_cutoff        : 8.42051700181961 -> 9.247483297348023
1:55:42.636280 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:55:42.792181 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:55:43.226654 INFO: === checking if optimization conditions were reached ===
1:55:43.227044 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:55:43.230552 INFO: Updating optimization_manager: rt_error            : 612.51119506129 -> 633.6658101610951
1:55:43.230697 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 633.6658.
1:55:43.230783 INFO: ==============================================
1:55:43.230880 INFO: Starting optimization step 2.
1:55:43.230957 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:55:43.231057 INFO: Using rust extraction backend
1:55:43.231146 PROGRESS: Extracting batch of 252182 precursors
1:55:43.707273 INFO: === Search parameters used ===
1:55:43.707552 INFO: rt_error       : 633.6658101610951
1:55:43.707623 INFO: mobility_error : 0.1
1:55:43.707676 INFO: num_candidates : 3
1:55:43.707723 INFO: ms1_error      : 20
1:55:43.707766 INFO: ms2_error      : 10.0
1:55:43.707811 INFO: fwhm_rt        : 3.0
1:55:43.707864 INFO: quant_window   : 3
1:55:43.707909 INFO: ==============================================
1:55:47.804175 INFO: performing precursor FDR with 40 features
1:55:47.804359 INFO: Decoy channel: -1
1:55:47.804404 INFO: competitive: True
1:55:48.070004 INFO: Setting torch num_threads to 2 for FDR classification task
1:55:48.449775 INFO: Estimating optimal hyperparameters - samples: 603,864, batch_size: 2,473, learning_rate: 7.77e-04
1:55:48.451167 INFO: Using random state 743242 for train-test-split
1:56:05.015151 INFO: Test AUC: 0.609
1:56:05.015375 INFO: Train AUC: 0.621
1:56:05.015430 INFO: AUC difference: 2.04%
1:56:05.657501 INFO: Resetting torch num_threads to 32
1:56:05.704315 PROGRESS: === Extracted 754830 precursors and 3858851 fragments ===
1:56:05.705176 INFO: === FDR correction performed with classifier version 12 ===
1:56:05.705942 PROGRESS: ============================= Precursor FDR =============================
1:56:05.706043 PROGRESS: Total precursors accumulated: 1,325
1:56:05.706111 PROGRESS: Target precursors: 1,312 (99.02%)
1:56:05.706171 PROGRESS: Decoy precursors: 13 (0.98%)
1:56:05.706235 PROGRESS: 
1:56:05.706287 PROGRESS: Precursor Summary:
1:56:05.707664 PROGRESS: Channel   0:	 0.050 FDR: 1,312; 0.010 FDR: 1,312; 0.001 FDR: 1,050
1:56:05.707766 PROGRESS: 
1:56:05.707827 PROGRESS: Protein Summary:
1:56:05.709628 PROGRESS: Channel   0:	 0.050 FDR: 1,147; 0.010 FDR: 1,147; 0.001 FDR:   923
1:56:05.709733 PROGRESS: =========================================================================
1:56:05.727778 INFO: Target number of precursors reached.
1:56:06.209658 INFO: fragments_df: keeping 5000 of 3858851 [sum(precursor_idx_mask)=30759 sum(mass_error_mask)=3858851 stop_rank=5000
1:56:06.731252 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:56:07.050735 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:56:07.936793 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:56:07.937284 INFO: Using score_cutoff 8.044364794063569 (fac=0.99, q=1)
1:56:07.937635 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:56:07.937726 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:56:07.937793 INFO: Updating optimization_manager: score_cutoff        : 9.247483297348023 -> 8.044364794063569
1:56:07.937862 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:56:08.095688 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:56:08.474854 INFO: === checking if optimization conditions were reached ===
1:56:08.475244 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:56:08.478593 INFO: Updating optimization_manager: rt_error            : 633.6658101610951 -> 605.8422539239855
1:56:08.478735 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 605.8423.
1:56:08.478833 INFO: ==============================================
1:56:08.478930 INFO: Starting optimization step 3.
1:56:08.479014 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:56:08.479122 INFO: Using rust extraction backend
1:56:08.479210 PROGRESS: Extracting batch of 252182 precursors
1:56:08.979546 INFO: === Search parameters used ===
1:56:08.979817 INFO: rt_error       : 605.8422539239855
1:56:08.979888 INFO: mobility_error : 0.1
1:56:08.979940 INFO: num_candidates : 3
1:56:08.979987 INFO: ms1_error      : 20
1:56:08.980030 INFO: ms2_error      : 10.0
1:56:08.980072 INFO: fwhm_rt        : 3.0
1:56:08.980114 INFO: quant_window   : 3
1:56:08.980156 INFO: ==============================================
1:56:13.020924 INFO: performing precursor FDR with 40 features
1:56:13.021050 INFO: Decoy channel: -1
1:56:13.021079 INFO: competitive: True
1:56:13.264006 INFO: Setting torch num_threads to 2 for FDR classification task
1:56:13.708044 INFO: Estimating optimal hyperparameters - samples: 603,865, batch_size: 2,473, learning_rate: 7.77e-04
1:56:13.709367 INFO: Using random state 743242 for train-test-split
1:56:28.896224 INFO: Test AUC: 0.606
1:56:28.896438 INFO: Train AUC: 0.619
1:56:28.896489 INFO: AUC difference: 2.04%
1:56:29.388520 INFO: Resetting torch num_threads to 32
1:56:29.420774 PROGRESS: === Extracted 754832 precursors and 3857263 fragments ===
1:56:29.421276 INFO: === FDR correction performed with classifier version 12 ===
1:56:29.421974 PROGRESS: ============================= Precursor FDR =============================
1:56:29.422074 PROGRESS: Total precursors accumulated: 1,281
1:56:29.422161 PROGRESS: Target precursors: 1,269 (99.06%)
1:56:29.422220 PROGRESS: Decoy precursors: 12 (0.94%)
1:56:29.422271 PROGRESS: 
1:56:29.422323 PROGRESS: Precursor Summary:
1:56:29.423624 PROGRESS: Channel   0:	 0.050 FDR: 1,269; 0.010 FDR: 1,269; 0.001 FDR:   893
1:56:29.423719 PROGRESS: 
1:56:29.423780 PROGRESS: Protein Summary:
1:56:29.425476 PROGRESS: Channel   0:	 0.050 FDR: 1,109; 0.010 FDR: 1,109; 0.001 FDR:   797
1:56:29.425583 PROGRESS: =========================================================================
1:56:29.445294 INFO: Target number of precursors reached.
1:56:30.006649 INFO: fragments_df: keeping 5000 of 3857263 [sum(precursor_idx_mask)=30145 sum(mass_error_mask)=3857263 stop_rank=5000
1:56:30.566145 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:56:30.916752 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:56:31.742054 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:56:31.742581 INFO: Using score_cutoff 9.531885480880737 (fac=0.99, q=1)
1:56:31.742960 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:56:31.743064 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:56:31.743141 INFO: Updating optimization_manager: score_cutoff        : 8.044364794063569 -> 9.531885480880737
1:56:31.743225 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:56:31.933520 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:56:32.366721 INFO: === checking if optimization conditions were reached ===
1:56:32.367075 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:56:32.371078 INFO: Updating optimization_manager: rt_error            : 605.8422539239855 -> 590.1037309174421
1:56:32.371228 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 590.1037.
1:56:32.371325 INFO: ==============================================
1:56:32.371441 INFO: Starting optimization step 4.
1:56:32.371527 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:56:32.371642 INFO: Using rust extraction backend
1:56:32.371749 PROGRESS: Extracting batch of 252182 precursors
1:56:32.867390 INFO: === Search parameters used ===
1:56:32.867669 INFO: rt_error       : 590.1037309174421
1:56:32.867735 INFO: mobility_error : 0.1
1:56:32.867789 INFO: num_candidates : 3
1:56:32.867837 INFO: ms1_error      : 20
1:56:32.867883 INFO: ms2_error      : 10.0
1:56:32.867929 INFO: fwhm_rt        : 3.0
1:56:32.867976 INFO: quant_window   : 3
1:56:32.868019 INFO: ==============================================
1:56:36.769298 INFO: performing precursor FDR with 40 features
1:56:36.769430 INFO: Decoy channel: -1
1:56:36.769459 INFO: competitive: True
1:56:37.041995 INFO: Setting torch num_threads to 2 for FDR classification task
1:56:37.432889 INFO: Estimating optimal hyperparameters - samples: 603,827, batch_size: 2,473, learning_rate: 7.77e-04
1:56:37.434228 INFO: Using random state 743242 for train-test-split
1:56:48.287812 INFO: Test AUC: 0.609
1:56:48.287989 INFO: Train AUC: 0.620
1:56:48.288024 INFO: AUC difference: 1.77%
1:56:48.836493 INFO: Resetting torch num_threads to 32
1:56:48.885806 PROGRESS: === Extracted 754784 precursors and 3852484 fragments ===
1:56:48.886438 INFO: === FDR correction performed with classifier version 12 ===
1:56:48.887416 PROGRESS: ============================= Precursor FDR =============================
1:56:48.887563 PROGRESS: Total precursors accumulated: 1,279
1:56:48.887645 PROGRESS: Target precursors: 1,267 (99.06%)
1:56:48.887712 PROGRESS: Decoy precursors: 12 (0.94%)
1:56:48.887774 PROGRESS: 
1:56:48.887834 PROGRESS: Precursor Summary:
1:56:48.889623 PROGRESS: Channel   0:	 0.050 FDR: 1,267; 0.010 FDR: 1,267; 0.001 FDR:   607
1:56:48.889747 PROGRESS: 
1:56:48.889819 PROGRESS: Protein Summary:
1:56:48.891981 PROGRESS: Channel   0:	 0.050 FDR: 1,114; 0.010 FDR: 1,114; 0.001 FDR:   553
1:56:48.892106 PROGRESS: =========================================================================
1:56:48.922097 INFO: Target number of precursors reached.
1:56:49.425079 INFO: fragments_df: keeping 5000 of 3852484 [sum(precursor_idx_mask)=29542 sum(mass_error_mask)=3852484 stop_rank=5000
1:56:49.922780 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:56:50.183264 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:56:51.042454 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:56:51.043082 INFO: Using score_cutoff 7.195515079593658 (fac=0.99, q=1)
1:56:51.043561 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:56:51.043680 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:56:51.043780 INFO: Updating optimization_manager: score_cutoff        : 9.531885480880737 -> 7.195515079593658
1:56:51.043901 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:56:51.204361 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:56:51.589146 INFO: === checking if optimization conditions were reached ===
1:56:51.589477 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:56:51.590617 INFO: Updating optimization_manager: rt_error            : 590.1037309174421 -> 805.5982666015625
1:56:51.590785 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
1:56:51.590906 INFO: Updating optimization_manager: score_cutoff        : 7.195515079593658 -> 8.42051700181961
1:56:51.591019 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:56:51.591126 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:56:51.591242 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 805.5983 found after 5 searches.
1:56:51.591321 INFO: ==============================================
1:56:51.591410 PROGRESS: Optimization finished for rt_error.
1:56:52.113124 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:56:52.274676 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:56:52.733321 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:56:52.733591 PROGRESS: ==============================================
1:56:52.733696 PROGRESS: ms2_error      : 10.0000
1:56:52.733773 PROGRESS: rt_error       : 805.5983
1:56:52.733840 PROGRESS: ==============================================
1:56:52.734737 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:57:02.419805 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:57:30.174711 INFO: Using rust extraction backend
1:57:30.175087 PROGRESS: Extracting batch of 15081856 precursors
1:57:57.411400 INFO: === Search parameters used ===
1:57:57.411779 INFO: rt_error       : 805.5982666015625
1:57:57.411856 INFO: mobility_error : 0.1
1:57:57.411916 INFO: num_candidates : 3
1:57:57.411969 INFO: ms1_error      : 20
1:57:57.412021 INFO: ms2_error      : 10.0
1:57:57.412067 INFO: fwhm_rt        : 3.0
1:57:57.412119 INFO: quant_window   : 3
1:57:57.412164 INFO: ==============================================
1:59:37.533729 INFO: Removed 5424249 precursors with score below cutoff 8.42051700181961
2:00:22.216351 INFO: performing precursor FDR with 40 features
2:00:22.216570 INFO: Decoy channel: -1
2:00:22.216604 INFO: competitive: True
2:00:27.104380 INFO: Setting torch num_threads to 2 for FDR classification task
2:00:48.404194 INFO: Estimating optimal hyperparameters - samples: 31,856,773, batch_size: 4,096, learning_rate: 1.00e-03
2:00:48.508689 INFO: Using random state 10619 for train-test-split
2:13:22.437131 INFO: Test AUC: 0.615
2:13:22.437432 INFO: Train AUC: 0.615
2:13:22.437510 INFO: AUC difference: 0.05%
2:13:30.794344 INFO: Resetting torch num_threads to 32
2:13:33.955083 PROGRESS: ============================= Precursor FDR =============================
2:13:33.955361 PROGRESS: Total precursors accumulated: 86,579
2:13:33.955439 PROGRESS: Target precursors: 85,722 (99.01%)
2:13:33.955501 PROGRESS: Decoy precursors: 857 (0.99%)
2:13:33.955557 PROGRESS: 
2:13:33.955614 PROGRESS: Precursor Summary:
2:13:33.983696 PROGRESS: Channel   0:	 0.050 FDR: 85,722; 0.010 FDR: 85,722; 0.001 FDR: 45,353
2:13:33.983936 PROGRESS: 
2:13:33.984017 PROGRESS: Protein Summary:
2:13:34.023995 PROGRESS: Channel   0:	 0.050 FDR: 11,970; 0.010 FDR: 11,970; 0.001 FDR: 7,780
2:13:34.024224 PROGRESS: =========================================================================
2:13:34.369559 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/psm.parquet
2:13:34.579044 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.parquet
2:13:34.841424 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:13:35.752865 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 
2:13:35.753018 INFO: Quantification results path: /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant
2:13:35.753093 INFO: Creating folder /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/figures
2:13:35.753290 INFO: Initializing TimingManager
2:13:35.753767 INFO: Initializing RawFileManager
2:14:33.063854 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.
2:14:33.075581 INFO: Determining DIA cycle
2:14:33.095140 INFO: Found cycle with start 0.00 min and length 300.
2:14:33.307142 INFO: RT (min)            : 0.0 - 26.9
2:14:33.307250 INFO: RT duration (sec)   : 1611.2
2:14:33.307296 INFO: RT duration (min)   : 26.9
2:14:33.307331 INFO: Cycle len (scans)   : 300
2:14:33.307362 INFO: Cycle len (sec)     : 1.65
2:14:33.307391 INFO: Number of cycles    : 977
2:14:33.307420 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:14:33.307462 INFO: Creating DIA data object took: 57.55358815193176
2:14:35.004099 INFO: Creating DIA data NG object took: 1.6964590549468994
2:14:37.036805 INFO: Initializing CalibrationManager
2:14:37.037096 INFO: Setting up calibration estimators ..
2:14:37.037168 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:14:37.037272 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'}' ..
2:14:37.037370 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:14:37.037437 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:14:37.037499 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}}' ..
2:14:37.037555 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:14:37.037605 INFO: Done setting up calibration estimators.
2:14:37.037835 INFO: Initializing OptimizationManager
2:14:37.038010 INFO: initial parameter: ms1_error = 20
2:14:37.038068 INFO: initial parameter: ms2_error = 20
2:14:37.038119 INFO: initial parameter: rt_error = 805.6002197265625
2:14:37.038165 INFO: initial parameter: mobility_error = 0.1
2:14:37.038210 INFO: initial parameter: num_candidates = 1
2:14:37.038254 INFO: initial parameter: fwhm_rt = 5
2:14:37.038296 INFO: initial parameter: fwhm_mobility = 0.01
2:14:37.038342 INFO: initial parameter: score_cutoff = 0
2:14:37.038385 INFO: initial parameter: classifier_version = -1
2:14:37.038460 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:14:37.038734 INFO: FDRManager: loading saved state not requested, will be initialized.
2:14:37.038767 INFO: Initializing FDRManager
2:14:37.038810 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2:14:39.496214 PROGRESS: Initializing spectral library: 7,536,970 target precursors potentially observable (1,230,167 removed)
2:14:41.187637 INFO: Updating optimization_manager: ms2_error           : 20 -> 20
2:14:41.188065 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
2:14:41.188183 PROGRESS: Starting initial search for precursors.
2:14:41.188282 INFO: Starting optimization step 0.
2:14:41.188353 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:14:41.188423 INFO: Using rust extraction backend
2:14:41.188489 PROGRESS: Extracting batch of 1988 precursors
2:14:41.193920 INFO: === Search parameters used ===
2:14:41.194069 INFO: rt_error       : 805.6002197265625
2:14:41.194130 INFO: mobility_error : 0.1
2:14:41.194184 INFO: num_candidates : 1
2:14:41.194232 INFO: ms1_error      : 20
2:14:41.194278 INFO: ms2_error      : 20
2:14:41.194327 INFO: fwhm_rt        : 5
2:14:41.194376 INFO: quant_window   : 3
2:14:41.194422 INFO: ==============================================
2:14:41.233351 INFO: performing precursor FDR with 40 features
2:14:41.233449 INFO: Decoy channel: -1
2:14:41.233476 INFO: competitive: True
2:14:41.234899 INFO: Setting torch num_threads to 2 for FDR classification task
2:14:41.237024 INFO: Estimating optimal hyperparameters - samples: 1,582, batch_size: 128, learning_rate: 1.77e-04
2:14:41.237864 INFO: Using random state 414455 for train-test-split
2:14:41.420952 INFO: Test AUC: 0.509
2:14:41.421083 INFO: Train AUC: 0.574
2:14:41.421125 INFO: AUC difference: 11.18%
2:14:41.421157 WARNING: AUC difference > 5%. This may indicate overfitting.
2:14:41.746912 INFO: Resetting torch num_threads to 32
2:14:41.749005 PROGRESS: === Extracted 1978 precursors and 9357 fragments ===
2:14:41.749466 INFO: === FDR correction performed with classifier version -1 ===
2:14:41.750016 PROGRESS: ============================= Precursor FDR =============================
2:14:41.750128 PROGRESS: Total precursors accumulated: 4
2:14:41.750192 PROGRESS: Target precursors: 4 (100.00%)
2:14:41.750247 PROGRESS: Decoy precursors: 0 (0.00%)
2:14:41.750299 PROGRESS: 
2:14:41.750345 PROGRESS: Precursor Summary:
2:14:41.751433 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
2:14:41.751529 PROGRESS: 
2:14:41.751592 PROGRESS: Protein Summary:
2:14:41.752802 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
2:14:41.752905 PROGRESS: =========================================================================
2:14:41.753188 INFO: Target number of precursors not reached yet.
2:14:41.865669 INFO: Starting optimization step 1.
2:14:41.865931 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:14:41.866055 INFO: Using rust extraction backend
2:14:41.866158 PROGRESS: Extracting batch of 3976 precursors
2:14:41.876428 INFO: === Search parameters used ===
2:14:41.876682 INFO: rt_error       : 805.6002197265625
2:14:41.876769 INFO: mobility_error : 0.1
2:14:41.876839 INFO: num_candidates : 1
2:14:41.876903 INFO: ms1_error      : 20
2:14:41.876964 INFO: ms2_error      : 20
2:14:41.877025 INFO: fwhm_rt        : 5
2:14:41.877092 INFO: quant_window   : 3
2:14:41.877160 INFO: ==============================================
2:14:41.943759 INFO: performing precursor FDR with 40 features
2:14:41.943886 INFO: Decoy channel: -1
2:14:41.943917 INFO: competitive: True
2:14:41.948471 INFO: Setting torch num_threads to 2 for FDR classification task
2:14:41.951000 INFO: Estimating optimal hyperparameters - samples: 4,743, batch_size: 128, learning_rate: 1.77e-04
2:14:41.951118 INFO: Using random state 430564 for train-test-split
2:14:42.547649 INFO: Test AUC: 0.524
2:14:42.547805 INFO: Train AUC: 0.589
2:14:42.547853 INFO: AUC difference: 11.00%
2:14:42.547893 WARNING: AUC difference > 5%. This may indicate overfitting.
2:14:42.875647 INFO: Resetting torch num_threads to 32
2:14:42.880429 PROGRESS: === Extracted 5929 precursors and 28056 fragments ===
2:14:42.881039 INFO: === FDR correction performed with classifier version -1 ===
2:14:42.881840 PROGRESS: ============================= Precursor FDR =============================
2:14:42.881977 PROGRESS: Total precursors accumulated: 17
2:14:42.882086 PROGRESS: Target precursors: 17 (100.00%)
2:14:42.882180 PROGRESS: Decoy precursors: 0 (0.00%)
2:14:42.882258 PROGRESS: 
2:14:42.882331 PROGRESS: Precursor Summary:
2:14:42.884108 PROGRESS: Channel   0:	 0.050 FDR:    17; 0.010 FDR:    17; 0.001 FDR:    17
2:14:42.884239 PROGRESS: 
2:14:42.884337 PROGRESS: Protein Summary:
2:14:42.886412 PROGRESS: Channel   0:	 0.050 FDR:    17; 0.010 FDR:    17; 0.001 FDR:    17
2:14:42.886554 PROGRESS: =========================================================================
2:14:42.887079 INFO: Target number of precursors not reached yet.
2:14:43.018092 INFO: Starting optimization step 2.
2:14:43.018375 PROGRESS: === Extracting elution groups 3000 to 7000 ===
2:14:43.018518 INFO: Using rust extraction backend
2:14:43.018635 PROGRESS: Extracting batch of 7946 precursors
2:14:43.037296 INFO: === Search parameters used ===
2:14:43.037573 INFO: rt_error       : 805.6002197265625
2:14:43.037673 INFO: mobility_error : 0.1
2:14:43.037778 INFO: num_candidates : 1
2:14:43.037871 INFO: ms1_error      : 20
2:14:43.037957 INFO: ms2_error      : 20
2:14:43.038040 INFO: fwhm_rt        : 5
2:14:43.038116 INFO: quant_window   : 3
2:14:43.038191 INFO: ==============================================
2:14:43.152164 INFO: performing precursor FDR with 40 features
2:14:43.152277 INFO: Decoy channel: -1
2:14:43.152304 INFO: competitive: True
2:14:43.159250 INFO: Setting torch num_threads to 2 for FDR classification task
2:14:43.163542 INFO: Estimating optimal hyperparameters - samples: 11,062, batch_size: 128, learning_rate: 1.77e-04
2:14:43.163720 INFO: Using random state 106453 for train-test-split
2:14:44.506957 INFO: Test AUC: 0.558
2:14:44.507091 INFO: Train AUC: 0.593
2:14:44.507128 INFO: AUC difference: 5.93%
2:14:44.507156 WARNING: AUC difference > 5%. This may indicate overfitting.
2:14:44.816640 INFO: Resetting torch num_threads to 32
2:14:44.821252 PROGRESS: === Extracted 13828 precursors and 65442 fragments ===
2:14:44.821722 INFO: === FDR correction performed with classifier version -1 ===
2:14:44.822268 PROGRESS: ============================= Precursor FDR =============================
2:14:44.822377 PROGRESS: Total precursors accumulated: 36
2:14:44.822442 PROGRESS: Target precursors: 36 (100.00%)
2:14:44.822497 PROGRESS: Decoy precursors: 0 (0.00%)
2:14:44.822548 PROGRESS: 
2:14:44.822597 PROGRESS: Precursor Summary:
2:14:44.823679 PROGRESS: Channel   0:	 0.050 FDR:    36; 0.010 FDR:    36; 0.001 FDR:    36
2:14:44.823779 PROGRESS: 
2:14:44.823837 PROGRESS: Protein Summary:
2:14:44.825052 PROGRESS: Channel   0:	 0.050 FDR:    36; 0.010 FDR:    36; 0.001 FDR:    36
2:14:44.825150 PROGRESS: =========================================================================
2:14:44.825554 INFO: Target number of precursors not reached yet.
2:14:44.961908 INFO: Starting optimization step 3.
2:14:44.962213 PROGRESS: === Extracting elution groups 7000 to 15000 ===
2:14:44.962320 INFO: Using rust extraction backend
2:14:44.962400 PROGRESS: Extracting batch of 15879 precursors
2:14:44.994514 INFO: === Search parameters used ===
2:14:44.994816 INFO: rt_error       : 805.6002197265625
2:14:44.994885 INFO: mobility_error : 0.1
2:14:44.994945 INFO: num_candidates : 1
2:14:44.995001 INFO: ms1_error      : 20
2:14:44.995055 INFO: ms2_error      : 20
2:14:44.995120 INFO: fwhm_rt        : 5
2:14:44.995178 INFO: quant_window   : 3
2:14:44.995229 INFO: ==============================================
2:14:45.219555 INFO: performing precursor FDR with 40 features
2:14:45.219719 INFO: Decoy channel: -1
2:14:45.219750 INFO: competitive: True
2:14:45.237082 INFO: Setting torch num_threads to 2 for FDR classification task
2:14:45.247235 INFO: Estimating optimal hyperparameters - samples: 23,666, batch_size: 128, learning_rate: 1.77e-04
2:14:45.247463 INFO: Using random state 852722 for train-test-split
2:14:47.390261 INFO: Test AUC: 0.563
2:14:47.390409 INFO: Train AUC: 0.606
2:14:47.390456 INFO: AUC difference: 7.09%
2:14:47.390490 WARNING: AUC difference > 5%. This may indicate overfitting.
2:14:49.261812 INFO: Resetting torch num_threads to 32
2:14:49.273281 PROGRESS: === Extracted 29583 precursors and 140153 fragments ===
2:14:49.274045 INFO: === FDR correction performed with classifier version -1 ===
2:14:49.274890 PROGRESS: ============================= Precursor FDR =============================
2:14:49.275028 PROGRESS: Total precursors accumulated: 62
2:14:49.275116 PROGRESS: Target precursors: 62 (100.00%)
2:14:49.275192 PROGRESS: Decoy precursors: 0 (0.00%)
2:14:49.275268 PROGRESS: 
2:14:49.275342 PROGRESS: Precursor Summary:
2:14:49.277024 PROGRESS: Channel   0:	 0.050 FDR:    62; 0.010 FDR:    62; 0.001 FDR:    62
2:14:49.277153 PROGRESS: 
2:14:49.277242 PROGRESS: Protein Summary:
2:14:49.278967 PROGRESS: Channel   0:	 0.050 FDR:    62; 0.010 FDR:    62; 0.001 FDR:    62
2:14:49.279084 PROGRESS: =========================================================================
2:14:49.279964 INFO: Target number of precursors not reached yet.
2:14:49.468277 INFO: Starting optimization step 4.
2:14:49.468566 PROGRESS: === Extracting elution groups 15000 to 31000 ===
2:14:49.468707 INFO: Using rust extraction backend
2:14:49.468815 PROGRESS: Extracting batch of 31750 precursors
2:14:49.534669 INFO: === Search parameters used ===
2:14:49.534933 INFO: rt_error       : 805.6002197265625
2:14:49.535001 INFO: mobility_error : 0.1
2:14:49.535056 INFO: num_candidates : 1
2:14:49.535108 INFO: ms1_error      : 20
2:14:49.535155 INFO: ms2_error      : 20
2:14:49.535201 INFO: fwhm_rt        : 5
2:14:49.535247 INFO: quant_window   : 3
2:14:49.535292 INFO: ==============================================
2:14:49.883572 INFO: performing precursor FDR with 40 features
2:14:49.883717 INFO: Decoy channel: -1
2:14:49.883750 INFO: competitive: True
2:14:49.920163 INFO: Setting torch num_threads to 2 for FDR classification task
2:14:49.943783 INFO: Estimating optimal hyperparameters - samples: 48,884, batch_size: 200, learning_rate: 2.21e-04
2:14:49.944078 INFO: Using random state 42856 for train-test-split
2:14:53.139039 INFO: Test AUC: 0.565
2:14:53.139184 INFO: Train AUC: 0.613
2:14:53.139224 INFO: AUC difference: 7.90%
2:14:53.139257 WARNING: AUC difference > 5%. This may indicate overfitting.
2:14:53.476226 INFO: Resetting torch num_threads to 32
2:14:53.492413 PROGRESS: === Extracted 61106 precursors and 290025 fragments ===
2:14:53.493073 INFO: === FDR correction performed with classifier version -1 ===
2:14:53.493660 PROGRESS: ============================= Precursor FDR =============================
2:14:53.493775 PROGRESS: Total precursors accumulated: 137
2:14:53.493841 PROGRESS: Target precursors: 136 (99.27%)
2:14:53.493906 PROGRESS: Decoy precursors: 1 (0.73%)
2:14:53.493958 PROGRESS: 
2:14:53.494006 PROGRESS: Precursor Summary:
2:14:53.495020 PROGRESS: Channel   0:	 0.050 FDR:   136; 0.010 FDR:   136; 0.001 FDR:    56
2:14:53.495121 PROGRESS: 
2:14:53.495181 PROGRESS: Protein Summary:
2:14:53.496335 PROGRESS: Channel   0:	 0.050 FDR:   134; 0.010 FDR:   134; 0.001 FDR:    55
2:14:53.496433 PROGRESS: =========================================================================
2:14:53.497851 INFO: Target number of precursors not reached yet.
2:14:53.734873 INFO: Starting optimization step 5.
2:14:53.735142 PROGRESS: === Extracting elution groups 31000 to 63000 ===
2:14:53.735239 INFO: Using rust extraction backend
2:14:53.735318 PROGRESS: Extracting batch of 63536 precursors
2:14:53.856293 INFO: === Search parameters used ===
2:14:53.856632 INFO: rt_error       : 805.6002197265625
2:14:53.856724 INFO: mobility_error : 0.1
2:14:53.856787 INFO: num_candidates : 1
2:14:53.856847 INFO: ms1_error      : 20
2:14:53.856904 INFO: ms2_error      : 20
2:14:53.856958 INFO: fwhm_rt        : 5
2:14:53.857012 INFO: quant_window   : 3
2:14:53.857066 INFO: ==============================================
2:14:54.542005 INFO: performing precursor FDR with 40 features
2:14:54.542142 INFO: Decoy channel: -1
2:14:54.542172 INFO: competitive: True
2:14:54.622344 INFO: Setting torch num_threads to 2 for FDR classification task
2:14:54.672859 INFO: Estimating optimal hyperparameters - samples: 99,396, batch_size: 407, learning_rate: 3.15e-04
2:14:54.673265 INFO: Using random state 688669 for train-test-split
2:14:58.793173 INFO: Test AUC: 0.580
2:14:58.793324 INFO: Train AUC: 0.612
2:14:58.793358 INFO: AUC difference: 5.32%
2:14:58.793384 WARNING: AUC difference > 5%. This may indicate overfitting.
2:14:59.112545 INFO: Resetting torch num_threads to 32
2:14:59.140314 PROGRESS: === Extracted 124246 precursors and 590092 fragments ===
2:14:59.141004 INFO: === FDR correction performed with classifier version -1 ===
2:14:59.141680 PROGRESS: ============================= Precursor FDR =============================
2:14:59.141780 PROGRESS: Total precursors accumulated: 415
2:14:59.141859 PROGRESS: Target precursors: 411 (99.04%)
2:14:59.141919 PROGRESS: Decoy precursors: 4 (0.96%)
2:14:59.141972 PROGRESS: 
2:14:59.142026 PROGRESS: Precursor Summary:
2:14:59.143157 PROGRESS: Channel   0:	 0.050 FDR:   411; 0.010 FDR:   411; 0.001 FDR:   297
2:14:59.143257 PROGRESS: 
2:14:59.143327 PROGRESS: Protein Summary:
2:14:59.144780 PROGRESS: Channel   0:	 0.050 FDR:   395; 0.010 FDR:   395; 0.001 FDR:   286
2:14:59.144922 PROGRESS: =========================================================================
2:14:59.148432 INFO: Target number of precursors not reached yet.
2:14:59.586798 INFO: Starting optimization step 6.
2:14:59.587112 PROGRESS: === Extracting elution groups 63000 to 127000 ===
2:14:59.587229 INFO: Using rust extraction backend
2:14:59.587316 PROGRESS: Extracting batch of 127107 precursors
2:14:59.834367 INFO: === Search parameters used ===
2:14:59.834672 INFO: rt_error       : 805.6002197265625
2:14:59.834740 INFO: mobility_error : 0.1
2:14:59.834795 INFO: num_candidates : 1
2:14:59.834847 INFO: ms1_error      : 20
2:14:59.834893 INFO: ms2_error      : 20
2:14:59.834941 INFO: fwhm_rt        : 5
2:14:59.834991 INFO: quant_window   : 3
2:14:59.835043 INFO: ==============================================
2:15:01.128599 INFO: performing precursor FDR with 40 features
2:15:01.128766 INFO: Decoy channel: -1
2:15:01.128804 INFO: competitive: True
2:15:01.247754 INFO: Setting torch num_threads to 2 for FDR classification task
2:15:01.346586 INFO: Estimating optimal hyperparameters - samples: 200,430, batch_size: 820, learning_rate: 4.47e-04
2:15:01.346994 INFO: Using random state 360741 for train-test-split
2:15:06.708024 INFO: Test AUC: 0.585
2:15:06.708161 INFO: Train AUC: 0.611
2:15:06.708206 INFO: AUC difference: 4.14%
2:15:07.062275 INFO: Resetting torch num_threads to 32
2:15:07.119587 PROGRESS: === Extracted 250538 precursors and 1187789 fragments ===
2:15:07.120264 INFO: === FDR correction performed with classifier version -1 ===
2:15:07.121066 PROGRESS: ============================= Precursor FDR =============================
2:15:07.121171 PROGRESS: Total precursors accumulated: 773
2:15:07.121239 PROGRESS: Target precursors: 766 (99.09%)
2:15:07.121297 PROGRESS: Decoy precursors: 7 (0.91%)
2:15:07.121350 PROGRESS: 
2:15:07.121400 PROGRESS: Precursor Summary:
2:15:07.122636 PROGRESS: Channel   0:	 0.050 FDR:   766; 0.010 FDR:   766; 0.001 FDR:   443
2:15:07.122735 PROGRESS: 
2:15:07.122797 PROGRESS: Protein Summary:
2:15:07.124461 PROGRESS: Channel   0:	 0.050 FDR:   690; 0.010 FDR:   690; 0.001 FDR:   410
2:15:07.124561 PROGRESS: =========================================================================
2:15:07.131684 INFO: Target number of precursors not reached yet.
2:15:07.733148 INFO: Starting optimization step 7.
2:15:07.733428 PROGRESS: === Extracting elution groups 127000 to 255000 ===
2:15:07.733522 INFO: Using rust extraction backend
2:15:07.733591 PROGRESS: Extracting batch of 254254 precursors
2:15:08.206733 INFO: === Search parameters used ===
2:15:08.207046 INFO: rt_error       : 805.6002197265625
2:15:08.207145 INFO: mobility_error : 0.1
2:15:08.207237 INFO: num_candidates : 1
2:15:08.207325 INFO: ms1_error      : 20
2:15:08.207404 INFO: ms2_error      : 20
2:15:08.207498 INFO: fwhm_rt        : 5
2:15:08.207589 INFO: quant_window   : 3
2:15:08.207668 INFO: ==============================================
2:15:10.731093 INFO: performing precursor FDR with 40 features
2:15:10.731274 INFO: Decoy channel: -1
2:15:10.731323 INFO: competitive: True
2:15:10.972968 INFO: Setting torch num_threads to 2 for FDR classification task
2:15:11.229346 INFO: Estimating optimal hyperparameters - samples: 402,493, batch_size: 1,648, learning_rate: 6.34e-04
2:15:11.230323 INFO: Using random state 720865 for train-test-split
2:15:22.719756 INFO: Test AUC: 0.588
2:15:22.719887 INFO: Train AUC: 0.607
2:15:22.719923 INFO: AUC difference: 3.13%
2:15:23.206118 INFO: Resetting torch num_threads to 32
2:15:23.360257 PROGRESS: === Extracted 503117 precursors and 2385912 fragments ===
2:15:23.361071 INFO: === FDR correction performed with classifier version -1 ===
2:15:23.362299 PROGRESS: ============================= Precursor FDR =============================
2:15:23.362416 PROGRESS: Total precursors accumulated: 1,760
2:15:23.362494 PROGRESS: Target precursors: 1,743 (99.03%)
2:15:23.362566 PROGRESS: Decoy precursors: 17 (0.97%)
2:15:23.362634 PROGRESS: 
2:15:23.362697 PROGRESS: Precursor Summary:
2:15:23.364647 PROGRESS: Channel   0:	 0.050 FDR: 1,743; 0.010 FDR: 1,743; 0.001 FDR: 1,296
2:15:23.364766 PROGRESS: 
2:15:23.364854 PROGRESS: Protein Summary:
2:15:23.367423 PROGRESS: Channel   0:	 0.050 FDR: 1,421; 0.010 FDR: 1,421; 0.001 FDR: 1,088
2:15:23.367544 PROGRESS: =========================================================================
2:15:23.380531 INFO: Target number of precursors reached.
2:15:23.662035 INFO: fragments_df: keeping 5000 of 2385912 [sum(precursor_idx_mask)=18554 sum(mass_error_mask)=2385912 stop_rank=5000
2:15:24.628733 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:15:24.996991 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:15:25.833574 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:15:25.834073 INFO: Using score_cutoff 12.675979294395447 (fac=0.99, q=1)
2:15:25.834450 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:15:25.834547 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:15:25.834613 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.675979294395447
2:15:25.834675 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:15:26.156518 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:15:26.986845 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
2:15:26.987083 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:15:26.987192 INFO: Starting optimization step 8.
2:15:26.987260 PROGRESS: === Extracting elution groups 0 to 255000 ===
2:15:26.987335 INFO: Using rust extraction backend
2:15:26.987403 PROGRESS: Extracting batch of 506436 precursors
2:15:27.924892 INFO: === Search parameters used ===
2:15:27.925158 INFO: rt_error       : 805.6002197265625
2:15:27.925228 INFO: mobility_error : 0.1
2:15:27.925284 INFO: num_candidates : 3
2:15:27.925332 INFO: ms1_error      : 20
2:15:27.925380 INFO: ms2_error      : 20
2:15:27.925427 INFO: fwhm_rt        : 3.0
2:15:27.925474 INFO: quant_window   : 3
2:15:27.925531 INFO: ==============================================
2:15:36.521230 INFO: performing precursor FDR with 40 features
2:15:36.521364 INFO: Decoy channel: -1
2:15:36.521393 INFO: competitive: True
2:15:37.065458 INFO: Setting torch num_threads to 2 for FDR classification task
2:15:37.884182 INFO: Estimating optimal hyperparameters - samples: 1,206,311, batch_size: 4,096, learning_rate: 1.00e-03
2:15:37.886908 INFO: Using random state 41931 for train-test-split
2:16:05.521720 INFO: Test AUC: 0.594
2:16:05.521885 INFO: Train AUC: 0.603
2:16:05.521929 INFO: AUC difference: 1.44%
2:16:06.295026 INFO: Resetting torch num_threads to 32
2:16:06.352282 PROGRESS: === Extracted 1507889 precursors and 6933784 fragments ===
2:16:06.352788 INFO: === FDR correction performed with classifier version 7 ===
2:16:06.353658 PROGRESS: ============================= Precursor FDR =============================
2:16:06.353760 PROGRESS: Total precursors accumulated: 1,946
2:16:06.353828 PROGRESS: Target precursors: 1,927 (99.02%)
2:16:06.353887 PROGRESS: Decoy precursors: 19 (0.98%)
2:16:06.353941 PROGRESS: 
2:16:06.353994 PROGRESS: Precursor Summary:
2:16:06.355499 PROGRESS: Channel   0:	 0.050 FDR: 1,927; 0.010 FDR: 1,927; 0.001 FDR: 1,308
2:16:06.355601 PROGRESS: 
2:16:06.355666 PROGRESS: Protein Summary:
2:16:06.357676 PROGRESS: Channel   0:	 0.050 FDR: 1,559; 0.010 FDR: 1,559; 0.001 FDR: 1,093
2:16:06.357787 PROGRESS: =========================================================================
2:16:06.391237 INFO: Target number of precursors reached.
2:16:07.302578 INFO: fragments_df: keeping 5000 of 6933784 [sum(precursor_idx_mask)=44591 sum(mass_error_mask)=6933784 stop_rank=5000
2:16:08.286983 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:16:08.661345 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:16:09.604236 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:16:09.604873 INFO: Using score_cutoff 13.036643642807007 (fac=0.99, q=1)
2:16:09.605334 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:16:09.605448 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:16:09.605536 INFO: Updating optimization_manager: score_cutoff        : 12.675979294395447 -> 13.036643642807007
2:16:09.605626 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:16:09.935479 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:16:10.787413 INFO: === checking if optimization conditions were reached ===
2:16:10.789664 INFO: Updating optimization_manager: ms2_error           : 20 -> 10.0
2:16:10.789778 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
2:16:10.789854 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:16:10.789919 INFO: ==============================================
2:16:10.789991 INFO: Starting optimization step 9.
2:16:10.790053 PROGRESS: === Extracting elution groups 0 to 255000 ===
2:16:10.790118 INFO: Using rust extraction backend
2:16:10.790183 PROGRESS: Extracting batch of 506436 precursors
2:16:11.731517 INFO: === Search parameters used ===
2:16:11.731789 INFO: rt_error       : 805.6002197265625
2:16:11.731866 INFO: mobility_error : 0.1
2:16:11.731927 INFO: num_candidates : 3
2:16:11.731990 INFO: ms1_error      : 20
2:16:11.732060 INFO: ms2_error      : 10.0
2:16:11.732148 INFO: fwhm_rt        : 3.0
2:16:11.732221 INFO: quant_window   : 3
2:16:11.732284 INFO: ==============================================
2:16:20.418307 INFO: performing precursor FDR with 40 features
2:16:20.418433 INFO: Decoy channel: -1
2:16:20.418464 INFO: competitive: True
2:16:20.929850 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:21.757421 INFO: Estimating optimal hyperparameters - samples: 1,212,479, batch_size: 4,096, learning_rate: 1.00e-03
2:16:21.760121 INFO: Using random state 786845 for train-test-split
2:16:42.273435 INFO: Test AUC: 0.601
2:16:42.273584 INFO: Train AUC: 0.607
2:16:42.273623 INFO: AUC difference: 1.03%
2:16:43.112374 INFO: Resetting torch num_threads to 32
2:16:43.173664 PROGRESS: === Extracted 1515599 precursors and 7721354 fragments ===
2:16:43.174169 INFO: === FDR correction performed with classifier version 8 ===
2:16:43.175184 PROGRESS: ============================= Precursor FDR =============================
2:16:43.175282 PROGRESS: Total precursors accumulated: 2,432
2:16:43.175350 PROGRESS: Target precursors: 2,408 (99.01%)
2:16:43.175410 PROGRESS: Decoy precursors: 24 (0.99%)
2:16:43.175462 PROGRESS: 
2:16:43.175514 PROGRESS: Precursor Summary:
2:16:43.177154 PROGRESS: Channel   0:	 0.050 FDR: 2,408; 0.010 FDR: 2,408; 0.001 FDR: 1,348
2:16:43.177261 PROGRESS: 
2:16:43.177330 PROGRESS: Protein Summary:
2:16:43.179533 PROGRESS: Channel   0:	 0.050 FDR: 1,907; 0.010 FDR: 1,907; 0.001 FDR: 1,125
2:16:43.179636 PROGRESS: =========================================================================
2:16:43.218048 INFO: Target number of precursors reached.
2:16:44.212472 INFO: fragments_df: keeping 5000 of 7721354 [sum(precursor_idx_mask)=57108 sum(mass_error_mask)=7721354 stop_rank=5000
2:16:44.777783 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:16:45.169376 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:16:46.156740 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:16:46.157280 INFO: Using score_cutoff 10.264249248218535 (fac=0.99, q=1)
2:16:46.157623 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:16:46.157712 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:16:46.157774 INFO: Updating optimization_manager: score_cutoff        : 13.036643642807007 -> 10.264249248218535
2:16:46.157836 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:16:46.324231 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:16:46.841597 INFO: === checking if optimization conditions were reached ===
2:16:46.844470 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:16:46.844601 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
2:16:46.845124 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:16:46.845416 INFO: ==============================================
2:16:46.845706 INFO: Starting optimization step 10.
2:16:46.845837 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:16:46.845917 INFO: Using rust extraction backend
2:16:46.845991 PROGRESS: Extracting batch of 252182 precursors
2:16:47.341759 INFO: === Search parameters used ===
2:16:47.342032 INFO: rt_error       : 805.6002197265625
2:16:47.342107 INFO: mobility_error : 0.1
2:16:47.342162 INFO: num_candidates : 3
2:16:47.342213 INFO: ms1_error      : 20
2:16:47.342273 INFO: ms2_error      : 10.0
2:16:47.342324 INFO: fwhm_rt        : 3.0
2:16:47.342370 INFO: quant_window   : 3
2:16:47.342416 INFO: ==============================================
2:16:51.596661 INFO: performing precursor FDR with 40 features
2:16:51.596791 INFO: Decoy channel: -1
2:16:51.596819 INFO: competitive: True
2:16:51.839021 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:52.196813 INFO: Estimating optimal hyperparameters - samples: 603,795, batch_size: 2,473, learning_rate: 7.77e-04
2:16:52.198037 INFO: Using random state 883123 for train-test-split
2:17:02.756198 INFO: Test AUC: 0.602
2:17:02.756366 INFO: Train AUC: 0.614
2:17:02.756406 INFO: AUC difference: 1.93%
2:17:03.342033 INFO: Resetting torch num_threads to 32
2:17:03.373804 PROGRESS: === Extracted 754744 precursors and 3844651 fragments ===
2:17:03.374293 INFO: === FDR correction performed with classifier version 9 ===
2:17:03.375000 PROGRESS: ============================= Precursor FDR =============================
2:17:03.375100 PROGRESS: Total precursors accumulated: 1,339
2:17:03.375169 PROGRESS: Target precursors: 1,326 (99.03%)
2:17:03.375231 PROGRESS: Decoy precursors: 13 (0.97%)
2:17:03.375283 PROGRESS: 
2:17:03.375332 PROGRESS: Precursor Summary:
2:17:03.376687 PROGRESS: Channel   0:	 0.050 FDR: 1,326; 0.010 FDR: 1,326; 0.001 FDR:   774
2:17:03.376795 PROGRESS: 
2:17:03.376858 PROGRESS: Protein Summary:
2:17:03.378594 PROGRESS: Channel   0:	 0.050 FDR: 1,154; 0.010 FDR: 1,154; 0.001 FDR:   690
2:17:03.378697 PROGRESS: =========================================================================
2:17:03.396224 INFO: Target number of precursors reached.
2:17:03.872808 INFO: fragments_df: keeping 5000 of 3844651 [sum(precursor_idx_mask)=31256 sum(mass_error_mask)=3844651 stop_rank=5000
2:17:04.438044 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:17:04.695480 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:17:05.576724 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:17:05.577293 INFO: Using score_cutoff 10.249930665493011 (fac=0.99, q=1)
2:17:05.577743 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:17:05.577855 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:17:05.577925 INFO: Updating optimization_manager: score_cutoff        : 10.264249248218535 -> 10.249930665493011
2:17:05.577994 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:17:05.738925 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:17:06.341448 INFO: === checking if optimization conditions were reached ===
2:17:06.344106 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:17:06.344236 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
2:17:06.344325 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:17:06.344402 INFO: ==============================================
2:17:06.344490 INFO: Starting optimization step 11.
2:17:06.344570 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:17:06.344671 INFO: Using rust extraction backend
2:17:06.344754 PROGRESS: Extracting batch of 252182 precursors
2:17:06.824882 INFO: === Search parameters used ===
2:17:06.825210 INFO: rt_error       : 805.6002197265625
2:17:06.825326 INFO: mobility_error : 0.1
2:17:06.825439 INFO: num_candidates : 3
2:17:06.825532 INFO: ms1_error      : 20
2:17:06.825613 INFO: ms2_error      : 10.0
2:17:06.825682 INFO: fwhm_rt        : 3.0
2:17:06.825741 INFO: quant_window   : 3
2:17:06.825805 INFO: ==============================================
2:17:11.017684 INFO: performing precursor FDR with 40 features
2:17:11.017808 INFO: Decoy channel: -1
2:17:11.017837 INFO: competitive: True
2:17:11.285386 INFO: Setting torch num_threads to 2 for FDR classification task
2:17:11.689698 INFO: Estimating optimal hyperparameters - samples: 603,801, batch_size: 2,473, learning_rate: 7.77e-04
2:17:11.690980 INFO: Using random state 360991 for train-test-split
2:17:26.925424 INFO: Test AUC: 0.606
2:17:26.925562 INFO: Train AUC: 0.616
2:17:26.925598 INFO: AUC difference: 1.74%
2:17:27.505512 INFO: Resetting torch num_threads to 32
2:17:27.554670 PROGRESS: === Extracted 754752 precursors and 3845152 fragments ===
2:17:27.555286 INFO: === FDR correction performed with classifier version 10 ===
2:17:27.556396 PROGRESS: ============================= Precursor FDR =============================
2:17:27.556552 PROGRESS: Total precursors accumulated: 1,276
2:17:27.556649 PROGRESS: Target precursors: 1,264 (99.06%)
2:17:27.556726 PROGRESS: Decoy precursors: 12 (0.94%)
2:17:27.556792 PROGRESS: 
2:17:27.556859 PROGRESS: Precursor Summary:
2:17:27.558825 PROGRESS: Channel   0:	 0.050 FDR: 1,264; 0.010 FDR: 1,264; 0.001 FDR: 1,137
2:17:27.558964 PROGRESS: 
2:17:27.559033 PROGRESS: Protein Summary:
2:17:27.561397 PROGRESS: Channel   0:	 0.050 FDR: 1,107; 0.010 FDR: 1,107; 0.001 FDR: 1,003
2:17:27.561533 PROGRESS: =========================================================================
2:17:27.594092 INFO: Target number of precursors reached.
2:17:28.083695 INFO: fragments_df: keeping 5000 of 3845152 [sum(precursor_idx_mask)=29806 sum(mass_error_mask)=3845152 stop_rank=5000
2:17:28.624643 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:17:28.895523 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:17:29.765627 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:17:29.766338 INFO: Using score_cutoff 9.665368821716308 (fac=0.99, q=1)
2:17:29.766872 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:17:29.766983 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:17:29.767055 INFO: Updating optimization_manager: score_cutoff        : 10.249930665493011 -> 9.665368821716308
2:17:29.767130 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:17:29.924310 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:17:30.359603 INFO: === checking if optimization conditions were reached ===
2:17:30.362319 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:17:30.362464 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
2:17:30.362560 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:17:30.362645 INFO: ==============================================
2:17:30.362740 INFO: Starting optimization step 12.
2:17:30.362827 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:17:30.362929 INFO: Using rust extraction backend
2:17:30.363015 PROGRESS: Extracting batch of 252182 precursors
2:17:30.852568 INFO: === Search parameters used ===
2:17:30.852942 INFO: rt_error       : 805.6002197265625
2:17:30.853073 INFO: mobility_error : 0.1
2:17:30.853173 INFO: num_candidates : 3
2:17:30.853266 INFO: ms1_error      : 20
2:17:30.853344 INFO: ms2_error      : 10.0
2:17:30.853417 INFO: fwhm_rt        : 3.0
2:17:30.853495 INFO: quant_window   : 3
2:17:30.853578 INFO: ==============================================
2:17:34.957726 INFO: performing precursor FDR with 40 features
2:17:34.957904 INFO: Decoy channel: -1
2:17:34.957947 INFO: competitive: True
2:17:35.228824 INFO: Setting torch num_threads to 2 for FDR classification task
2:17:35.595214 INFO: Estimating optimal hyperparameters - samples: 603,803, batch_size: 2,473, learning_rate: 7.77e-04
2:17:35.596466 INFO: Using random state 313031 for train-test-split
2:17:50.970431 INFO: Test AUC: 0.607
2:17:50.970623 INFO: Train AUC: 0.620
2:17:50.970660 INFO: AUC difference: 2.15%
2:17:51.554991 INFO: Resetting torch num_threads to 32
2:17:51.589859 PROGRESS: === Extracted 754754 precursors and 3844972 fragments ===
2:17:51.590584 INFO: === FDR correction performed with classifier version 11 ===
2:17:51.591789 PROGRESS: ============================= Precursor FDR =============================
2:17:51.591926 PROGRESS: Total precursors accumulated: 1,376
2:17:51.592037 PROGRESS: Target precursors: 1,363 (99.06%)
2:17:51.592141 PROGRESS: Decoy precursors: 13 (0.94%)
2:17:51.592236 PROGRESS: 
2:17:51.592332 PROGRESS: Precursor Summary:
2:17:51.595064 PROGRESS: Channel   0:	 0.050 FDR: 1,363; 0.010 FDR: 1,363; 0.001 FDR: 1,094
2:17:51.595205 PROGRESS: 
2:17:51.595300 PROGRESS: Protein Summary:
2:17:51.598413 PROGRESS: Channel   0:	 0.050 FDR: 1,193; 0.010 FDR: 1,193; 0.001 FDR:   963
2:17:51.598553 PROGRESS: =========================================================================
2:17:51.626276 INFO: Target number of precursors reached.
2:17:52.064792 INFO: fragments_df: keeping 5000 of 3844972 [sum(precursor_idx_mask)=31791 sum(mass_error_mask)=3844972 stop_rank=5000
2:17:52.558449 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:17:52.846148 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:17:53.690519 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:17:53.691243 INFO: Using score_cutoff 8.473456315612793 (fac=0.99, q=1)
2:17:53.691674 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:17:53.691765 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:17:53.691823 INFO: Updating optimization_manager: score_cutoff        : 9.665368821716308 -> 8.473456315612793
2:17:53.691887 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:17:53.848228 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:17:54.239753 INFO: === checking if optimization conditions were reached ===
2:17:54.242417 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:17:54.242554 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
2:17:54.242640 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:17:54.242719 INFO: ==============================================
2:17:54.242808 PROGRESS: Optimization finished for ms2_error.
2:17:54.742803 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:17:54.903461 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:17:55.300263 INFO: Starting optimization step 0.
2:17:55.300647 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:17:55.300808 INFO: Using rust extraction backend
2:17:55.300938 PROGRESS: Extracting batch of 252182 precursors
2:17:55.779752 INFO: === Search parameters used ===
2:17:55.780068 INFO: rt_error       : 805.6002197265625
2:17:55.780151 INFO: mobility_error : 0.1
2:17:55.780211 INFO: num_candidates : 3
2:17:55.780265 INFO: ms1_error      : 20
2:17:55.780314 INFO: ms2_error      : 10.0
2:17:55.780363 INFO: fwhm_rt        : 3.0
2:17:55.780411 INFO: quant_window   : 3
2:17:55.780458 INFO: ==============================================
2:17:59.697345 INFO: performing precursor FDR with 40 features
2:17:59.697495 INFO: Decoy channel: -1
2:17:59.697522 INFO: competitive: True
2:17:59.913095 INFO: Setting torch num_threads to 2 for FDR classification task
2:18:00.258313 INFO: Estimating optimal hyperparameters - samples: 603,801, batch_size: 2,473, learning_rate: 7.77e-04
2:18:00.259510 INFO: Using random state 409839 for train-test-split
2:18:15.001034 INFO: Test AUC: 0.605
2:18:15.001224 INFO: Train AUC: 0.622
2:18:15.001261 INFO: AUC difference: 2.86%
2:18:15.481317 INFO: Resetting torch num_threads to 32
2:18:15.513941 PROGRESS: === Extracted 754752 precursors and 3844948 fragments ===
2:18:15.514444 INFO: === FDR correction performed with classifier version 12 ===
2:18:15.515159 PROGRESS: ============================= Precursor FDR =============================
2:18:15.515261 PROGRESS: Total precursors accumulated: 1,398
2:18:15.515331 PROGRESS: Target precursors: 1,385 (99.07%)
2:18:15.515389 PROGRESS: Decoy precursors: 13 (0.93%)
2:18:15.515441 PROGRESS: 
2:18:15.515492 PROGRESS: Precursor Summary:
2:18:15.516876 PROGRESS: Channel   0:	 0.050 FDR: 1,385; 0.010 FDR: 1,385; 0.001 FDR: 1,088
2:18:15.516983 PROGRESS: 
2:18:15.517056 PROGRESS: Protein Summary:
2:18:15.518830 PROGRESS: Channel   0:	 0.050 FDR: 1,208; 0.010 FDR: 1,208; 0.001 FDR:   962
2:18:15.518927 PROGRESS: =========================================================================
2:18:15.536273 INFO: Target number of precursors reached.
2:18:15.975570 INFO: fragments_df: keeping 5000 of 3844948 [sum(precursor_idx_mask)=32231 sum(mass_error_mask)=3844948 stop_rank=5000
2:18:16.466641 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:18:16.713457 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:18:17.463663 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:18:17.464284 INFO: Using score_cutoff 7.302084202194213 (fac=0.99, q=1)
2:18:17.464706 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:18:17.464796 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:18:17.464857 INFO: Updating optimization_manager: score_cutoff        : 8.473456315612793 -> 7.302084202194213
2:18:17.464931 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:18:17.623141 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:18:18.014726 INFO: === checking if optimization conditions were reached ===
2:18:18.015016 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:18:18.018280 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 734.4994998035329
2:18:18.018461 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 734.4995.
2:18:18.018551 INFO: ==============================================
2:18:18.018651 INFO: Starting optimization step 1.
2:18:18.018727 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:18:18.018826 INFO: Using rust extraction backend
2:18:18.018912 PROGRESS: Extracting batch of 252182 precursors
2:18:18.492261 INFO: === Search parameters used ===
2:18:18.492559 INFO: rt_error       : 734.4994998035329
2:18:18.492656 INFO: mobility_error : 0.1
2:18:18.492722 INFO: num_candidates : 3
2:18:18.492779 INFO: ms1_error      : 20
2:18:18.492833 INFO: ms2_error      : 10.0
2:18:18.492888 INFO: fwhm_rt        : 3.0
2:18:18.492940 INFO: quant_window   : 3
2:18:18.492991 INFO: ==============================================
2:18:22.528758 INFO: performing precursor FDR with 40 features
2:18:22.528879 INFO: Decoy channel: -1
2:18:22.528908 INFO: competitive: True
2:18:22.773714 INFO: Setting torch num_threads to 2 for FDR classification task
2:18:23.120965 INFO: Estimating optimal hyperparameters - samples: 603,836, batch_size: 2,473, learning_rate: 7.77e-04
2:18:23.122511 INFO: Using random state 409839 for train-test-split
2:18:38.046251 INFO: Test AUC: 0.609
2:18:38.046406 INFO: Train AUC: 0.622
2:18:38.046442 INFO: AUC difference: 2.18%
2:18:38.564480 INFO: Resetting torch num_threads to 32
2:18:38.596597 PROGRESS: === Extracted 754796 precursors and 3845409 fragments ===
2:18:38.597107 INFO: === FDR correction performed with classifier version 12 ===
2:18:38.597826 PROGRESS: ============================= Precursor FDR =============================
2:18:38.597926 PROGRESS: Total precursors accumulated: 1,367
2:18:38.597995 PROGRESS: Target precursors: 1,354 (99.05%)
2:18:38.598053 PROGRESS: Decoy precursors: 13 (0.95%)
2:18:38.598108 PROGRESS: 
2:18:38.598159 PROGRESS: Precursor Summary:
2:18:38.599537 PROGRESS: Channel   0:	 0.050 FDR: 1,354; 0.010 FDR: 1,354; 0.001 FDR: 1,085
2:18:38.599644 PROGRESS: 
2:18:38.599707 PROGRESS: Protein Summary:
2:18:38.601460 PROGRESS: Channel   0:	 0.050 FDR: 1,182; 0.010 FDR: 1,182; 0.001 FDR:   954
2:18:38.601564 PROGRESS: =========================================================================
2:18:38.619189 INFO: Target number of precursors reached.
2:18:39.093986 INFO: fragments_df: keeping 5000 of 3845409 [sum(precursor_idx_mask)=31791 sum(mass_error_mask)=3845409 stop_rank=5000
2:18:39.607703 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:18:39.879356 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:18:40.704423 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:18:40.704938 INFO: Using score_cutoff 10.120435711097718 (fac=0.99, q=1)
2:18:40.705295 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:18:40.705384 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:18:40.705443 INFO: Updating optimization_manager: score_cutoff        : 7.302084202194213 -> 10.120435711097718
2:18:40.705504 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:18:40.860939 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:18:41.248670 INFO: === checking if optimization conditions were reached ===
2:18:41.248945 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:18:41.252054 INFO: Updating optimization_manager: rt_error            : 734.4994998035329 -> 657.7364130018906
2:18:41.252199 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 657.7364.
2:18:41.252283 INFO: ==============================================
2:18:41.252375 INFO: Starting optimization step 2.
2:18:41.252449 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:18:41.252529 INFO: Using rust extraction backend
2:18:41.252604 PROGRESS: Extracting batch of 252182 precursors
2:18:41.721892 INFO: === Search parameters used ===
2:18:41.722222 INFO: rt_error       : 657.7364130018906
2:18:41.722305 INFO: mobility_error : 0.1
2:18:41.722376 INFO: num_candidates : 3
2:18:41.722433 INFO: ms1_error      : 20
2:18:41.722488 INFO: ms2_error      : 10.0
2:18:41.722541 INFO: fwhm_rt        : 3.0
2:18:41.722591 INFO: quant_window   : 3
2:18:41.722648 INFO: ==============================================
2:18:45.534100 INFO: performing precursor FDR with 40 features
2:18:45.534226 INFO: Decoy channel: -1
2:18:45.534256 INFO: competitive: True
2:18:45.760514 INFO: Setting torch num_threads to 2 for FDR classification task
2:18:46.112502 INFO: Estimating optimal hyperparameters - samples: 603,802, batch_size: 2,473, learning_rate: 7.77e-04
2:18:46.113755 INFO: Using random state 409839 for train-test-split
2:18:56.111700 INFO: Test AUC: 0.608
2:18:56.111863 INFO: Train AUC: 0.622
2:18:56.111899 INFO: AUC difference: 2.31%
2:18:56.617180 INFO: Resetting torch num_threads to 32
2:18:56.648033 PROGRESS: === Extracted 754753 precursors and 3837703 fragments ===
2:18:56.648532 INFO: === FDR correction performed with classifier version 12 ===
2:18:56.649256 PROGRESS: ============================= Precursor FDR =============================
2:18:56.649360 PROGRESS: Total precursors accumulated: 1,299
2:18:56.649431 PROGRESS: Target precursors: 1,287 (99.08%)
2:18:56.649492 PROGRESS: Decoy precursors: 12 (0.92%)
2:18:56.649557 PROGRESS: 
2:18:56.649610 PROGRESS: Precursor Summary:
2:18:56.650936 PROGRESS: Channel   0:	 0.050 FDR: 1,287; 0.010 FDR: 1,287; 0.001 FDR:   975
2:18:56.651037 PROGRESS: 
2:18:56.651101 PROGRESS: Protein Summary:
2:18:56.652851 PROGRESS: Channel   0:	 0.050 FDR: 1,132; 0.010 FDR: 1,132; 0.001 FDR:   863
2:18:56.652958 PROGRESS: =========================================================================
2:18:56.712934 INFO: Target number of precursors reached.
2:18:57.213771 INFO: fragments_df: keeping 5000 of 3837703 [sum(precursor_idx_mask)=30037 sum(mass_error_mask)=3837703 stop_rank=5000
2:18:57.732806 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:18:57.946232 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:18:58.800394 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:18:58.801087 INFO: Using score_cutoff 7.306781522655487 (fac=0.99, q=1)
2:18:58.801581 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:18:58.801693 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:18:58.801765 INFO: Updating optimization_manager: score_cutoff        : 10.120435711097718 -> 7.306781522655487
2:18:58.801842 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:18:58.959121 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:18:59.410078 INFO: === checking if optimization conditions were reached ===
2:18:59.410383 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:18:59.414214 INFO: Updating optimization_manager: rt_error            : 657.7364130018906 -> 601.9358529040303
2:18:59.414356 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 601.9359.
2:18:59.414471 INFO: ==============================================
2:18:59.414613 INFO: Starting optimization step 3.
2:18:59.414731 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:18:59.414873 INFO: Using rust extraction backend
2:18:59.415007 PROGRESS: Extracting batch of 252182 precursors
2:18:59.891666 INFO: === Search parameters used ===
2:18:59.891947 INFO: rt_error       : 601.9358529040303
2:18:59.892025 INFO: mobility_error : 0.1
2:18:59.892079 INFO: num_candidates : 3
2:18:59.892130 INFO: ms1_error      : 20
2:18:59.892174 INFO: ms2_error      : 10.0
2:18:59.892218 INFO: fwhm_rt        : 3.0
2:18:59.892261 INFO: quant_window   : 3
2:18:59.892303 INFO: ==============================================
2:19:03.259648 INFO: performing precursor FDR with 40 features
2:19:03.259773 INFO: Decoy channel: -1
2:19:03.259801 INFO: competitive: True
2:19:03.481986 INFO: Setting torch num_threads to 2 for FDR classification task
2:19:03.804685 INFO: Estimating optimal hyperparameters - samples: 603,852, batch_size: 2,473, learning_rate: 7.77e-04
2:19:03.805653 INFO: Using random state 409839 for train-test-split
2:19:17.448859 INFO: Test AUC: 0.605
2:19:17.449042 INFO: Train AUC: 0.623
2:19:17.449084 INFO: AUC difference: 2.93%
2:19:17.996585 INFO: Resetting torch num_threads to 32
2:19:18.039112 PROGRESS: === Extracted 754816 precursors and 3842871 fragments ===
2:19:18.039623 INFO: === FDR correction performed with classifier version 12 ===
2:19:18.040344 PROGRESS: ============================= Precursor FDR =============================
2:19:18.040447 PROGRESS: Total precursors accumulated: 1,343
2:19:18.040529 PROGRESS: Target precursors: 1,330 (99.03%)
2:19:18.040591 PROGRESS: Decoy precursors: 13 (0.97%)
2:19:18.040659 PROGRESS: 
2:19:18.040711 PROGRESS: Precursor Summary:
2:19:18.042043 PROGRESS: Channel   0:	 0.050 FDR: 1,330; 0.010 FDR: 1,330; 0.001 FDR:   822
2:19:18.042145 PROGRESS: 
2:19:18.042206 PROGRESS: Protein Summary:
2:19:18.043917 PROGRESS: Channel   0:	 0.050 FDR: 1,159; 0.010 FDR: 1,159; 0.001 FDR:   730
2:19:18.044020 PROGRESS: =========================================================================
2:19:18.061187 INFO: Target number of precursors reached.
2:19:18.593276 INFO: fragments_df: keeping 5000 of 3842871 [sum(precursor_idx_mask)=31626 sum(mass_error_mask)=3842871 stop_rank=5000
2:19:19.135510 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:19:19.414747 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:19:20.149912 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:19:20.150389 INFO: Using score_cutoff 11.457096752643587 (fac=0.99, q=1)
2:19:20.150743 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:19:20.150829 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:19:20.150890 INFO: Updating optimization_manager: score_cutoff        : 7.306781522655487 -> 11.457096752643587
2:19:20.150952 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:19:20.303889 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:19:20.678967 INFO: === checking if optimization conditions were reached ===
2:19:20.679245 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:19:20.682481 INFO: Updating optimization_manager: rt_error            : 601.9358529040303 -> 400.718420399725
2:19:20.682614 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 400.7184.
2:19:20.682699 INFO: ==============================================
2:19:20.682797 INFO: Starting optimization step 4.
2:19:20.682877 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:19:20.682974 INFO: Using rust extraction backend
2:19:20.683070 PROGRESS: Extracting batch of 252182 precursors
2:19:21.149069 INFO: === Search parameters used ===
2:19:21.149335 INFO: rt_error       : 400.718420399725
2:19:21.149402 INFO: mobility_error : 0.1
2:19:21.149456 INFO: num_candidates : 3
2:19:21.149507 INFO: ms1_error      : 20
2:19:21.149557 INFO: ms2_error      : 10.0
2:19:21.149603 INFO: fwhm_rt        : 3.0
2:19:21.149651 INFO: quant_window   : 3
2:19:21.149698 INFO: ==============================================
2:19:24.533378 INFO: performing precursor FDR with 40 features
2:19:24.533537 INFO: Decoy channel: -1
2:19:24.533571 INFO: competitive: True
2:19:24.742646 INFO: Setting torch num_threads to 2 for FDR classification task
2:19:25.109973 INFO: Estimating optimal hyperparameters - samples: 603,001, batch_size: 2,469, learning_rate: 7.76e-04
2:19:25.111256 INFO: Using random state 409839 for train-test-split
2:19:39.935553 INFO: Test AUC: 0.606
2:19:39.935750 INFO: Train AUC: 0.620
2:19:39.935804 INFO: AUC difference: 2.15%
2:19:40.533340 INFO: Resetting torch num_threads to 32
2:19:40.584091 PROGRESS: === Extracted 753752 precursors and 3733176 fragments ===
2:19:40.584735 INFO: === FDR correction performed with classifier version 12 ===
2:19:40.585835 PROGRESS: ============================= Precursor FDR =============================
2:19:40.585984 PROGRESS: Total precursors accumulated: 1,340
2:19:40.586064 PROGRESS: Target precursors: 1,327 (99.03%)
2:19:40.586131 PROGRESS: Decoy precursors: 13 (0.97%)
2:19:40.586195 PROGRESS: 
2:19:40.586256 PROGRESS: Precursor Summary:
2:19:40.588162 PROGRESS: Channel   0:	 0.050 FDR: 1,327; 0.010 FDR: 1,327; 0.001 FDR: 1,074
2:19:40.588291 PROGRESS: 
2:19:40.588363 PROGRESS: Protein Summary:
2:19:40.590708 PROGRESS: Channel   0:	 0.050 FDR: 1,157; 0.010 FDR: 1,157; 0.001 FDR:   951
2:19:40.590841 PROGRESS: =========================================================================
2:19:40.621212 INFO: Target number of precursors reached.
2:19:41.107281 INFO: fragments_df: keeping 5000 of 3733176 [sum(precursor_idx_mask)=31216 sum(mass_error_mask)=3733176 stop_rank=5000
2:19:41.689541 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:19:41.927465 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:19:42.781004 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:19:42.781619 INFO: Using score_cutoff 10.896404047393798 (fac=0.99, q=1)
2:19:42.782097 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:19:42.782218 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:19:42.782316 INFO: Updating optimization_manager: score_cutoff        : 11.457096752643587 -> 10.896404047393798
2:19:42.782416 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:19:42.945367 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:19:43.346642 INFO: === checking if optimization conditions were reached ===
2:19:43.346961 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:19:43.350167 INFO: Updating optimization_manager: rt_error            : 400.718420399725 -> 412.54699544019405
2:19:43.350287 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 412.5470.
2:19:43.350367 INFO: ==============================================
2:19:43.350456 INFO: Starting optimization step 5.
2:19:43.350529 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:19:43.350608 INFO: Using rust extraction backend
2:19:43.350679 PROGRESS: Extracting batch of 252182 precursors
2:19:43.827628 INFO: === Search parameters used ===
2:19:43.827890 INFO: rt_error       : 412.54699544019405
2:19:43.827963 INFO: mobility_error : 0.1
2:19:43.828017 INFO: num_candidates : 3
2:19:43.828068 INFO: ms1_error      : 20
2:19:43.828116 INFO: ms2_error      : 10.0
2:19:43.828163 INFO: fwhm_rt        : 3.0
2:19:43.828208 INFO: quant_window   : 3
2:19:43.828250 INFO: ==============================================
2:19:46.919381 INFO: performing precursor FDR with 40 features
2:19:46.919534 INFO: Decoy channel: -1
2:19:46.919563 INFO: competitive: True
2:19:47.143822 INFO: Setting torch num_threads to 2 for FDR classification task
2:19:47.467171 INFO: Estimating optimal hyperparameters - samples: 603,051, batch_size: 2,470, learning_rate: 7.77e-04
2:19:47.468361 INFO: Using random state 409839 for train-test-split
2:20:00.509225 INFO: Test AUC: 0.606
2:20:00.509409 INFO: Train AUC: 0.619
2:20:00.509445 INFO: AUC difference: 2.02%
2:20:01.024064 INFO: Resetting torch num_threads to 32
2:20:01.055112 PROGRESS: === Extracted 753814 precursors and 3742559 fragments ===
2:20:01.055707 INFO: === FDR correction performed with classifier version 12 ===
2:20:01.056390 PROGRESS: ============================= Precursor FDR =============================
2:20:01.056493 PROGRESS: Total precursors accumulated: 1,365
2:20:01.056558 PROGRESS: Target precursors: 1,352 (99.05%)
2:20:01.056644 PROGRESS: Decoy precursors: 13 (0.95%)
2:20:01.056713 PROGRESS: 
2:20:01.056762 PROGRESS: Precursor Summary:
2:20:01.058136 PROGRESS: Channel   0:	 0.050 FDR: 1,352; 0.010 FDR: 1,352; 0.001 FDR: 1,058
2:20:01.058234 PROGRESS: 
2:20:01.058293 PROGRESS: Protein Summary:
2:20:01.060121 PROGRESS: Channel   0:	 0.050 FDR: 1,177; 0.010 FDR: 1,177; 0.001 FDR:   937
2:20:01.060217 PROGRESS: =========================================================================
2:20:01.076560 INFO: Target number of precursors reached.
2:20:01.473160 INFO: fragments_df: keeping 5000 of 3742559 [sum(precursor_idx_mask)=31715 sum(mass_error_mask)=3742559 stop_rank=5000
2:20:01.954494 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:20:02.183965 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:20:02.921020 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:20:02.921509 INFO: Using score_cutoff 11.097238414478303 (fac=0.99, q=1)
2:20:02.921840 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:20:02.921920 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:20:02.921980 INFO: Updating optimization_manager: score_cutoff        : 10.896404047393798 -> 11.097238414478303
2:20:02.922042 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:20:03.076994 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:20:03.513560 INFO: === checking if optimization conditions were reached ===
2:20:03.513909 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:20:03.515059 INFO: Updating optimization_manager: rt_error            : 412.54699544019405 -> 805.6002197265625
2:20:03.515212 INFO: Updating optimization_manager: classifier_version  : 12 -> 13
2:20:03.515335 INFO: Updating optimization_manager: score_cutoff        : 11.097238414478303 -> 7.302084202194213
2:20:03.515443 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:20:03.515546 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:20:03.515658 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 805.6002 found after 6 searches.
2:20:03.515736 INFO: ==============================================
2:20:03.515826 PROGRESS: Optimization finished for rt_error.
2:20:03.959872 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:20:04.111519 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:20:05.504002 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:20:05.504343 PROGRESS: ==============================================
2:20:05.504431 PROGRESS: ms2_error      : 10.0000
2:20:05.504503 PROGRESS: rt_error       : 805.6002
2:20:05.504578 PROGRESS: ==============================================
2:20:05.507251 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:20:15.532647 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:20:49.531410 INFO: Using rust extraction backend
2:20:49.531915 PROGRESS: Extracting batch of 15081856 precursors
2:21:16.712568 INFO: === Search parameters used ===
2:21:16.713005 INFO: rt_error       : 805.6002197265625
2:21:16.713089 INFO: mobility_error : 0.1
2:21:16.713155 INFO: num_candidates : 3
2:21:16.713211 INFO: ms1_error      : 20
2:21:16.713270 INFO: ms2_error      : 10.0
2:21:16.713327 INFO: fwhm_rt        : 3.0
2:21:16.713383 INFO: quant_window   : 3
2:21:16.713434 INFO: ==============================================
2:22:51.001767 INFO: Removed 3210437 precursors with score below cutoff 7.302084202194213
2:23:37.604213 INFO: performing precursor FDR with 40 features
2:23:37.604403 INFO: Decoy channel: -1
2:23:37.604438 INFO: competitive: True
2:23:42.663915 INFO: Setting torch num_threads to 2 for FDR classification task
2:24:06.757320 INFO: Estimating optimal hyperparameters - samples: 33,627,761, batch_size: 4,096, learning_rate: 1.00e-03
2:24:06.873155 INFO: Using random state 2211 for train-test-split
2:40:00.604837 INFO: Test AUC: 0.615
2:40:00.605135 INFO: Train AUC: 0.615
2:40:00.605212 INFO: AUC difference: 0.09%
2:40:09.548635 INFO: Resetting torch num_threads to 32
2:40:12.583786 PROGRESS: ============================= Precursor FDR =============================
2:40:12.584132 PROGRESS: Total precursors accumulated: 87,899
2:40:12.584214 PROGRESS: Target precursors: 87,029 (99.01%)
2:40:12.584276 PROGRESS: Decoy precursors: 870 (0.99%)
2:40:12.584330 PROGRESS: 
2:40:12.584382 PROGRESS: Precursor Summary:
2:40:12.614614 PROGRESS: Channel   0:	 0.050 FDR: 87,029; 0.010 FDR: 87,029; 0.001 FDR: 55,500
2:40:12.614846 PROGRESS: 
2:40:12.614914 PROGRESS: Protein Summary:
2:40:12.655783 PROGRESS: Channel   0:	 0.050 FDR: 12,148; 0.010 FDR: 12,148; 0.001 FDR: 8,706
2:40:12.655999 PROGRESS: =========================================================================
2:40:12.999666 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/psm.parquet
2:40:13.176976 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.parquet
2:40:13.427505 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:40:14.149220 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 
2:40:14.149381 INFO: Quantification results path: /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant
2:40:14.149450 INFO: Creating folder /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/figures
2:40:14.149637 INFO: Initializing TimingManager
2:40:14.150120 INFO: Initializing RawFileManager
2:41:12.231905 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.
2:41:12.241616 INFO: Determining DIA cycle
2:41:12.262514 INFO: Found cycle with start 0.00 min and length 300.
2:41:12.466788 INFO: RT (min)            : 0.0 - 26.9
2:41:12.466913 INFO: RT duration (sec)   : 1611.2
2:41:12.466949 INFO: RT duration (min)   : 26.9
2:41:12.466982 INFO: Cycle len (scans)   : 300
2:41:12.467010 INFO: Cycle len (sec)     : 1.65
2:41:12.467039 INFO: Number of cycles    : 978
2:41:12.467066 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:41:12.467130 INFO: Creating DIA data object took: 58.31690335273743
2:41:14.130364 INFO: Creating DIA data NG object took: 1.6630771160125732
2:41:16.138572 INFO: Initializing CalibrationManager
2:41:16.138906 INFO: Setting up calibration estimators ..
2:41:16.139006 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:41:16.139150 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'}' ..
2:41:16.139292 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:41:16.139381 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:41:16.139473 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}}' ..
2:41:16.139555 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:41:16.139627 INFO: Done setting up calibration estimators.
2:41:16.139938 INFO: Initializing OptimizationManager
2:41:16.140151 INFO: initial parameter: ms1_error = 20
2:41:16.140234 INFO: initial parameter: ms2_error = 20
2:41:16.140310 INFO: initial parameter: rt_error = 805.611083984375
2:41:16.140393 INFO: initial parameter: mobility_error = 0.1
2:41:16.140462 INFO: initial parameter: num_candidates = 1
2:41:16.140530 INFO: initial parameter: fwhm_rt = 5
2:41:16.140595 INFO: initial parameter: fwhm_mobility = 0.01
2:41:16.140678 INFO: initial parameter: score_cutoff = 0
2:41:16.140743 INFO: initial parameter: classifier_version = -1
2:41:16.140859 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:41:16.141249 INFO: FDRManager: loading saved state not requested, will be initialized.
2:41:16.141302 INFO: Initializing FDRManager
2:41:16.141354 INFO: Loading classifier store from /home/robbe/.pyenv/versions/3.11.11/envs/alphaida/lib/python3.11/site-packages/alphadia/constants/classifier
2:41:18.435813 PROGRESS: Initializing spectral library: 7,536,970 target precursors potentially observable (1,230,167 removed)
2:41:20.101423 INFO: Updating optimization_manager: ms2_error           : 20 -> 20
2:41:20.101857 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
2:41:20.101980 PROGRESS: Starting initial search for precursors.
2:41:20.102077 INFO: Starting optimization step 0.
2:41:20.102147 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:41:20.102233 INFO: Using rust extraction backend
2:41:20.102312 PROGRESS: Extracting batch of 1988 precursors
2:41:20.107543 INFO: === Search parameters used ===
2:41:20.107666 INFO: rt_error       : 805.611083984375
2:41:20.107727 INFO: mobility_error : 0.1
2:41:20.107778 INFO: num_candidates : 1
2:41:20.107826 INFO: ms1_error      : 20
2:41:20.107871 INFO: ms2_error      : 20
2:41:20.107915 INFO: fwhm_rt        : 5
2:41:20.107963 INFO: quant_window   : 3
2:41:20.108007 INFO: ==============================================
2:41:20.167031 INFO: performing precursor FDR with 40 features
2:41:20.167163 INFO: Decoy channel: -1
2:41:20.167206 INFO: competitive: True
2:41:20.169510 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:20.172900 INFO: Estimating optimal hyperparameters - samples: 1,581, batch_size: 128, learning_rate: 1.77e-04
2:41:20.174265 INFO: Using random state 509747 for train-test-split
2:41:20.352959 INFO: Test AUC: 0.527
2:41:20.353048 INFO: Train AUC: 0.516
2:41:20.353081 INFO: AUC difference: 2.03%
2:41:20.636693 INFO: Resetting torch num_threads to 32
2:41:20.638290 PROGRESS: === Extracted 1977 precursors and 9426 fragments ===
2:41:20.638665 INFO: === FDR correction performed with classifier version -1 ===
2:41:20.639149 PROGRESS: ============================= Precursor FDR =============================
2:41:20.639244 PROGRESS: Total precursors accumulated: 0
2:41:20.639308 PROGRESS: Target precursors: 0 (0.00%)
2:41:20.639365 PROGRESS: Decoy precursors: 0 (0.00%)
2:41:20.639415 PROGRESS: 
2:41:20.639467 PROGRESS: Precursor Summary:
2:41:20.639587 PROGRESS: 
2:41:20.639655 PROGRESS: Protein Summary:
2:41:20.639733 PROGRESS: =========================================================================
2:41:20.639962 INFO: Target number of precursors not reached yet.
2:41:20.757351 INFO: Starting optimization step 1.
2:41:20.757563 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:41:20.757663 INFO: Using rust extraction backend
2:41:20.757732 PROGRESS: Extracting batch of 3976 precursors
2:41:20.766782 INFO: === Search parameters used ===
2:41:20.766942 INFO: rt_error       : 805.611083984375
2:41:20.767001 INFO: mobility_error : 0.1
2:41:20.767052 INFO: num_candidates : 1
2:41:20.767099 INFO: ms1_error      : 20
2:41:20.767145 INFO: ms2_error      : 20
2:41:20.767189 INFO: fwhm_rt        : 5
2:41:20.767235 INFO: quant_window   : 3
2:41:20.767279 INFO: ==============================================
2:41:20.847358 INFO: performing precursor FDR with 40 features
2:41:20.847648 INFO: Decoy channel: -1
2:41:20.847682 INFO: competitive: True
2:41:20.854478 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:20.858102 INFO: Estimating optimal hyperparameters - samples: 4,739, batch_size: 128, learning_rate: 1.77e-04
2:41:20.858245 INFO: Using random state 93829 for train-test-split
2:41:21.310853 INFO: Test AUC: 0.530
2:41:21.310987 INFO: Train AUC: 0.551
2:41:21.311017 INFO: AUC difference: 3.81%
2:41:21.594690 INFO: Resetting torch num_threads to 32
2:41:21.599516 PROGRESS: === Extracted 5924 precursors and 28277 fragments ===
2:41:21.600090 INFO: === FDR correction performed with classifier version -1 ===
2:41:21.600711 PROGRESS: ============================= Precursor FDR =============================
2:41:21.600826 PROGRESS: Total precursors accumulated: 11
2:41:21.600906 PROGRESS: Target precursors: 11 (100.00%)
2:41:21.600974 PROGRESS: Decoy precursors: 0 (0.00%)
2:41:21.601038 PROGRESS: 
2:41:21.601101 PROGRESS: Precursor Summary:
2:41:21.602346 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
2:41:21.602449 PROGRESS: 
2:41:21.602528 PROGRESS: Protein Summary:
2:41:21.603873 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
2:41:21.603977 PROGRESS: =========================================================================
2:41:21.604655 INFO: Target number of precursors not reached yet.
2:41:21.759062 INFO: Starting optimization step 2.
2:41:21.759352 PROGRESS: === Extracting elution groups 3000 to 7000 ===
2:41:21.759444 INFO: Using rust extraction backend
2:41:21.759509 PROGRESS: Extracting batch of 7946 precursors
2:41:21.775417 INFO: === Search parameters used ===
2:41:21.775629 INFO: rt_error       : 805.611083984375
2:41:21.775697 INFO: mobility_error : 0.1
2:41:21.775761 INFO: num_candidates : 1
2:41:21.775818 INFO: ms1_error      : 20
2:41:21.775872 INFO: ms2_error      : 20
2:41:21.775925 INFO: fwhm_rt        : 5
2:41:21.775979 INFO: quant_window   : 3
2:41:21.776031 INFO: ==============================================
2:41:21.864273 INFO: performing precursor FDR with 40 features
2:41:21.864409 INFO: Decoy channel: -1
2:41:21.864437 INFO: competitive: True
2:41:21.871222 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:21.875262 INFO: Estimating optimal hyperparameters - samples: 11,047, batch_size: 128, learning_rate: 1.77e-04
2:41:21.875401 INFO: Using random state 311020 for train-test-split
2:41:23.005070 INFO: Test AUC: 0.534
2:41:23.005185 INFO: Train AUC: 0.576
2:41:23.005219 INFO: AUC difference: 7.20%
2:41:23.005243 WARNING: AUC difference > 5%. This may indicate overfitting.
2:41:23.307615 INFO: Resetting torch num_threads to 32
2:41:23.314503 PROGRESS: === Extracted 13809 precursors and 65688 fragments ===
2:41:23.315166 INFO: === FDR correction performed with classifier version -1 ===
2:41:23.315959 PROGRESS: ============================= Precursor FDR =============================
2:41:23.316088 PROGRESS: Total precursors accumulated: 31
2:41:23.316183 PROGRESS: Target precursors: 31 (100.00%)
2:41:23.316284 PROGRESS: Decoy precursors: 0 (0.00%)
2:41:23.316366 PROGRESS: 
2:41:23.316442 PROGRESS: Precursor Summary:
2:41:23.317926 PROGRESS: Channel   0:	 0.050 FDR:    31; 0.010 FDR:    31; 0.001 FDR:    31
2:41:23.318044 PROGRESS: 
2:41:23.318116 PROGRESS: Protein Summary:
2:41:23.319405 PROGRESS: Channel   0:	 0.050 FDR:    31; 0.010 FDR:    31; 0.001 FDR:    31
2:41:23.319504 PROGRESS: =========================================================================
2:41:23.319989 INFO: Target number of precursors not reached yet.
2:41:23.483217 INFO: Starting optimization step 3.
2:41:23.483443 PROGRESS: === Extracting elution groups 7000 to 15000 ===
2:41:23.483555 INFO: Using rust extraction backend
2:41:23.483640 PROGRESS: Extracting batch of 15879 precursors
2:41:23.514793 INFO: === Search parameters used ===
2:41:23.515150 INFO: rt_error       : 805.611083984375
2:41:23.515254 INFO: mobility_error : 0.1
2:41:23.515347 INFO: num_candidates : 1
2:41:23.515428 INFO: ms1_error      : 20
2:41:23.515507 INFO: ms2_error      : 20
2:41:23.515587 INFO: fwhm_rt        : 5
2:41:23.515663 INFO: quant_window   : 3
2:41:23.515749 INFO: ==============================================
2:41:23.686913 INFO: performing precursor FDR with 40 features
2:41:23.687056 INFO: Decoy channel: -1
2:41:23.687098 INFO: competitive: True
2:41:23.698421 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:23.705408 INFO: Estimating optimal hyperparameters - samples: 23,664, batch_size: 128, learning_rate: 1.77e-04
2:41:23.705590 INFO: Using random state 290647 for train-test-split
2:41:26.463648 INFO: Test AUC: 0.560
2:41:26.463803 INFO: Train AUC: 0.581
2:41:26.463835 INFO: AUC difference: 3.48%
2:41:26.794022 INFO: Resetting torch num_threads to 32
2:41:26.801479 PROGRESS: === Extracted 29581 precursors and 140327 fragments ===
2:41:26.802081 INFO: === FDR correction performed with classifier version -1 ===
2:41:26.802680 PROGRESS: ============================= Precursor FDR =============================
2:41:26.802776 PROGRESS: Total precursors accumulated: 53
2:41:26.802841 PROGRESS: Target precursors: 53 (100.00%)
2:41:26.802896 PROGRESS: Decoy precursors: 0 (0.00%)
2:41:26.802945 PROGRESS: 
2:41:26.802994 PROGRESS: Precursor Summary:
2:41:26.804111 PROGRESS: Channel   0:	 0.050 FDR:    53; 0.010 FDR:    53; 0.001 FDR:    53
2:41:26.804208 PROGRESS: 
2:41:26.804265 PROGRESS: Protein Summary:
2:41:26.805468 PROGRESS: Channel   0:	 0.050 FDR:    53; 0.010 FDR:    53; 0.001 FDR:    53
2:41:26.805566 PROGRESS: =========================================================================
2:41:26.806176 INFO: Target number of precursors not reached yet.
2:41:27.003252 INFO: Starting optimization step 4.
2:41:27.003518 PROGRESS: === Extracting elution groups 15000 to 31000 ===
2:41:27.003635 INFO: Using rust extraction backend
2:41:27.003731 PROGRESS: Extracting batch of 31750 precursors
2:41:27.065708 INFO: === Search parameters used ===
2:41:27.065999 INFO: rt_error       : 805.611083984375
2:41:27.066075 INFO: mobility_error : 0.1
2:41:27.066151 INFO: num_candidates : 1
2:41:27.066212 INFO: ms1_error      : 20
2:41:27.066270 INFO: ms2_error      : 20
2:41:27.066326 INFO: fwhm_rt        : 5
2:41:27.066385 INFO: quant_window   : 3
2:41:27.066439 INFO: ==============================================
2:41:27.400144 INFO: performing precursor FDR with 40 features
2:41:27.400265 INFO: Decoy channel: -1
2:41:27.400293 INFO: competitive: True
2:41:27.427463 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:27.445485 INFO: Estimating optimal hyperparameters - samples: 48,898, batch_size: 200, learning_rate: 2.21e-04
2:41:27.445759 INFO: Using random state 896918 for train-test-split
2:41:31.537294 INFO: Test AUC: 0.574
2:41:31.537407 INFO: Train AUC: 0.599
2:41:31.537439 INFO: AUC difference: 4.21%
2:41:31.848935 INFO: Resetting torch num_threads to 32
2:41:31.871864 PROGRESS: === Extracted 61123 precursors and 290798 fragments ===
2:41:31.872644 INFO: === FDR correction performed with classifier version -1 ===
2:41:31.873420 PROGRESS: ============================= Precursor FDR =============================
2:41:31.873534 PROGRESS: Total precursors accumulated: 0
2:41:31.873613 PROGRESS: Target precursors: 0 (0.00%)
2:41:31.873682 PROGRESS: Decoy precursors: 0 (0.00%)
2:41:31.873748 PROGRESS: 
2:41:31.873811 PROGRESS: Precursor Summary:
2:41:31.873959 PROGRESS: 
2:41:31.874037 PROGRESS: Protein Summary:
2:41:31.874131 PROGRESS: =========================================================================
2:41:31.876099 INFO: Target number of precursors not reached yet.
2:41:32.130002 INFO: Starting optimization step 5.
2:41:32.130247 PROGRESS: === Extracting elution groups 31000 to 63000 ===
2:41:32.130340 INFO: Using rust extraction backend
2:41:32.130411 PROGRESS: Extracting batch of 63536 precursors
2:41:32.247757 INFO: === Search parameters used ===
2:41:32.248035 INFO: rt_error       : 805.611083984375
2:41:32.248107 INFO: mobility_error : 0.1
2:41:32.248159 INFO: num_candidates : 1
2:41:32.248208 INFO: ms1_error      : 20
2:41:32.248253 INFO: ms2_error      : 20
2:41:32.248300 INFO: fwhm_rt        : 5
2:41:32.248349 INFO: quant_window   : 3
2:41:32.248394 INFO: ==============================================
2:41:32.869818 INFO: performing precursor FDR with 40 features
2:41:32.869941 INFO: Decoy channel: -1
2:41:32.869980 INFO: competitive: True
2:41:32.927788 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:32.970266 INFO: Estimating optimal hyperparameters - samples: 99,395, batch_size: 407, learning_rate: 3.15e-04
2:41:32.970703 INFO: Using random state 785587 for train-test-split
2:41:37.043385 INFO: Test AUC: 0.578
2:41:37.043540 INFO: Train AUC: 0.601
2:41:37.043592 INFO: AUC difference: 3.87%
2:41:37.409003 INFO: Resetting torch num_threads to 32
2:41:37.469984 PROGRESS: === Extracted 124244 precursors and 590595 fragments ===
2:41:37.470833 INFO: === FDR correction performed with classifier version -1 ===
2:41:37.471905 PROGRESS: ============================= Precursor FDR =============================
2:41:37.472089 PROGRESS: Total precursors accumulated: 310
2:41:37.472202 PROGRESS: Target precursors: 307 (99.03%)
2:41:37.472306 PROGRESS: Decoy precursors: 3 (0.97%)
2:41:37.472406 PROGRESS: 
2:41:37.472501 PROGRESS: Precursor Summary:
2:41:37.474237 PROGRESS: Channel   0:	 0.050 FDR:   307; 0.010 FDR:   307; 0.001 FDR:    66
2:41:37.474376 PROGRESS: 
2:41:37.474462 PROGRESS: Protein Summary:
2:41:37.476367 PROGRESS: Channel   0:	 0.050 FDR:   295; 0.010 FDR:   295; 0.001 FDR:    65
2:41:37.476514 PROGRESS: =========================================================================
2:41:37.480949 INFO: Target number of precursors not reached yet.
2:41:38.055054 INFO: Starting optimization step 6.
2:41:38.055347 PROGRESS: === Extracting elution groups 63000 to 127000 ===
2:41:38.055461 INFO: Using rust extraction backend
2:41:38.055533 PROGRESS: Extracting batch of 127107 precursors
2:41:38.286281 INFO: === Search parameters used ===
2:41:38.286658 INFO: rt_error       : 805.611083984375
2:41:38.286766 INFO: mobility_error : 0.1
2:41:38.286864 INFO: num_candidates : 1
2:41:38.286948 INFO: ms1_error      : 20
2:41:38.287015 INFO: ms2_error      : 20
2:41:38.287078 INFO: fwhm_rt        : 5
2:41:38.287137 INFO: quant_window   : 3
2:41:38.287200 INFO: ==============================================
2:41:39.638535 INFO: performing precursor FDR with 40 features
2:41:39.638776 INFO: Decoy channel: -1
2:41:39.638808 INFO: competitive: True
2:41:41.308189 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:41.395016 INFO: Estimating optimal hyperparameters - samples: 200,431, batch_size: 820, learning_rate: 4.47e-04
2:41:41.395528 INFO: Using random state 333082 for train-test-split
2:41:48.905977 INFO: Test AUC: 0.585
2:41:48.906205 INFO: Train AUC: 0.603
2:41:48.906243 INFO: AUC difference: 2.90%
2:41:49.279664 INFO: Resetting torch num_threads to 32
2:41:49.346233 PROGRESS: === Extracted 250539 precursors and 1189568 fragments ===
2:41:49.347173 INFO: === FDR correction performed with classifier version -1 ===
2:41:49.348389 PROGRESS: ============================= Precursor FDR =============================
2:41:49.348526 PROGRESS: Total precursors accumulated: 855
2:41:49.348655 PROGRESS: Target precursors: 847 (99.06%)
2:41:49.348765 PROGRESS: Decoy precursors: 8 (0.94%)
2:41:49.348860 PROGRESS: 
2:41:49.348968 PROGRESS: Precursor Summary:
2:41:49.351140 PROGRESS: Channel   0:	 0.050 FDR:   847; 0.010 FDR:   847; 0.001 FDR:   680
2:41:49.351278 PROGRESS: 
2:41:49.351381 PROGRESS: Protein Summary:
2:41:49.353991 PROGRESS: Channel   0:	 0.050 FDR:   758; 0.010 FDR:   758; 0.001 FDR:   611
2:41:49.354125 PROGRESS: =========================================================================
2:41:49.361171 INFO: Target number of precursors not reached yet.
2:41:49.937497 INFO: Starting optimization step 7.
2:41:49.937766 PROGRESS: === Extracting elution groups 127000 to 255000 ===
2:41:49.937905 INFO: Using rust extraction backend
2:41:49.937986 PROGRESS: Extracting batch of 254254 precursors
2:41:50.418972 INFO: === Search parameters used ===
2:41:50.419294 INFO: rt_error       : 805.611083984375
2:41:50.419431 INFO: mobility_error : 0.1
2:41:50.419532 INFO: num_candidates : 1
2:41:50.419627 INFO: ms1_error      : 20
2:41:50.419717 INFO: ms2_error      : 20
2:41:50.419825 INFO: fwhm_rt        : 5
2:41:50.419916 INFO: quant_window   : 3
2:41:50.420000 INFO: ==============================================
2:41:52.827479 INFO: performing precursor FDR with 40 features
2:41:52.827597 INFO: Decoy channel: -1
2:41:52.827623 INFO: competitive: True
2:41:53.149783 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:53.435278 INFO: Estimating optimal hyperparameters - samples: 402,492, batch_size: 1,648, learning_rate: 6.34e-04
2:41:53.436225 INFO: Using random state 198429 for train-test-split
2:42:04.865327 INFO: Test AUC: 0.591
2:42:04.865523 INFO: Train AUC: 0.602
2:42:04.865559 INFO: AUC difference: 1.84%
2:42:05.290601 INFO: Resetting torch num_threads to 32
2:42:05.449530 PROGRESS: === Extracted 503116 precursors and 2387579 fragments ===
2:42:05.450348 INFO: === FDR correction performed with classifier version -1 ===
2:42:05.451591 PROGRESS: ============================= Precursor FDR =============================
2:42:05.451703 PROGRESS: Total precursors accumulated: 1,748
2:42:05.451780 PROGRESS: Target precursors: 1,731 (99.03%)
2:42:05.451846 PROGRESS: Decoy precursors: 17 (0.97%)
2:42:05.451912 PROGRESS: 
2:42:05.451971 PROGRESS: Precursor Summary:
2:42:05.453950 PROGRESS: Channel   0:	 0.050 FDR: 1,731; 0.010 FDR: 1,731; 0.001 FDR: 1,397
2:42:05.454072 PROGRESS: 
2:42:05.454146 PROGRESS: Protein Summary:
2:42:05.456716 PROGRESS: Channel   0:	 0.050 FDR: 1,398; 0.010 FDR: 1,398; 0.001 FDR: 1,156
2:42:05.456839 PROGRESS: =========================================================================
2:42:05.469714 INFO: Target number of precursors reached.
2:42:05.765556 INFO: fragments_df: keeping 5000 of 2387579 [sum(precursor_idx_mask)=18684 sum(mass_error_mask)=2387579 stop_rank=5000
2:42:06.678626 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:06.962763 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:07.752717 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:42:07.753186 INFO: Using score_cutoff 12.646959111213684 (fac=0.99, q=1)
2:42:07.753527 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:42:07.753616 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:42:07.753675 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.646959111213684
2:42:07.753750 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:08.076249 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:10.279214 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
2:42:10.279515 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:42:10.279642 INFO: Starting optimization step 8.
2:42:10.279719 PROGRESS: === Extracting elution groups 0 to 255000 ===
2:42:10.279813 INFO: Using rust extraction backend
2:42:10.279889 PROGRESS: Extracting batch of 506436 precursors
2:42:11.190668 INFO: === Search parameters used ===
2:42:11.190926 INFO: rt_error       : 805.611083984375
2:42:11.190997 INFO: mobility_error : 0.1
2:42:11.191053 INFO: num_candidates : 3
2:42:11.191107 INFO: ms1_error      : 20
2:42:11.191157 INFO: ms2_error      : 20
2:42:11.191207 INFO: fwhm_rt        : 3.0
2:42:11.191253 INFO: quant_window   : 3
2:42:11.191298 INFO: ==============================================
2:42:19.773554 INFO: performing precursor FDR with 40 features
2:42:19.773731 INFO: Decoy channel: -1
2:42:19.773762 INFO: competitive: True
2:42:20.306927 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:21.168275 INFO: Estimating optimal hyperparameters - samples: 1,206,276, batch_size: 4,096, learning_rate: 1.00e-03
2:42:21.171174 INFO: Using random state 137367 for train-test-split
2:42:49.457907 INFO: Test AUC: 0.597
2:42:49.458100 INFO: Train AUC: 0.601
2:42:49.458137 INFO: AUC difference: 0.75%
2:42:50.303217 INFO: Resetting torch num_threads to 32
2:42:50.411334 PROGRESS: === Extracted 1507845 precursors and 6934634 fragments ===
2:42:50.411875 INFO: === FDR correction performed with classifier version 7 ===
2:42:50.413123 PROGRESS: ============================= Precursor FDR =============================
2:42:50.413260 PROGRESS: Total precursors accumulated: 2,232
2:42:50.413346 PROGRESS: Target precursors: 2,210 (99.01%)
2:42:50.413421 PROGRESS: Decoy precursors: 22 (0.99%)
2:42:50.413489 PROGRESS: 
2:42:50.413555 PROGRESS: Precursor Summary:
2:42:50.415605 PROGRESS: Channel   0:	 0.050 FDR: 2,210; 0.010 FDR: 2,210; 0.001 FDR: 1,122
2:42:50.415723 PROGRESS: 
2:42:50.415800 PROGRESS: Protein Summary:
2:42:50.418944 PROGRESS: Channel   0:	 0.050 FDR: 1,740; 0.010 FDR: 1,740; 0.001 FDR:   945
2:42:50.419071 PROGRESS: =========================================================================
2:42:50.468048 INFO: Target number of precursors reached.
2:42:51.322392 INFO: fragments_df: keeping 5000 of 6934634 [sum(precursor_idx_mask)=50261 sum(mass_error_mask)=6934634 stop_rank=5000
2:42:51.893249 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:52.313881 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:53.170382 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:53.170940 INFO: Using score_cutoff 12.117102921009064 (fac=0.99, q=1)
2:42:53.171349 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:53.171447 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:53.171509 INFO: Updating optimization_manager: score_cutoff        : 12.646959111213684 -> 12.117102921009064
2:42:53.171584 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:53.329064 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:53.748019 INFO: === checking if optimization conditions were reached ===
2:42:53.750705 INFO: Updating optimization_manager: ms2_error           : 20 -> 10.0
2:42:53.750904 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
2:42:53.750989 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:42:53.751069 INFO: ==============================================
2:42:53.751164 INFO: Starting optimization step 9.
2:42:53.751268 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:42:53.751369 INFO: Using rust extraction backend
2:42:53.751457 PROGRESS: Extracting batch of 252182 precursors
2:42:54.216778 INFO: === Search parameters used ===
2:42:54.217141 INFO: rt_error       : 805.611083984375
2:42:54.217252 INFO: mobility_error : 0.1
2:42:54.217326 INFO: num_candidates : 3
2:42:54.217396 INFO: ms1_error      : 20
2:42:54.217460 INFO: ms2_error      : 10.0
2:42:54.217522 INFO: fwhm_rt        : 3.0
2:42:54.217585 INFO: quant_window   : 3
2:42:54.217648 INFO: ==============================================
2:42:58.485665 INFO: performing precursor FDR with 40 features
2:42:58.485816 INFO: Decoy channel: -1
2:42:58.485850 INFO: competitive: True
2:42:58.731929 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:59.150414 INFO: Estimating optimal hyperparameters - samples: 603,732, batch_size: 2,472, learning_rate: 7.77e-04
2:42:59.151712 INFO: Using random state 453291 for train-test-split
2:43:14.006772 INFO: Test AUC: 0.599
2:43:14.006998 INFO: Train AUC: 0.609
2:43:14.007038 INFO: AUC difference: 1.67%
2:43:14.584820 INFO: Resetting torch num_threads to 32
2:43:14.619094 PROGRESS: === Extracted 754665 precursors and 3843521 fragments ===
2:43:14.619619 INFO: === FDR correction performed with classifier version 8 ===
2:43:14.620417 PROGRESS: ============================= Precursor FDR =============================
2:43:14.620520 PROGRESS: Total precursors accumulated: 1,370
2:43:14.620591 PROGRESS: Target precursors: 1,357 (99.05%)
2:43:14.620671 PROGRESS: Decoy precursors: 13 (0.95%)
2:43:14.620727 PROGRESS: 
2:43:14.620780 PROGRESS: Precursor Summary:
2:43:14.622187 PROGRESS: Channel   0:	 0.050 FDR: 1,357; 0.010 FDR: 1,357; 0.001 FDR: 1,078
2:43:14.622297 PROGRESS: 
2:43:14.622359 PROGRESS: Protein Summary:
2:43:14.624128 PROGRESS: Channel   0:	 0.050 FDR: 1,178; 0.010 FDR: 1,178; 0.001 FDR:   943
2:43:14.624232 PROGRESS: =========================================================================
2:43:14.642624 INFO: Target number of precursors reached.
2:43:15.108506 INFO: fragments_df: keeping 5000 of 3843521 [sum(precursor_idx_mask)=31860 sum(mass_error_mask)=3843521 stop_rank=5000
2:43:15.644825 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:15.977082 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:16.780173 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:16.780666 INFO: Using score_cutoff 9.20412589416504 (fac=0.99, q=1)
2:43:16.781019 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:16.781106 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:16.781166 INFO: Updating optimization_manager: score_cutoff        : 12.117102921009064 -> 9.20412589416504
2:43:16.781233 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:16.939289 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:17.337390 INFO: === checking if optimization conditions were reached ===
2:43:17.340115 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:43:17.340302 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
2:43:17.340410 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:43:17.340485 INFO: ==============================================
2:43:17.340574 INFO: Starting optimization step 10.
2:43:17.340667 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:43:17.340768 INFO: Using rust extraction backend
2:43:17.340857 PROGRESS: Extracting batch of 252182 precursors
2:43:17.820513 INFO: === Search parameters used ===
2:43:17.820874 INFO: rt_error       : 805.611083984375
2:43:17.820975 INFO: mobility_error : 0.1
2:43:17.821047 INFO: num_candidates : 3
2:43:17.821110 INFO: ms1_error      : 20
2:43:17.821170 INFO: ms2_error      : 10.0
2:43:17.821231 INFO: fwhm_rt        : 3.0
2:43:17.821290 INFO: quant_window   : 3
2:43:17.821352 INFO: ==============================================
2:43:22.290929 INFO: performing precursor FDR with 40 features
2:43:22.291127 INFO: Decoy channel: -1
2:43:22.291172 INFO: competitive: True
2:43:22.540001 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:22.938210 INFO: Estimating optimal hyperparameters - samples: 603,744, batch_size: 2,472, learning_rate: 7.77e-04
2:43:22.939538 INFO: Using random state 421192 for train-test-split
2:43:37.722331 INFO: Test AUC: 0.605
2:43:37.722567 INFO: Train AUC: 0.611
2:43:37.722621 INFO: AUC difference: 0.91%
2:43:38.341302 INFO: Resetting torch num_threads to 32
2:43:38.391146 PROGRESS: === Extracted 754680 precursors and 3843953 fragments ===
2:43:38.391873 INFO: === FDR correction performed with classifier version 9 ===
2:43:38.393036 PROGRESS: ============================= Precursor FDR =============================
2:43:38.393171 PROGRESS: Total precursors accumulated: 1,233
2:43:38.393266 PROGRESS: Target precursors: 1,221 (99.03%)
2:43:38.393365 PROGRESS: Decoy precursors: 12 (0.97%)
2:43:38.393461 PROGRESS: 
2:43:38.393549 PROGRESS: Precursor Summary:
2:43:38.395653 PROGRESS: Channel   0:	 0.050 FDR: 1,221; 0.010 FDR: 1,221; 0.001 FDR:     0
2:43:38.395778 PROGRESS: 
2:43:38.395874 PROGRESS: Protein Summary:
2:43:38.398494 PROGRESS: Channel   0:	 0.050 FDR: 1,060; 0.010 FDR: 1,060; 0.001 FDR:     0
2:43:38.398633 PROGRESS: =========================================================================
2:43:38.421924 INFO: Target number of precursors reached.
2:43:38.870892 INFO: fragments_df: keeping 5000 of 3843953 [sum(precursor_idx_mask)=29128 sum(mass_error_mask)=3843953 stop_rank=5000
2:43:39.415545 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:39.679721 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:40.489295 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:40.489871 INFO: Using score_cutoff 11.24814952468872 (fac=0.99, q=1)
2:43:40.490315 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:40.490447 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:40.490539 INFO: Updating optimization_manager: score_cutoff        : 9.20412589416504 -> 11.24814952468872
2:43:40.490626 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:40.655313 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:41.048471 INFO: === checking if optimization conditions were reached ===
2:43:41.051084 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:43:41.051220 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
2:43:41.051301 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:43:41.051374 INFO: ==============================================
2:43:41.051461 INFO: Starting optimization step 11.
2:43:41.051534 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:43:41.051629 INFO: Using rust extraction backend
2:43:41.051714 PROGRESS: Extracting batch of 252182 precursors
2:43:41.532533 INFO: === Search parameters used ===
2:43:41.532854 INFO: rt_error       : 805.611083984375
2:43:41.532934 INFO: mobility_error : 0.1
2:43:41.532999 INFO: num_candidates : 3
2:43:41.533061 INFO: ms1_error      : 20
2:43:41.533119 INFO: ms2_error      : 10.0
2:43:41.533175 INFO: fwhm_rt        : 3.0
2:43:41.533231 INFO: quant_window   : 3
2:43:41.533288 INFO: ==============================================
2:43:45.857553 INFO: performing precursor FDR with 40 features
2:43:45.857754 INFO: Decoy channel: -1
2:43:45.857794 INFO: competitive: True
2:43:46.133817 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:46.497359 INFO: Estimating optimal hyperparameters - samples: 603,728, batch_size: 2,472, learning_rate: 7.77e-04
2:43:46.498826 INFO: Using random state 295720 for train-test-split
2:44:00.950135 INFO: Test AUC: 0.606
2:44:00.950324 INFO: Train AUC: 0.615
2:44:00.950359 INFO: AUC difference: 1.37%
2:44:01.530712 INFO: Resetting torch num_threads to 32
2:44:01.586972 PROGRESS: === Extracted 754660 precursors and 3843782 fragments ===
2:44:01.587648 INFO: === FDR correction performed with classifier version 10 ===
2:44:01.588923 PROGRESS: ============================= Precursor FDR =============================
2:44:01.589094 PROGRESS: Total precursors accumulated: 1,473
2:44:01.589180 PROGRESS: Target precursors: 1,459 (99.05%)
2:44:01.589252 PROGRESS: Decoy precursors: 14 (0.95%)
2:44:01.589321 PROGRESS: 
2:44:01.589382 PROGRESS: Precursor Summary:
2:44:01.591448 PROGRESS: Channel   0:	 0.050 FDR: 1,459; 0.010 FDR: 1,459; 0.001 FDR: 1,143
2:44:01.591594 PROGRESS: 
2:44:01.591672 PROGRESS: Protein Summary:
2:44:01.594209 PROGRESS: Channel   0:	 0.050 FDR: 1,263; 0.010 FDR: 1,263; 0.001 FDR:   998
2:44:01.594356 PROGRESS: =========================================================================
2:44:01.625442 INFO: Target number of precursors reached.
2:44:02.125309 INFO: fragments_df: keeping 5000 of 3843782 [sum(precursor_idx_mask)=34211 sum(mass_error_mask)=3843782 stop_rank=5000
2:44:02.723225 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:03.060558 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:03.908531 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:03.909027 INFO: Using score_cutoff 10.30646718120575 (fac=0.99, q=1)
2:44:03.909396 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:03.909494 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:03.909557 INFO: Updating optimization_manager: score_cutoff        : 11.24814952468872 -> 10.30646718120575
2:44:03.909621 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:04.064719 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:04.515576 INFO: === checking if optimization conditions were reached ===
2:44:04.517945 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:44:04.518123 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
2:44:04.518213 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:44:04.518274 INFO: ==============================================
2:44:04.518352 INFO: Starting optimization step 12.
2:44:04.518416 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:44:04.518497 INFO: Using rust extraction backend
2:44:04.518570 PROGRESS: Extracting batch of 252182 precursors
2:44:04.989016 INFO: === Search parameters used ===
2:44:04.989296 INFO: rt_error       : 805.611083984375
2:44:04.989359 INFO: mobility_error : 0.1
2:44:04.989410 INFO: num_candidates : 3
2:44:04.989455 INFO: ms1_error      : 20
2:44:04.989501 INFO: ms2_error      : 10.0
2:44:04.989543 INFO: fwhm_rt        : 3.0
2:44:04.989605 INFO: quant_window   : 3
2:44:04.989649 INFO: ==============================================
2:44:09.174069 INFO: performing precursor FDR with 40 features
2:44:09.174245 INFO: Decoy channel: -1
2:44:09.174277 INFO: competitive: True
2:44:09.457237 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:09.843352 INFO: Estimating optimal hyperparameters - samples: 603,732, batch_size: 2,472, learning_rate: 7.77e-04
2:44:09.844554 INFO: Using random state 970728 for train-test-split
2:44:20.387594 INFO: Test AUC: 0.606
2:44:20.387740 INFO: Train AUC: 0.618
2:44:20.387781 INFO: AUC difference: 2.02%
2:44:20.955073 INFO: Resetting torch num_threads to 32
2:44:21.005294 PROGRESS: === Extracted 754666 precursors and 3844186 fragments ===
2:44:21.005926 INFO: === FDR correction performed with classifier version 11 ===
2:44:21.006990 PROGRESS: ============================= Precursor FDR =============================
2:44:21.007123 PROGRESS: Total precursors accumulated: 1,472
2:44:21.007197 PROGRESS: Target precursors: 1,458 (99.05%)
2:44:21.007262 PROGRESS: Decoy precursors: 14 (0.95%)
2:44:21.007324 PROGRESS: 
2:44:21.007382 PROGRESS: Precursor Summary:
2:44:21.009339 PROGRESS: Channel   0:	 0.050 FDR: 1,458; 0.010 FDR: 1,458; 0.001 FDR: 1,134
2:44:21.009465 PROGRESS: 
2:44:21.009540 PROGRESS: Protein Summary:
2:44:21.011960 PROGRESS: Channel   0:	 0.050 FDR: 1,256; 0.010 FDR: 1,256; 0.001 FDR:   990
2:44:21.012078 PROGRESS: =========================================================================
2:44:21.040739 INFO: Target number of precursors reached.
2:44:21.532754 INFO: fragments_df: keeping 5000 of 3844186 [sum(precursor_idx_mask)=34148 sum(mass_error_mask)=3844186 stop_rank=5000
2:44:22.057589 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:22.306347 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:23.137811 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:23.138399 INFO: Using score_cutoff 10.435110136413574 (fac=0.99, q=1)
2:44:23.138842 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:23.138940 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:23.139004 INFO: Updating optimization_manager: score_cutoff        : 10.30646718120575 -> 10.435110136413574
2:44:23.139077 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:23.301762 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:23.700247 INFO: === checking if optimization conditions were reached ===
2:44:23.702892 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:44:23.703038 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
2:44:23.703120 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:44:23.703194 INFO: ==============================================
2:44:23.703284 PROGRESS: Optimization finished for ms2_error.
2:44:24.297797 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:24.451207 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:24.850345 INFO: Starting optimization step 0.
2:44:24.850630 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:44:24.850764 INFO: Using rust extraction backend
2:44:24.850870 PROGRESS: Extracting batch of 252182 precursors
2:44:25.335920 INFO: === Search parameters used ===
2:44:25.336239 INFO: rt_error       : 805.611083984375
2:44:25.336339 INFO: mobility_error : 0.1
2:44:25.336406 INFO: num_candidates : 3
2:44:25.336467 INFO: ms1_error      : 20
2:44:25.336522 INFO: ms2_error      : 10.0
2:44:25.336576 INFO: fwhm_rt        : 3.0
2:44:25.336647 INFO: quant_window   : 3
2:44:25.336707 INFO: ==============================================
2:44:29.468691 INFO: performing precursor FDR with 40 features
2:44:29.468864 INFO: Decoy channel: -1
2:44:29.468893 INFO: competitive: True
2:44:29.699627 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:30.070818 INFO: Estimating optimal hyperparameters - samples: 603,732, batch_size: 2,472, learning_rate: 7.77e-04
2:44:30.072047 INFO: Using random state 927534 for train-test-split
2:44:40.454083 INFO: Test AUC: 0.609
2:44:40.454227 INFO: Train AUC: 0.619
2:44:40.454263 INFO: AUC difference: 1.68%
2:44:40.991316 INFO: Resetting torch num_threads to 32
2:44:41.028600 PROGRESS: === Extracted 754665 precursors and 3844470 fragments ===
2:44:41.029222 INFO: === FDR correction performed with classifier version 12 ===
2:44:41.030268 PROGRESS: ============================= Precursor FDR =============================
2:44:41.030419 PROGRESS: Total precursors accumulated: 1,515
2:44:41.030535 PROGRESS: Target precursors: 1,500 (99.01%)
2:44:41.030638 PROGRESS: Decoy precursors: 15 (0.99%)
2:44:41.030704 PROGRESS: 
2:44:41.030759 PROGRESS: Precursor Summary:
2:44:41.032771 PROGRESS: Channel   0:	 0.050 FDR: 1,500; 0.010 FDR: 1,497; 0.001 FDR: 1,159
2:44:41.032917 PROGRESS: 
2:44:41.032992 PROGRESS: Protein Summary:
2:44:41.035460 PROGRESS: Channel   0:	 0.050 FDR: 1,302; 0.010 FDR: 1,299; 0.001 FDR: 1,010
2:44:41.035572 PROGRESS: =========================================================================
2:44:41.057138 INFO: Target number of precursors reached.
2:44:41.574085 INFO: fragments_df: keeping 5000 of 3844470 [sum(precursor_idx_mask)=34389 sum(mass_error_mask)=3844470 stop_rank=5000
2:44:42.108868 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:42.396582 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:43.273087 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:43.273693 INFO: Using score_cutoff 9.106297229003905 (fac=0.99, q=1)
2:44:43.274169 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:43.274298 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:43.274404 INFO: Updating optimization_manager: score_cutoff        : 10.435110136413574 -> 9.106297229003905
2:44:43.274509 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:43.428954 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:43.918453 INFO: === checking if optimization conditions were reached ===
2:44:43.918808 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:44:43.922055 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 584.2209433169187
2:44:43.922236 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 584.2209.
2:44:43.922322 INFO: ==============================================
2:44:43.922417 INFO: Starting optimization step 1.
2:44:43.922494 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:44:43.922593 INFO: Using rust extraction backend
2:44:43.922678 PROGRESS: Extracting batch of 252182 precursors
2:44:44.399848 INFO: === Search parameters used ===
2:44:44.400187 INFO: rt_error       : 584.2209433169187
2:44:44.400316 INFO: mobility_error : 0.1
2:44:44.400419 INFO: num_candidates : 3
2:44:44.400511 INFO: ms1_error      : 20
2:44:44.400601 INFO: ms2_error      : 10.0
2:44:44.400701 INFO: fwhm_rt        : 3.0
2:44:44.400781 INFO: quant_window   : 3
2:44:44.400867 INFO: ==============================================
2:44:48.492098 INFO: performing precursor FDR with 40 features
2:44:48.492226 INFO: Decoy channel: -1
2:44:48.492254 INFO: competitive: True
2:44:48.725417 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:49.182431 INFO: Estimating optimal hyperparameters - samples: 603,848, batch_size: 2,473, learning_rate: 7.77e-04
2:44:49.183770 INFO: Using random state 927534 for train-test-split
2:45:04.582086 INFO: Test AUC: 0.609
2:45:04.582298 INFO: Train AUC: 0.618
2:45:04.582342 INFO: AUC difference: 1.55%
2:45:05.223091 INFO: Resetting torch num_threads to 32
2:45:05.288361 PROGRESS: === Extracted 754811 precursors and 3844918 fragments ===
2:45:05.288921 INFO: === FDR correction performed with classifier version 12 ===
2:45:05.289750 PROGRESS: ============================= Precursor FDR =============================
2:45:05.289850 PROGRESS: Total precursors accumulated: 1,370
2:45:05.289933 PROGRESS: Target precursors: 1,357 (99.05%)
2:45:05.289990 PROGRESS: Decoy precursors: 13 (0.95%)
2:45:05.290041 PROGRESS: 
2:45:05.290092 PROGRESS: Precursor Summary:
2:45:05.291497 PROGRESS: Channel   0:	 0.050 FDR: 1,357; 0.010 FDR: 1,357; 0.001 FDR: 1,129
2:45:05.291596 PROGRESS: 
2:45:05.291659 PROGRESS: Protein Summary:
2:45:05.293452 PROGRESS: Channel   0:	 0.050 FDR: 1,178; 0.010 FDR: 1,178; 0.001 FDR:   985
2:45:05.293554 PROGRESS: =========================================================================
2:45:05.311620 INFO: Target number of precursors reached.
2:45:05.724607 INFO: fragments_df: keeping 5000 of 3844918 [sum(precursor_idx_mask)=32172 sum(mass_error_mask)=3844918 stop_rank=5000
2:45:06.367813 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:45:06.638289 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:45:07.442468 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:45:07.442986 INFO: Using score_cutoff 11.153870627975463 (fac=0.99, q=1)
2:45:07.443357 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:45:07.443446 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:45:07.443506 INFO: Updating optimization_manager: score_cutoff        : 9.106297229003905 -> 11.153870627975463
2:45:07.443573 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:45:07.604074 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:45:07.998846 INFO: === checking if optimization conditions were reached ===
2:45:07.999181 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:45:08.003052 INFO: Updating optimization_manager: rt_error            : 584.2209433169187 -> 350.2457031667846
2:45:08.003217 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 350.2457.
2:45:08.003328 INFO: ==============================================
2:45:08.003467 INFO: Starting optimization step 2.
2:45:08.003592 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:45:08.003748 INFO: Using rust extraction backend
2:45:08.003882 PROGRESS: Extracting batch of 252182 precursors
2:45:08.480103 INFO: === Search parameters used ===
2:45:08.480364 INFO: rt_error       : 350.2457031667846
2:45:08.480430 INFO: mobility_error : 0.1
2:45:08.480489 INFO: num_candidates : 3
2:45:08.480541 INFO: ms1_error      : 20
2:45:08.480589 INFO: ms2_error      : 10.0
2:45:08.480673 INFO: fwhm_rt        : 3.0
2:45:08.480731 INFO: quant_window   : 3
2:45:08.480780 INFO: ==============================================
2:45:11.980511 INFO: performing precursor FDR with 40 features
2:45:11.980663 INFO: Decoy channel: -1
2:45:11.980693 INFO: competitive: True
2:45:12.255870 INFO: Setting torch num_threads to 2 for FDR classification task
2:45:12.643270 INFO: Estimating optimal hyperparameters - samples: 602,648, batch_size: 2,468, learning_rate: 7.76e-04
2:45:12.644525 INFO: Using random state 927534 for train-test-split
2:45:27.477304 INFO: Test AUC: 0.602
2:45:27.477528 INFO: Train AUC: 0.616
2:45:27.477572 INFO: AUC difference: 2.31%
2:45:28.038893 INFO: Resetting torch num_threads to 32
2:45:28.083720 PROGRESS: === Extracted 753311 precursors and 3689257 fragments ===
2:45:28.084286 INFO: === FDR correction performed with classifier version 12 ===
2:45:28.085186 PROGRESS: ============================= Precursor FDR =============================
2:45:28.085314 PROGRESS: Total precursors accumulated: 1,535
2:45:28.085383 PROGRESS: Target precursors: 1,520 (99.02%)
2:45:28.085442 PROGRESS: Decoy precursors: 15 (0.98%)
2:45:28.085494 PROGRESS: 
2:45:28.085542 PROGRESS: Precursor Summary:
2:45:28.087057 PROGRESS: Channel   0:	 0.050 FDR: 1,520; 0.010 FDR: 1,520; 0.001 FDR: 1,126
2:45:28.087170 PROGRESS: 
2:45:28.087230 PROGRESS: Protein Summary:
2:45:28.089171 PROGRESS: Channel   0:	 0.050 FDR: 1,316; 0.010 FDR: 1,316; 0.001 FDR:   983
2:45:28.089285 PROGRESS: =========================================================================
2:45:28.108171 INFO: Target number of precursors reached.
2:45:28.551039 INFO: fragments_df: keeping 5000 of 3689257 [sum(precursor_idx_mask)=34919 sum(mass_error_mask)=3689257 stop_rank=5000
2:45:29.166827 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:45:29.485964 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:45:30.311503 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:45:30.312075 INFO: Using score_cutoff 9.256653082466126 (fac=0.99, q=1)
2:45:30.312523 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:45:30.312646 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:45:30.312721 INFO: Updating optimization_manager: score_cutoff        : 11.153870627975463 -> 9.256653082466126
2:45:30.312793 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:45:30.471134 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:45:30.876455 INFO: === checking if optimization conditions were reached ===
2:45:30.876751 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:45:30.880439 INFO: Updating optimization_manager: rt_error            : 350.2457031667846 -> 380.1160508532871
2:45:30.880622 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 380.1161.
2:45:30.880719 INFO: ==============================================
2:45:30.880820 INFO: Starting optimization step 3.
2:45:30.880913 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:45:30.881016 INFO: Using rust extraction backend
2:45:30.881106 PROGRESS: Extracting batch of 252182 precursors
2:45:31.355982 INFO: === Search parameters used ===
2:45:31.356293 INFO: rt_error       : 380.1160508532871
2:45:31.356361 INFO: mobility_error : 0.1
2:45:31.356418 INFO: num_candidates : 3
2:45:31.356471 INFO: ms1_error      : 20
2:45:31.356518 INFO: ms2_error      : 10.0
2:45:31.356567 INFO: fwhm_rt        : 3.0
2:45:31.356643 INFO: quant_window   : 3
2:45:31.356699 INFO: ==============================================
2:45:35.118913 INFO: performing precursor FDR with 40 features
2:45:35.119049 INFO: Decoy channel: -1
2:45:35.119077 INFO: competitive: True
2:45:35.336377 INFO: Setting torch num_threads to 2 for FDR classification task
2:45:35.777864 INFO: Estimating optimal hyperparameters - samples: 602,917, batch_size: 2,469, learning_rate: 7.76e-04
2:45:35.779207 INFO: Using random state 927534 for train-test-split
2:45:50.084239 INFO: Test AUC: 0.605
2:45:50.084437 INFO: Train AUC: 0.616
2:45:50.084477 INFO: AUC difference: 1.70%
2:45:50.654683 INFO: Resetting torch num_threads to 32
2:45:50.689438 PROGRESS: === Extracted 753647 precursors and 3726653 fragments ===
2:45:50.689960 INFO: === FDR correction performed with classifier version 12 ===
2:45:50.690717 PROGRESS: ============================= Precursor FDR =============================
2:45:50.690819 PROGRESS: Total precursors accumulated: 1,537
2:45:50.690886 PROGRESS: Target precursors: 1,522 (99.02%)
2:45:50.690944 PROGRESS: Decoy precursors: 15 (0.98%)
2:45:50.690996 PROGRESS: 
2:45:50.691048 PROGRESS: Precursor Summary:
2:45:50.692428 PROGRESS: Channel   0:	 0.050 FDR: 1,522; 0.010 FDR: 1,522; 0.001 FDR: 1,232
2:45:50.692542 PROGRESS: 
2:45:50.692608 PROGRESS: Protein Summary:
2:45:50.694508 PROGRESS: Channel   0:	 0.050 FDR: 1,312; 0.010 FDR: 1,312; 0.001 FDR: 1,070
2:45:50.694606 PROGRESS: =========================================================================
2:45:50.720536 INFO: Target number of precursors reached.
2:45:51.265677 INFO: fragments_df: keeping 5000 of 3726653 [sum(precursor_idx_mask)=35416 sum(mass_error_mask)=3726653 stop_rank=5000
2:45:51.887321 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:45:52.197709 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:45:53.036508 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:45:53.037115 INFO: Using score_cutoff 10.031393303489686 (fac=0.99, q=1)
2:45:53.037576 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:45:53.037682 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:45:53.037750 INFO: Updating optimization_manager: score_cutoff        : 9.256653082466126 -> 10.031393303489686
2:45:53.037826 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:45:53.197530 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:45:53.696600 INFO: === checking if optimization conditions were reached ===
2:45:53.696921 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:45:53.700295 INFO: Updating optimization_manager: rt_error            : 380.1160508532871 -> 385.1693225949019
2:45:53.700424 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 385.1693.
2:45:53.700523 INFO: ==============================================
2:45:53.700638 INFO: Starting optimization step 4.
2:45:53.700722 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:45:53.700820 INFO: Using rust extraction backend
2:45:53.700913 PROGRESS: Extracting batch of 252182 precursors
2:45:54.186726 INFO: === Search parameters used ===
2:45:54.186979 INFO: rt_error       : 385.1693225949019
2:45:54.187046 INFO: mobility_error : 0.1
2:45:54.187100 INFO: num_candidates : 3
2:45:54.187150 INFO: ms1_error      : 20
2:45:54.187196 INFO: ms2_error      : 10.0
2:45:54.187242 INFO: fwhm_rt        : 3.0
2:45:54.187288 INFO: quant_window   : 3
2:45:54.187335 INFO: ==============================================
2:45:57.716246 INFO: performing precursor FDR with 40 features
2:45:57.716418 INFO: Decoy channel: -1
2:45:57.716446 INFO: competitive: True
2:45:57.930633 INFO: Setting torch num_threads to 2 for FDR classification task
2:45:58.289732 INFO: Estimating optimal hyperparameters - samples: 602,938, batch_size: 2,469, learning_rate: 7.76e-04
2:45:58.291051 INFO: Using random state 927534 for train-test-split
2:46:12.954257 INFO: Test AUC: 0.606
2:46:12.954392 INFO: Train AUC: 0.616
2:46:12.954427 INFO: AUC difference: 1.74%
2:46:13.593419 INFO: Resetting torch num_threads to 32
2:46:13.629315 PROGRESS: === Extracted 753673 precursors and 3732295 fragments ===
2:46:13.630012 INFO: === FDR correction performed with classifier version 12 ===
2:46:13.631264 PROGRESS: ============================= Precursor FDR =============================
2:46:13.631413 PROGRESS: Total precursors accumulated: 1,549
2:46:13.631525 PROGRESS: Target precursors: 1,534 (99.03%)
2:46:13.631618 PROGRESS: Decoy precursors: 15 (0.97%)
2:46:13.631711 PROGRESS: 
2:46:13.631805 PROGRESS: Precursor Summary:
2:46:13.634291 PROGRESS: Channel   0:	 0.050 FDR: 1,534; 0.010 FDR: 1,534; 0.001 FDR: 1,153
2:46:13.634435 PROGRESS: 
2:46:13.634537 PROGRESS: Protein Summary:
2:46:13.637681 PROGRESS: Channel   0:	 0.050 FDR: 1,321; 0.010 FDR: 1,321; 0.001 FDR: 1,008
2:46:13.637833 PROGRESS: =========================================================================
2:46:13.666650 INFO: Target number of precursors reached.
2:46:14.170752 INFO: fragments_df: keeping 5000 of 3732295 [sum(precursor_idx_mask)=35619 sum(mass_error_mask)=3732295 stop_rank=5000
2:46:14.747876 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:46:15.137341 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:46:15.956572 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:46:15.957098 INFO: Using score_cutoff 10.068219455623627 (fac=0.99, q=1)
2:46:15.957450 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:46:15.957541 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:46:15.957601 INFO: Updating optimization_manager: score_cutoff        : 10.031393303489686 -> 10.068219455623627
2:46:15.957667 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:16.115879 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:16.656167 INFO: === checking if optimization conditions were reached ===
2:46:16.656529 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:46:16.657702 INFO: Updating optimization_manager: rt_error            : 385.1693225949019 -> 385.1693225949019
2:46:16.657883 INFO: Updating optimization_manager: classifier_version  : 12 -> 17
2:46:16.658005 INFO: Updating optimization_manager: score_cutoff        : 10.068219455623627 -> 10.068219455623627
2:46:16.658116 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:46:16.658223 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:46:16.658334 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 385.1693 found after 5 searches.
2:46:16.658412 INFO: ==============================================
2:46:16.658504 PROGRESS: Optimization finished for rt_error.
2:46:17.224589 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:17.383645 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:17.886470 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:46:17.886869 PROGRESS: ==============================================
2:46:17.886963 PROGRESS: ms2_error      : 10.0000
2:46:17.887041 PROGRESS: rt_error       : 385.1693
2:46:17.887121 PROGRESS: ==============================================
2:46:17.888127 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:27.979849 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:47:00.892754 INFO: Using rust extraction backend
2:47:00.893228 PROGRESS: Extracting batch of 15081856 precursors
2:47:26.856637 INFO: === Search parameters used ===
2:47:26.857068 INFO: rt_error       : 385.1693225949019
2:47:26.857146 INFO: mobility_error : 0.1
2:47:26.857202 INFO: num_candidates : 3
2:47:26.857257 INFO: ms1_error      : 20
2:47:26.857305 INFO: ms2_error      : 10.0
2:47:26.857351 INFO: fwhm_rt        : 3.0
2:47:26.857395 INFO: quant_window   : 3
2:47:26.857440 INFO: ==============================================
2:48:27.965561 INFO: Removed 12131772 precursors with score below cutoff 10.068219455623627
2:49:06.326641 INFO: performing precursor FDR with 40 features
2:49:06.326887 INFO: Decoy channel: -1
2:49:06.326926 INFO: competitive: True
2:49:10.350531 INFO: Setting torch num_threads to 2 for FDR classification task
2:49:27.954442 INFO: Estimating optimal hyperparameters - samples: 26,487,978, batch_size: 4,096, learning_rate: 1.00e-03
2:49:28.043303 INFO: Using random state 818641 for train-test-split
3:00:20.248571 INFO: Test AUC: 0.613
3:00:20.248844 INFO: Train AUC: 0.613
3:00:20.248899 INFO: AUC difference: 0.07%
3:00:27.982834 INFO: Resetting torch num_threads to 32
3:00:31.145496 PROGRESS: ============================= Precursor FDR =============================
3:00:31.145890 PROGRESS: Total precursors accumulated: 88,607
3:00:31.145978 PROGRESS: Target precursors: 87,730 (99.01%)
3:00:31.146048 PROGRESS: Decoy precursors: 877 (0.99%)
3:00:31.146112 PROGRESS: 
3:00:31.146171 PROGRESS: Precursor Summary:
3:00:31.187229 PROGRESS: Channel   0:	 0.050 FDR: 87,730; 0.010 FDR: 87,730; 0.001 FDR: 60,333
3:00:31.187498 PROGRESS: 
3:00:31.187576 PROGRESS: Protein Summary:
3:00:31.246595 PROGRESS: Channel   0:	 0.050 FDR: 12,523; 0.010 FDR: 12,523; 0.001 FDR: 9,256
3:00:31.246847 PROGRESS: =========================================================================
3:00:31.519225 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/psm.parquet
3:00:31.684224 INFO: Saving results to /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.parquet
3:00:32.010424 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:01:35.710912 PROGRESS: Processing search outputs
3:01:35.711100 PROGRESS: Performing protein grouping and FDR
3:01:35.711151 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:01:35.769946 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:01:35.809258 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:01:35.851732 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:01:35.894835 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:01:35.935906 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:01:35.984957 INFO: Building combined output
3:01:36.021790 INFO: Performing protein inference
3:01:36.936709 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
3:02:37.081556 INFO: Performing protein FDR
3:02:44.977640 INFO: Normalizing q-values using 17,553 targets and 3,761 decoys
3:02:44.982621 INFO: Test AUC: 0.862
3:02:44.982819 INFO: Train AUC: 0.865
3:02:44.982960 INFO: AUC difference: 0.37%
3:02:45.688277 INFO: ================ Protein FDR =================
3:02:45.688416 INFO: Unique protein groups in output
3:02:45.688447 INFO:   1% protein FDR: 9,736
3:02:45.688471 INFO: 
3:02:45.688494 INFO: Unique precursor in output
3:02:45.688515 INFO:   1% protein FDR: 121,693
3:02:45.688535 INFO: ================================================
3:02:45.745358 PROGRESS: Building search statistics
3:02:45.867800 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
3:02:45.868003 INFO: Initializing OptimizationManager
3:02:45.868268 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
3:02:45.868358 INFO: Initializing CalibrationManager
3:02:45.869230 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
3:02:45.869336 INFO: Initializing RawFileManager
3:02:45.901403 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
3:02:45.901597 INFO: Initializing OptimizationManager
3:02:45.901830 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
3:02:45.901919 INFO: Initializing CalibrationManager
3:02:45.902720 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
3:02:45.902811 INFO: Initializing RawFileManager
3:02:45.934173 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
3:02:45.934367 INFO: Initializing OptimizationManager
3:02:45.934593 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
3:02:45.934678 INFO: Initializing CalibrationManager
3:02:45.934895 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
3:02:45.934976 INFO: Initializing RawFileManager
3:02:45.968532 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
3:02:45.968728 INFO: Initializing OptimizationManager
3:02:45.968953 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
3:02:45.969257 INFO: Initializing CalibrationManager
3:02:45.969492 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
3:02:45.969578 INFO: Initializing RawFileManager
3:02:46.003115 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
3:02:46.003291 INFO: Initializing OptimizationManager
3:02:46.003512 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
3:02:46.003592 INFO: Initializing CalibrationManager
3:02:46.003805 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
3:02:46.003884 INFO: Initializing RawFileManager
3:02:46.036935 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
3:02:46.037124 INFO: Initializing OptimizationManager
3:02:46.037341 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
3:02:46.037419 INFO: Initializing CalibrationManager
3:02:46.037627 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
3:02:46.037705 INFO: Initializing RawFileManager
3:02:46.041320 INFO: Writing stat output to disk
3:02:46.041404 INFO: Saving /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/stat.tsv to disk
3:02:46.053145 PROGRESS: Building internal statistics
3:02:46.053483 INFO: Loaded TimingManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
3:02:46.053531 INFO: Initializing TimingManager
3:02:46.053973 INFO: Loaded TimingManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
3:02:46.054017 INFO: Initializing TimingManager
3:02:46.054239 INFO: Loaded TimingManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
3:02:46.054280 INFO: Initializing TimingManager
3:02:46.054489 INFO: Loaded TimingManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
3:02:46.054527 INFO: Initializing TimingManager
3:02:46.054723 INFO: Loaded TimingManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
3:02:46.054759 INFO: Initializing TimingManager
3:02:46.054951 INFO: Loaded TimingManager from /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
3:02:46.054989 INFO: Initializing TimingManager
3:02:46.055445 INFO: Writing internal output to disk
3:02:46.055491 INFO: Saving /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/internal.tsv to disk
3:02:46.133883 INFO: Performing label free quantification
3:02:46.134011 INFO: Accumulating fragment data
3:02:46.134069 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
3:02:46.354448 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
3:02:47.717803 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
3:02:49.096716 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
3:02:50.634621 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
3:02:52.324440 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
3:02:54.380892 INFO: Performing label free quantification on the precursor level
3:02:54.381043 INFO: Filtering fragments by quality
3:02:54.805583 INFO: Performing label-free quantification with directlfq normalization
3:02:55.387794 INFO: Applying directLFQ normalization
3:02:56.591603 INFO: 121693 lfq-groups total
3:03:46.892249 INFO: using 32 processes
3:03:47.500297 INFO: lfq-object 0
3:03:47.675330 INFO: lfq-object 100
3:03:47.837451 INFO: lfq-object 200
3:03:47.903091 INFO: lfq-object 1000
3:03:48.013270 INFO: lfq-object 300
3:03:48.071633 INFO: lfq-object 1100
3:03:48.189717 INFO: lfq-object 400
3:03:48.252163 INFO: lfq-object 1200
3:03:48.295484 INFO: lfq-object 2000
3:03:48.306753 INFO: lfq-object 500
3:03:48.411262 INFO: lfq-object 1300
3:03:48.423428 INFO: lfq-object 2100
3:03:48.424554 INFO: lfq-object 600
3:03:48.526143 INFO: lfq-object 1400
3:03:48.544161 INFO: lfq-object 700
3:03:48.573534 INFO: lfq-object 2200
3:03:48.594619 INFO: lfq-object 2900
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3:08:13.545828 INFO: Performing label free quantification on the pg level
3:08:13.546295 INFO: Filtering fragments by quality
3:08:14.072869 INFO: Performing label-free quantification with directlfq normalization
3:08:14.271362 INFO: Applying directLFQ normalization
3:08:14.464839 INFO: 9736 lfq-groups total
3:08:40.436033 INFO: using 32 processes
3:08:40.521611 INFO: lfq-object 0
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3:08:44.655407 INFO: lfq-object 5000
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3:08:44.921773 INFO: lfq-object 6300
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3:08:45.050059 INFO: lfq-object 7100
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3:08:45.193243 INFO: lfq-object 7300
3:08:45.211218 INFO: lfq-object 7000
3:08:45.211136 INFO: lfq-object 6600
3:08:45.324379 INFO: lfq-object 7700
3:08:45.344346 INFO: lfq-object 7500
3:08:45.381274 INFO: lfq-object 7600
3:08:45.525391 INFO: lfq-object 7900
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3:08:45.754736 INFO: lfq-object 8000
3:08:47.933407 INFO: lfq-object 8400
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3:08:48.235246 INFO: lfq-object 8800
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3:08:48.283657 INFO: lfq-object 8600
3:08:48.365233 INFO: lfq-object 8900
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3:08:48.413001 INFO: lfq-object 8700
3:08:48.418684 INFO: lfq-object 9400
3:08:48.457896 INFO: lfq-object 9200
3:08:48.545062 INFO: lfq-object 9000
3:08:48.577643 INFO: lfq-object 9300
3:08:48.867018 INFO: lfq-object 9600
3:08:48.911615 INFO: lfq-object 9500
3:08:49.123023 INFO: lfq-object 9700
3:08:51.994868 INFO: Writing psm output to disk
3:08:52.093711 INFO: Saving /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/precursors.parquet to disk
3:08:52.858318 INFO: Writing precursor output to disk
3:08:52.861913 INFO: Saving /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/precursor.matrix.parquet to disk
3:08:52.950902 INFO: Writing peptide output to disk
3:08:52.955562 INFO: Saving /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/peptide.matrix.parquet to disk
3:08:53.035056 INFO: Writing pg output to disk
3:08:53.038333 INFO: Saving /home/robbe/PB_output/results/test_run/HYE_Astral/alphadia_v2.1.1/pg.matrix.parquet to disk
3:08:53.131673 PROGRESS: Building MBR spectral library
3:08:53.131854 INFO: Running MbrLibraryBuilder
3:08:57.252045 INFO: MBR spectral library contains 121,693 precursors, 9,736 proteins
3:08:57.252204 INFO: Writing MBR spectral library to disk
3:08:58.330436 PROGRESS: =================== Search step 'library' finished ===================
3:09:00.628390 INFO: =================== Search Finished ===================
