0:00:00.000048 INFO: Output directory: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1, cwd: /home/robbe/PB_output/work/af/5bf8f78295acd382a6ac31d117a164.
0:00:00.000153 INFO: User provided config file: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/alphadia_config.yaml.
0:00:00.014242 PROGRESS:           _      _         ___ ___   _   
0:00:00.014309 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.014341 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.014364 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.014385 PROGRESS:            |_|                           
0:00:00.014408 PROGRESS: 
0:00:00.014437 PROGRESS: version: 2.1.1
0:00:00.014456 PROGRESS: Please cite: Wallmann, et al., Nature Biotechnology (2025), https://doi.org/10.1038/s41587-025-02791-w
0:00:00.014480 INFO: hostname: thestral
0:00:00.014505 PROGRESS: os: Linux 6.12.85+deb13-amd64 (x86_64)
0:00:00.014531 PROGRESS: python: 3.11.11 (CPython)
0:00:00.014579 INFO: date: 2026-07-09 17:46:17
0:00:00.014599 INFO: ================ AlphaX Environment ===============
0:00:00.014617 INFO: alphabase       : 1.8.1
0:00:00.014635 INFO: alpharaw        : 0.5.0
0:00:00.014653 INFO: alphatims       : 1.0.9
0:00:00.014670 INFO: alphapeptdeep   : 1.4.2
0:00:00.014687 INFO: directlfq       : 0.3.3
0:00:00.014702 INFO: ===================================================
0:00:00.014718 INFO: ================= Pip Environment =================
0:00:00.083554 INFO: comm==0.2.3 alphadia==2.1.1 ipython_pygments_lexers==1.1.1 peptdeep==1.4.2 ipython==9.15.0 et_xmlfile==2.0.0 httpcore==1.0.9 scikit-learn==1.7.2 packaging==26.1 h5py==3.16.0 multiprocess==0.70.19 asttokens==3.0.1 nvidia-nvjitlink-cu12==12.4.127 filelock==3.28.0 decorator==5.3.1 regex==2026.4.4 prompt_toolkit==3.0.52 rocket-fft==0.3.1 matplotlib==3.10.7 tokenizers==0.22.2 tqdm==4.67.1 MarkupSafe==3.0.3 transformers==5.5.4 ipykernel==7.3.0 pytz==2026.1.post1 pip==24.0 numpy==1.26.4 wcwidth==0.8.2 contextlib2==21.6.0 directlfq==0.3.3 debugpy==1.8.21 traitlets==5.15.1 argparse==1.4.0 pyzmq==27.1.0 nvidia-cuda-cupti-cu12==12.4.127 pandas==2.3.3 huggingface_hub==1.11.0 dill==0.4.1 matplotlib-inline==0.2.2 idna==3.11 pyzstd==0.19.1 safetensors==0.7.0 nvidia-cuda-nvrtc-cu12==12.4.127 pyteomics==4.7.5 PyYAML==6.0.3 pyarrow==23.0.1 mpmath==1.3.0 certifi==2026.2.25 six==1.17.0 narwhals==2.19.0 cycler==0.12.1 shellingham==1.5.4 rdkit==2026.3.1 threadpoolctl==3.6.0 pythonnet==3.0.5 triton==3.2.0 alphatims==1.0.9 typing_extensions==4.15.0 hf-xet==1.4.3 joblib==1.5.3 torchmetrics==1.9.0 pillow==12.2.0 Pygments==2.20.0 click==8.3.1 python-dateutil==2.9.0.post0 stack-data==0.6.3 alpharaw==0.5.0 rich==15.0.0 h11==0.16.0 pexpect==4.9.0 torch==2.6.0 plotly==6.7.0 openpyxl==3.1.5 nvidia-cusparse-cu12==12.3.1.170 contourpy==1.3.3 pyopenms==3.3.0 jedi==0.20.0 numba==0.62.1 alphabase==1.8.1 backports.zstd==1.3.0 fsspec==2026.3.0 quantselect==0.1.3 platformdirs==4.10.0 statsmodels==0.14.6 jupyter_client==8.9.1 mdurl==0.1.2 kiwisolver==1.5.0 markdown-it-py==4.0.0 patsy==1.0.2 seaborn==0.13.2 alphadia-search-rs==1.1.1 owlready2==0.50 executing==2.2.1 psutil==7.2.2 biopython==1.86 pycparser==3.0 pyahocorasick==2.3.0 typer==0.24.1 fonttools==4.62.1 fragpipe-speclib==0.1.59 nest-asyncio2==1.7.2 Jinja2==3.1.6 scipy==1.17.1 nvidia-nvtx-cu12==12.4.127 nvidia-cusolver-cu12==11.6.1.9 llvmlite==0.45.1 nvidia-cufft-cu12==11.2.1.3 tzdata==2026.1 sympy==1.13.1 pure_eval==0.2.3 tornado==6.5.7 nvidia-cublas-cu12==12.4.5.8 nvidia-cudnn-cu12==9.1.0.70 ptyprocess==0.7.0 parso==0.8.7 nvidia-curand-cu12==10.3.5.147 lightning-utilities==0.15.3 lxml==6.1.0 networkx==3.6.1 httpx==0.28.1 clr_loader==0.2.10 cffi==2.0.0 setuptools==65.5.0 nvidia-cuda-runtime-cu12==12.4.127 jupyter_core==5.9.1 nvidia-nccl-cu12==2.21.5 xxhash==3.6.0 anyio==4.13.0 pyparsing==3.3.2 nvidia-cusparselt-cu12==0.6.2 annotated-doc==0.0.4
0:00:00.083638 INFO: ===================================================
0:00:00.083679 INFO: =================== Running step 'transfer' ===================
0:00:00.083819 INFO: loading default config from /home/robbe/bin/alphadia/alphadia/constants/default.yaml
0:00:00.096089 INFO: loading additional config provided via CLI
0:00:00.096155 INFO: loading additional config provided via CLI parameters
0:00:00.096514 INFO: Updating config with 'user defined'
0:00:00.096588 INFO: Updating config with 'user defined (cli)'
0:00:00.096654 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/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1', 'general': {'thread_count': 100, 'mbr_step_enabled': True, 'transfer_step_enabled': True}, 'library_prediction': {'enabled': True, 'enzyme': 'trypsin/p', 'missed_cleavages': 1, 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M', 'max_var_mod_num': 1, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [380.0, 980.0], 'fragment_mz': [150.0, 2000.0]}, 'search': {'target_ms1_tolerance': 3, 'target_ms2_tolerance': 10, 'extraction_backend': 'rust'}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins'}, 'search_output': {'normalize_directlfq': True}, 'search_initial': {'ms1_tolerance': 3, 'ms2_tolerance': 10}}, {'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']}, {'transfer_library': {'enabled': True}, 'transfer_learning': {'enabled': True}, 'quant_directory': None, 'general': {'save_library': False}, 'output_directory': '/home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer'}]
0:00:00.096856 INFO: Updating config with 'user defined'
0:00:00.096901 INFO: Updating config with 'user defined (cli)'
0:00:00.096920 INFO: Updating config with 'multistep search'
0:00:00.096957 INFO: ├──version: None
0:00:00.096980 INFO: ├──workflow_name: None
0:00:00.097001 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer [multistep search, default: None][0m
0:00:00.097021 INFO: ├──library_path: None
0:00:00.097039 INFO: ├──raw_paths:
0:00:00.097057 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:00:00.097074 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:00:00.097091 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:00:00.097111 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:00:00.097129 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:00:00.097155 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:00:00.097175 INFO: ├──fasta_paths:
0:00:00.097193 INFO: │   [32;20m- /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta [user defined, default: None][0m
0:00:00.097212 INFO: ├──quant_directory: None
0:00:00.097228 INFO: ├──general
0:00:00.097247 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
0:00:00.097266 INFO: │   [32;20m├──transfer_step_enabled: True [user defined, default: False][0m
0:00:00.097283 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
0:00:00.097300 INFO: │   ├──reuse_calibration: False
0:00:00.097317 INFO: │   ├──reuse_quant: False
0:00:00.097335 INFO: │   ├──log_level: INFO
0:00:00.097352 INFO: │   ├──use_gpu: True
0:00:00.097370 INFO: │   ├──save_figures: True
0:00:00.097390 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.097408 INFO: │   ├──save_flat_library: False
0:00:00.097426 INFO: │   ├──input_library_type: base
0:00:00.097443 INFO: │   ├──save_mbr_library: True
0:00:00.097461 INFO: │   ├──random_state: None
0:00:00.097478 INFO: │   └──fail_fast: False
0:00:00.097496 INFO: ├──library_loading
0:00:00.097515 INFO: │   └──drop_decoys: False
0:00:00.097533 INFO: ├──library_prediction
0:00:00.097552 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.097570 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.097587 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.097604 INFO: │   [32;20m├──variable_modifications: Oxidation@M [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
0:00:00.097622 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.097640 INFO: │   ├──missed_cleavages: 1
0:00:00.097657 INFO: │   ├──precursor_len:
0:00:00.097677 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.097695 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.097711 INFO: │   ├──precursor_charge:
0:00:00.097728 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.097744 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.097760 INFO: │   ├──precursor_mz:
0:00:00.097778 INFO: │   │   [32;20m- 380.0 [user defined, default: 400][0m
0:00:00.097795 INFO: │   │   [32;20m- 980.0 [user defined, default: 1200][0m
0:00:00.097811 INFO: │   ├──fragment_mz:
0:00:00.097827 INFO: │   │   [32;20m- 150.0 [user defined, default: 200][0m
0:00:00.097844 INFO: │   │   - 2000.0
0:00:00.097861 INFO: │   ├──nce: 25.0
0:00:00.097878 INFO: │   ├──fragment_types:
0:00:00.097894 INFO: │   │   - b
0:00:00.097910 INFO: │   │   - y
0:00:00.097928 INFO: │   ├──max_fragment_charge: 2
0:00:00.097945 INFO: │   ├──instrument: Lumos
0:00:00.097962 INFO: │   ├──peptdeep_model_path: None
0:00:00.097978 INFO: │   ├──peptdeep_model_type: generic
0:00:00.097995 INFO: │   ├──predict_charge: False
0:00:00.098013 INFO: │   └──min_charge_probability: 0.1
0:00:00.098030 INFO: ├──custom_modifications:
0:00:00.098047 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.098064 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.098081 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.098098 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.098115 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.098132 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.098149 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.098165 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.098182 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.098199 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.098224 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.098244 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.098261 INFO: │   ├──name: Label:13C(12)@K
0:00:00.098278 INFO: │   └──composition: C(12)
0:00:00.098293 INFO: ├──search
0:00:00.098310 INFO: │   ├──extraction_backend: rust
0:00:00.098328 INFO: │   [32;20m├──target_ms1_tolerance: 3 [user defined, default: 5][0m
0:00:00.098345 INFO: │   ├──target_ms2_tolerance: 10
0:00:00.098362 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.098379 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.098396 INFO: │   ├──quant_window: 3
0:00:00.098413 INFO: │   ├──target_num_candidates: 3
0:00:00.098430 INFO: │   ├──channel_filter: 
0:00:00.098446 INFO: │   ├──compete_for_fragments: True
0:00:00.098463 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.098480 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.098497 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.098514 INFO: │   ├──optimized_peak_group_score: False
0:00:00.098531 INFO: │   ├──exclude_shared_ions: True
0:00:00.098547 INFO: │   ├──quant_all: True
0:00:00.098565 INFO: │   └──experimental_xic: True
0:00:00.098582 INFO: ├──calibration
0:00:00.098601 INFO: │   ├──batch_size: 1000
0:00:00.098619 INFO: │   ├──optimization_lock_target: 1000
0:00:00.098637 INFO: │   ├──max_steps: 20
0:00:00.098654 INFO: │   ├──min_steps: 5
0:00:00.098672 INFO: │   ├──max_skips: 1
0:00:00.098689 INFO: │   ├──max_fragments: 5000
0:00:00.098707 INFO: │   └──min_correlation: 0.7
0:00:00.098724 INFO: ├──search_initial
0:00:00.098742 INFO: │   ├──num_candidates: 1
0:00:00.098759 INFO: │   [32;20m├──ms1_tolerance: 3 [user defined, default: 30][0m
0:00:00.098776 INFO: │   [32;20m├──ms2_tolerance: 10 [user defined, default: 30][0m
0:00:00.098794 INFO: │   ├──mobility_tolerance: 0.1
0:00:00.098812 INFO: │   └──rt_tolerance: 0.5
0:00:00.098829 INFO: ├──library_multiplexing
0:00:00.098848 INFO: │   ├──enabled: False
0:00:00.098866 INFO: │   ├──input_channel: 0
0:00:00.098882 INFO: │   └──multiplex_mapping:
0:00:00.098899 INFO: ├──multiplexing
0:00:00.098916 INFO: │   ├──enabled: False
0:00:00.098933 INFO: │   ├──target_channels: 4,8
0:00:00.098950 INFO: │   ├──decoy_channel: 12
0:00:00.098966 INFO: │   ├──reference_channel: 0
0:00:00.098983 INFO: │   └──competitive_scoring: True
0:00:00.099000 INFO: ├──fdr
0:00:00.099017 INFO: │   ├──fdr: 0.01
0:00:00.099033 INFO: │   ├──group_level: proteins
0:00:00.099050 INFO: │   ├──inference_strategy: heuristic
0:00:00.099067 INFO: │   ├──competitive_scoring: True
0:00:00.099084 INFO: │   ├──keep_decoys: False
0:00:00.099101 INFO: │   ├──keep_decoys_in_mbr_library: False
0:00:00.099118 INFO: │   ├──channel_wise_fdr: False
0:00:00.099136 INFO: │   └──enable_nn_hyperparameter_tuning: True
0:00:00.099163 INFO: ├──search_output
0:00:00.099182 INFO: │   ├──file_format: parquet
0:00:00.099199 INFO: │   ├──precursor_level_lfq: True
0:00:00.099216 INFO: │   ├──peptide_level_lfq: True
0:00:00.099233 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.099249 INFO: │   ├──min_k_fragments: 12
0:00:00.099266 INFO: │   ├──min_correlation: 0.9
0:00:00.099283 INFO: │   ├──num_samples_quadratic: 50
0:00:00.099300 INFO: │   ├──min_nonnan: 3
0:00:00.099317 INFO: │   ├──normalization_method: directlfq
0:00:00.099334 INFO: │   └──normalize_directlfq: True
0:00:00.099350 INFO: ├──optimization
0:00:00.099368 INFO: │   ├──order_of_optimization: None
0:00:00.099385 INFO: │   ├──ms2_error
0:00:00.099403 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.099424 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.099443 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.099462 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.099479 INFO: │   │   ├──try_narrower_values: True
0:00:00.099496 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.099513 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.099530 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.099546 INFO: │   ├──ms1_error
0:00:00.099564 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.099581 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.099598 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.099615 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.099631 INFO: │   │   ├──try_narrower_values: False
0:00:00.099648 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.099665 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.099682 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.099698 INFO: │   ├──mobility_error
0:00:00.099715 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.099732 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.099750 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.099768 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.099786 INFO: │   │   ├──try_narrower_values: False
0:00:00.099803 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.099821 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.099838 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.099855 INFO: │   └──rt_error
0:00:00.099873 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.099891 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.099909 INFO: │       ├──automatic_update_percentile_range: 0.999
0:00:00.099927 INFO: │       ├──automatic_update_factor: 1.5
0:00:00.099945 INFO: │       ├──try_narrower_values: True
0:00:00.099962 INFO: │       ├──maximal_decrease: 0.1
0:00:00.099980 INFO: │       ├──favour_narrower_optimum: False
0:00:00.099997 INFO: │       └──maximum_decrease_from_maximum: 0.5
0:00:00.100015 INFO: ├──optimization_manager
0:00:00.100033 INFO: │   ├──fwhm_rt: 5
0:00:00.100051 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.100069 INFO: │   └──score_cutoff: 0
0:00:00.100085 INFO: ├──transfer_library
0:00:00.100102 INFO: │   [32;20m├──enabled: True [multistep search, default: False][0m
0:00:00.100119 INFO: │   ├──fragment_types:
0:00:00.100136 INFO: │   │   - b
0:00:00.100152 INFO: │   │   - y
0:00:00.100169 INFO: │   ├──max_charge: 2
0:00:00.100186 INFO: │   ├──top_k_samples: 3
0:00:00.100202 INFO: │   ├──norm_delta_max: True
0:00:00.100219 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.100236 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.100252 INFO: └──transfer_learning
0:00:00.100270 INFO:     [32;20m├──enabled: True [multistep search, default: False][0m
0:00:00.100287 INFO:     ├──batch_size: 2000
0:00:00.100304 INFO:     ├──max_lr: 0.0001
0:00:00.100321 INFO:     ├──train_fraction: 0.7
0:00:00.100338 INFO:     ├──validation_fraction: 0.2
0:00:00.100355 INFO:     ├──test_fraction: 0.1
0:00:00.100372 INFO:     ├──test_interval: 1
0:00:00.100388 INFO:     ├──lr_patience: 3
0:00:00.100405 INFO:     ├──epochs: 51
0:00:00.100421 INFO:     ├──warmup_epochs: 5
0:00:00.100438 INFO:     ├──nce: 25
0:00:00.100455 INFO:     └──instrument: Lumos
0:00:00.105611 INFO: Registering 7 custom modifications
0:00:00.147422 INFO: Searching 6 files:
0:00:00.147573 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:00:00.147597 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:00:00.147625 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:00:00.147645 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:00:00.147662 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:00:00.147678 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:00:00.147694 INFO: Using 1 fasta files:
0:00:00.147712 INFO:   /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
0:00:00.147731 INFO: Using library: None
0:00:00.147748 INFO: Saving output to: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer
0:00:00.147784 PROGRESS: Loading spectral library
0:00:00.147813 PROGRESS: No library provided. Building library from fasta files.
0:00:00.147860 INFO: Running FastaDigest
0:00:00.150241 INFO: Digesting fasta file
0:00:07.034920 INFO: Adding modifications
0:01:55.148591 INFO: Removing non-canonical amino acids
0:02:01.735715 INFO: Fasta library contains 6,091,314 precursors
0:02:01.736013 PROGRESS: Predicting library properties.
0:02:01.736108 INFO: Running PeptDeepPrediction
0:02:01.737568 INFO: Device set to cpu
0:02:03.669295 INFO: Loading PeptDeep models of type generic
0:02:05.147583 INFO: Predicting RT, MS2 and mobility
0:02:05.147815 INFO: Using multiprocessing with 100 processes ...
0:02:05.780227 INFO: Predicting rt,ms2,mobility ...
0:08:29.189967 INFO: Adding fragment mz information
0:08:29.492707 INFO: Adding fragment intensity information
0:08:29.795503 INFO: Adding precursor information
0:08:30.124160 INFO: Running PrecursorInitializer
0:08:30.147684 INFO: Running AnnotateFasta
0:08:56.860157 INFO: Running IsotopeGenerator
0:08:56.861659 WARNING: Multiprocessing not compatible with custom modifications yet, falling back to single process.
0:13:26.540014 INFO: Running RTNormalization
0:13:26.540383 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:13:26.540501 INFO: Saving library to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/speclib.hdf
0:14:01.295951 INFO: Running DecoyGenerator
0:16:01.362455 INFO: Running FlattenLibrary
0:16:30.508083 INFO: Running InitFlatColumns
0:16:30.745329 INFO: Running LogFlatLibraryStats
0:16:30.745477 INFO: ============ Library Stats ============
0:16:30.745516 INFO: Number of precursors: 12,150,378
0:16:32.568936 INFO: 	thereof targets:6,091,314
0:16:32.569085 INFO: 	thereof decoys: 6,059,064
0:16:32.656204 INFO: Number of elution groups: 6,091,314
0:16:32.656348 INFO: 	average size: 1.99
0:16:32.944676 INFO: Number of proteins: 117,993
0:16:32.977320 INFO: Number of channels: 1 ([0])
0:16:32.977497 INFO: Isotopes Distribution for 4 isotopes
0:16:32.977526 INFO: =======================================
0:16:32.977612 PROGRESS: =================== Starting Search Workflows for step transfer ===================
0:16:32.977777 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 
0:16:32.977844 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant
0:16:32.977944 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/figures
0:16:32.978212 INFO: Initializing TimingManager
0:16:32.978700 INFO: Initializing RawFileManager
0:16:42.750922 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.
0:16:42.759653 INFO: Determining DIA cycle
0:16:43.084144 INFO: Found cycle with start 0.00 min and length 300.
0:16:43.247230 INFO: RT (min)            : 0.0 - 26.9
0:16:43.247338 INFO: RT duration (sec)   : 1611.2
0:16:43.247367 INFO: RT duration (min)   : 26.9
0:16:43.247392 INFO: Cycle len (scans)   : 300
0:16:43.247413 INFO: Cycle len (sec)     : 1.65
0:16:43.247433 INFO: Number of cycles    : 977
0:16:43.247452 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:16:43.247490 INFO: Creating DIA data object took: 10.2686927318573
0:16:44.067837 INFO: Creating DIA data NG object took: 0.8202023506164551
0:16:45.335432 INFO: Initializing CalibrationManager
0:16:45.335720 INFO: Setting up calibration estimators ..
0:16:45.335788 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:16:45.335876 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'}' ..
0:16:45.335974 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:16:45.336032 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:16:45.336093 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}}' ..
0:16:45.336148 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:16:45.336195 INFO: Done setting up calibration estimators.
0:16:45.336391 INFO: Initializing OptimizationManager
0:16:45.336532 INFO: initial parameter: ms1_error = 3
0:16:45.336588 INFO: initial parameter: ms2_error = 10
0:16:45.336635 INFO: initial parameter: rt_error = 805.5992431640625
0:16:45.336680 INFO: initial parameter: mobility_error = 0.1
0:16:45.336723 INFO: initial parameter: num_candidates = 1
0:16:45.336763 INFO: initial parameter: fwhm_rt = 5
0:16:45.336806 INFO: initial parameter: fwhm_mobility = 0.01
0:16:45.336848 INFO: initial parameter: score_cutoff = 0
0:16:45.336895 INFO: initial parameter: classifier_version = -1
0:16:45.336968 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:16:45.337252 INFO: FDRManager: loading saved state not requested, will be initialized.
0:16:45.337287 INFO: Initializing FDRManager
0:16:45.337325 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
0:16:46.748857 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
0:16:48.225786 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
0:16:48.226254 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
0:16:48.226380 PROGRESS: Starting initial search for precursors.
0:16:48.226471 INFO: Starting optimization step 0.
0:16:48.226540 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:16:48.226603 INFO: Using rust extraction backend
0:16:48.226674 PROGRESS: Extracting batch of 1963 precursors
0:16:48.232026 INFO: === Search parameters used ===
0:16:48.232124 INFO: rt_error       : 805.5992431640625
0:16:48.232173 INFO: mobility_error : 0.1
0:16:48.232218 INFO: num_candidates : 1
0:16:48.232260 INFO: ms1_error      : 3
0:16:48.232301 INFO: ms2_error      : 10
0:16:48.232343 INFO: fwhm_rt        : 5
0:16:48.232387 INFO: quant_window   : 3
0:16:48.232428 INFO: ==============================================
0:16:48.257794 INFO: performing precursor FDR with 40 features
0:16:48.257864 INFO: Decoy channel: -1
0:16:48.257891 INFO: competitive: True
0:16:48.259082 INFO: Setting torch num_threads to 2 for FDR classification task
0:16:48.261260 INFO: Estimating optimal hyperparameters - samples: 1,565, batch_size: 128, learning_rate: 1.77e-04
0:16:48.262074 INFO: Using random state 582637 for train-test-split
0:16:48.422255 INFO: Test AUC: 0.505
0:16:48.422343 INFO: Train AUC: 0.579
0:16:48.422371 INFO: AUC difference: 12.77%
0:16:48.422394 WARNING: AUC difference > 5%. This may indicate overfitting.
0:16:48.708055 INFO: Resetting torch num_threads to 100
0:16:48.709555 PROGRESS: === Extracted 1957 precursors and 10979 fragments ===
0:16:48.709907 INFO: === FDR correction performed with classifier version -1 ===
0:16:48.710393 PROGRESS: ============================= Precursor FDR =============================
0:16:48.710478 PROGRESS: Total precursors accumulated: 10
0:16:48.710536 PROGRESS: Target precursors: 10 (100.00%)
0:16:48.710592 PROGRESS: Decoy precursors: 0 (0.00%)
0:16:48.710637 PROGRESS: 
0:16:48.710679 PROGRESS: Precursor Summary:
0:16:48.711775 PROGRESS: Channel   0:	 0.050 FDR:    10; 0.010 FDR:    10; 0.001 FDR:    10
0:16:48.711861 PROGRESS: 
0:16:48.711914 PROGRESS: Protein Summary:
0:16:48.713092 PROGRESS: Channel   0:	 0.050 FDR:    10; 0.010 FDR:    10; 0.001 FDR:    10
0:16:48.713175 PROGRESS: =========================================================================
0:16:48.713360 INFO: Target number of precursors not reached yet.
0:16:48.797716 INFO: Starting optimization step 1.
0:16:48.797948 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:16:48.798030 INFO: Using rust extraction backend
0:16:48.798092 PROGRESS: Extracting batch of 3911 precursors
0:16:48.806878 INFO: === Search parameters used ===
0:16:48.807013 INFO: rt_error       : 805.5992431640625
0:16:48.807064 INFO: mobility_error : 0.1
0:16:48.807107 INFO: num_candidates : 1
0:16:48.807158 INFO: ms1_error      : 3
0:16:48.807204 INFO: ms2_error      : 10
0:16:48.807245 INFO: fwhm_rt        : 5
0:16:48.807283 INFO: quant_window   : 3
0:16:48.807322 INFO: ==============================================
0:16:48.851738 INFO: performing precursor FDR with 40 features
0:16:48.851831 INFO: Decoy channel: -1
0:16:48.851854 INFO: competitive: True
0:16:48.856683 INFO: Setting torch num_threads to 2 for FDR classification task
0:16:48.859593 INFO: Estimating optimal hyperparameters - samples: 4,687, batch_size: 128, learning_rate: 1.77e-04
0:16:48.859677 INFO: Using random state 718521 for train-test-split
0:16:49.310811 INFO: Test AUC: 0.548
0:16:49.310897 INFO: Train AUC: 0.588
0:16:49.310926 INFO: AUC difference: 6.67%
0:16:49.310950 WARNING: AUC difference > 5%. This may indicate overfitting.
0:16:49.558982 INFO: Resetting torch num_threads to 100
0:16:49.566803 PROGRESS: === Extracted 5859 precursors and 32958 fragments ===
0:16:49.567204 INFO: === FDR correction performed with classifier version -1 ===
0:16:49.567697 PROGRESS: ============================= Precursor FDR =============================
0:16:49.567783 PROGRESS: Total precursors accumulated: 12
0:16:49.567842 PROGRESS: Target precursors: 12 (100.00%)
0:16:49.567893 PROGRESS: Decoy precursors: 0 (0.00%)
0:16:49.567941 PROGRESS: 
0:16:49.567987 PROGRESS: Precursor Summary:
0:16:49.569054 PROGRESS: Channel   0:	 0.050 FDR:    12; 0.010 FDR:    12; 0.001 FDR:    12
0:16:49.569139 PROGRESS: 
0:16:49.569194 PROGRESS: Protein Summary:
0:16:49.570385 PROGRESS: Channel   0:	 0.050 FDR:    12; 0.010 FDR:    12; 0.001 FDR:    12
0:16:49.570470 PROGRESS: =========================================================================
0:16:49.570753 INFO: Target number of precursors not reached yet.
0:16:49.674429 INFO: Starting optimization step 2.
0:16:49.674663 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:16:49.674744 INFO: Using rust extraction backend
0:16:49.674810 PROGRESS: Extracting batch of 7891 precursors
0:16:49.689669 INFO: === Search parameters used ===
0:16:49.689806 INFO: rt_error       : 805.5992431640625
0:16:49.689860 INFO: mobility_error : 0.1
0:16:49.689907 INFO: num_candidates : 1
0:16:49.689952 INFO: ms1_error      : 3
0:16:49.689996 INFO: ms2_error      : 10
0:16:49.690039 INFO: fwhm_rt        : 5
0:16:49.690082 INFO: quant_window   : 3
0:16:49.690124 INFO: ==============================================
0:16:49.767125 INFO: performing precursor FDR with 40 features
0:16:49.767234 INFO: Decoy channel: -1
0:16:49.767259 INFO: competitive: True
0:16:49.774877 INFO: Setting torch num_threads to 2 for FDR classification task
0:16:49.778392 INFO: Estimating optimal hyperparameters - samples: 10,986, batch_size: 128, learning_rate: 1.77e-04
0:16:49.778493 INFO: Using random state 167479 for train-test-split
0:16:50.845951 INFO: Test AUC: 0.550
0:16:50.846050 INFO: Train AUC: 0.588
0:16:50.846081 INFO: AUC difference: 6.48%
0:16:50.846105 WARNING: AUC difference > 5%. This may indicate overfitting.
0:16:51.571726 INFO: Resetting torch num_threads to 100
0:16:51.575614 PROGRESS: === Extracted 13733 precursors and 77029 fragments ===
0:16:51.576009 INFO: === FDR correction performed with classifier version -1 ===
0:16:51.576507 PROGRESS: ============================= Precursor FDR =============================
0:16:51.576589 PROGRESS: Total precursors accumulated: 26
0:16:51.576645 PROGRESS: Target precursors: 26 (100.00%)
0:16:51.576694 PROGRESS: Decoy precursors: 0 (0.00%)
0:16:51.576739 PROGRESS: 
0:16:51.576784 PROGRESS: Precursor Summary:
0:16:51.577838 PROGRESS: Channel   0:	 0.050 FDR:    26; 0.010 FDR:    26; 0.001 FDR:    26
0:16:51.577919 PROGRESS: 
0:16:51.577971 PROGRESS: Protein Summary:
0:16:51.579131 PROGRESS: Channel   0:	 0.050 FDR:    26; 0.010 FDR:    26; 0.001 FDR:    26
0:16:51.579233 PROGRESS: =========================================================================
0:16:51.579537 INFO: Target number of precursors not reached yet.
0:16:51.691644 INFO: Starting optimization step 3.
0:16:51.691887 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:16:51.691966 INFO: Using rust extraction backend
0:16:51.692029 PROGRESS: Extracting batch of 15777 precursors
0:16:51.720338 INFO: === Search parameters used ===
0:16:51.720505 INFO: rt_error       : 805.5992431640625
0:16:51.720557 INFO: mobility_error : 0.1
0:16:51.720604 INFO: num_candidates : 1
0:16:51.720648 INFO: ms1_error      : 3
0:16:51.720689 INFO: ms2_error      : 10
0:16:51.720743 INFO: fwhm_rt        : 5
0:16:51.720785 INFO: quant_window   : 3
0:16:51.720827 INFO: ==============================================
0:16:51.851010 INFO: performing precursor FDR with 40 features
0:16:51.851121 INFO: Decoy channel: -1
0:16:51.851162 INFO: competitive: True
0:16:51.862435 INFO: Setting torch num_threads to 2 for FDR classification task
0:16:51.868997 INFO: Estimating optimal hyperparameters - samples: 23,579, batch_size: 128, learning_rate: 1.77e-04
0:16:51.869157 INFO: Using random state 792441 for train-test-split
0:16:54.206095 INFO: Test AUC: 0.576
0:16:54.206232 INFO: Train AUC: 0.602
0:16:54.206262 INFO: AUC difference: 4.41%
0:16:54.467677 INFO: Resetting torch num_threads to 100
0:16:54.477675 PROGRESS: === Extracted 29474 precursors and 165979 fragments ===
0:16:54.478125 INFO: === FDR correction performed with classifier version -1 ===
0:16:54.478624 PROGRESS: ============================= Precursor FDR =============================
0:16:54.478712 PROGRESS: Total precursors accumulated: 105
0:16:54.478771 PROGRESS: Target precursors: 104 (99.05%)
0:16:54.478822 PROGRESS: Decoy precursors: 1 (0.95%)
0:16:54.478869 PROGRESS: 
0:16:54.478915 PROGRESS: Precursor Summary:
0:16:54.479896 PROGRESS: Channel   0:	 0.050 FDR:   104; 0.010 FDR:   104; 0.001 FDR:    44
0:16:54.479986 PROGRESS: 
0:16:54.480043 PROGRESS: Protein Summary:
0:16:54.481137 PROGRESS: Channel   0:	 0.050 FDR:   102; 0.010 FDR:   102; 0.001 FDR:    44
0:16:54.481225 PROGRESS: =========================================================================
0:16:54.481822 INFO: Target number of precursors not reached yet.
0:16:54.622855 INFO: Starting optimization step 4.
0:16:54.623108 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:16:54.623234 INFO: Using rust extraction backend
0:16:54.623307 PROGRESS: Extracting batch of 31516 precursors
0:16:54.681448 INFO: === Search parameters used ===
0:16:54.681677 INFO: rt_error       : 805.5992431640625
0:16:54.681730 INFO: mobility_error : 0.1
0:16:54.681775 INFO: num_candidates : 1
0:16:54.681818 INFO: ms1_error      : 3
0:16:54.681858 INFO: ms2_error      : 10
0:16:54.681898 INFO: fwhm_rt        : 5
0:16:54.681937 INFO: quant_window   : 3
0:16:54.681976 INFO: ==============================================
0:16:54.900716 INFO: performing precursor FDR with 40 features
0:16:54.900830 INFO: Decoy channel: -1
0:16:54.900855 INFO: competitive: True
0:16:54.922975 INFO: Setting torch num_threads to 2 for FDR classification task
0:16:54.937086 INFO: Estimating optimal hyperparameters - samples: 48,725, batch_size: 199, learning_rate: 2.20e-04
0:16:54.937290 INFO: Using random state 469163 for train-test-split
0:16:58.501150 INFO: Test AUC: 0.577
0:16:58.501257 INFO: Train AUC: 0.609
0:16:58.501286 INFO: AUC difference: 5.28%
0:16:58.501307 WARNING: AUC difference > 5%. This may indicate overfitting.
0:16:58.764567 INFO: Resetting torch num_threads to 100
0:16:58.775670 PROGRESS: === Extracted 60907 precursors and 342868 fragments ===
0:16:58.776205 INFO: === FDR correction performed with classifier version -1 ===
0:16:58.776735 PROGRESS: ============================= Precursor FDR =============================
0:16:58.776816 PROGRESS: Total precursors accumulated: 228
0:16:58.776873 PROGRESS: Target precursors: 226 (99.12%)
0:16:58.776921 PROGRESS: Decoy precursors: 2 (0.88%)
0:16:58.776965 PROGRESS: 
0:16:58.777007 PROGRESS: Precursor Summary:
0:16:58.778018 PROGRESS: Channel   0:	 0.050 FDR:   226; 0.010 FDR:   226; 0.001 FDR:   216
0:16:58.778099 PROGRESS: 
0:16:58.778151 PROGRESS: Protein Summary:
0:16:58.780377 PROGRESS: Channel   0:	 0.050 FDR:   216; 0.010 FDR:   216; 0.001 FDR:   207
0:16:58.780484 PROGRESS: =========================================================================
0:16:58.781476 INFO: Target number of precursors not reached yet.
0:16:58.964357 INFO: Starting optimization step 5.
0:16:58.964615 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:16:58.964697 INFO: Using rust extraction backend
0:16:58.964761 PROGRESS: Extracting batch of 63010 precursors
0:16:59.073814 INFO: === Search parameters used ===
0:16:59.074064 INFO: rt_error       : 805.5992431640625
0:16:59.074116 INFO: mobility_error : 0.1
0:16:59.074159 INFO: num_candidates : 1
0:16:59.074200 INFO: ms1_error      : 3
0:16:59.074239 INFO: ms2_error      : 10
0:16:59.074278 INFO: fwhm_rt        : 5
0:16:59.074315 INFO: quant_window   : 3
0:16:59.074353 INFO: ==============================================
0:16:59.449993 INFO: performing precursor FDR with 40 features
0:16:59.450107 INFO: Decoy channel: -1
0:16:59.450134 INFO: competitive: True
0:16:59.499765 INFO: Setting torch num_threads to 2 for FDR classification task
0:16:59.532579 INFO: Estimating optimal hyperparameters - samples: 99,000, batch_size: 405, learning_rate: 3.14e-04
0:16:59.533072 INFO: Using random state 766651 for train-test-split
0:17:04.067224 INFO: Test AUC: 0.588
0:17:04.067337 INFO: Train AUC: 0.612
0:17:04.067367 INFO: AUC difference: 3.93%
0:17:04.351545 INFO: Resetting torch num_threads to 100
0:17:04.375328 PROGRESS: === Extracted 123750 precursors and 696310 fragments ===
0:17:04.375962 INFO: === FDR correction performed with classifier version -1 ===
0:17:04.376599 PROGRESS: ============================= Precursor FDR =============================
0:17:04.376691 PROGRESS: Total precursors accumulated: 556
0:17:04.376752 PROGRESS: Target precursors: 551 (99.10%)
0:17:04.376806 PROGRESS: Decoy precursors: 5 (0.90%)
0:17:04.376854 PROGRESS: 
0:17:04.376918 PROGRESS: Precursor Summary:
0:17:04.378058 PROGRESS: Channel   0:	 0.050 FDR:   551; 0.010 FDR:   551; 0.001 FDR:   427
0:17:04.378147 PROGRESS: 
0:17:04.378203 PROGRESS: Protein Summary:
0:17:04.379621 PROGRESS: Channel   0:	 0.050 FDR:   496; 0.010 FDR:   496; 0.001 FDR:   392
0:17:04.379719 PROGRESS: =========================================================================
0:17:04.381526 INFO: Target number of precursors not reached yet.
0:17:04.663207 INFO: Starting optimization step 6.
0:17:04.663476 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:17:04.663562 INFO: Using rust extraction backend
0:17:04.663628 PROGRESS: Extracting batch of 126188 precursors
0:17:04.879451 INFO: === Search parameters used ===
0:17:04.879704 INFO: rt_error       : 805.5992431640625
0:17:04.879760 INFO: mobility_error : 0.1
0:17:04.879809 INFO: num_candidates : 1
0:17:04.879854 INFO: ms1_error      : 3
0:17:04.879895 INFO: ms2_error      : 10
0:17:04.879936 INFO: fwhm_rt        : 5
0:17:04.879977 INFO: quant_window   : 3
0:17:04.880017 INFO: ==============================================
0:17:05.568062 INFO: performing precursor FDR with 40 features
0:17:05.568192 INFO: Decoy channel: -1
0:17:05.568218 INFO: competitive: True
0:17:05.682835 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:05.766093 INFO: Estimating optimal hyperparameters - samples: 199,720, batch_size: 818, learning_rate: 4.47e-04
0:17:05.766496 INFO: Using random state 470671 for train-test-split
0:17:11.927386 INFO: Test AUC: 0.594
0:17:11.927527 INFO: Train AUC: 0.612
0:17:11.927561 INFO: AUC difference: 3.03%
0:17:12.249460 INFO: Resetting torch num_threads to 100
0:17:12.300538 PROGRESS: === Extracted 249650 precursors and 1403607 fragments ===
0:17:12.301221 INFO: === FDR correction performed with classifier version -1 ===
0:17:12.302014 PROGRESS: ============================= Precursor FDR =============================
0:17:12.302109 PROGRESS: Total precursors accumulated: 1,259
0:17:12.302167 PROGRESS: Target precursors: 1,247 (99.05%)
0:17:12.302217 PROGRESS: Decoy precursors: 12 (0.95%)
0:17:12.302263 PROGRESS: 
0:17:12.302307 PROGRESS: Precursor Summary:
0:17:12.303609 PROGRESS: Channel   0:	 0.050 FDR: 1,247; 0.010 FDR: 1,247; 0.001 FDR:   626
0:17:12.303701 PROGRESS: 
0:17:12.303755 PROGRESS: Protein Summary:
0:17:12.305360 PROGRESS: Channel   0:	 0.050 FDR: 1,056; 0.010 FDR: 1,056; 0.001 FDR:   558
0:17:12.305446 PROGRESS: =========================================================================
0:17:12.309853 INFO: Target number of precursors reached.
0:17:12.477065 INFO: fragments_df: keeping 5000 of 1403607 [sum(precursor_idx_mask)=13264 sum(mass_error_mask)=1403607 stop_rank=5000
0:17:12.978054 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:13.200564 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:13.913597 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:17:13.914038 INFO: Using score_cutoff 12.41551369857788 (fac=0.99, q=1)
0:17:13.914373 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:17:13.914450 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:17:13.914510 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.41551369857788
0:17:13.914570 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:14.070398 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:14.403630 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
0:17:14.403915 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:17:14.404044 INFO: Starting optimization step 7.
0:17:14.404123 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:17:14.404210 INFO: Using rust extraction backend
0:17:14.404292 PROGRESS: Extracting batch of 250256 precursors
0:17:14.832219 INFO: === Search parameters used ===
0:17:14.832493 INFO: rt_error       : 805.5992431640625
0:17:14.832553 INFO: mobility_error : 0.1
0:17:14.832603 INFO: num_candidates : 3
0:17:14.832649 INFO: ms1_error      : 3
0:17:14.832693 INFO: ms2_error      : 10
0:17:14.832736 INFO: fwhm_rt        : 3.0
0:17:14.832780 INFO: quant_window   : 3
0:17:14.832824 INFO: ==============================================
0:17:17.465580 INFO: performing precursor FDR with 40 features
0:17:17.465693 INFO: Decoy channel: -1
0:17:17.465719 INFO: competitive: True
0:17:17.658883 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:17.960108 INFO: Estimating optimal hyperparameters - samples: 599,210, batch_size: 2,454, learning_rate: 7.74e-04
0:17:17.961099 INFO: Using random state 176610 for train-test-split
0:17:30.653001 INFO: Test AUC: 0.595
0:17:30.653127 INFO: Train AUC: 0.608
0:17:30.653158 INFO: AUC difference: 2.10%
0:17:31.125610 INFO: Resetting torch num_threads to 100
0:17:31.153972 PROGRESS: === Extracted 749013 precursors and 4035118 fragments ===
0:17:31.154417 INFO: === FDR correction performed with classifier version 6 ===
0:17:31.155095 PROGRESS: ============================= Precursor FDR =============================
0:17:31.155216 PROGRESS: Total precursors accumulated: 1,451
0:17:31.155277 PROGRESS: Target precursors: 1,437 (99.04%)
0:17:31.155332 PROGRESS: Decoy precursors: 14 (0.96%)
0:17:31.155377 PROGRESS: 
0:17:31.155419 PROGRESS: Precursor Summary:
0:17:31.156744 PROGRESS: Channel   0:	 0.050 FDR: 1,437; 0.010 FDR: 1,437; 0.001 FDR: 1,024
0:17:31.156829 PROGRESS: 
0:17:31.156881 PROGRESS: Protein Summary:
0:17:31.158580 PROGRESS: Channel   0:	 0.050 FDR: 1,208; 0.010 FDR: 1,208; 0.001 FDR:   886
0:17:31.158666 PROGRESS: =========================================================================
0:17:31.172646 INFO: Target number of precursors reached.
0:17:31.617016 INFO: fragments_df: keeping 5000 of 4035118 [sum(precursor_idx_mask)=34114 sum(mass_error_mask)=4035118 stop_rank=5000
0:17:32.032227 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:32.342517 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:33.062711 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:17:33.063161 INFO: Using score_cutoff 11.625953538894652 (fac=0.99, q=1)
0:17:33.063470 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:33.063543 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:33.063595 INFO: Updating optimization_manager: score_cutoff        : 12.41551369857788 -> 11.625953538894652
0:17:33.063651 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:33.214989 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:33.545993 INFO: === checking if optimization conditions were reached ===
0:17:33.548586 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
0:17:33.548758 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:17:33.548838 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:17:33.548906 INFO: ==============================================
0:17:33.548989 INFO: Starting optimization step 8.
0:17:33.549057 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:17:33.549132 INFO: Using rust extraction backend
0:17:33.549200 PROGRESS: Extracting batch of 250256 precursors
0:17:33.975845 INFO: === Search parameters used ===
0:17:33.976101 INFO: rt_error       : 805.5992431640625
0:17:33.976157 INFO: mobility_error : 0.1
0:17:33.976203 INFO: num_candidates : 3
0:17:33.976246 INFO: ms1_error      : 3
0:17:33.976286 INFO: ms2_error      : 10.0
0:17:33.976326 INFO: fwhm_rt        : 3.0
0:17:33.976364 INFO: quant_window   : 3
0:17:33.976402 INFO: ==============================================
0:17:36.394917 INFO: performing precursor FDR with 40 features
0:17:36.395037 INFO: Decoy channel: -1
0:17:36.395063 INFO: competitive: True
0:17:36.578082 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:36.859974 INFO: Estimating optimal hyperparameters - samples: 599,221, batch_size: 2,454, learning_rate: 7.74e-04
0:17:36.861064 INFO: Using random state 493132 for train-test-split
0:17:49.690681 INFO: Test AUC: 0.604
0:17:49.690882 INFO: Train AUC: 0.614
0:17:49.690916 INFO: AUC difference: 1.53%
0:17:50.172143 INFO: Resetting torch num_threads to 100
0:17:50.201310 PROGRESS: === Extracted 749027 precursors and 4034880 fragments ===
0:17:50.201806 INFO: === FDR correction performed with classifier version 7 ===
0:17:50.202562 PROGRESS: ============================= Precursor FDR =============================
0:17:50.202707 PROGRESS: Total precursors accumulated: 1,554
0:17:50.202766 PROGRESS: Target precursors: 1,539 (99.03%)
0:17:50.202816 PROGRESS: Decoy precursors: 15 (0.97%)
0:17:50.202863 PROGRESS: 
0:17:50.202907 PROGRESS: Precursor Summary:
0:17:50.204269 PROGRESS: Channel   0:	 0.050 FDR: 1,539; 0.010 FDR: 1,539; 0.001 FDR: 1,108
0:17:50.204361 PROGRESS: 
0:17:50.204416 PROGRESS: Protein Summary:
0:17:50.206164 PROGRESS: Channel   0:	 0.050 FDR: 1,287; 0.010 FDR: 1,287; 0.001 FDR:   953
0:17:50.206252 PROGRESS: =========================================================================
0:17:50.221662 INFO: Target number of precursors reached.
0:17:50.668238 INFO: fragments_df: keeping 5000 of 4034880 [sum(precursor_idx_mask)=36427 sum(mass_error_mask)=4034880 stop_rank=5000
0:17:51.086664 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:17:51.335561 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:17:52.048871 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:17:52.049310 INFO: Using score_cutoff 11.919555304527282 (fac=0.99, q=1)
0:17:52.049644 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:17:52.049723 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:17:52.049779 INFO: Updating optimization_manager: score_cutoff        : 11.625953538894652 -> 11.919555304527282
0:17:52.049843 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:17:52.203622 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:17:52.541595 INFO: === checking if optimization conditions were reached ===
0:17:52.544247 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:17:52.544409 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:17:52.544488 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:17:52.544558 INFO: ==============================================
0:17:52.544636 INFO: Starting optimization step 9.
0:17:52.544703 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:17:52.544781 INFO: Using rust extraction backend
0:17:52.544852 PROGRESS: Extracting batch of 250256 precursors
0:17:52.973643 INFO: === Search parameters used ===
0:17:52.973902 INFO: rt_error       : 805.5992431640625
0:17:52.973959 INFO: mobility_error : 0.1
0:17:52.974008 INFO: num_candidates : 3
0:17:52.974055 INFO: ms1_error      : 3
0:17:52.974099 INFO: ms2_error      : 10.0
0:17:52.974143 INFO: fwhm_rt        : 3.0
0:17:52.974184 INFO: quant_window   : 3
0:17:52.974225 INFO: ==============================================
0:17:55.423126 INFO: performing precursor FDR with 40 features
0:17:55.423262 INFO: Decoy channel: -1
0:17:55.423288 INFO: competitive: True
0:17:55.610247 INFO: Setting torch num_threads to 2 for FDR classification task
0:17:55.899613 INFO: Estimating optimal hyperparameters - samples: 599,217, batch_size: 2,454, learning_rate: 7.74e-04
0:17:55.900638 INFO: Using random state 326588 for train-test-split
0:18:08.889235 INFO: Test AUC: 0.606
0:18:08.889366 INFO: Train AUC: 0.620
0:18:08.889398 INFO: AUC difference: 2.27%
0:18:09.349787 INFO: Resetting torch num_threads to 100
0:18:09.378552 PROGRESS: === Extracted 749022 precursors and 4034550 fragments ===
0:18:09.379032 INFO: === FDR correction performed with classifier version 8 ===
0:18:09.379746 PROGRESS: ============================= Precursor FDR =============================
0:18:09.379844 PROGRESS: Total precursors accumulated: 1,543
0:18:09.379902 PROGRESS: Target precursors: 1,528 (99.03%)
0:18:09.379951 PROGRESS: Decoy precursors: 15 (0.97%)
0:18:09.379997 PROGRESS: 
0:18:09.380042 PROGRESS: Precursor Summary:
0:18:09.381440 PROGRESS: Channel   0:	 0.050 FDR: 1,528; 0.010 FDR: 1,528; 0.001 FDR: 1,199
0:18:09.381531 PROGRESS: 
0:18:09.381589 PROGRESS: Protein Summary:
0:18:09.383394 PROGRESS: Channel   0:	 0.050 FDR: 1,279; 0.010 FDR: 1,279; 0.001 FDR: 1,025
0:18:09.383489 PROGRESS: =========================================================================
0:18:09.398067 INFO: Target number of precursors reached.
0:18:09.843715 INFO: fragments_df: keeping 5000 of 4034550 [sum(precursor_idx_mask)=36418 sum(mass_error_mask)=4034550 stop_rank=5000
0:18:10.353383 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:10.585203 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:11.297898 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:11.298338 INFO: Using score_cutoff 12.212347755432129 (fac=0.99, q=1)
0:18:11.298662 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:11.298742 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:11.298804 INFO: Updating optimization_manager: score_cutoff        : 11.919555304527282 -> 12.212347755432129
0:18:11.298867 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:11.448168 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:11.787065 INFO: === checking if optimization conditions were reached ===
0:18:11.789560 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:18:11.789685 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:18:11.789763 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:18:11.789834 INFO: ==============================================
0:18:11.789916 INFO: Starting optimization step 10.
0:18:11.789984 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:18:11.790054 INFO: Using rust extraction backend
0:18:11.790121 PROGRESS: Extracting batch of 250256 precursors
0:18:12.213395 INFO: === Search parameters used ===
0:18:12.213648 INFO: rt_error       : 805.5992431640625
0:18:12.213703 INFO: mobility_error : 0.1
0:18:12.213751 INFO: num_candidates : 3
0:18:12.213794 INFO: ms1_error      : 3
0:18:12.213836 INFO: ms2_error      : 10.0
0:18:12.213878 INFO: fwhm_rt        : 3.0
0:18:12.213918 INFO: quant_window   : 3
0:18:12.213959 INFO: ==============================================
0:18:14.637309 INFO: performing precursor FDR with 40 features
0:18:14.637452 INFO: Decoy channel: -1
0:18:14.637479 INFO: competitive: True
0:18:14.816365 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:15.099644 INFO: Estimating optimal hyperparameters - samples: 599,214, batch_size: 2,454, learning_rate: 7.74e-04
0:18:15.100630 INFO: Using random state 783767 for train-test-split
0:18:27.796552 INFO: Test AUC: 0.611
0:18:27.796680 INFO: Train AUC: 0.622
0:18:27.796712 INFO: AUC difference: 1.76%
0:18:28.667392 INFO: Resetting torch num_threads to 100
0:18:28.762294 PROGRESS: === Extracted 749018 precursors and 4034727 fragments ===
0:18:28.762786 INFO: === FDR correction performed with classifier version 9 ===
0:18:28.763617 PROGRESS: ============================= Precursor FDR =============================
0:18:28.763721 PROGRESS: Total precursors accumulated: 1,682
0:18:28.763783 PROGRESS: Target precursors: 1,666 (99.05%)
0:18:28.763835 PROGRESS: Decoy precursors: 16 (0.95%)
0:18:28.763883 PROGRESS: 
0:18:28.763928 PROGRESS: Precursor Summary:
0:18:28.765303 PROGRESS: Channel   0:	 0.050 FDR: 1,666; 0.010 FDR: 1,666; 0.001 FDR:   637
0:18:28.765396 PROGRESS: 
0:18:28.765453 PROGRESS: Protein Summary:
0:18:28.767194 PROGRESS: Channel   0:	 0.050 FDR: 1,387; 0.010 FDR: 1,387; 0.001 FDR:   566
0:18:28.767290 PROGRESS: =========================================================================
0:18:28.781508 INFO: Target number of precursors reached.
0:18:29.220211 INFO: fragments_df: keeping 5000 of 4034727 [sum(precursor_idx_mask)=39335 sum(mass_error_mask)=4034727 stop_rank=5000
0:18:29.659374 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:29.921202 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:30.633152 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:30.633591 INFO: Using score_cutoff 11.490290647029877 (fac=0.99, q=1)
0:18:30.633917 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:30.634002 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:30.634059 INFO: Updating optimization_manager: score_cutoff        : 12.212347755432129 -> 11.490290647029877
0:18:30.634116 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:30.784462 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:31.120907 INFO: === checking if optimization conditions were reached ===
0:18:31.123386 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:18:31.123517 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:18:31.123600 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:18:31.123685 INFO: ==============================================
0:18:31.123766 INFO: Starting optimization step 11.
0:18:31.123855 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:18:31.123929 INFO: Using rust extraction backend
0:18:31.123997 PROGRESS: Extracting batch of 250256 precursors
0:18:31.553786 INFO: === Search parameters used ===
0:18:31.554047 INFO: rt_error       : 805.5992431640625
0:18:31.554104 INFO: mobility_error : 0.1
0:18:31.554152 INFO: num_candidates : 3
0:18:31.554196 INFO: ms1_error      : 3
0:18:31.554238 INFO: ms2_error      : 10.0
0:18:31.554279 INFO: fwhm_rt        : 3.0
0:18:31.554350 INFO: quant_window   : 3
0:18:31.554393 INFO: ==============================================
0:18:33.978415 INFO: performing precursor FDR with 40 features
0:18:33.978567 INFO: Decoy channel: -1
0:18:33.978596 INFO: competitive: True
0:18:34.162665 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:34.458107 INFO: Estimating optimal hyperparameters - samples: 599,211, batch_size: 2,454, learning_rate: 7.74e-04
0:18:34.459125 INFO: Using random state 240954 for train-test-split
0:18:47.173262 INFO: Test AUC: 0.610
0:18:47.173391 INFO: Train AUC: 0.623
0:18:47.173422 INFO: AUC difference: 2.10%
0:18:47.654071 INFO: Resetting torch num_threads to 100
0:18:47.679796 PROGRESS: === Extracted 749014 precursors and 4034822 fragments ===
0:18:47.680248 INFO: === FDR correction performed with classifier version 10 ===
0:18:47.680952 PROGRESS: ============================= Precursor FDR =============================
0:18:47.681044 PROGRESS: Total precursors accumulated: 1,691
0:18:47.681104 PROGRESS: Target precursors: 1,675 (99.05%)
0:18:47.681155 PROGRESS: Decoy precursors: 16 (0.95%)
0:18:47.681203 PROGRESS: 
0:18:47.681248 PROGRESS: Precursor Summary:
0:18:47.682662 PROGRESS: Channel   0:	 0.050 FDR: 1,675; 0.010 FDR: 1,675; 0.001 FDR: 1,220
0:18:47.682749 PROGRESS: 
0:18:47.682804 PROGRESS: Protein Summary:
0:18:47.684671 PROGRESS: Channel   0:	 0.050 FDR: 1,427; 0.010 FDR: 1,427; 0.001 FDR: 1,043
0:18:47.684767 PROGRESS: =========================================================================
0:18:47.702589 INFO: Target number of precursors reached.
0:18:48.143894 INFO: fragments_df: keeping 5000 of 4034822 [sum(precursor_idx_mask)=38242 sum(mass_error_mask)=4034822 stop_rank=5000
0:18:48.558452 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:18:48.814070 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:18:49.526595 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:18:49.527035 INFO: Using score_cutoff 7.462826305389404 (fac=0.99, q=1)
0:18:49.527360 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:18:49.527441 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:18:49.527497 INFO: Updating optimization_manager: score_cutoff        : 11.490290647029877 -> 7.462826305389404
0:18:49.527552 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:49.677909 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:50.018316 INFO: === checking if optimization conditions were reached ===
0:18:50.020841 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:18:50.020959 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:18:50.021037 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:18:50.021105 INFO: ==============================================
0:18:50.021190 PROGRESS: Optimization finished for ms2_error.
0:18:50.413925 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:18:50.566290 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:18:50.900003 INFO: Starting optimization step 0.
0:18:50.900287 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:18:50.900385 INFO: Using rust extraction backend
0:18:50.900463 PROGRESS: Extracting batch of 250256 precursors
0:18:51.331432 INFO: === Search parameters used ===
0:18:51.331695 INFO: rt_error       : 805.5992431640625
0:18:51.331770 INFO: mobility_error : 0.1
0:18:51.331820 INFO: num_candidates : 3
0:18:51.331865 INFO: ms1_error      : 3
0:18:51.331913 INFO: ms2_error      : 10.0
0:18:51.331956 INFO: fwhm_rt        : 3.0
0:18:51.332004 INFO: quant_window   : 3
0:18:51.332047 INFO: ==============================================
0:18:53.814370 INFO: performing precursor FDR with 40 features
0:18:53.814515 INFO: Decoy channel: -1
0:18:53.814542 INFO: competitive: True
0:18:53.992853 INFO: Setting torch num_threads to 2 for FDR classification task
0:18:54.280790 INFO: Estimating optimal hyperparameters - samples: 599,264, batch_size: 2,454, learning_rate: 7.74e-04
0:18:54.281895 INFO: Using random state 878016 for train-test-split
0:19:07.258180 INFO: Test AUC: 0.612
0:19:07.258373 INFO: Train AUC: 0.626
0:19:07.258408 INFO: AUC difference: 2.22%
0:19:07.730168 INFO: Resetting torch num_threads to 100
0:19:07.758637 PROGRESS: === Extracted 749080 precursors and 4035768 fragments ===
0:19:07.759121 INFO: === FDR correction performed with classifier version 11 ===
0:19:07.759837 PROGRESS: ============================= Precursor FDR =============================
0:19:07.759926 PROGRESS: Total precursors accumulated: 1,748
0:19:07.759987 PROGRESS: Target precursors: 1,731 (99.03%)
0:19:07.760040 PROGRESS: Decoy precursors: 17 (0.97%)
0:19:07.760087 PROGRESS: 
0:19:07.760133 PROGRESS: Precursor Summary:
0:19:07.761525 PROGRESS: Channel   0:	 0.050 FDR: 1,731; 0.010 FDR: 1,731; 0.001 FDR: 1,162
0:19:07.761612 PROGRESS: 
0:19:07.761668 PROGRESS: Protein Summary:
0:19:07.763471 PROGRESS: Channel   0:	 0.050 FDR: 1,449; 0.010 FDR: 1,449; 0.001 FDR: 1,003
0:19:07.763566 PROGRESS: =========================================================================
0:19:07.776918 INFO: Target number of precursors reached.
0:19:08.207227 INFO: fragments_df: keeping 5000 of 4035768 [sum(precursor_idx_mask)=40009 sum(mass_error_mask)=4035768 stop_rank=5000
0:19:08.637240 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:08.898288 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:09.611286 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:09.611726 INFO: Using score_cutoff 9.004861372947692 (fac=0.99, q=1)
0:19:09.612046 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:09.612123 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:09.612178 INFO: Updating optimization_manager: score_cutoff        : 7.462826305389404 -> 9.004861372947692
0:19:09.612235 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:09.762920 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:10.100291 INFO: === checking if optimization conditions were reached ===
0:19:10.100616 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:19:10.103870 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 692.2912035618517
0:19:10.104041 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 692.2912.
0:19:10.104118 INFO: ==============================================
0:19:10.104207 INFO: Starting optimization step 1.
0:19:10.104278 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:19:10.104358 INFO: Using rust extraction backend
0:19:10.104432 PROGRESS: Extracting batch of 250256 precursors
0:19:10.535763 INFO: === Search parameters used ===
0:19:10.536028 INFO: rt_error       : 692.2912035618517
0:19:10.536088 INFO: mobility_error : 0.1
0:19:10.536137 INFO: num_candidates : 3
0:19:10.536183 INFO: ms1_error      : 3
0:19:10.536247 INFO: ms2_error      : 10.0
0:19:10.536290 INFO: fwhm_rt        : 3.0
0:19:10.536331 INFO: quant_window   : 3
0:19:10.536370 INFO: ==============================================
0:19:12.938522 INFO: performing precursor FDR with 40 features
0:19:12.938643 INFO: Decoy channel: -1
0:19:12.938669 INFO: competitive: True
0:19:13.120397 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:13.416197 INFO: Estimating optimal hyperparameters - samples: 599,205, batch_size: 2,454, learning_rate: 7.74e-04
0:19:13.417307 INFO: Using random state 878016 for train-test-split
0:19:25.990251 INFO: Test AUC: 0.615
0:19:25.990379 INFO: Train AUC: 0.627
0:19:25.990414 INFO: AUC difference: 1.99%
0:19:26.466878 INFO: Resetting torch num_threads to 100
0:19:26.491520 PROGRESS: === Extracted 749007 precursors and 4030789 fragments ===
0:19:26.491951 INFO: === FDR correction performed with classifier version 11 ===
0:19:26.492646 PROGRESS: ============================= Precursor FDR =============================
0:19:26.492733 PROGRESS: Total precursors accumulated: 1,754
0:19:26.492794 PROGRESS: Target precursors: 1,737 (99.03%)
0:19:26.492851 PROGRESS: Decoy precursors: 17 (0.97%)
0:19:26.492905 PROGRESS: 
0:19:26.492954 PROGRESS: Precursor Summary:
0:19:26.494365 PROGRESS: Channel   0:	 0.050 FDR: 1,737; 0.010 FDR: 1,737; 0.001 FDR: 1,189
0:19:26.494456 PROGRESS: 
0:19:26.494513 PROGRESS: Protein Summary:
0:19:26.496365 PROGRESS: Channel   0:	 0.050 FDR: 1,464; 0.010 FDR: 1,464; 0.001 FDR: 1,013
0:19:26.496468 PROGRESS: =========================================================================
0:19:26.509044 INFO: Target number of precursors reached.
0:19:26.948592 INFO: fragments_df: keeping 5000 of 4030789 [sum(precursor_idx_mask)=39763 sum(mass_error_mask)=4030789 stop_rank=5000
0:19:27.349028 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:27.614463 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:28.328789 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:28.329236 INFO: Using score_cutoff 8.982621060562135 (fac=0.99, q=1)
0:19:28.329539 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:28.329619 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:28.329676 INFO: Updating optimization_manager: score_cutoff        : 9.004861372947692 -> 8.982621060562135
0:19:28.329731 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:28.480510 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:28.810110 INFO: === checking if optimization conditions were reached ===
0:19:28.810420 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:19:28.813698 INFO: Updating optimization_manager: rt_error            : 692.2912035618517 -> 802.2747984700425
0:19:28.813828 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 802.2748.
0:19:28.813906 INFO: ==============================================
0:19:28.813992 INFO: Starting optimization step 2.
0:19:28.814062 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:19:28.814156 INFO: Using rust extraction backend
0:19:28.814230 PROGRESS: Extracting batch of 250256 precursors
0:19:29.239995 INFO: === Search parameters used ===
0:19:29.240258 INFO: rt_error       : 802.2747984700425
0:19:29.240313 INFO: mobility_error : 0.1
0:19:29.240360 INFO: num_candidates : 3
0:19:29.240404 INFO: ms1_error      : 3
0:19:29.240446 INFO: ms2_error      : 10.0
0:19:29.240487 INFO: fwhm_rt        : 3.0
0:19:29.240528 INFO: quant_window   : 3
0:19:29.240568 INFO: ==============================================
0:19:31.676791 INFO: performing precursor FDR with 40 features
0:19:31.676906 INFO: Decoy channel: -1
0:19:31.676931 INFO: competitive: True
0:19:31.842359 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:32.129857 INFO: Estimating optimal hyperparameters - samples: 599,258, batch_size: 2,454, learning_rate: 7.74e-04
0:19:32.130958 INFO: Using random state 878016 for train-test-split
0:19:45.189747 INFO: Test AUC: 0.611
0:19:45.189900 INFO: Train AUC: 0.627
0:19:45.189933 INFO: AUC difference: 2.63%
0:19:45.668350 INFO: Resetting torch num_threads to 100
0:19:45.693938 PROGRESS: === Extracted 749073 precursors and 4035284 fragments ===
0:19:45.694395 INFO: === FDR correction performed with classifier version 11 ===
0:19:45.695060 PROGRESS: ============================= Precursor FDR =============================
0:19:45.695179 PROGRESS: Total precursors accumulated: 1,583
0:19:45.695257 PROGRESS: Target precursors: 1,568 (99.05%)
0:19:45.695310 PROGRESS: Decoy precursors: 15 (0.95%)
0:19:45.695356 PROGRESS: 
0:19:45.695401 PROGRESS: Precursor Summary:
0:19:45.696766 PROGRESS: Channel   0:	 0.050 FDR: 1,568; 0.010 FDR: 1,568; 0.001 FDR: 1,364
0:19:45.696853 PROGRESS: 
0:19:45.696908 PROGRESS: Protein Summary:
0:19:45.698707 PROGRESS: Channel   0:	 0.050 FDR: 1,344; 0.010 FDR: 1,344; 0.001 FDR: 1,166
0:19:45.698797 PROGRESS: =========================================================================
0:19:45.712085 INFO: Target number of precursors reached.
0:19:46.150733 INFO: fragments_df: keeping 5000 of 4035284 [sum(precursor_idx_mask)=35771 sum(mass_error_mask)=4035284 stop_rank=5000
0:19:46.578422 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:19:46.820831 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:19:47.535789 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:19:47.536227 INFO: Using score_cutoff 7.535643789052964 (fac=0.99, q=1)
0:19:47.536547 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:19:47.536623 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:19:47.536680 INFO: Updating optimization_manager: score_cutoff        : 8.982621060562135 -> 7.535643789052964
0:19:47.536732 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:19:47.687851 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:19:48.031122 INFO: === checking if optimization conditions were reached ===
0:19:48.031453 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:19:48.034785 INFO: Updating optimization_manager: rt_error            : 802.2747984700425 -> 883.87410403317
0:19:48.034901 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 883.8741.
0:19:48.034997 INFO: ==============================================
0:19:48.035080 INFO: Starting optimization step 3.
0:19:48.035163 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:19:48.035246 INFO: Using rust extraction backend
0:19:48.035317 PROGRESS: Extracting batch of 250256 precursors
0:19:48.466279 INFO: === Search parameters used ===
0:19:48.466763 INFO: rt_error       : 883.87410403317
0:19:48.466823 INFO: mobility_error : 0.1
0:19:48.466869 INFO: num_candidates : 3
0:19:48.466912 INFO: ms1_error      : 3
0:19:48.466953 INFO: ms2_error      : 10.0
0:19:48.466991 INFO: fwhm_rt        : 3.0
0:19:48.467029 INFO: quant_window   : 3
0:19:48.467066 INFO: ==============================================
0:19:50.953533 INFO: performing precursor FDR with 40 features
0:19:50.953654 INFO: Decoy channel: -1
0:19:50.953680 INFO: competitive: True
0:19:51.131122 INFO: Setting torch num_threads to 2 for FDR classification task
0:19:51.416729 INFO: Estimating optimal hyperparameters - samples: 599,231, batch_size: 2,454, learning_rate: 7.74e-04
0:19:51.417853 INFO: Using random state 878016 for train-test-split
0:20:03.941439 INFO: Test AUC: 0.612
0:20:03.941568 INFO: Train AUC: 0.627
0:20:03.941600 INFO: AUC difference: 2.50%
0:20:04.413427 INFO: Resetting torch num_threads to 100
0:20:04.438677 PROGRESS: === Extracted 749039 precursors and 4035369 fragments ===
0:20:04.439125 INFO: === FDR correction performed with classifier version 11 ===
0:20:04.439852 PROGRESS: ============================= Precursor FDR =============================
0:20:04.439939 PROGRESS: Total precursors accumulated: 1,791
0:20:04.439999 PROGRESS: Target precursors: 1,774 (99.05%)
0:20:04.440050 PROGRESS: Decoy precursors: 17 (0.95%)
0:20:04.440099 PROGRESS: 
0:20:04.440146 PROGRESS: Precursor Summary:
0:20:04.441554 PROGRESS: Channel   0:	 0.050 FDR: 1,774; 0.010 FDR: 1,774; 0.001 FDR: 1,371
0:20:04.441655 PROGRESS: 
0:20:04.441713 PROGRESS: Protein Summary:
0:20:04.443651 PROGRESS: Channel   0:	 0.050 FDR: 1,482; 0.010 FDR: 1,482; 0.001 FDR: 1,156
0:20:04.443762 PROGRESS: =========================================================================
0:20:04.460449 INFO: Target number of precursors reached.
0:20:04.900078 INFO: fragments_df: keeping 5000 of 4035369 [sum(precursor_idx_mask)=41371 sum(mass_error_mask)=4035369 stop_rank=5000
0:20:05.305068 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:20:05.564760 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:20:06.274798 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:20:06.275264 INFO: Using score_cutoff 10.783176347351073 (fac=0.99, q=1)
0:20:06.275572 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:20:06.275650 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:20:06.275706 INFO: Updating optimization_manager: score_cutoff        : 7.535643789052964 -> 10.783176347351073
0:20:06.275760 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:20:06.424534 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:20:06.753826 INFO: === checking if optimization conditions were reached ===
0:20:06.754134 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:20:06.757739 INFO: Updating optimization_manager: rt_error            : 883.87410403317 -> 504.96745095334285
0:20:06.757905 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 504.9675.
0:20:06.758008 INFO: ==============================================
0:20:06.758094 INFO: Starting optimization step 4.
0:20:06.758164 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:20:06.758236 INFO: Using rust extraction backend
0:20:06.758303 PROGRESS: Extracting batch of 250256 precursors
0:20:07.183792 INFO: === Search parameters used ===
0:20:07.184054 INFO: rt_error       : 504.96745095334285
0:20:07.184112 INFO: mobility_error : 0.1
0:20:07.184160 INFO: num_candidates : 3
0:20:07.184206 INFO: ms1_error      : 3
0:20:07.184254 INFO: ms2_error      : 10.0
0:20:07.184299 INFO: fwhm_rt        : 3.0
0:20:07.184345 INFO: quant_window   : 3
0:20:07.184386 INFO: ==============================================
0:20:09.511634 INFO: performing precursor FDR with 40 features
0:20:09.511755 INFO: Decoy channel: -1
0:20:09.511781 INFO: competitive: True
0:20:09.690495 INFO: Setting torch num_threads to 2 for FDR classification task
0:20:09.981754 INFO: Estimating optimal hyperparameters - samples: 598,601, batch_size: 2,451, learning_rate: 7.74e-04
0:20:09.982880 INFO: Using random state 878016 for train-test-split
0:20:22.567642 INFO: Test AUC: 0.608
0:20:22.567848 INFO: Train AUC: 0.625
0:20:22.567883 INFO: AUC difference: 2.57%
0:20:23.043979 INFO: Resetting torch num_threads to 100
0:20:23.068629 PROGRESS: === Extracted 748252 precursors and 3981244 fragments ===
0:20:23.069102 INFO: === FDR correction performed with classifier version 11 ===
0:20:23.069787 PROGRESS: ============================= Precursor FDR =============================
0:20:23.069877 PROGRESS: Total precursors accumulated: 1,633
0:20:23.069938 PROGRESS: Target precursors: 1,617 (99.02%)
0:20:23.069992 PROGRESS: Decoy precursors: 16 (0.98%)
0:20:23.070049 PROGRESS: 
0:20:23.070098 PROGRESS: Precursor Summary:
0:20:23.071414 PROGRESS: Channel   0:	 0.050 FDR: 1,617; 0.010 FDR: 1,617; 0.001 FDR:     0
0:20:23.071509 PROGRESS: 
0:20:23.071565 PROGRESS: Protein Summary:
0:20:23.073201 PROGRESS: Channel   0:	 0.050 FDR: 1,358; 0.010 FDR: 1,358; 0.001 FDR:     0
0:20:23.073292 PROGRESS: =========================================================================
0:20:23.086388 INFO: Target number of precursors reached.
0:20:23.519637 INFO: fragments_df: keeping 5000 of 3981244 [sum(precursor_idx_mask)=38160 sum(mass_error_mask)=3981244 stop_rank=5000
0:20:23.924841 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:20:24.170708 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:20:24.884790 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:20:24.885231 INFO: Using score_cutoff 11.433609867095948 (fac=0.99, q=1)
0:20:24.885541 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:20:24.885625 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:20:24.885678 INFO: Updating optimization_manager: score_cutoff        : 10.783176347351073 -> 11.433609867095948
0:20:24.885732 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:20:25.037035 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:20:25.368229 INFO: === checking if optimization conditions were reached ===
0:20:25.368531 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:20:25.371937 INFO: Updating optimization_manager: rt_error            : 504.96745095334285 -> 446.6054226735776
0:20:25.372112 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 446.6054.
0:20:25.372187 INFO: ==============================================
0:20:25.372275 INFO: Starting optimization step 5.
0:20:25.372343 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:20:25.372427 INFO: Using rust extraction backend
0:20:25.372503 PROGRESS: Extracting batch of 250256 precursors
0:20:25.797730 INFO: === Search parameters used ===
0:20:25.797988 INFO: rt_error       : 446.6054226735776
0:20:25.798044 INFO: mobility_error : 0.1
0:20:25.798090 INFO: num_candidates : 3
0:20:25.798132 INFO: ms1_error      : 3
0:20:25.798176 INFO: ms2_error      : 10.0
0:20:25.798218 INFO: fwhm_rt        : 3.0
0:20:25.798259 INFO: quant_window   : 3
0:20:25.798304 INFO: ==============================================
0:20:28.078689 INFO: performing precursor FDR with 40 features
0:20:28.078809 INFO: Decoy channel: -1
0:20:28.078835 INFO: competitive: True
0:20:28.257638 INFO: Setting torch num_threads to 2 for FDR classification task
0:20:28.546834 INFO: Estimating optimal hyperparameters - samples: 598,181, batch_size: 2,450, learning_rate: 7.73e-04
0:20:28.547956 INFO: Using random state 878016 for train-test-split
0:20:40.997326 INFO: Test AUC: 0.608
0:20:40.997478 INFO: Train AUC: 0.624
0:20:40.997510 INFO: AUC difference: 2.55%
0:20:41.472481 INFO: Resetting torch num_threads to 100
0:20:41.498189 PROGRESS: === Extracted 747727 precursors and 3937948 fragments ===
0:20:41.498653 INFO: === FDR correction performed with classifier version 11 ===
0:20:41.499450 PROGRESS: ============================= Precursor FDR =============================
0:20:41.499549 PROGRESS: Total precursors accumulated: 1,754
0:20:41.499611 PROGRESS: Target precursors: 1,737 (99.03%)
0:20:41.499663 PROGRESS: Decoy precursors: 17 (0.97%)
0:20:41.499722 PROGRESS: 
0:20:41.499769 PROGRESS: Precursor Summary:
0:20:41.501214 PROGRESS: Channel   0:	 0.050 FDR: 1,737; 0.010 FDR: 1,737; 0.001 FDR: 1,159
0:20:41.501306 PROGRESS: 
0:20:41.501361 PROGRESS: Protein Summary:
0:20:41.503223 PROGRESS: Channel   0:	 0.050 FDR: 1,459; 0.010 FDR: 1,459; 0.001 FDR:   996
0:20:41.503319 PROGRESS: =========================================================================
0:20:41.517117 INFO: Target number of precursors reached.
0:20:41.949308 INFO: fragments_df: keeping 5000 of 3937948 [sum(precursor_idx_mask)=40235 sum(mass_error_mask)=3937948 stop_rank=5000
0:20:42.368364 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:20:42.633885 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:20:43.348125 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:20:43.348561 INFO: Using score_cutoff 9.558041339492798 (fac=0.99, q=1)
0:20:43.348875 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:20:43.348955 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:20:43.349010 INFO: Updating optimization_manager: score_cutoff        : 11.433609867095948 -> 9.558041339492798
0:20:43.349067 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:20:43.498795 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:20:43.836390 INFO: === checking if optimization conditions were reached ===
0:20:43.836725 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
0:20:43.840247 INFO: Updating optimization_manager: rt_error            : 446.6054226735776 -> 589.1120892264278
0:20:43.840409 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 589.1121.
0:20:43.840487 INFO: ==============================================
0:20:43.840571 INFO: Starting optimization step 6.
0:20:43.840642 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:20:43.840721 INFO: Using rust extraction backend
0:20:43.840792 PROGRESS: Extracting batch of 250256 precursors
0:20:44.270438 INFO: === Search parameters used ===
0:20:44.270704 INFO: rt_error       : 589.1120892264278
0:20:44.270761 INFO: mobility_error : 0.1
0:20:44.270808 INFO: num_candidates : 3
0:20:44.270853 INFO: ms1_error      : 3
0:20:44.270894 INFO: ms2_error      : 10.0
0:20:44.270934 INFO: fwhm_rt        : 3.0
0:20:44.270973 INFO: quant_window   : 3
0:20:44.271012 INFO: ==============================================
0:20:46.612602 INFO: performing precursor FDR with 40 features
0:20:46.612720 INFO: Decoy channel: -1
0:20:46.612745 INFO: competitive: True
0:20:46.795626 INFO: Setting torch num_threads to 2 for FDR classification task
0:20:47.087735 INFO: Estimating optimal hyperparameters - samples: 598,937, batch_size: 2,453, learning_rate: 7.74e-04
0:20:47.088878 INFO: Using random state 878016 for train-test-split
0:20:59.937934 INFO: Test AUC: 0.611
0:20:59.938067 INFO: Train AUC: 0.627
0:20:59.938100 INFO: AUC difference: 2.49%
0:21:00.908751 INFO: Resetting torch num_threads to 100
0:21:00.933875 PROGRESS: === Extracted 748672 precursors and 4010820 fragments ===
0:21:00.934329 INFO: === FDR correction performed with classifier version 11 ===
0:21:00.935054 PROGRESS: ============================= Precursor FDR =============================
0:21:00.935164 PROGRESS: Total precursors accumulated: 1,725
0:21:00.935242 PROGRESS: Target precursors: 1,708 (99.01%)
0:21:00.935297 PROGRESS: Decoy precursors: 17 (0.99%)
0:21:00.935344 PROGRESS: 
0:21:00.935389 PROGRESS: Precursor Summary:
0:21:00.936848 PROGRESS: Channel   0:	 0.050 FDR: 1,708; 0.010 FDR: 1,708; 0.001 FDR: 1,245
0:21:00.936950 PROGRESS: 
0:21:00.937005 PROGRESS: Protein Summary:
0:21:00.938868 PROGRESS: Channel   0:	 0.050 FDR: 1,430; 0.010 FDR: 1,430; 0.001 FDR: 1,060
0:21:00.938958 PROGRESS: =========================================================================
0:21:00.954116 INFO: Target number of precursors reached.
0:21:01.376497 INFO: fragments_df: keeping 5000 of 4010820 [sum(precursor_idx_mask)=39966 sum(mass_error_mask)=4010820 stop_rank=5000
0:21:01.780944 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:21:02.037856 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:21:02.758635 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:21:02.759084 INFO: Using score_cutoff 10.697152659130097 (fac=0.99, q=1)
0:21:02.759414 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:21:02.759493 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:21:02.759547 INFO: Updating optimization_manager: score_cutoff        : 9.558041339492798 -> 10.697152659130097
0:21:02.759606 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:21:02.910213 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:21:03.242041 INFO: === checking if optimization conditions were reached ===
0:21:03.242348 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
0:21:03.245879 INFO: Updating optimization_manager: rt_error            : 589.1120892264278 -> 670.7427924383727
0:21:03.246033 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 670.7428.
0:21:03.246111 INFO: ==============================================
0:21:03.246197 INFO: Starting optimization step 7.
0:21:03.246270 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:21:03.246343 INFO: Using rust extraction backend
0:21:03.246410 PROGRESS: Extracting batch of 250256 precursors
0:21:03.672740 INFO: === Search parameters used ===
0:21:03.673013 INFO: rt_error       : 670.7427924383727
0:21:03.673074 INFO: mobility_error : 0.1
0:21:03.673126 INFO: num_candidates : 3
0:21:03.673178 INFO: ms1_error      : 3
0:21:03.673223 INFO: ms2_error      : 10.0
0:21:03.673265 INFO: fwhm_rt        : 3.0
0:21:03.673308 INFO: quant_window   : 3
0:21:03.673350 INFO: ==============================================
0:21:06.160152 INFO: performing precursor FDR with 40 features
0:21:06.160268 INFO: Decoy channel: -1
0:21:06.160294 INFO: competitive: True
0:21:06.334679 INFO: Setting torch num_threads to 2 for FDR classification task
0:21:06.631842 INFO: Estimating optimal hyperparameters - samples: 599,155, batch_size: 2,454, learning_rate: 7.74e-04
0:21:06.632988 INFO: Using random state 878016 for train-test-split
0:21:19.276491 INFO: Test AUC: 0.612
0:21:19.276649 INFO: Train AUC: 0.626
0:21:19.276684 INFO: AUC difference: 2.19%
0:21:19.753714 INFO: Resetting torch num_threads to 100
0:21:19.782283 PROGRESS: === Extracted 748944 precursors and 4027693 fragments ===
0:21:19.782756 INFO: === FDR correction performed with classifier version 11 ===
0:21:19.783542 PROGRESS: ============================= Precursor FDR =============================
0:21:19.783644 PROGRESS: Total precursors accumulated: 1,746
0:21:19.783710 PROGRESS: Target precursors: 1,729 (99.03%)
0:21:19.783761 PROGRESS: Decoy precursors: 17 (0.97%)
0:21:19.783805 PROGRESS: 
0:21:19.783848 PROGRESS: Precursor Summary:
0:21:19.785357 PROGRESS: Channel   0:	 0.050 FDR: 1,729; 0.010 FDR: 1,729; 0.001 FDR: 1,312
0:21:19.785450 PROGRESS: 
0:21:19.785504 PROGRESS: Protein Summary:
0:21:19.787377 PROGRESS: Channel   0:	 0.050 FDR: 1,456; 0.010 FDR: 1,456; 0.001 FDR: 1,117
0:21:19.787475 PROGRESS: =========================================================================
0:21:19.801123 INFO: Target number of precursors reached.
0:21:20.227461 INFO: fragments_df: keeping 5000 of 4027693 [sum(precursor_idx_mask)=40371 sum(mass_error_mask)=4027693 stop_rank=5000
0:21:20.654707 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:21:20.915644 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:21:21.632754 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:21:21.633197 INFO: Using score_cutoff 10.9798012298584 (fac=0.99, q=1)
0:21:21.633499 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:21:21.633575 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:21:21.633629 INFO: Updating optimization_manager: score_cutoff        : 10.697152659130097 -> 10.9798012298584
0:21:21.633691 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:21:21.783772 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:21:22.114345 INFO: === checking if optimization conditions were reached ===
0:21:22.114655 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
0:21:22.118170 INFO: Updating optimization_manager: rt_error            : 670.7427924383727 -> 607.1795644101994
0:21:22.118325 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 607.1796.
0:21:22.118402 INFO: ==============================================
0:21:22.118493 INFO: Starting optimization step 8.
0:21:22.118564 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:21:22.118651 INFO: Using rust extraction backend
0:21:22.118731 PROGRESS: Extracting batch of 250256 precursors
0:21:22.542865 INFO: === Search parameters used ===
0:21:22.543128 INFO: rt_error       : 607.1795644101994
0:21:22.543205 INFO: mobility_error : 0.1
0:21:22.543255 INFO: num_candidates : 3
0:21:22.543301 INFO: ms1_error      : 3
0:21:22.543344 INFO: ms2_error      : 10.0
0:21:22.543393 INFO: fwhm_rt        : 3.0
0:21:22.543442 INFO: quant_window   : 3
0:21:22.543484 INFO: ==============================================
0:21:24.867958 INFO: performing precursor FDR with 40 features
0:21:24.868081 INFO: Decoy channel: -1
0:21:24.868124 INFO: competitive: True
0:21:25.045194 INFO: Setting torch num_threads to 2 for FDR classification task
0:21:25.331199 INFO: Estimating optimal hyperparameters - samples: 598,994, batch_size: 2,453, learning_rate: 7.74e-04
0:21:25.332192 INFO: Using random state 878016 for train-test-split
0:21:38.283608 INFO: Test AUC: 0.615
0:21:38.283748 INFO: Train AUC: 0.626
0:21:38.283782 INFO: AUC difference: 1.80%
0:21:38.759641 INFO: Resetting torch num_threads to 100
0:21:38.784268 PROGRESS: === Extracted 748743 precursors and 4016296 fragments ===
0:21:38.784730 INFO: === FDR correction performed with classifier version 11 ===
0:21:38.785450 PROGRESS: ============================= Precursor FDR =============================
0:21:38.785544 PROGRESS: Total precursors accumulated: 1,610
0:21:38.785603 PROGRESS: Target precursors: 1,595 (99.07%)
0:21:38.785654 PROGRESS: Decoy precursors: 15 (0.93%)
0:21:38.785701 PROGRESS: 
0:21:38.785746 PROGRESS: Precursor Summary:
0:21:38.787184 PROGRESS: Channel   0:	 0.050 FDR: 1,595; 0.010 FDR: 1,595; 0.001 FDR: 1,154
0:21:38.787287 PROGRESS: 
0:21:38.787341 PROGRESS: Protein Summary:
0:21:38.789160 PROGRESS: Channel   0:	 0.050 FDR: 1,341; 0.010 FDR: 1,341; 0.001 FDR:   989
0:21:38.789253 PROGRESS: =========================================================================
0:21:38.802524 INFO: Target number of precursors reached.
0:21:39.243708 INFO: fragments_df: keeping 5000 of 4016296 [sum(precursor_idx_mask)=37953 sum(mass_error_mask)=4016296 stop_rank=5000
0:21:39.646275 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:21:39.889666 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:21:40.602934 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:21:40.603379 INFO: Using score_cutoff 11.536078439712524 (fac=0.99, q=1)
0:21:40.603681 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:21:40.603759 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:21:40.603822 INFO: Updating optimization_manager: score_cutoff        : 10.9798012298584 -> 11.536078439712524
0:21:40.603877 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:21:40.755475 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:21:41.082316 INFO: === checking if optimization conditions were reached ===
0:21:41.082618 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
0:21:41.087295 INFO: Updating optimization_manager: rt_error            : 607.1795644101994 -> 492.8569217287116
0:21:41.087456 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 492.8569.
0:21:41.087537 INFO: ==============================================
0:21:41.087622 INFO: Starting optimization step 9.
0:21:41.087692 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:21:41.087766 INFO: Using rust extraction backend
0:21:41.087834 PROGRESS: Extracting batch of 250256 precursors
0:21:41.514061 INFO: === Search parameters used ===
0:21:41.514328 INFO: rt_error       : 492.8569217287116
0:21:41.514386 INFO: mobility_error : 0.1
0:21:41.514458 INFO: num_candidates : 3
0:21:41.514504 INFO: ms1_error      : 3
0:21:41.514547 INFO: ms2_error      : 10.0
0:21:41.514589 INFO: fwhm_rt        : 3.0
0:21:41.514629 INFO: quant_window   : 3
0:21:41.514674 INFO: ==============================================
0:21:43.793414 INFO: performing precursor FDR with 40 features
0:21:43.793530 INFO: Decoy channel: -1
0:21:43.793555 INFO: competitive: True
0:21:43.958143 INFO: Setting torch num_threads to 2 for FDR classification task
0:21:44.243448 INFO: Estimating optimal hyperparameters - samples: 598,444, batch_size: 2,451, learning_rate: 7.74e-04
0:21:44.244536 INFO: Using random state 878016 for train-test-split
0:21:56.884521 INFO: Test AUC: 0.613
0:21:56.884670 INFO: Train AUC: 0.625
0:21:56.884703 INFO: AUC difference: 1.92%
0:21:57.362029 INFO: Resetting torch num_threads to 100
0:21:57.387302 PROGRESS: === Extracted 748056 precursors and 3969254 fragments ===
0:21:57.387767 INFO: === FDR correction performed with classifier version 11 ===
0:21:57.388504 PROGRESS: ============================= Precursor FDR =============================
0:21:57.388602 PROGRESS: Total precursors accumulated: 1,706
0:21:57.388661 PROGRESS: Target precursors: 1,690 (99.06%)
0:21:57.388710 PROGRESS: Decoy precursors: 16 (0.94%)
0:21:57.388757 PROGRESS: 
0:21:57.388801 PROGRESS: Precursor Summary:
0:21:57.390225 PROGRESS: Channel   0:	 0.050 FDR: 1,690; 0.010 FDR: 1,690; 0.001 FDR: 1,122
0:21:57.390318 PROGRESS: 
0:21:57.390374 PROGRESS: Protein Summary:
0:21:57.392229 PROGRESS: Channel   0:	 0.050 FDR: 1,450; 0.010 FDR: 1,450; 0.001 FDR:   971
0:21:57.392324 PROGRESS: =========================================================================
0:21:57.408252 INFO: Target number of precursors reached.
0:21:57.837527 INFO: fragments_df: keeping 5000 of 3969254 [sum(precursor_idx_mask)=38315 sum(mass_error_mask)=3969254 stop_rank=5000
0:21:58.239496 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:21:58.499829 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:21:59.210914 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:21:59.211362 INFO: Using score_cutoff 8.199225958728789 (fac=0.99, q=1)
0:21:59.211678 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:21:59.211755 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:21:59.211809 INFO: Updating optimization_manager: score_cutoff        : 11.536078439712524 -> 8.199225958728789
0:21:59.211861 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:21:59.363739 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:21:59.695660 INFO: === checking if optimization conditions were reached ===
0:21:59.695953 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
0:21:59.699378 INFO: Updating optimization_manager: rt_error            : 492.8569217287116 -> 593.8682016858003
0:21:59.699532 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 593.8682.
0:21:59.699608 INFO: ==============================================
0:21:59.699691 INFO: Starting optimization step 10.
0:21:59.699759 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:21:59.699854 INFO: Using rust extraction backend
0:21:59.699920 PROGRESS: Extracting batch of 250256 precursors
0:22:00.126041 INFO: === Search parameters used ===
0:22:00.126302 INFO: rt_error       : 593.8682016858003
0:22:00.126358 INFO: mobility_error : 0.1
0:22:00.126404 INFO: num_candidates : 3
0:22:00.126446 INFO: ms1_error      : 3
0:22:00.126486 INFO: ms2_error      : 10.0
0:22:00.126542 INFO: fwhm_rt        : 3.0
0:22:00.126584 INFO: quant_window   : 3
0:22:00.126622 INFO: ==============================================
0:22:02.459725 INFO: performing precursor FDR with 40 features
0:22:02.459848 INFO: Decoy channel: -1
0:22:02.459874 INFO: competitive: True
0:22:02.634128 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:02.918848 INFO: Estimating optimal hyperparameters - samples: 599,085, batch_size: 2,453, learning_rate: 7.74e-04
0:22:02.919992 INFO: Using random state 878016 for train-test-split
0:22:15.528644 INFO: Test AUC: 0.611
0:22:15.528772 INFO: Train AUC: 0.626
0:22:15.528806 INFO: AUC difference: 2.36%
0:22:16.002871 INFO: Resetting torch num_threads to 100
0:22:16.031569 PROGRESS: === Extracted 748857 precursors and 4020939 fragments ===
0:22:16.032015 INFO: === FDR correction performed with classifier version 11 ===
0:22:16.032728 PROGRESS: ============================= Precursor FDR =============================
0:22:16.032823 PROGRESS: Total precursors accumulated: 1,569
0:22:16.032884 PROGRESS: Target precursors: 1,554 (99.04%)
0:22:16.032936 PROGRESS: Decoy precursors: 15 (0.96%)
0:22:16.032983 PROGRESS: 
0:22:16.033028 PROGRESS: Precursor Summary:
0:22:16.034346 PROGRESS: Channel   0:	 0.050 FDR: 1,554; 0.010 FDR: 1,554; 0.001 FDR:   332
0:22:16.034452 PROGRESS: 
0:22:16.034507 PROGRESS: Protein Summary:
0:22:16.036161 PROGRESS: Channel   0:	 0.050 FDR: 1,307; 0.010 FDR: 1,307; 0.001 FDR:   308
0:22:16.036257 PROGRESS: =========================================================================
0:22:16.049495 INFO: Target number of precursors reached.
0:22:16.499005 INFO: fragments_df: keeping 5000 of 4020939 [sum(precursor_idx_mask)=36915 sum(mass_error_mask)=4020939 stop_rank=5000
0:22:16.900147 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:22:17.136061 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:22:17.849333 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:22:17.849758 INFO: Using score_cutoff 11.450567805290223 (fac=0.99, q=1)
0:22:17.850061 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:22:17.850136 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:22:17.850190 INFO: Updating optimization_manager: score_cutoff        : 8.199225958728789 -> 11.450567805290223
0:22:17.850240 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:22:18.001463 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:22:18.329247 INFO: === checking if optimization conditions were reached ===
0:22:18.329547 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
0:22:18.332868 INFO: Updating optimization_manager: rt_error            : 593.8682016858003 -> 441.1070990449143
0:22:18.333049 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 441.1071.
0:22:18.333127 INFO: ==============================================
0:22:18.333220 INFO: Starting optimization step 11.
0:22:18.333289 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:22:18.333360 INFO: Using rust extraction backend
0:22:18.333433 PROGRESS: Extracting batch of 250256 precursors
0:22:18.759742 INFO: === Search parameters used ===
0:22:18.760012 INFO: rt_error       : 441.1070990449143
0:22:18.760071 INFO: mobility_error : 0.1
0:22:18.760120 INFO: num_candidates : 3
0:22:18.760182 INFO: ms1_error      : 3
0:22:18.760227 INFO: ms2_error      : 10.0
0:22:18.760269 INFO: fwhm_rt        : 3.0
0:22:18.760312 INFO: quant_window   : 3
0:22:18.760354 INFO: ==============================================
0:22:21.031757 INFO: performing precursor FDR with 40 features
0:22:21.031872 INFO: Decoy channel: -1
0:22:21.031899 INFO: competitive: True
0:22:21.213892 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:21.515541 INFO: Estimating optimal hyperparameters - samples: 598,023, batch_size: 2,449, learning_rate: 7.73e-04
0:22:21.516551 INFO: Using random state 878016 for train-test-split
0:22:34.058511 INFO: Test AUC: 0.609
0:22:34.058644 INFO: Train AUC: 0.624
0:22:34.058676 INFO: AUC difference: 2.37%
0:22:34.528985 INFO: Resetting torch num_threads to 100
0:22:34.553974 PROGRESS: === Extracted 747529 precursors and 3926798 fragments ===
0:22:34.554426 INFO: === FDR correction performed with classifier version 11 ===
0:22:34.555162 PROGRESS: ============================= Precursor FDR =============================
0:22:34.555261 PROGRESS: Total precursors accumulated: 1,744
0:22:34.555321 PROGRESS: Target precursors: 1,727 (99.03%)
0:22:34.555372 PROGRESS: Decoy precursors: 17 (0.97%)
0:22:34.555418 PROGRESS: 
0:22:34.555463 PROGRESS: Precursor Summary:
0:22:34.556878 PROGRESS: Channel   0:	 0.050 FDR: 1,727; 0.010 FDR: 1,727; 0.001 FDR: 1,200
0:22:34.556967 PROGRESS: 
0:22:34.557023 PROGRESS: Protein Summary:
0:22:34.558865 PROGRESS: Channel   0:	 0.050 FDR: 1,447; 0.010 FDR: 1,447; 0.001 FDR: 1,029
0:22:34.558955 PROGRESS: =========================================================================
0:22:34.571971 INFO: Target number of precursors reached.
0:22:34.994859 INFO: fragments_df: keeping 5000 of 3926798 [sum(precursor_idx_mask)=40156 sum(mass_error_mask)=3926798 stop_rank=5000
0:22:35.396567 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:22:35.662056 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:22:36.374261 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:22:36.374697 INFO: Using score_cutoff 10.103080423164368 (fac=0.99, q=1)
0:22:36.374993 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:22:36.375067 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:22:36.375121 INFO: Updating optimization_manager: score_cutoff        : 11.450567805290223 -> 10.103080423164368
0:22:36.375188 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:22:36.524406 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:22:36.847538 INFO: === checking if optimization conditions were reached ===
0:22:36.847831 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 5 ===
0:22:36.851263 INFO: Updating optimization_manager: rt_error            : 441.1070990449143 -> 573.9381893185555
0:22:36.851413 PROGRESS: ❌ rt_error       : optimization incomplete after 12 search(es). Will search with parameter 573.9382.
0:22:36.851490 INFO: ==============================================
0:22:36.851572 INFO: Starting optimization step 12.
0:22:36.851638 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:22:36.851708 INFO: Using rust extraction backend
0:22:36.851774 PROGRESS: Extracting batch of 250256 precursors
0:22:37.278341 INFO: === Search parameters used ===
0:22:37.278605 INFO: rt_error       : 573.9381893185555
0:22:37.278680 INFO: mobility_error : 0.1
0:22:37.278726 INFO: num_candidates : 3
0:22:37.278769 INFO: ms1_error      : 3
0:22:37.278812 INFO: ms2_error      : 10.0
0:22:37.278854 INFO: fwhm_rt        : 3.0
0:22:37.278894 INFO: quant_window   : 3
0:22:37.278933 INFO: ==============================================
0:22:39.610697 INFO: performing precursor FDR with 40 features
0:22:39.610818 INFO: Decoy channel: -1
0:22:39.610842 INFO: competitive: True
0:22:39.787602 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:40.068857 INFO: Estimating optimal hyperparameters - samples: 598,938, batch_size: 2,453, learning_rate: 7.74e-04
0:22:40.069963 INFO: Using random state 878016 for train-test-split
0:22:52.603761 INFO: Test AUC: 0.613
0:22:52.603887 INFO: Train AUC: 0.626
0:22:52.603919 INFO: AUC difference: 2.14%
0:22:53.077974 INFO: Resetting torch num_threads to 100
0:22:53.102632 PROGRESS: === Extracted 748673 precursors and 4009825 fragments ===
0:22:53.103070 INFO: === FDR correction performed with classifier version 11 ===
0:22:53.103801 PROGRESS: ============================= Precursor FDR =============================
0:22:53.103892 PROGRESS: Total precursors accumulated: 1,710
0:22:53.103952 PROGRESS: Target precursors: 1,694 (99.06%)
0:22:53.104006 PROGRESS: Decoy precursors: 16 (0.94%)
0:22:53.104054 PROGRESS: 
0:22:53.104101 PROGRESS: Precursor Summary:
0:22:53.105470 PROGRESS: Channel   0:	 0.050 FDR: 1,694; 0.010 FDR: 1,694; 0.001 FDR: 1,116
0:22:53.105561 PROGRESS: 
0:22:53.105617 PROGRESS: Protein Summary:
0:22:53.107416 PROGRESS: Channel   0:	 0.050 FDR: 1,435; 0.010 FDR: 1,435; 0.001 FDR:   961
0:22:53.107517 PROGRESS: =========================================================================
0:22:53.120801 INFO: Target number of precursors reached.
0:22:53.544502 INFO: fragments_df: keeping 5000 of 4009825 [sum(precursor_idx_mask)=39155 sum(mass_error_mask)=4009825 stop_rank=5000
0:22:53.947706 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:22:54.198675 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:22:54.913515 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:22:54.913952 INFO: Using score_cutoff 8.725769727230071 (fac=0.99, q=1)
0:22:54.914252 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:22:54.914335 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:22:54.914390 INFO: Updating optimization_manager: score_cutoff        : 10.103080423164368 -> 8.725769727230071
0:22:54.914442 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:22:55.064104 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:22:55.389910 INFO: === checking if optimization conditions were reached ===
0:22:55.390211 PROGRESS: === Optimization of rt_error has been performed 13 time(s); minimum number is 5 ===
0:22:55.393655 INFO: Updating optimization_manager: rt_error            : 573.9381893185555 -> 761.9054345175148
0:22:55.393808 PROGRESS: ❌ rt_error       : optimization incomplete after 13 search(es). Will search with parameter 761.9054.
0:22:55.393883 INFO: ==============================================
0:22:55.393964 INFO: Starting optimization step 13.
0:22:55.394030 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:22:55.394100 INFO: Using rust extraction backend
0:22:55.394166 PROGRESS: Extracting batch of 250256 precursors
0:22:55.819496 INFO: === Search parameters used ===
0:22:55.819762 INFO: rt_error       : 761.9054345175148
0:22:55.819820 INFO: mobility_error : 0.1
0:22:55.819870 INFO: num_candidates : 3
0:22:55.819915 INFO: ms1_error      : 3
0:22:55.819959 INFO: ms2_error      : 10.0
0:22:55.820002 INFO: fwhm_rt        : 3.0
0:22:55.820044 INFO: quant_window   : 3
0:22:55.820086 INFO: ==============================================
0:22:58.199250 INFO: performing precursor FDR with 40 features
0:22:58.199364 INFO: Decoy channel: -1
0:22:58.199389 INFO: competitive: True
0:22:58.381456 INFO: Setting torch num_threads to 2 for FDR classification task
0:22:58.680876 INFO: Estimating optimal hyperparameters - samples: 599,240, batch_size: 2,454, learning_rate: 7.74e-04
0:22:58.681962 INFO: Using random state 878016 for train-test-split
0:23:11.243477 INFO: Test AUC: 0.613
0:23:11.243615 INFO: Train AUC: 0.627
0:23:11.243649 INFO: AUC difference: 2.26%
0:23:11.714369 INFO: Resetting torch num_threads to 100
0:23:11.739312 PROGRESS: === Extracted 749051 precursors and 4035046 fragments ===
0:23:11.739765 INFO: === FDR correction performed with classifier version 11 ===
0:23:11.740488 PROGRESS: ============================= Precursor FDR =============================
0:23:11.740582 PROGRESS: Total precursors accumulated: 1,770
0:23:11.740642 PROGRESS: Target precursors: 1,753 (99.04%)
0:23:11.740694 PROGRESS: Decoy precursors: 17 (0.96%)
0:23:11.740741 PROGRESS: 
0:23:11.740788 PROGRESS: Precursor Summary:
0:23:11.742253 PROGRESS: Channel   0:	 0.050 FDR: 1,753; 0.010 FDR: 1,753; 0.001 FDR: 1,366
0:23:11.742346 PROGRESS: 
0:23:11.742402 PROGRESS: Protein Summary:
0:23:11.744309 PROGRESS: Channel   0:	 0.050 FDR: 1,481; 0.010 FDR: 1,481; 0.001 FDR: 1,159
0:23:11.744406 PROGRESS: =========================================================================
0:23:11.756853 INFO: Target number of precursors reached.
0:23:12.187783 INFO: fragments_df: keeping 5000 of 4035046 [sum(precursor_idx_mask)=40200 sum(mass_error_mask)=4035046 stop_rank=5000
0:23:12.592478 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:23:12.855346 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:23:13.568089 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:23:13.568518 INFO: Using score_cutoff 8.700715403366088 (fac=0.99, q=1)
0:23:13.568812 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:13.568891 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:13.568945 INFO: Updating optimization_manager: score_cutoff        : 8.725769727230071 -> 8.700715403366088
0:23:13.568996 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:13.717946 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:14.045759 INFO: === checking if optimization conditions were reached ===
0:23:14.046053 PROGRESS: === Optimization of rt_error has been performed 14 time(s); minimum number is 5 ===
0:23:14.049515 INFO: Updating optimization_manager: rt_error            : 761.9054345175148 -> 820.7333986493286
0:23:14.049682 PROGRESS: ❌ rt_error       : optimization incomplete after 14 search(es). Will search with parameter 820.7334.
0:23:14.049783 INFO: ==============================================
0:23:14.049865 INFO: Starting optimization step 14.
0:23:14.049932 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:23:14.050009 INFO: Using rust extraction backend
0:23:14.050079 PROGRESS: Extracting batch of 250256 precursors
0:23:14.475273 INFO: === Search parameters used ===
0:23:14.475533 INFO: rt_error       : 820.7333986493286
0:23:14.475588 INFO: mobility_error : 0.1
0:23:14.475633 INFO: num_candidates : 3
0:23:14.475676 INFO: ms1_error      : 3
0:23:14.475716 INFO: ms2_error      : 10.0
0:23:14.475754 INFO: fwhm_rt        : 3.0
0:23:14.475792 INFO: quant_window   : 3
0:23:14.475829 INFO: ==============================================
0:23:16.913633 INFO: performing precursor FDR with 40 features
0:23:16.913752 INFO: Decoy channel: -1
0:23:16.913779 INFO: competitive: True
0:23:17.090252 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:17.374651 INFO: Estimating optimal hyperparameters - samples: 599,247, batch_size: 2,454, learning_rate: 7.74e-04
0:23:17.375686 INFO: Using random state 878016 for train-test-split
0:23:29.864599 INFO: Test AUC: 0.613
0:23:29.864738 INFO: Train AUC: 0.627
0:23:29.864769 INFO: AUC difference: 2.20%
0:23:30.338690 INFO: Resetting torch num_threads to 100
0:23:30.363297 PROGRESS: === Extracted 749059 precursors and 4035566 fragments ===
0:23:30.363733 INFO: === FDR correction performed with classifier version 11 ===
0:23:30.364429 PROGRESS: ============================= Precursor FDR =============================
0:23:30.364517 PROGRESS: Total precursors accumulated: 1,818
0:23:30.364578 PROGRESS: Target precursors: 1,800 (99.01%)
0:23:30.364630 PROGRESS: Decoy precursors: 18 (0.99%)
0:23:30.364677 PROGRESS: 
0:23:30.364723 PROGRESS: Precursor Summary:
0:23:30.366146 PROGRESS: Channel   0:	 0.050 FDR: 1,800; 0.010 FDR: 1,790; 0.001 FDR: 1,297
0:23:30.366234 PROGRESS: 
0:23:30.366289 PROGRESS: Protein Summary:
0:23:30.368191 PROGRESS: Channel   0:	 0.050 FDR: 1,531; 0.010 FDR: 1,525; 0.001 FDR: 1,114
0:23:30.368294 PROGRESS: =========================================================================
0:23:30.381704 INFO: Target number of precursors reached.
0:23:30.827529 INFO: fragments_df: keeping 5000 of 4035566 [sum(precursor_idx_mask)=40485 sum(mass_error_mask)=4035566 stop_rank=5000
0:23:31.231704 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:23:31.498671 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:23:32.213922 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:23:32.214365 INFO: Using score_cutoff 8.160946051883696 (fac=0.99, q=1)
0:23:32.214669 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:32.214745 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:32.214799 INFO: Updating optimization_manager: score_cutoff        : 8.700715403366088 -> 8.160946051883696
0:23:32.214851 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:32.365118 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:32.696556 INFO: === checking if optimization conditions were reached ===
0:23:32.696854 PROGRESS: === Optimization of rt_error has been performed 15 time(s); minimum number is 5 ===
0:23:32.700304 INFO: Updating optimization_manager: rt_error            : 820.7333986493286 -> 878.9118232094844
0:23:32.700428 PROGRESS: ❌ rt_error       : optimization incomplete after 15 search(es). Will search with parameter 878.9118.
0:23:32.700504 INFO: ==============================================
0:23:32.700588 INFO: Starting optimization step 15.
0:23:32.700678 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:23:32.700752 INFO: Using rust extraction backend
0:23:32.700819 PROGRESS: Extracting batch of 250256 precursors
0:23:33.124689 INFO: === Search parameters used ===
0:23:33.125843 INFO: rt_error       : 878.9118232094844
0:23:33.125909 INFO: mobility_error : 0.1
0:23:33.125960 INFO: num_candidates : 3
0:23:33.126006 INFO: ms1_error      : 3
0:23:33.126067 INFO: ms2_error      : 10.0
0:23:33.126114 INFO: fwhm_rt        : 3.0
0:23:33.126157 INFO: quant_window   : 3
0:23:33.126198 INFO: ==============================================
0:23:35.584590 INFO: performing precursor FDR with 40 features
0:23:35.584706 INFO: Decoy channel: -1
0:23:35.584731 INFO: competitive: True
0:23:35.759569 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:36.050341 INFO: Estimating optimal hyperparameters - samples: 599,240, batch_size: 2,454, learning_rate: 7.74e-04
0:23:36.051257 INFO: Using random state 878016 for train-test-split
0:23:48.640863 INFO: Test AUC: 0.613
0:23:48.640999 INFO: Train AUC: 0.627
0:23:48.641033 INFO: AUC difference: 2.20%
0:23:49.655969 INFO: Resetting torch num_threads to 100
0:23:49.680985 PROGRESS: === Extracted 749051 precursors and 4036103 fragments ===
0:23:49.681416 INFO: === FDR correction performed with classifier version 11 ===
0:23:49.682103 PROGRESS: ============================= Precursor FDR =============================
0:23:49.682190 PROGRESS: Total precursors accumulated: 1,755
0:23:49.682249 PROGRESS: Target precursors: 1,738 (99.03%)
0:23:49.682301 PROGRESS: Decoy precursors: 17 (0.97%)
0:23:49.682349 PROGRESS: 
0:23:49.682406 PROGRESS: Precursor Summary:
0:23:49.683823 PROGRESS: Channel   0:	 0.050 FDR: 1,738; 0.010 FDR: 1,738; 0.001 FDR: 1,108
0:23:49.683925 PROGRESS: 
0:23:49.683981 PROGRESS: Protein Summary:
0:23:49.685830 PROGRESS: Channel   0:	 0.050 FDR: 1,468; 0.010 FDR: 1,468; 0.001 FDR:   954
0:23:49.685924 PROGRESS: =========================================================================
0:23:49.699625 INFO: Target number of precursors reached.
0:23:50.134891 INFO: fragments_df: keeping 5000 of 4036103 [sum(precursor_idx_mask)=40050 sum(mass_error_mask)=4036103 stop_rank=5000
0:23:50.536202 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:23:50.797228 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:23:51.509731 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:23:51.510173 INFO: Using score_cutoff 9.210139106369018 (fac=0.99, q=1)
0:23:51.510479 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:23:51.510554 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:23:51.510607 INFO: Updating optimization_manager: score_cutoff        : 8.160946051883696 -> 9.210139106369018
0:23:51.510660 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:23:51.660759 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:23:51.990771 INFO: === checking if optimization conditions were reached ===
0:23:51.991067 PROGRESS: === Optimization of rt_error has been performed 16 time(s); minimum number is 5 ===
0:23:51.994560 INFO: Updating optimization_manager: rt_error            : 878.9118232094844 -> 757.7699226411232
0:23:51.994715 PROGRESS: ❌ rt_error       : optimization incomplete after 16 search(es). Will search with parameter 757.7699.
0:23:51.994815 INFO: ==============================================
0:23:51.994902 INFO: Starting optimization step 16.
0:23:51.994977 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:23:51.995053 INFO: Using rust extraction backend
0:23:51.995121 PROGRESS: Extracting batch of 250256 precursors
0:23:52.420482 INFO: === Search parameters used ===
0:23:52.420743 INFO: rt_error       : 757.7699226411232
0:23:52.420801 INFO: mobility_error : 0.1
0:23:52.420852 INFO: num_candidates : 3
0:23:52.420898 INFO: ms1_error      : 3
0:23:52.420943 INFO: ms2_error      : 10.0
0:23:52.420987 INFO: fwhm_rt        : 3.0
0:23:52.421029 INFO: quant_window   : 3
0:23:52.421070 INFO: ==============================================
0:23:54.835302 INFO: performing precursor FDR with 40 features
0:23:54.835430 INFO: Decoy channel: -1
0:23:54.835457 INFO: competitive: True
0:23:55.011275 INFO: Setting torch num_threads to 2 for FDR classification task
0:23:55.299942 INFO: Estimating optimal hyperparameters - samples: 599,245, batch_size: 2,454, learning_rate: 7.74e-04
0:23:55.301059 INFO: Using random state 878016 for train-test-split
0:24:07.801682 INFO: Test AUC: 0.613
0:24:07.801810 INFO: Train AUC: 0.627
0:24:07.801842 INFO: AUC difference: 2.32%
0:24:08.277620 INFO: Resetting torch num_threads to 100
0:24:08.302371 PROGRESS: === Extracted 749057 precursors and 4034681 fragments ===
0:24:08.302825 INFO: === FDR correction performed with classifier version 11 ===
0:24:08.303581 PROGRESS: ============================= Precursor FDR =============================
0:24:08.303692 PROGRESS: Total precursors accumulated: 1,671
0:24:08.303753 PROGRESS: Target precursors: 1,655 (99.04%)
0:24:08.303804 PROGRESS: Decoy precursors: 16 (0.96%)
0:24:08.303851 PROGRESS: 
0:24:08.303895 PROGRESS: Precursor Summary:
0:24:08.305348 PROGRESS: Channel   0:	 0.050 FDR: 1,655; 0.010 FDR: 1,655; 0.001 FDR: 1,075
0:24:08.305442 PROGRESS: 
0:24:08.305497 PROGRESS: Protein Summary:
0:24:08.307372 PROGRESS: Channel   0:	 0.050 FDR: 1,393; 0.010 FDR: 1,393; 0.001 FDR:   924
0:24:08.307467 PROGRESS: =========================================================================
0:24:08.322590 INFO: Target number of precursors reached.
0:24:08.769266 INFO: fragments_df: keeping 5000 of 4034681 [sum(precursor_idx_mask)=38728 sum(mass_error_mask)=4034681 stop_rank=5000
0:24:09.169441 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:24:09.394856 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:24:10.115315 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:24:10.115760 INFO: Using score_cutoff 10.064279069137573 (fac=0.99, q=1)
0:24:10.116067 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:24:10.116147 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:24:10.116203 INFO: Updating optimization_manager: score_cutoff        : 9.210139106369018 -> 10.064279069137573
0:24:10.116256 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:24:10.266882 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:10.596557 INFO: === checking if optimization conditions were reached ===
0:24:10.596851 PROGRESS: === Optimization of rt_error has been performed 17 time(s); minimum number is 5 ===
0:24:10.600269 INFO: Updating optimization_manager: rt_error            : 757.7699226411232 -> 787.8549144182027
0:24:10.600451 PROGRESS: ❌ rt_error       : optimization incomplete after 17 search(es). Will search with parameter 787.8549.
0:24:10.600532 INFO: ==============================================
0:24:10.600616 INFO: Starting optimization step 17.
0:24:10.600686 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:24:10.600761 INFO: Using rust extraction backend
0:24:10.600830 PROGRESS: Extracting batch of 250256 precursors
0:24:11.024821 INFO: === Search parameters used ===
0:24:11.025084 INFO: rt_error       : 787.8549144182027
0:24:11.025141 INFO: mobility_error : 0.1
0:24:11.025189 INFO: num_candidates : 3
0:24:11.025235 INFO: ms1_error      : 3
0:24:11.025280 INFO: ms2_error      : 10.0
0:24:11.025323 INFO: fwhm_rt        : 3.0
0:24:11.025365 INFO: quant_window   : 3
0:24:11.025407 INFO: ==============================================
0:24:13.442253 INFO: performing precursor FDR with 40 features
0:24:13.442369 INFO: Decoy channel: -1
0:24:13.442395 INFO: competitive: True
0:24:13.609401 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:13.905553 INFO: Estimating optimal hyperparameters - samples: 599,230, batch_size: 2,454, learning_rate: 7.74e-04
0:24:13.906665 INFO: Using random state 878016 for train-test-split
0:24:26.734192 INFO: Test AUC: 0.614
0:24:26.734337 INFO: Train AUC: 0.627
0:24:26.734369 INFO: AUC difference: 2.21%
0:24:27.212031 INFO: Resetting torch num_threads to 100
0:24:27.236892 PROGRESS: === Extracted 749038 precursors and 4034990 fragments ===
0:24:27.237328 INFO: === FDR correction performed with classifier version 11 ===
0:24:27.238000 PROGRESS: ============================= Precursor FDR =============================
0:24:27.238087 PROGRESS: Total precursors accumulated: 1,630
0:24:27.238159 PROGRESS: Target precursors: 1,614 (99.02%)
0:24:27.238209 PROGRESS: Decoy precursors: 16 (0.98%)
0:24:27.238263 PROGRESS: 
0:24:27.238310 PROGRESS: Precursor Summary:
0:24:27.239683 PROGRESS: Channel   0:	 0.050 FDR: 1,614; 0.010 FDR: 1,614; 0.001 FDR: 1,111
0:24:27.239775 PROGRESS: 
0:24:27.239829 PROGRESS: Protein Summary:
0:24:27.241599 PROGRESS: Channel   0:	 0.050 FDR: 1,380; 0.010 FDR: 1,380; 0.001 FDR:   958
0:24:27.241685 PROGRESS: =========================================================================
0:24:27.257224 INFO: Target number of precursors reached.
0:24:27.695354 INFO: fragments_df: keeping 5000 of 4034990 [sum(precursor_idx_mask)=37135 sum(mass_error_mask)=4034990 stop_rank=5000
0:24:28.100871 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:24:28.346971 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:24:29.059505 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:24:29.059937 INFO: Using score_cutoff 8.423288423252107 (fac=0.99, q=1)
0:24:29.060235 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:24:29.060308 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:24:29.060359 INFO: Updating optimization_manager: score_cutoff        : 10.064279069137573 -> 8.423288423252107
0:24:29.060410 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:24:29.211800 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:29.556818 INFO: === checking if optimization conditions were reached ===
0:24:29.557142 PROGRESS: === Optimization of rt_error has been performed 18 time(s); minimum number is 5 ===
0:24:29.558194 INFO: Updating optimization_manager: rt_error            : 787.8549144182027 -> 820.7333986493286
0:24:29.558335 INFO: Updating optimization_manager: classifier_version  : 11 -> 26
0:24:29.558447 INFO: Updating optimization_manager: score_cutoff        : 8.423288423252107 -> 8.160946051883696
0:24:29.558553 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:24:29.558654 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:24:29.558762 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 820.7334 found after 18 searches.
0:24:29.558831 INFO: ==============================================
0:24:29.558911 PROGRESS: Optimization finished for rt_error.
0:24:29.952108 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:24:30.103015 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:30.449089 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:24:30.449378 PROGRESS: ==============================================
0:24:30.449459 PROGRESS: ms2_error      : 10.0000
0:24:30.449523 PROGRESS: rt_error       : 820.7334
0:24:30.449579 PROGRESS: ==============================================
0:24:30.450380 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:24:38.086774 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:54.711702 INFO: Using rust extraction backend
0:24:54.712296 PROGRESS: Extracting batch of 11997144 precursors
0:25:10.893371 INFO: === Search parameters used ===
0:25:10.893862 INFO: rt_error       : 820.7333986493286
0:25:10.893936 INFO: mobility_error : 0.1
0:25:10.893996 INFO: num_candidates : 3
0:25:10.894061 INFO: ms1_error      : 3
0:25:10.894112 INFO: ms2_error      : 10.0
0:25:10.894161 INFO: fwhm_rt        : 3.0
0:25:10.894209 INFO: quant_window   : 3
0:25:10.894254 INFO: ==============================================
0:25:43.938667 INFO: Removed 3610483 precursors with score below cutoff 8.160946051883696
0:26:08.692257 INFO: performing precursor FDR with 40 features
0:26:08.692484 INFO: Decoy channel: -1
0:26:08.692514 INFO: competitive: True
0:26:12.116679 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:25.916726 INFO: Estimating optimal hyperparameters - samples: 25,904,493, batch_size: 4,096, learning_rate: 1.00e-03
0:26:26.002527 INFO: Using random state 301621 for train-test-split
0:35:48.747165 INFO: Test AUC: 0.621
0:35:48.747816 INFO: Train AUC: 0.621
0:35:48.747884 INFO: AUC difference: 0.07%
0:35:55.843349 INFO: Resetting torch num_threads to 100
0:35:59.277616 PROGRESS: ============================= Precursor FDR =============================
0:35:59.278062 PROGRESS: Total precursors accumulated: 92,545
0:35:59.278137 PROGRESS: Target precursors: 91,629 (99.01%)
0:35:59.278193 PROGRESS: Decoy precursors: 916 (0.99%)
0:35:59.278241 PROGRESS: 
0:35:59.278287 PROGRESS: Precursor Summary:
0:35:59.304312 PROGRESS: Channel   0:	 0.050 FDR: 91,629; 0.010 FDR: 91,629; 0.001 FDR: 61,037
0:35:59.304562 PROGRESS: 
0:35:59.304625 PROGRESS: Protein Summary:
0:35:59.340009 PROGRESS: Channel   0:	 0.050 FDR: 14,336; 0.010 FDR: 14,336; 0.001 FDR: 9,845
0:35:59.340273 PROGRESS: =========================================================================
0:35:59.609074 PROGRESS: === Transfer learning quantification ===
0:35:59.609374 INFO: creating library for charged fragment types: ['b', 'y']
0:36:00.820062 INFO: Calibrating library
0:36:00.820347 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:00.874828 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:01.418022 INFO: quantifying 92,545 precursors with 4,031,010 fragments
0:36:01.418295 INFO: Using rust extraction backend
0:36:02.395647 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/psm.parquet
0:36:02.564801 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.parquet
0:36:02.791539 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.transfer.parquet
0:36:03.333418 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:36:04.048414 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 
0:36:04.048733 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant
0:36:04.048853 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/figures
0:36:04.049089 INFO: Initializing TimingManager
0:36:04.049727 INFO: Initializing RawFileManager
0:36:13.909520 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.
0:36:13.917290 INFO: Determining DIA cycle
0:36:13.933635 INFO: Found cycle with start 0.00 min and length 300.
0:36:14.099525 INFO: RT (min)            : 0.0 - 26.9
0:36:14.099620 INFO: RT duration (sec)   : 1611.2
0:36:14.099648 INFO: RT duration (min)   : 26.9
0:36:14.099670 INFO: Cycle len (scans)   : 300
0:36:14.099689 INFO: Cycle len (sec)     : 1.65
0:36:14.099707 INFO: Number of cycles    : 978
0:36:14.099725 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:36:14.099750 INFO: Creating DIA data object took: 10.04992938041687
0:36:14.772950 INFO: Creating DIA data NG object took: 0.673065185546875
0:36:16.564221 INFO: Initializing CalibrationManager
0:36:16.564517 INFO: Setting up calibration estimators ..
0:36:16.564586 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:36:16.564677 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'}' ..
0:36:16.564810 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:36:16.564864 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:36:16.564929 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}}' ..
0:36:16.564984 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:36:16.565031 INFO: Done setting up calibration estimators.
0:36:16.565244 INFO: Initializing OptimizationManager
0:36:16.565385 INFO: initial parameter: ms1_error = 3
0:36:16.565434 INFO: initial parameter: ms2_error = 10
0:36:16.565479 INFO: initial parameter: rt_error = 805.6019897460938
0:36:16.565521 INFO: initial parameter: mobility_error = 0.1
0:36:16.565560 INFO: initial parameter: num_candidates = 1
0:36:16.565599 INFO: initial parameter: fwhm_rt = 5
0:36:16.565638 INFO: initial parameter: fwhm_mobility = 0.01
0:36:16.565675 INFO: initial parameter: score_cutoff = 0
0:36:16.565713 INFO: initial parameter: classifier_version = -1
0:36:16.565779 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:36:16.566107 INFO: FDRManager: loading saved state not requested, will be initialized.
0:36:16.566138 INFO: Initializing FDRManager
0:36:16.566176 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
0:36:18.013162 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
0:36:18.885118 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
0:36:18.885547 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
0:36:18.885652 PROGRESS: Starting initial search for precursors.
0:36:18.885743 INFO: Starting optimization step 0.
0:36:18.885809 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:36:18.885871 INFO: Using rust extraction backend
0:36:18.885942 PROGRESS: Extracting batch of 1963 precursors
0:36:18.892004 INFO: === Search parameters used ===
0:36:18.892113 INFO: rt_error       : 805.6019897460938
0:36:18.892168 INFO: mobility_error : 0.1
0:36:18.892213 INFO: num_candidates : 1
0:36:18.892254 INFO: ms1_error      : 3
0:36:18.892294 INFO: ms2_error      : 10
0:36:18.892335 INFO: fwhm_rt        : 5
0:36:18.892376 INFO: quant_window   : 3
0:36:18.892415 INFO: ==============================================
0:36:18.920324 INFO: performing precursor FDR with 40 features
0:36:18.920393 INFO: Decoy channel: -1
0:36:18.920417 INFO: competitive: True
0:36:18.921864 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:18.924083 INFO: Estimating optimal hyperparameters - samples: 1,567, batch_size: 128, learning_rate: 1.77e-04
0:36:18.924925 INFO: Using random state 312002 for train-test-split
0:36:19.079065 INFO: Test AUC: 0.465
0:36:19.079151 INFO: Train AUC: 0.593
0:36:19.079183 INFO: AUC difference: 21.62%
0:36:19.079203 WARNING: AUC difference > 5%. This may indicate overfitting.
0:36:19.318098 INFO: Resetting torch num_threads to 100
0:36:19.319678 PROGRESS: === Extracted 1959 precursors and 10835 fragments ===
0:36:19.320039 INFO: === FDR correction performed with classifier version -1 ===
0:36:19.320538 PROGRESS: ============================= Precursor FDR =============================
0:36:19.320617 PROGRESS: Total precursors accumulated: 0
0:36:19.320671 PROGRESS: Target precursors: 0 (0.00%)
0:36:19.320718 PROGRESS: Decoy precursors: 0 (0.00%)
0:36:19.320762 PROGRESS: 
0:36:19.320803 PROGRESS: Precursor Summary:
0:36:19.320915 PROGRESS: 
0:36:19.320971 PROGRESS: Protein Summary:
0:36:19.321043 PROGRESS: =========================================================================
0:36:19.321235 INFO: Target number of precursors not reached yet.
0:36:19.405408 INFO: Starting optimization step 1.
0:36:19.405639 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:36:19.405717 INFO: Using rust extraction backend
0:36:19.405774 PROGRESS: Extracting batch of 3911 precursors
0:36:19.415463 INFO: === Search parameters used ===
0:36:19.415591 INFO: rt_error       : 805.6019897460938
0:36:19.415650 INFO: mobility_error : 0.1
0:36:19.415694 INFO: num_candidates : 1
0:36:19.415735 INFO: ms1_error      : 3
0:36:19.415774 INFO: ms2_error      : 10
0:36:19.415812 INFO: fwhm_rt        : 5
0:36:19.415850 INFO: quant_window   : 3
0:36:19.415888 INFO: ==============================================
0:36:19.462902 INFO: performing precursor FDR with 40 features
0:36:19.462990 INFO: Decoy channel: -1
0:36:19.463014 INFO: competitive: True
0:36:19.467530 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:19.469933 INFO: Estimating optimal hyperparameters - samples: 4,684, batch_size: 128, learning_rate: 1.77e-04
0:36:19.470013 INFO: Using random state 6298 for train-test-split
0:36:19.941028 INFO: Test AUC: 0.574
0:36:19.941123 INFO: Train AUC: 0.600
0:36:19.941151 INFO: AUC difference: 4.38%
0:36:20.191257 INFO: Resetting torch num_threads to 100
0:36:20.194783 PROGRESS: === Extracted 5856 precursors and 32539 fragments ===
0:36:20.195159 INFO: === FDR correction performed with classifier version -1 ===
0:36:20.195647 PROGRESS: ============================= Precursor FDR =============================
0:36:20.195730 PROGRESS: Total precursors accumulated: 8
0:36:20.195786 PROGRESS: Target precursors: 8 (100.00%)
0:36:20.195834 PROGRESS: Decoy precursors: 0 (0.00%)
0:36:20.195878 PROGRESS: 
0:36:20.195919 PROGRESS: Precursor Summary:
0:36:20.196984 PROGRESS: Channel   0:	 0.050 FDR:     8; 0.010 FDR:     8; 0.001 FDR:     8
0:36:20.197063 PROGRESS: 
0:36:20.197124 PROGRESS: Protein Summary:
0:36:20.198288 PROGRESS: Channel   0:	 0.050 FDR:     8; 0.010 FDR:     8; 0.001 FDR:     8
0:36:20.198368 PROGRESS: =========================================================================
0:36:20.198690 INFO: Target number of precursors not reached yet.
0:36:20.298203 INFO: Starting optimization step 2.
0:36:20.298429 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:36:20.298511 INFO: Using rust extraction backend
0:36:20.298570 PROGRESS: Extracting batch of 7891 precursors
0:36:20.314875 INFO: === Search parameters used ===
0:36:20.315023 INFO: rt_error       : 805.6019897460938
0:36:20.315073 INFO: mobility_error : 0.1
0:36:20.315116 INFO: num_candidates : 1
0:36:20.315167 INFO: ms1_error      : 3
0:36:20.315214 INFO: ms2_error      : 10
0:36:20.315253 INFO: fwhm_rt        : 5
0:36:20.315293 INFO: quant_window   : 3
0:36:20.315333 INFO: ==============================================
0:36:20.396555 INFO: performing precursor FDR with 40 features
0:36:20.396665 INFO: Decoy channel: -1
0:36:20.396689 INFO: competitive: True
0:36:20.403347 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:20.406918 INFO: Estimating optimal hyperparameters - samples: 10,980, batch_size: 128, learning_rate: 1.77e-04
0:36:20.407027 INFO: Using random state 100000 for train-test-split
0:36:21.499637 INFO: Test AUC: 0.557
0:36:21.499747 INFO: Train AUC: 0.602
0:36:21.499777 INFO: AUC difference: 7.43%
0:36:21.499801 WARNING: AUC difference > 5%. This may indicate overfitting.
0:36:21.750258 INFO: Resetting torch num_threads to 100
0:36:21.754521 PROGRESS: === Extracted 13725 precursors and 76386 fragments ===
0:36:21.754921 INFO: === FDR correction performed with classifier version -1 ===
0:36:21.755444 PROGRESS: ============================= Precursor FDR =============================
0:36:21.755536 PROGRESS: Total precursors accumulated: 24
0:36:21.755606 PROGRESS: Target precursors: 24 (100.00%)
0:36:21.755659 PROGRESS: Decoy precursors: 0 (0.00%)
0:36:21.755705 PROGRESS: 
0:36:21.755749 PROGRESS: Precursor Summary:
0:36:21.756822 PROGRESS: Channel   0:	 0.050 FDR:    24; 0.010 FDR:    24; 0.001 FDR:    24
0:36:21.756905 PROGRESS: 
0:36:21.756960 PROGRESS: Protein Summary:
0:36:21.758142 PROGRESS: Channel   0:	 0.050 FDR:    24; 0.010 FDR:    24; 0.001 FDR:    24
0:36:21.758229 PROGRESS: =========================================================================
0:36:21.758564 INFO: Target number of precursors not reached yet.
0:36:21.870141 INFO: Starting optimization step 3.
0:36:21.870395 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:36:21.870486 INFO: Using rust extraction backend
0:36:21.870559 PROGRESS: Extracting batch of 15777 precursors
0:36:21.900782 INFO: === Search parameters used ===
0:36:21.900966 INFO: rt_error       : 805.6019897460938
0:36:21.901021 INFO: mobility_error : 0.1
0:36:21.901067 INFO: num_candidates : 1
0:36:21.901110 INFO: ms1_error      : 3
0:36:21.901152 INFO: ms2_error      : 10
0:36:21.901192 INFO: fwhm_rt        : 5
0:36:21.901233 INFO: quant_window   : 3
0:36:21.901284 INFO: ==============================================
0:36:22.031989 INFO: performing precursor FDR with 40 features
0:36:22.032103 INFO: Decoy channel: -1
0:36:22.032128 INFO: competitive: True
0:36:22.043375 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:22.050672 INFO: Estimating optimal hyperparameters - samples: 23,567, batch_size: 128, learning_rate: 1.77e-04
0:36:22.050839 INFO: Using random state 502742 for train-test-split
0:36:24.424750 INFO: Test AUC: 0.573
0:36:24.424881 INFO: Train AUC: 0.608
0:36:24.424910 INFO: AUC difference: 5.76%
0:36:24.424930 WARNING: AUC difference > 5%. This may indicate overfitting.
0:36:24.682937 INFO: Resetting torch num_threads to 100
0:36:24.689646 PROGRESS: === Extracted 29459 precursors and 164266 fragments ===
0:36:24.690089 INFO: === FDR correction performed with classifier version -1 ===
0:36:24.690609 PROGRESS: ============================= Precursor FDR =============================
0:36:24.690695 PROGRESS: Total precursors accumulated: 133
0:36:24.690752 PROGRESS: Target precursors: 132 (99.25%)
0:36:24.690803 PROGRESS: Decoy precursors: 1 (0.75%)
0:36:24.690846 PROGRESS: 
0:36:24.690889 PROGRESS: Precursor Summary:
0:36:24.691883 PROGRESS: Channel   0:	 0.050 FDR:   132; 0.010 FDR:   132; 0.001 FDR:   110
0:36:24.691972 PROGRESS: 
0:36:24.692026 PROGRESS: Protein Summary:
0:36:24.693227 PROGRESS: Channel   0:	 0.050 FDR:   131; 0.010 FDR:   131; 0.001 FDR:   109
0:36:24.693311 PROGRESS: =========================================================================
0:36:24.693800 INFO: Target number of precursors not reached yet.
0:36:24.830138 INFO: Starting optimization step 4.
0:36:24.830399 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:36:24.830489 INFO: Using rust extraction backend
0:36:24.830555 PROGRESS: Extracting batch of 31516 precursors
0:36:24.887102 INFO: === Search parameters used ===
0:36:24.887354 INFO: rt_error       : 805.6019897460938
0:36:24.887421 INFO: mobility_error : 0.1
0:36:24.887470 INFO: num_candidates : 1
0:36:24.887512 INFO: ms1_error      : 3
0:36:24.887552 INFO: ms2_error      : 10
0:36:24.887593 INFO: fwhm_rt        : 5
0:36:24.887632 INFO: quant_window   : 3
0:36:24.887672 INFO: ==============================================
0:36:25.113371 INFO: performing precursor FDR with 40 features
0:36:25.113487 INFO: Decoy channel: -1
0:36:25.113510 INFO: competitive: True
0:36:25.136945 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:25.151445 INFO: Estimating optimal hyperparameters - samples: 48,720, batch_size: 199, learning_rate: 2.20e-04
0:36:25.151652 INFO: Using random state 86508 for train-test-split
0:36:28.780803 INFO: Test AUC: 0.576
0:36:28.780922 INFO: Train AUC: 0.616
0:36:28.780954 INFO: AUC difference: 6.47%
0:36:28.780977 WARNING: AUC difference > 5%. This may indicate overfitting.
0:36:29.042922 INFO: Resetting torch num_threads to 100
0:36:29.054593 PROGRESS: === Extracted 60900 precursors and 339463 fragments ===
0:36:29.055246 INFO: === FDR correction performed with classifier version -1 ===
0:36:29.055872 PROGRESS: ============================= Precursor FDR =============================
0:36:29.055963 PROGRESS: Total precursors accumulated: 259
0:36:29.056024 PROGRESS: Target precursors: 257 (99.23%)
0:36:29.056075 PROGRESS: Decoy precursors: 2 (0.77%)
0:36:29.056121 PROGRESS: 
0:36:29.056167 PROGRESS: Precursor Summary:
0:36:29.057197 PROGRESS: Channel   0:	 0.050 FDR:   257; 0.010 FDR:   257; 0.001 FDR:   199
0:36:29.057284 PROGRESS: 
0:36:29.057350 PROGRESS: Protein Summary:
0:36:29.058538 PROGRESS: Channel   0:	 0.050 FDR:   244; 0.010 FDR:   244; 0.001 FDR:   190
0:36:29.058623 PROGRESS: =========================================================================
0:36:29.059648 INFO: Target number of precursors not reached yet.
0:36:29.238403 INFO: Starting optimization step 5.
0:36:29.238688 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:36:29.238771 INFO: Using rust extraction backend
0:36:29.238834 PROGRESS: Extracting batch of 63010 precursors
0:36:29.348906 INFO: === Search parameters used ===
0:36:29.349192 INFO: rt_error       : 805.6019897460938
0:36:29.349250 INFO: mobility_error : 0.1
0:36:29.349298 INFO: num_candidates : 1
0:36:29.349342 INFO: ms1_error      : 3
0:36:29.349384 INFO: ms2_error      : 10
0:36:29.349424 INFO: fwhm_rt        : 5
0:36:29.349464 INFO: quant_window   : 3
0:36:29.349503 INFO: ==============================================
0:36:29.730837 INFO: performing precursor FDR with 40 features
0:36:29.730950 INFO: Decoy channel: -1
0:36:29.730974 INFO: competitive: True
0:36:29.779559 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:29.812485 INFO: Estimating optimal hyperparameters - samples: 99,009, batch_size: 405, learning_rate: 3.14e-04
0:36:29.812791 INFO: Using random state 59108 for train-test-split
0:36:34.400744 INFO: Test AUC: 0.589
0:36:34.400854 INFO: Train AUC: 0.615
0:36:34.400886 INFO: AUC difference: 4.17%
0:36:34.684265 INFO: Resetting torch num_threads to 100
0:36:34.704398 PROGRESS: === Extracted 123762 precursors and 690307 fragments ===
0:36:34.705050 INFO: === FDR correction performed with classifier version -1 ===
0:36:34.705619 PROGRESS: ============================= Precursor FDR =============================
0:36:34.705706 PROGRESS: Total precursors accumulated: 0
0:36:34.705766 PROGRESS: Target precursors: 0 (0.00%)
0:36:34.705818 PROGRESS: Decoy precursors: 0 (0.00%)
0:36:34.705865 PROGRESS: 
0:36:34.705912 PROGRESS: Precursor Summary:
0:36:34.706040 PROGRESS: 
0:36:34.706102 PROGRESS: Protein Summary:
0:36:34.706192 PROGRESS: =========================================================================
0:36:34.708227 INFO: Target number of precursors not reached yet.
0:36:34.968413 INFO: Starting optimization step 6.
0:36:34.968737 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:36:34.968820 INFO: Using rust extraction backend
0:36:34.968884 PROGRESS: Extracting batch of 126188 precursors
0:36:35.187808 INFO: === Search parameters used ===
0:36:35.188069 INFO: rt_error       : 805.6019897460938
0:36:35.188130 INFO: mobility_error : 0.1
0:36:35.188178 INFO: num_candidates : 1
0:36:35.188222 INFO: ms1_error      : 3
0:36:35.188265 INFO: ms2_error      : 10
0:36:35.188308 INFO: fwhm_rt        : 5
0:36:35.188350 INFO: quant_window   : 3
0:36:35.188391 INFO: ==============================================
0:36:35.880070 INFO: performing precursor FDR with 40 features
0:36:35.880210 INFO: Decoy channel: -1
0:36:35.880235 INFO: competitive: True
0:36:35.980743 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:36.058654 INFO: Estimating optimal hyperparameters - samples: 199,700, batch_size: 817, learning_rate: 4.47e-04
0:36:36.059087 INFO: Using random state 377900 for train-test-split
0:36:42.495317 INFO: Test AUC: 0.591
0:36:42.495487 INFO: Train AUC: 0.613
0:36:42.495521 INFO: AUC difference: 3.47%
0:36:42.823312 INFO: Resetting torch num_threads to 100
0:36:42.877332 PROGRESS: === Extracted 249625 precursors and 1390915 fragments ===
0:36:42.878094 INFO: === FDR correction performed with classifier version -1 ===
0:36:42.878912 PROGRESS: ============================= Precursor FDR =============================
0:36:42.879003 PROGRESS: Total precursors accumulated: 1,099
0:36:42.879066 PROGRESS: Target precursors: 1,089 (99.09%)
0:36:42.879117 PROGRESS: Decoy precursors: 10 (0.91%)
0:36:42.879187 PROGRESS: 
0:36:42.879237 PROGRESS: Precursor Summary:
0:36:42.880458 PROGRESS: Channel   0:	 0.050 FDR: 1,089; 0.010 FDR: 1,089; 0.001 FDR:     0
0:36:42.880553 PROGRESS: 
0:36:42.880608 PROGRESS: Protein Summary:
0:36:42.882064 PROGRESS: Channel   0:	 0.050 FDR:   934; 0.010 FDR:   934; 0.001 FDR:     0
0:36:42.882151 PROGRESS: =========================================================================
0:36:42.886444 INFO: Target number of precursors reached.
0:36:43.047358 INFO: fragments_df: keeping 5000 of 1390915 [sum(precursor_idx_mask)=11675 sum(mass_error_mask)=1390915 stop_rank=5000
0:36:43.461702 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:36:43.631454 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:36:44.284726 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:36:44.285191 INFO: Using score_cutoff 12.782347136306763 (fac=0.99, q=1)
0:36:44.285519 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:36:44.285595 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:36:44.285650 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.782347136306763
0:36:44.285712 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:36:44.440683 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:36:44.785371 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
0:36:44.785643 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:36:44.785757 INFO: Starting optimization step 7.
0:36:44.785824 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:36:44.785894 INFO: Using rust extraction backend
0:36:44.785958 PROGRESS: Extracting batch of 250256 precursors
0:36:45.218781 INFO: === Search parameters used ===
0:36:45.219071 INFO: rt_error       : 805.6019897460938
0:36:45.219130 INFO: mobility_error : 0.1
0:36:45.219207 INFO: num_candidates : 3
0:36:45.219253 INFO: ms1_error      : 3
0:36:45.219306 INFO: ms2_error      : 10
0:36:45.219346 INFO: fwhm_rt        : 3.0
0:36:45.219384 INFO: quant_window   : 3
0:36:45.219422 INFO: ==============================================
0:36:47.816526 INFO: performing precursor FDR with 40 features
0:36:47.816653 INFO: Decoy channel: -1
0:36:47.816680 INFO: competitive: True
0:36:47.999084 INFO: Setting torch num_threads to 2 for FDR classification task
0:36:48.311078 INFO: Estimating optimal hyperparameters - samples: 599,223, batch_size: 2,454, learning_rate: 7.74e-04
0:36:48.312041 INFO: Using random state 641914 for train-test-split
0:37:01.097574 INFO: Test AUC: 0.599
0:37:01.097702 INFO: Train AUC: 0.609
0:37:01.097735 INFO: AUC difference: 1.65%
0:37:01.581407 INFO: Resetting torch num_threads to 100
0:37:01.609604 PROGRESS: === Extracted 749029 precursors and 4011304 fragments ===
0:37:01.610079 INFO: === FDR correction performed with classifier version 6 ===
0:37:01.610723 PROGRESS: ============================= Precursor FDR =============================
0:37:01.610815 PROGRESS: Total precursors accumulated: 1,234
0:37:01.610876 PROGRESS: Target precursors: 1,222 (99.03%)
0:37:01.610928 PROGRESS: Decoy precursors: 12 (0.97%)
0:37:01.610976 PROGRESS: 
0:37:01.611021 PROGRESS: Precursor Summary:
0:37:01.612239 PROGRESS: Channel   0:	 0.050 FDR: 1,222; 0.010 FDR: 1,222; 0.001 FDR:     0
0:37:01.612331 PROGRESS: 
0:37:01.612386 PROGRESS: Protein Summary:
0:37:01.613870 PROGRESS: Channel   0:	 0.050 FDR: 1,042; 0.010 FDR: 1,042; 0.001 FDR:     0
0:37:01.613957 PROGRESS: =========================================================================
0:37:01.636720 INFO: Target number of precursors reached.
0:37:02.086937 INFO: fragments_df: keeping 5000 of 4011304 [sum(precursor_idx_mask)=29514 sum(mass_error_mask)=4011304 stop_rank=5000
0:37:02.515805 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:37:02.698936 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:37:03.355539 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:37:03.355978 INFO: Using score_cutoff 12.724078468036652 (fac=0.99, q=1)
0:37:03.356283 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:37:03.356368 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:37:03.356422 INFO: Updating optimization_manager: score_cutoff        : 12.782347136306763 -> 12.724078468036652
0:37:03.356476 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:37:03.509882 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:37:03.851846 INFO: === checking if optimization conditions were reached ===
0:37:03.854228 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
0:37:03.854334 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:37:03.854438 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:37:03.854507 INFO: ==============================================
0:37:03.854591 INFO: Starting optimization step 8.
0:37:03.854656 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:37:03.854721 INFO: Using rust extraction backend
0:37:03.854783 PROGRESS: Extracting batch of 250256 precursors
0:37:04.280158 INFO: === Search parameters used ===
0:37:04.280430 INFO: rt_error       : 805.6019897460938
0:37:04.280491 INFO: mobility_error : 0.1
0:37:04.280541 INFO: num_candidates : 3
0:37:04.280590 INFO: ms1_error      : 3
0:37:04.280634 INFO: ms2_error      : 10.0
0:37:04.280677 INFO: fwhm_rt        : 3.0
0:37:04.280721 INFO: quant_window   : 3
0:37:04.280762 INFO: ==============================================
0:37:06.782643 INFO: performing precursor FDR with 40 features
0:37:06.782758 INFO: Decoy channel: -1
0:37:06.782784 INFO: competitive: True
0:37:06.968022 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:07.260708 INFO: Estimating optimal hyperparameters - samples: 599,239, batch_size: 2,454, learning_rate: 7.74e-04
0:37:07.261853 INFO: Using random state 611499 for train-test-split
0:37:20.234795 INFO: Test AUC: 0.601
0:37:20.234976 INFO: Train AUC: 0.615
0:37:20.235012 INFO: AUC difference: 2.22%
0:37:21.377655 INFO: Resetting torch num_threads to 100
0:37:21.408324 PROGRESS: === Extracted 749049 precursors and 4011501 fragments ===
0:37:21.408797 INFO: === FDR correction performed with classifier version 7 ===
0:37:21.409439 PROGRESS: ============================= Precursor FDR =============================
0:37:21.409527 PROGRESS: Total precursors accumulated: 1,347
0:37:21.409587 PROGRESS: Target precursors: 1,334 (99.03%)
0:37:21.409639 PROGRESS: Decoy precursors: 13 (0.97%)
0:37:21.409686 PROGRESS: 
0:37:21.409741 PROGRESS: Precursor Summary:
0:37:21.410937 PROGRESS: Channel   0:	 0.050 FDR: 1,334; 0.010 FDR: 1,334; 0.001 FDR:     0
0:37:21.411023 PROGRESS: 
0:37:21.411077 PROGRESS: Protein Summary:
0:37:21.412606 PROGRESS: Channel   0:	 0.050 FDR: 1,142; 0.010 FDR: 1,142; 0.001 FDR:     0
0:37:21.412697 PROGRESS: =========================================================================
0:37:21.430509 INFO: Target number of precursors reached.
0:37:21.861959 INFO: fragments_df: keeping 5000 of 4011501 [sum(precursor_idx_mask)=31422 sum(mass_error_mask)=4011501 stop_rank=5000
0:37:22.298612 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:37:22.510572 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:37:23.162080 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:37:23.162534 INFO: Using score_cutoff 9.819556202602385 (fac=0.99, q=1)
0:37:23.162839 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:37:23.162916 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:37:23.162971 INFO: Updating optimization_manager: score_cutoff        : 12.724078468036652 -> 9.819556202602385
0:37:23.163024 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:37:23.314479 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:37:23.653324 INFO: === checking if optimization conditions were reached ===
0:37:23.655556 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:37:23.655671 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:37:23.655739 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:37:23.655804 INFO: ==============================================
0:37:23.655868 INFO: Starting optimization step 9.
0:37:23.655923 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:37:23.655980 INFO: Using rust extraction backend
0:37:23.656033 PROGRESS: Extracting batch of 250256 precursors
0:37:24.081399 INFO: === Search parameters used ===
0:37:24.081668 INFO: rt_error       : 805.6019897460938
0:37:24.081724 INFO: mobility_error : 0.1
0:37:24.081771 INFO: num_candidates : 3
0:37:24.081813 INFO: ms1_error      : 3
0:37:24.081852 INFO: ms2_error      : 10.0
0:37:24.081891 INFO: fwhm_rt        : 3.0
0:37:24.081929 INFO: quant_window   : 3
0:37:24.081967 INFO: ==============================================
0:37:26.622340 INFO: performing precursor FDR with 40 features
0:37:26.622463 INFO: Decoy channel: -1
0:37:26.622490 INFO: competitive: True
0:37:26.809782 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:27.105198 INFO: Estimating optimal hyperparameters - samples: 599,262, batch_size: 2,454, learning_rate: 7.74e-04
0:37:27.106137 INFO: Using random state 601068 for train-test-split
0:37:39.849051 INFO: Test AUC: 0.606
0:37:39.849179 INFO: Train AUC: 0.619
0:37:39.849212 INFO: AUC difference: 2.02%
0:37:40.323206 INFO: Resetting torch num_threads to 100
0:37:40.353006 PROGRESS: === Extracted 749078 precursors and 4011766 fragments ===
0:37:40.353478 INFO: === FDR correction performed with classifier version 8 ===
0:37:40.354206 PROGRESS: ============================= Precursor FDR =============================
0:37:40.354300 PROGRESS: Total precursors accumulated: 1,464
0:37:40.354359 PROGRESS: Target precursors: 1,450 (99.04%)
0:37:40.354411 PROGRESS: Decoy precursors: 14 (0.96%)
0:37:40.354467 PROGRESS: 
0:37:40.354515 PROGRESS: Precursor Summary:
0:37:40.355821 PROGRESS: Channel   0:	 0.050 FDR: 1,450; 0.010 FDR: 1,450; 0.001 FDR:    52
0:37:40.355915 PROGRESS: 
0:37:40.355972 PROGRESS: Protein Summary:
0:37:40.357560 PROGRESS: Channel   0:	 0.050 FDR: 1,232; 0.010 FDR: 1,232; 0.001 FDR:    50
0:37:40.357650 PROGRESS: =========================================================================
0:37:40.372360 INFO: Target number of precursors reached.
0:37:40.829770 INFO: fragments_df: keeping 5000 of 4011766 [sum(precursor_idx_mask)=34203 sum(mass_error_mask)=4011766 stop_rank=5000
0:37:41.247175 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:37:41.451962 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:37:42.104806 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:37:42.105265 INFO: Using score_cutoff 11.30177502822876 (fac=0.99, q=1)
0:37:42.105576 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:37:42.105654 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:37:42.105719 INFO: Updating optimization_manager: score_cutoff        : 9.819556202602385 -> 11.30177502822876
0:37:42.105774 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:37:42.256640 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:37:42.606117 INFO: === checking if optimization conditions were reached ===
0:37:42.608380 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:37:42.608488 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:37:42.608555 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:37:42.608613 INFO: ==============================================
0:37:42.608680 INFO: Starting optimization step 10.
0:37:42.608738 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:37:42.608799 INFO: Using rust extraction backend
0:37:42.608855 PROGRESS: Extracting batch of 250256 precursors
0:37:43.030946 INFO: === Search parameters used ===
0:37:43.031235 INFO: rt_error       : 805.6019897460938
0:37:43.031295 INFO: mobility_error : 0.1
0:37:43.031343 INFO: num_candidates : 3
0:37:43.031386 INFO: ms1_error      : 3
0:37:43.031427 INFO: ms2_error      : 10.0
0:37:43.031484 INFO: fwhm_rt        : 3.0
0:37:43.031524 INFO: quant_window   : 3
0:37:43.031563 INFO: ==============================================
0:37:45.500297 INFO: performing precursor FDR with 40 features
0:37:45.500416 INFO: Decoy channel: -1
0:37:45.500441 INFO: competitive: True
0:37:45.698347 INFO: Setting torch num_threads to 2 for FDR classification task
0:37:46.011342 INFO: Estimating optimal hyperparameters - samples: 599,249, batch_size: 2,454, learning_rate: 7.74e-04
0:37:46.012281 INFO: Using random state 34317 for train-test-split
0:37:58.698267 INFO: Test AUC: 0.609
0:37:58.698424 INFO: Train AUC: 0.621
0:37:58.698459 INFO: AUC difference: 1.86%
0:37:59.180844 INFO: Resetting torch num_threads to 100
0:37:59.213055 PROGRESS: === Extracted 749062 precursors and 4012012 fragments ===
0:37:59.213559 INFO: === FDR correction performed with classifier version 9 ===
0:37:59.214230 PROGRESS: ============================= Precursor FDR =============================
0:37:59.214319 PROGRESS: Total precursors accumulated: 1,455
0:37:59.214391 PROGRESS: Target precursors: 1,441 (99.04%)
0:37:59.214445 PROGRESS: Decoy precursors: 14 (0.96%)
0:37:59.214492 PROGRESS: 
0:37:59.214538 PROGRESS: Precursor Summary:
0:37:59.215875 PROGRESS: Channel   0:	 0.050 FDR: 1,441; 0.010 FDR: 1,441; 0.001 FDR:   639
0:37:59.215967 PROGRESS: 
0:37:59.216023 PROGRESS: Protein Summary:
0:37:59.217702 PROGRESS: Channel   0:	 0.050 FDR: 1,225; 0.010 FDR: 1,225; 0.001 FDR:   564
0:37:59.217791 PROGRESS: =========================================================================
0:37:59.231952 INFO: Target number of precursors reached.
0:37:59.669476 INFO: fragments_df: keeping 5000 of 4012012 [sum(precursor_idx_mask)=33714 sum(mass_error_mask)=4012012 stop_rank=5000
0:38:00.208982 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:38:00.411639 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:38:01.070517 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:38:01.070978 INFO: Using score_cutoff 10.084037715911865 (fac=0.99, q=1)
0:38:01.071310 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:38:01.071391 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:38:01.071445 INFO: Updating optimization_manager: score_cutoff        : 11.30177502822876 -> 10.084037715911865
0:38:01.071500 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:38:01.223135 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:38:01.573864 INFO: === checking if optimization conditions were reached ===
0:38:01.576094 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:38:01.576200 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:38:01.576265 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:38:01.576321 INFO: ==============================================
0:38:01.576390 INFO: Starting optimization step 11.
0:38:01.576451 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:38:01.576517 INFO: Using rust extraction backend
0:38:01.576578 PROGRESS: Extracting batch of 250256 precursors
0:38:02.002208 INFO: === Search parameters used ===
0:38:02.002485 INFO: rt_error       : 805.6019897460938
0:38:02.002539 INFO: mobility_error : 0.1
0:38:02.002585 INFO: num_candidates : 3
0:38:02.002628 INFO: ms1_error      : 3
0:38:02.002670 INFO: ms2_error      : 10.0
0:38:02.002712 INFO: fwhm_rt        : 3.0
0:38:02.002753 INFO: quant_window   : 3
0:38:02.002794 INFO: ==============================================
0:38:04.541940 INFO: performing precursor FDR with 40 features
0:38:04.542067 INFO: Decoy channel: -1
0:38:04.542095 INFO: competitive: True
0:38:04.741475 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:05.051234 INFO: Estimating optimal hyperparameters - samples: 599,253, batch_size: 2,454, learning_rate: 7.74e-04
0:38:05.052393 INFO: Using random state 142451 for train-test-split
0:38:17.520938 INFO: Test AUC: 0.611
0:38:17.521057 INFO: Train AUC: 0.623
0:38:17.521099 INFO: AUC difference: 1.84%
0:38:17.989262 INFO: Resetting torch num_threads to 100
0:38:18.018219 PROGRESS: === Extracted 749067 precursors and 4012143 fragments ===
0:38:18.018690 INFO: === FDR correction performed with classifier version 10 ===
0:38:18.019377 PROGRESS: ============================= Precursor FDR =============================
0:38:18.019482 PROGRESS: Total precursors accumulated: 1,360
0:38:18.019541 PROGRESS: Target precursors: 1,347 (99.04%)
0:38:18.019590 PROGRESS: Decoy precursors: 13 (0.96%)
0:38:18.019634 PROGRESS: 
0:38:18.019678 PROGRESS: Precursor Summary:
0:38:18.020954 PROGRESS: Channel   0:	 0.050 FDR: 1,347; 0.010 FDR: 1,347; 0.001 FDR:   615
0:38:18.021045 PROGRESS: 
0:38:18.021099 PROGRESS: Protein Summary:
0:38:18.022711 PROGRESS: Channel   0:	 0.050 FDR: 1,154; 0.010 FDR: 1,154; 0.001 FDR:   541
0:38:18.022800 PROGRESS: =========================================================================
0:38:18.037103 INFO: Target number of precursors reached.
0:38:18.495351 INFO: fragments_df: keeping 5000 of 4012143 [sum(precursor_idx_mask)=31368 sum(mass_error_mask)=4012143 stop_rank=5000
0:38:19.004884 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:38:19.196576 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:38:19.850997 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:38:19.851506 INFO: Using score_cutoff 8.931307145690917 (fac=0.99, q=1)
0:38:19.851811 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:38:19.851888 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:38:19.851941 INFO: Updating optimization_manager: score_cutoff        : 10.084037715911865 -> 8.931307145690917
0:38:19.852001 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:38:20.008677 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:38:20.355057 INFO: === checking if optimization conditions were reached ===
0:38:20.357388 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:38:20.357534 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:38:20.357615 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:38:20.357676 INFO: ==============================================
0:38:20.357746 PROGRESS: Optimization finished for ms2_error.
0:38:20.808716 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:38:20.960805 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:38:21.307978 INFO: Starting optimization step 0.
0:38:21.308244 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:38:21.308321 INFO: Using rust extraction backend
0:38:21.308383 PROGRESS: Extracting batch of 250256 precursors
0:38:21.732198 INFO: === Search parameters used ===
0:38:21.732489 INFO: rt_error       : 805.6019897460938
0:38:21.732550 INFO: mobility_error : 0.1
0:38:21.732599 INFO: num_candidates : 3
0:38:21.732650 INFO: ms1_error      : 3
0:38:21.732694 INFO: ms2_error      : 10.0
0:38:21.732737 INFO: fwhm_rt        : 3.0
0:38:21.732777 INFO: quant_window   : 3
0:38:21.732983 INFO: ==============================================
0:38:24.272391 INFO: performing precursor FDR with 40 features
0:38:24.272515 INFO: Decoy channel: -1
0:38:24.272549 INFO: competitive: True
0:38:24.462193 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:24.752031 INFO: Estimating optimal hyperparameters - samples: 599,253, batch_size: 2,454, learning_rate: 7.74e-04
0:38:24.752970 INFO: Using random state 249848 for train-test-split
0:38:37.324254 INFO: Test AUC: 0.613
0:38:37.324382 INFO: Train AUC: 0.627
0:38:37.324416 INFO: AUC difference: 2.24%
0:38:37.804044 INFO: Resetting torch num_threads to 100
0:38:37.833600 PROGRESS: === Extracted 749067 precursors and 4012095 fragments ===
0:38:37.834068 INFO: === FDR correction performed with classifier version 11 ===
0:38:37.834714 PROGRESS: ============================= Precursor FDR =============================
0:38:37.834804 PROGRESS: Total precursors accumulated: 1,486
0:38:37.834877 PROGRESS: Target precursors: 1,472 (99.06%)
0:38:37.834928 PROGRESS: Decoy precursors: 14 (0.94%)
0:38:37.834974 PROGRESS: 
0:38:37.835021 PROGRESS: Precursor Summary:
0:38:37.836324 PROGRESS: Channel   0:	 0.050 FDR: 1,472; 0.010 FDR: 1,472; 0.001 FDR:   150
0:38:37.836426 PROGRESS: 
0:38:37.836482 PROGRESS: Protein Summary:
0:38:37.838098 PROGRESS: Channel   0:	 0.050 FDR: 1,249; 0.010 FDR: 1,249; 0.001 FDR:   140
0:38:37.838189 PROGRESS: =========================================================================
0:38:37.852304 INFO: Target number of precursors reached.
0:38:38.302746 INFO: fragments_df: keeping 5000 of 4012095 [sum(precursor_idx_mask)=34631 sum(mass_error_mask)=4012095 stop_rank=5000
0:38:38.712569 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:38:38.912888 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:38:39.564562 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:38:39.565033 INFO: Using score_cutoff 11.162244118022919 (fac=0.99, q=1)
0:38:39.565350 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:38:39.565427 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:38:39.565480 INFO: Updating optimization_manager: score_cutoff        : 8.931307145690917 -> 11.162244118022919
0:38:39.565533 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:38:39.716843 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:38:40.053007 INFO: === checking if optimization conditions were reached ===
0:38:40.053293 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:38:40.056035 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 689.9194197955619
0:38:40.056166 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 689.9194.
0:38:40.056233 INFO: ==============================================
0:38:40.056304 INFO: Starting optimization step 1.
0:38:40.056362 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:38:40.056423 INFO: Using rust extraction backend
0:38:40.056481 PROGRESS: Extracting batch of 250256 precursors
0:38:40.477618 INFO: === Search parameters used ===
0:38:40.477885 INFO: rt_error       : 689.9194197955619
0:38:40.477942 INFO: mobility_error : 0.1
0:38:40.477989 INFO: num_candidates : 3
0:38:40.478033 INFO: ms1_error      : 3
0:38:40.478075 INFO: ms2_error      : 10.0
0:38:40.478137 INFO: fwhm_rt        : 3.0
0:38:40.478180 INFO: quant_window   : 3
0:38:40.478221 INFO: ==============================================
0:38:42.874637 INFO: performing precursor FDR with 40 features
0:38:42.874761 INFO: Decoy channel: -1
0:38:42.874787 INFO: competitive: True
0:38:43.064306 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:43.359106 INFO: Estimating optimal hyperparameters - samples: 599,224, batch_size: 2,454, learning_rate: 7.74e-04
0:38:43.360263 INFO: Using random state 249848 for train-test-split
0:38:56.273052 INFO: Test AUC: 0.611
0:38:56.273183 INFO: Train AUC: 0.626
0:38:56.273216 INFO: AUC difference: 2.45%
0:38:56.745235 INFO: Resetting torch num_threads to 100
0:38:56.774974 PROGRESS: === Extracted 749031 precursors and 4008959 fragments ===
0:38:56.775458 INFO: === FDR correction performed with classifier version 11 ===
0:38:56.776132 PROGRESS: ============================= Precursor FDR =============================
0:38:56.776225 PROGRESS: Total precursors accumulated: 1,487
0:38:56.776298 PROGRESS: Target precursors: 1,473 (99.06%)
0:38:56.776349 PROGRESS: Decoy precursors: 14 (0.94%)
0:38:56.776397 PROGRESS: 
0:38:56.776441 PROGRESS: Precursor Summary:
0:38:56.777752 PROGRESS: Channel   0:	 0.050 FDR: 1,473; 0.010 FDR: 1,473; 0.001 FDR:   565
0:38:56.777843 PROGRESS: 
0:38:56.777898 PROGRESS: Protein Summary:
0:38:56.779578 PROGRESS: Channel   0:	 0.050 FDR: 1,255; 0.010 FDR: 1,255; 0.001 FDR:   502
0:38:56.779673 PROGRESS: =========================================================================
0:38:56.793507 INFO: Target number of precursors reached.
0:38:57.234288 INFO: fragments_df: keeping 5000 of 4008959 [sum(precursor_idx_mask)=34476 sum(mass_error_mask)=4008959 stop_rank=5000
0:38:57.645849 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:38:57.856773 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:38:58.509519 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:38:58.509974 INFO: Using score_cutoff 10.176914266204834 (fac=0.99, q=1)
0:38:58.510273 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:38:58.510346 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:38:58.510397 INFO: Updating optimization_manager: score_cutoff        : 11.162244118022919 -> 10.176914266204834
0:38:58.510448 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:38:58.661634 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:38:58.999862 INFO: === checking if optimization conditions were reached ===
0:38:59.000128 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:38:59.002863 INFO: Updating optimization_manager: rt_error            : 689.9194197955619 -> 693.1704013641709
0:38:59.002964 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 693.1704.
0:38:59.003026 INFO: ==============================================
0:38:59.003093 INFO: Starting optimization step 2.
0:38:59.003163 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:38:59.003232 INFO: Using rust extraction backend
0:38:59.003287 PROGRESS: Extracting batch of 250256 precursors
0:38:59.424262 INFO: === Search parameters used ===
0:38:59.424529 INFO: rt_error       : 693.1704013641709
0:38:59.424583 INFO: mobility_error : 0.1
0:38:59.424629 INFO: num_candidates : 3
0:38:59.424684 INFO: ms1_error      : 3
0:38:59.424725 INFO: ms2_error      : 10.0
0:38:59.424764 INFO: fwhm_rt        : 3.0
0:38:59.424802 INFO: quant_window   : 3
0:38:59.424840 INFO: ==============================================
0:39:01.865089 INFO: performing precursor FDR with 40 features
0:39:01.865217 INFO: Decoy channel: -1
0:39:01.865243 INFO: competitive: True
0:39:02.053362 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:02.350044 INFO: Estimating optimal hyperparameters - samples: 599,224, batch_size: 2,454, learning_rate: 7.74e-04
0:39:02.351233 INFO: Using random state 249848 for train-test-split
0:39:14.950627 INFO: Test AUC: 0.613
0:39:14.950753 INFO: Train AUC: 0.626
0:39:14.950785 INFO: AUC difference: 2.11%
0:39:15.424599 INFO: Resetting torch num_threads to 100
0:39:15.454150 PROGRESS: === Extracted 749030 precursors and 4009860 fragments ===
0:39:15.454619 INFO: === FDR correction performed with classifier version 11 ===
0:39:15.455291 PROGRESS: ============================= Precursor FDR =============================
0:39:15.455382 PROGRESS: Total precursors accumulated: 1,466
0:39:15.455442 PROGRESS: Target precursors: 1,452 (99.05%)
0:39:15.455493 PROGRESS: Decoy precursors: 14 (0.95%)
0:39:15.455539 PROGRESS: 
0:39:15.455584 PROGRESS: Precursor Summary:
0:39:15.456812 PROGRESS: Channel   0:	 0.050 FDR: 1,452; 0.010 FDR: 1,452; 0.001 FDR:     0
0:39:15.456898 PROGRESS: 
0:39:15.456954 PROGRESS: Protein Summary:
0:39:15.458506 PROGRESS: Channel   0:	 0.050 FDR: 1,235; 0.010 FDR: 1,235; 0.001 FDR:     0
0:39:15.458596 PROGRESS: =========================================================================
0:39:15.473240 INFO: Target number of precursors reached.
0:39:15.906048 INFO: fragments_df: keeping 5000 of 4009860 [sum(precursor_idx_mask)=34185 sum(mass_error_mask)=4009860 stop_rank=5000
0:39:16.319283 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:16.519864 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:17.174635 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:17.175102 INFO: Using score_cutoff 11.225826845741272 (fac=0.99, q=1)
0:39:17.175429 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:17.175518 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:17.175574 INFO: Updating optimization_manager: score_cutoff        : 10.176914266204834 -> 11.225826845741272
0:39:17.175628 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:17.325019 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:17.644462 INFO: === checking if optimization conditions were reached ===
0:39:17.644729 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:39:17.647627 INFO: Updating optimization_manager: rt_error            : 693.1704013641709 -> 701.1068768269165
0:39:17.647732 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 701.1069.
0:39:17.647803 INFO: ==============================================
0:39:17.647874 INFO: Starting optimization step 3.
0:39:17.647933 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:39:17.647994 INFO: Using rust extraction backend
0:39:17.648054 PROGRESS: Extracting batch of 250256 precursors
0:39:18.069405 INFO: === Search parameters used ===
0:39:18.069686 INFO: rt_error       : 701.1068768269165
0:39:18.069765 INFO: mobility_error : 0.1
0:39:18.069818 INFO: num_candidates : 3
0:39:18.069864 INFO: ms1_error      : 3
0:39:18.069907 INFO: ms2_error      : 10.0
0:39:18.069950 INFO: fwhm_rt        : 3.0
0:39:18.069992 INFO: quant_window   : 3
0:39:18.070036 INFO: ==============================================
0:39:20.487344 INFO: performing precursor FDR with 40 features
0:39:20.487466 INFO: Decoy channel: -1
0:39:20.487492 INFO: competitive: True
0:39:20.672632 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:20.964533 INFO: Estimating optimal hyperparameters - samples: 599,214, batch_size: 2,454, learning_rate: 7.74e-04
0:39:20.965704 INFO: Using random state 249848 for train-test-split
0:39:33.625211 INFO: Test AUC: 0.613
0:39:33.625341 INFO: Train AUC: 0.625
0:39:33.625375 INFO: AUC difference: 2.07%
0:39:34.106485 INFO: Resetting torch num_threads to 100
0:39:34.138424 PROGRESS: === Extracted 749018 precursors and 4009189 fragments ===
0:39:34.138914 INFO: === FDR correction performed with classifier version 11 ===
0:39:34.139652 PROGRESS: ============================= Precursor FDR =============================
0:39:34.139755 PROGRESS: Total precursors accumulated: 1,475
0:39:34.139816 PROGRESS: Target precursors: 1,461 (99.05%)
0:39:34.139867 PROGRESS: Decoy precursors: 14 (0.95%)
0:39:34.139913 PROGRESS: 
0:39:34.139959 PROGRESS: Precursor Summary:
0:39:34.141268 PROGRESS: Channel   0:	 0.050 FDR: 1,461; 0.010 FDR: 1,461; 0.001 FDR:    17
0:39:34.141364 PROGRESS: 
0:39:34.141420 PROGRESS: Protein Summary:
0:39:34.143007 PROGRESS: Channel   0:	 0.050 FDR: 1,239; 0.010 FDR: 1,239; 0.001 FDR:    17
0:39:34.143100 PROGRESS: =========================================================================
0:39:34.156873 INFO: Target number of precursors reached.
0:39:34.590340 INFO: fragments_df: keeping 5000 of 4009189 [sum(precursor_idx_mask)=34401 sum(mass_error_mask)=4009189 stop_rank=5000
0:39:35.005073 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:35.203277 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:35.857089 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:35.857559 INFO: Using score_cutoff 11.261167671203614 (fac=0.99, q=1)
0:39:35.857874 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:35.857952 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:35.858006 INFO: Updating optimization_manager: score_cutoff        : 11.225826845741272 -> 11.261167671203614
0:39:35.858059 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:36.008636 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:36.351209 INFO: === checking if optimization conditions were reached ===
0:39:36.351498 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:39:36.354359 INFO: Updating optimization_manager: rt_error            : 701.1068768269165 -> 691.2143133425404
0:39:36.354460 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 691.2143.
0:39:36.354525 INFO: ==============================================
0:39:36.354595 INFO: Starting optimization step 4.
0:39:36.354653 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:39:36.354714 INFO: Using rust extraction backend
0:39:36.354774 PROGRESS: Extracting batch of 250256 precursors
0:39:36.776443 INFO: === Search parameters used ===
0:39:36.776775 INFO: rt_error       : 691.2143133425404
0:39:36.776834 INFO: mobility_error : 0.1
0:39:36.776882 INFO: num_candidates : 3
0:39:36.776926 INFO: ms1_error      : 3
0:39:36.776986 INFO: ms2_error      : 10.0
0:39:36.777030 INFO: fwhm_rt        : 3.0
0:39:36.777074 INFO: quant_window   : 3
0:39:36.777122 INFO: ==============================================
0:39:39.198240 INFO: performing precursor FDR with 40 features
0:39:39.198367 INFO: Decoy channel: -1
0:39:39.198394 INFO: competitive: True
0:39:39.389465 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:39.683038 INFO: Estimating optimal hyperparameters - samples: 599,216, batch_size: 2,454, learning_rate: 7.74e-04
0:39:39.684248 INFO: Using random state 249848 for train-test-split
0:39:52.351705 INFO: Test AUC: 0.613
0:39:52.351851 INFO: Train AUC: 0.627
0:39:52.351885 INFO: AUC difference: 2.31%
0:39:52.829236 INFO: Resetting torch num_threads to 100
0:39:52.858689 PROGRESS: === Extracted 749020 precursors and 4009263 fragments ===
0:39:52.859221 INFO: === FDR correction performed with classifier version 11 ===
0:39:52.859851 PROGRESS: ============================= Precursor FDR =============================
0:39:52.859942 PROGRESS: Total precursors accumulated: 1,123
0:39:52.860003 PROGRESS: Target precursors: 1,112 (99.02%)
0:39:52.860058 PROGRESS: Decoy precursors: 11 (0.98%)
0:39:52.860106 PROGRESS: 
0:39:52.860152 PROGRESS: Precursor Summary:
0:39:52.861335 PROGRESS: Channel   0:	 0.050 FDR: 1,112; 0.010 FDR: 1,112; 0.001 FDR:     0
0:39:52.861423 PROGRESS: 
0:39:52.861478 PROGRESS: Protein Summary:
0:39:52.862904 PROGRESS: Channel   0:	 0.050 FDR:   957; 0.010 FDR:   957; 0.001 FDR:     0
0:39:52.863003 PROGRESS: =========================================================================
0:39:52.877639 INFO: Target number of precursors reached.
0:39:53.326035 INFO: fragments_df: keeping 5000 of 4009263 [sum(precursor_idx_mask)=26813 sum(mass_error_mask)=4009263 stop_rank=5000
0:39:53.799296 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:53.970261 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:54.637716 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:54.638171 INFO: Using score_cutoff 12.498702623176575 (fac=0.99, q=1)
0:39:54.638499 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:54.638578 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:54.638635 INFO: Updating optimization_manager: score_cutoff        : 11.261167671203614 -> 12.498702623176575
0:39:54.638692 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:54.792508 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:55.148369 INFO: === checking if optimization conditions were reached ===
0:39:55.148715 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:39:55.149763 INFO: Updating optimization_manager: rt_error            : 691.2143133425404 -> 689.9194197955619
0:39:55.149932 INFO: Updating optimization_manager: classifier_version  : 11 -> 13
0:39:55.150036 INFO: Updating optimization_manager: score_cutoff        : 12.498702623176575 -> 10.176914266204834
0:39:55.150129 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:55.150224 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:55.150331 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 689.9194 found after 5 searches.
0:39:55.150404 INFO: ==============================================
0:39:55.150476 PROGRESS: Optimization finished for rt_error.
0:39:55.560127 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:55.714892 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:56.067083 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:39:56.067406 PROGRESS: ==============================================
0:39:56.067496 PROGRESS: ms2_error      : 10.0000
0:39:56.067565 PROGRESS: rt_error       : 689.9194
0:39:56.067621 PROGRESS: ==============================================
0:39:56.068642 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:03.772034 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:21.094504 INFO: Using rust extraction backend
0:40:21.094980 PROGRESS: Extracting batch of 11997144 precursors
0:40:37.244799 INFO: === Search parameters used ===
0:40:37.245447 INFO: rt_error       : 689.9194197955619
0:40:37.245522 INFO: mobility_error : 0.1
0:40:37.245581 INFO: num_candidates : 3
0:40:37.245633 INFO: ms1_error      : 3
0:40:37.245682 INFO: ms2_error      : 10.0
0:40:37.245739 INFO: fwhm_rt        : 3.0
0:40:37.245781 INFO: quant_window   : 3
0:40:37.245821 INFO: ==============================================
0:41:07.476562 INFO: Removed 7530453 precursors with score below cutoff 10.176914266204834
0:41:30.050575 INFO: performing precursor FDR with 40 features
0:41:30.050796 INFO: Decoy channel: -1
0:41:30.050830 INFO: competitive: True
0:41:33.040677 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:44.382737 INFO: Estimating optimal hyperparameters - samples: 22,768,308, batch_size: 4,096, learning_rate: 1.00e-03
0:41:44.451478 INFO: Using random state 892371 for train-test-split
0:48:52.460630 INFO: Test AUC: 0.621
0:48:52.460922 INFO: Train AUC: 0.621
0:48:52.460966 INFO: AUC difference: 0.04%
0:48:59.269791 INFO: Resetting torch num_threads to 100
0:49:01.424318 PROGRESS: ============================= Precursor FDR =============================
0:49:01.424638 PROGRESS: Total precursors accumulated: 92,771
0:49:01.424706 PROGRESS: Target precursors: 91,853 (99.01%)
0:49:01.424760 PROGRESS: Decoy precursors: 918 (0.99%)
0:49:01.424809 PROGRESS: 
0:49:01.424855 PROGRESS: Precursor Summary:
0:49:01.450588 PROGRESS: Channel   0:	 0.050 FDR: 91,853; 0.010 FDR: 91,853; 0.001 FDR: 54,350
0:49:01.450835 PROGRESS: 
0:49:01.450897 PROGRESS: Protein Summary:
0:49:01.486636 PROGRESS: Channel   0:	 0.050 FDR: 13,705; 0.010 FDR: 13,705; 0.001 FDR: 8,983
0:49:01.486889 PROGRESS: =========================================================================
0:49:01.629601 PROGRESS: === Transfer learning quantification ===
0:49:01.629892 INFO: creating library for charged fragment types: ['b', 'y']
0:49:02.752913 INFO: Calibrating library
0:49:02.753178 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:49:02.807231 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:49:03.331987 INFO: quantifying 92,771 precursors with 4,059,886 fragments
0:49:03.332332 INFO: Using rust extraction backend
0:49:04.264516 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/psm.parquet
0:49:04.421931 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.parquet
0:49:04.651673 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.transfer.parquet
0:49:05.130806 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:49:05.604848 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 
0:49:05.605015 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant
0:49:05.605115 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/figures
0:49:05.605272 INFO: Initializing TimingManager
0:49:05.605822 INFO: Initializing RawFileManager
0:49:16.579596 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.
0:49:16.588339 INFO: Determining DIA cycle
0:49:16.605047 INFO: Found cycle with start 0.00 min and length 300.
0:49:16.768598 INFO: RT (min)            : 0.0 - 26.9
0:49:16.768695 INFO: RT duration (sec)   : 1611.2
0:49:16.768723 INFO: RT duration (min)   : 26.9
0:49:16.768744 INFO: Cycle len (scans)   : 300
0:49:16.768763 INFO: Cycle len (sec)     : 1.65
0:49:16.768780 INFO: Number of cycles    : 977
0:49:16.768798 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:49:16.768824 INFO: Creating DIA data object took: 11.1629056930542
0:49:17.435392 INFO: Creating DIA data NG object took: 0.6664154529571533
0:49:18.633263 INFO: Initializing CalibrationManager
0:49:18.633551 INFO: Setting up calibration estimators ..
0:49:18.633613 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:49:18.633688 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'}' ..
0:49:18.633764 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:49:18.633815 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:49:18.633868 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}}' ..
0:49:18.633922 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:49:18.633968 INFO: Done setting up calibration estimators.
0:49:18.634174 INFO: Initializing OptimizationManager
0:49:18.634318 INFO: initial parameter: ms1_error = 3
0:49:18.634372 INFO: initial parameter: ms2_error = 10
0:49:18.634420 INFO: initial parameter: rt_error = 805.6004638671875
0:49:18.634465 INFO: initial parameter: mobility_error = 0.1
0:49:18.634507 INFO: initial parameter: num_candidates = 1
0:49:18.634548 INFO: initial parameter: fwhm_rt = 5
0:49:18.634589 INFO: initial parameter: fwhm_mobility = 0.01
0:49:18.634630 INFO: initial parameter: score_cutoff = 0
0:49:18.634670 INFO: initial parameter: classifier_version = -1
0:49:18.634737 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:49:18.635031 INFO: FDRManager: loading saved state not requested, will be initialized.
0:49:18.635065 INFO: Initializing FDRManager
0:49:18.635101 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
0:49:20.025058 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
0:49:20.894110 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
0:49:20.894514 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
0:49:20.894607 PROGRESS: Starting initial search for precursors.
0:49:20.894690 INFO: Starting optimization step 0.
0:49:20.894752 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:49:20.894809 INFO: Using rust extraction backend
0:49:20.894871 PROGRESS: Extracting batch of 1963 precursors
0:49:20.900187 INFO: === Search parameters used ===
0:49:20.900295 INFO: rt_error       : 805.6004638671875
0:49:20.900345 INFO: mobility_error : 0.1
0:49:20.900391 INFO: num_candidates : 1
0:49:20.900434 INFO: ms1_error      : 3
0:49:20.900488 INFO: ms2_error      : 10
0:49:20.900530 INFO: fwhm_rt        : 5
0:49:20.900578 INFO: quant_window   : 3
0:49:20.900618 INFO: ==============================================
0:49:20.927586 INFO: performing precursor FDR with 40 features
0:49:20.927653 INFO: Decoy channel: -1
0:49:20.927677 INFO: competitive: True
0:49:20.929060 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:20.930862 INFO: Estimating optimal hyperparameters - samples: 1,565, batch_size: 128, learning_rate: 1.77e-04
0:49:20.931930 INFO: Using random state 373786 for train-test-split
0:49:21.087602 INFO: Test AUC: 0.573
0:49:21.087680 INFO: Train AUC: 0.537
0:49:21.087708 INFO: AUC difference: 6.62%
0:49:21.087729 WARNING: AUC difference > 5%. This may indicate overfitting.
0:49:21.333138 INFO: Resetting torch num_threads to 100
0:49:21.334744 PROGRESS: === Extracted 1957 precursors and 10997 fragments ===
0:49:21.335109 INFO: === FDR correction performed with classifier version -1 ===
0:49:21.335608 PROGRESS: ============================= Precursor FDR =============================
0:49:21.335699 PROGRESS: Total precursors accumulated: 7
0:49:21.335755 PROGRESS: Target precursors: 7 (100.00%)
0:49:21.335802 PROGRESS: Decoy precursors: 0 (0.00%)
0:49:21.335850 PROGRESS: 
0:49:21.335893 PROGRESS: Precursor Summary:
0:49:21.336945 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
0:49:21.337027 PROGRESS: 
0:49:21.337079 PROGRESS: Protein Summary:
0:49:21.338257 PROGRESS: Channel   0:	 0.050 FDR:     7; 0.010 FDR:     7; 0.001 FDR:     7
0:49:21.338337 PROGRESS: =========================================================================
0:49:21.338534 INFO: Target number of precursors not reached yet.
0:49:21.422682 INFO: Starting optimization step 1.
0:49:21.422901 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:49:21.422980 INFO: Using rust extraction backend
0:49:21.423042 PROGRESS: Extracting batch of 3911 precursors
0:49:21.431826 INFO: === Search parameters used ===
0:49:21.431961 INFO: rt_error       : 805.6004638671875
0:49:21.432010 INFO: mobility_error : 0.1
0:49:21.432054 INFO: num_candidates : 1
0:49:21.432094 INFO: ms1_error      : 3
0:49:21.432134 INFO: ms2_error      : 10
0:49:21.432173 INFO: fwhm_rt        : 5
0:49:21.432211 INFO: quant_window   : 3
0:49:21.432249 INFO: ==============================================
0:49:21.478792 INFO: performing precursor FDR with 40 features
0:49:21.478883 INFO: Decoy channel: -1
0:49:21.478907 INFO: competitive: True
0:49:21.483332 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:21.485998 INFO: Estimating optimal hyperparameters - samples: 4,686, batch_size: 128, learning_rate: 1.77e-04
0:49:21.486083 INFO: Using random state 316086 for train-test-split
0:49:21.950143 INFO: Test AUC: 0.567
0:49:21.950248 INFO: Train AUC: 0.581
0:49:21.950276 INFO: AUC difference: 2.38%
0:49:22.197672 INFO: Resetting torch num_threads to 100
0:49:22.200910 PROGRESS: === Extracted 5858 precursors and 32826 fragments ===
0:49:22.201304 INFO: === FDR correction performed with classifier version -1 ===
0:49:22.201790 PROGRESS: ============================= Precursor FDR =============================
0:49:22.201876 PROGRESS: Total precursors accumulated: 16
0:49:22.201931 PROGRESS: Target precursors: 16 (100.00%)
0:49:22.201977 PROGRESS: Decoy precursors: 0 (0.00%)
0:49:22.202020 PROGRESS: 
0:49:22.202061 PROGRESS: Precursor Summary:
0:49:22.203121 PROGRESS: Channel   0:	 0.050 FDR:    16; 0.010 FDR:    16; 0.001 FDR:    16
0:49:22.203213 PROGRESS: 
0:49:22.203267 PROGRESS: Protein Summary:
0:49:22.204428 PROGRESS: Channel   0:	 0.050 FDR:    16; 0.010 FDR:    16; 0.001 FDR:    16
0:49:22.204507 PROGRESS: =========================================================================
0:49:22.204762 INFO: Target number of precursors not reached yet.
0:49:22.294988 INFO: Starting optimization step 2.
0:49:22.295238 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:49:22.295331 INFO: Using rust extraction backend
0:49:22.295397 PROGRESS: Extracting batch of 7891 precursors
0:49:22.310842 INFO: === Search parameters used ===
0:49:22.310991 INFO: rt_error       : 805.6004638671875
0:49:22.311044 INFO: mobility_error : 0.1
0:49:22.311091 INFO: num_candidates : 1
0:49:22.311136 INFO: ms1_error      : 3
0:49:22.311193 INFO: ms2_error      : 10
0:49:22.311238 INFO: fwhm_rt        : 5
0:49:22.311280 INFO: quant_window   : 3
0:49:22.311322 INFO: ==============================================
0:49:22.391607 INFO: performing precursor FDR with 40 features
0:49:22.391715 INFO: Decoy channel: -1
0:49:22.391740 INFO: competitive: True
0:49:22.399502 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:22.403128 INFO: Estimating optimal hyperparameters - samples: 10,987, batch_size: 128, learning_rate: 1.77e-04
0:49:22.403253 INFO: Using random state 412459 for train-test-split
0:49:23.487697 INFO: Test AUC: 0.564
0:49:23.487783 INFO: Train AUC: 0.589
0:49:23.487813 INFO: AUC difference: 4.28%
0:49:23.733242 INFO: Resetting torch num_threads to 100
0:49:23.737327 PROGRESS: === Extracted 13734 precursors and 76865 fragments ===
0:49:23.737728 INFO: === FDR correction performed with classifier version -1 ===
0:49:23.738212 PROGRESS: ============================= Precursor FDR =============================
0:49:23.738295 PROGRESS: Total precursors accumulated: 0
0:49:23.738353 PROGRESS: Target precursors: 0 (0.00%)
0:49:23.738402 PROGRESS: Decoy precursors: 0 (0.00%)
0:49:23.738446 PROGRESS: 
0:49:23.738490 PROGRESS: Precursor Summary:
0:49:23.738603 PROGRESS: 
0:49:23.738663 PROGRESS: Protein Summary:
0:49:23.738736 PROGRESS: =========================================================================
0:49:23.739048 INFO: Target number of precursors not reached yet.
0:49:23.837902 INFO: Starting optimization step 3.
0:49:23.838143 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:49:23.838224 INFO: Using rust extraction backend
0:49:23.838284 PROGRESS: Extracting batch of 15777 precursors
0:49:23.867125 INFO: === Search parameters used ===
0:49:23.867323 INFO: rt_error       : 805.6004638671875
0:49:23.867378 INFO: mobility_error : 0.1
0:49:23.867425 INFO: num_candidates : 1
0:49:23.867469 INFO: ms1_error      : 3
0:49:23.867512 INFO: ms2_error      : 10
0:49:23.867589 INFO: fwhm_rt        : 5
0:49:23.867628 INFO: quant_window   : 3
0:49:23.867674 INFO: ==============================================
0:49:24.004830 INFO: performing precursor FDR with 40 features
0:49:24.004942 INFO: Decoy channel: -1
0:49:24.004966 INFO: competitive: True
0:49:24.016379 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:24.023161 INFO: Estimating optimal hyperparameters - samples: 23,569, batch_size: 128, learning_rate: 1.77e-04
0:49:24.023330 INFO: Using random state 437996 for train-test-split
0:49:26.408365 INFO: Test AUC: 0.573
0:49:26.408455 INFO: Train AUC: 0.600
0:49:26.408483 INFO: AUC difference: 4.55%
0:49:26.656203 INFO: Resetting torch num_threads to 100
0:49:26.662523 PROGRESS: === Extracted 29462 precursors and 165128 fragments ===
0:49:26.663024 INFO: === FDR correction performed with classifier version -1 ===
0:49:26.663542 PROGRESS: ============================= Precursor FDR =============================
0:49:26.663629 PROGRESS: Total precursors accumulated: 0
0:49:26.663685 PROGRESS: Target precursors: 0 (0.00%)
0:49:26.663733 PROGRESS: Decoy precursors: 0 (0.00%)
0:49:26.663777 PROGRESS: 
0:49:26.663819 PROGRESS: Precursor Summary:
0:49:26.663933 PROGRESS: 
0:49:26.663991 PROGRESS: Protein Summary:
0:49:26.664063 PROGRESS: =========================================================================
0:49:26.664498 INFO: Target number of precursors not reached yet.
0:49:26.782426 INFO: Starting optimization step 4.
0:49:26.782686 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:49:26.782768 INFO: Using rust extraction backend
0:49:26.782831 PROGRESS: Extracting batch of 31516 precursors
0:49:26.838173 INFO: === Search parameters used ===
0:49:26.838418 INFO: rt_error       : 805.6004638671875
0:49:26.838471 INFO: mobility_error : 0.1
0:49:26.838536 INFO: num_candidates : 1
0:49:26.838579 INFO: ms1_error      : 3
0:49:26.838623 INFO: ms2_error      : 10
0:49:26.838665 INFO: fwhm_rt        : 5
0:49:26.838704 INFO: quant_window   : 3
0:49:26.838742 INFO: ==============================================
0:49:27.064443 INFO: performing precursor FDR with 40 features
0:49:27.064549 INFO: Decoy channel: -1
0:49:27.064573 INFO: competitive: True
0:49:27.087376 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:27.101075 INFO: Estimating optimal hyperparameters - samples: 48,728, batch_size: 199, learning_rate: 2.20e-04
0:49:27.101289 INFO: Using random state 172893 for train-test-split
0:49:30.736821 INFO: Test AUC: 0.586
0:49:30.736916 INFO: Train AUC: 0.614
0:49:30.736945 INFO: AUC difference: 4.54%
0:49:30.996554 INFO: Resetting torch num_threads to 100
0:49:31.007747 PROGRESS: === Extracted 60910 precursors and 341907 fragments ===
0:49:31.008373 INFO: === FDR correction performed with classifier version -1 ===
0:49:31.008957 PROGRESS: ============================= Precursor FDR =============================
0:49:31.009047 PROGRESS: Total precursors accumulated: 139
0:49:31.009107 PROGRESS: Target precursors: 138 (99.28%)
0:49:31.009160 PROGRESS: Decoy precursors: 1 (0.72%)
0:49:31.009207 PROGRESS: 
0:49:31.009253 PROGRESS: Precursor Summary:
0:49:31.010248 PROGRESS: Channel   0:	 0.050 FDR:   138; 0.010 FDR:   138; 0.001 FDR:     0
0:49:31.010332 PROGRESS: 
0:49:31.010386 PROGRESS: Protein Summary:
0:49:31.011515 PROGRESS: Channel   0:	 0.050 FDR:   133; 0.010 FDR:   133; 0.001 FDR:     0
0:49:31.011604 PROGRESS: =========================================================================
0:49:31.012642 INFO: Target number of precursors not reached yet.
0:49:31.172429 INFO: Starting optimization step 5.
0:49:31.172685 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:49:31.172769 INFO: Using rust extraction backend
0:49:31.172848 PROGRESS: Extracting batch of 63010 precursors
0:49:31.281366 INFO: === Search parameters used ===
0:49:31.281642 INFO: rt_error       : 805.6004638671875
0:49:31.281700 INFO: mobility_error : 0.1
0:49:31.281750 INFO: num_candidates : 1
0:49:31.281794 INFO: ms1_error      : 3
0:49:31.281836 INFO: ms2_error      : 10
0:49:31.281877 INFO: fwhm_rt        : 5
0:49:31.281919 INFO: quant_window   : 3
0:49:31.281961 INFO: ==============================================
0:49:31.667571 INFO: performing precursor FDR with 40 features
0:49:31.667686 INFO: Decoy channel: -1
0:49:31.667711 INFO: competitive: True
0:49:31.715928 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:31.747959 INFO: Estimating optimal hyperparameters - samples: 99,005, batch_size: 405, learning_rate: 3.14e-04
0:49:31.748258 INFO: Using random state 728173 for train-test-split
0:49:36.377788 INFO: Test AUC: 0.591
0:49:36.377904 INFO: Train AUC: 0.617
0:49:36.377934 INFO: AUC difference: 4.21%
0:49:36.663287 INFO: Resetting torch num_threads to 100
0:49:36.686268 PROGRESS: === Extracted 123757 precursors and 694089 fragments ===
0:49:36.686925 INFO: === FDR correction performed with classifier version -1 ===
0:49:36.687604 PROGRESS: ============================= Precursor FDR =============================
0:49:36.687702 PROGRESS: Total precursors accumulated: 536
0:49:36.687763 PROGRESS: Target precursors: 531 (99.07%)
0:49:36.687814 PROGRESS: Decoy precursors: 5 (0.93%)
0:49:36.687861 PROGRESS: 
0:49:36.687905 PROGRESS: Precursor Summary:
0:49:36.688999 PROGRESS: Channel   0:	 0.050 FDR:   531; 0.010 FDR:   531; 0.001 FDR:     0
0:49:36.689087 PROGRESS: 
0:49:36.689143 PROGRESS: Protein Summary:
0:49:36.690411 PROGRESS: Channel   0:	 0.050 FDR:   492; 0.010 FDR:   492; 0.001 FDR:     0
0:49:36.690505 PROGRESS: =========================================================================
0:49:36.692418 INFO: Target number of precursors not reached yet.
0:49:36.945842 INFO: Starting optimization step 6.
0:49:36.946116 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:49:36.946203 INFO: Using rust extraction backend
0:49:36.946284 PROGRESS: Extracting batch of 126188 precursors
0:49:37.163107 INFO: === Search parameters used ===
0:49:37.163396 INFO: rt_error       : 805.6004638671875
0:49:37.163453 INFO: mobility_error : 0.1
0:49:37.163500 INFO: num_candidates : 1
0:49:37.163543 INFO: ms1_error      : 3
0:49:37.163584 INFO: ms2_error      : 10
0:49:37.163625 INFO: fwhm_rt        : 5
0:49:37.163664 INFO: quant_window   : 3
0:49:37.163701 INFO: ==============================================
0:49:37.864660 INFO: performing precursor FDR with 40 features
0:49:37.864791 INFO: Decoy channel: -1
0:49:37.864818 INFO: competitive: True
0:49:37.968530 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:38.046491 INFO: Estimating optimal hyperparameters - samples: 199,712, batch_size: 818, learning_rate: 4.47e-04
0:49:38.046876 INFO: Using random state 100426 for train-test-split
0:49:44.369812 INFO: Test AUC: 0.589
0:49:44.369931 INFO: Train AUC: 0.613
0:49:44.369961 INFO: AUC difference: 3.83%
0:49:44.697292 INFO: Resetting torch num_threads to 100
0:49:44.741989 PROGRESS: === Extracted 249641 precursors and 1400381 fragments ===
0:49:44.742693 INFO: === FDR correction performed with classifier version -1 ===
0:49:44.743582 PROGRESS: ============================= Precursor FDR =============================
0:49:44.743675 PROGRESS: Total precursors accumulated: 1,271
0:49:44.743738 PROGRESS: Target precursors: 1,259 (99.06%)
0:49:44.743791 PROGRESS: Decoy precursors: 12 (0.94%)
0:49:44.743850 PROGRESS: 
0:49:44.743897 PROGRESS: Precursor Summary:
0:49:44.745187 PROGRESS: Channel   0:	 0.050 FDR: 1,259; 0.010 FDR: 1,259; 0.001 FDR:   470
0:49:44.745273 PROGRESS: 
0:49:44.745329 PROGRESS: Protein Summary:
0:49:44.746934 PROGRESS: Channel   0:	 0.050 FDR: 1,071; 0.010 FDR: 1,071; 0.001 FDR:   422
0:49:44.747024 PROGRESS: =========================================================================
0:49:44.751233 INFO: Target number of precursors reached.
0:49:44.916773 INFO: fragments_df: keeping 5000 of 1400381 [sum(precursor_idx_mask)=13364 sum(mass_error_mask)=1400381 stop_rank=5000
0:49:45.318912 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:49:45.501255 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:49:46.153844 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:49:46.154300 INFO: Using score_cutoff 12.202719629287719 (fac=0.99, q=1)
0:49:46.154616 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:49:46.154693 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:49:46.154748 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.202719629287719
0:49:46.154800 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:49:46.309844 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:49:46.664902 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
0:49:46.665163 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:49:46.665272 INFO: Starting optimization step 7.
0:49:46.665342 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:49:46.665410 INFO: Using rust extraction backend
0:49:46.665469 PROGRESS: Extracting batch of 250256 precursors
0:49:47.096468 INFO: === Search parameters used ===
0:49:47.096736 INFO: rt_error       : 805.6004638671875
0:49:47.096794 INFO: mobility_error : 0.1
0:49:47.096842 INFO: num_candidates : 3
0:49:47.096885 INFO: ms1_error      : 3
0:49:47.096927 INFO: ms2_error      : 10
0:49:47.096967 INFO: fwhm_rt        : 3.0
0:49:47.097010 INFO: quant_window   : 3
0:49:47.097050 INFO: ==============================================
0:49:49.641277 INFO: performing precursor FDR with 40 features
0:49:49.641404 INFO: Decoy channel: -1
0:49:49.641431 INFO: competitive: True
0:49:49.828627 INFO: Setting torch num_threads to 2 for FDR classification task
0:49:50.115815 INFO: Estimating optimal hyperparameters - samples: 599,204, batch_size: 2,454, learning_rate: 7.74e-04
0:49:50.116941 INFO: Using random state 239676 for train-test-split
0:50:02.565511 INFO: Test AUC: 0.598
0:50:02.565653 INFO: Train AUC: 0.608
0:50:02.565688 INFO: AUC difference: 1.61%
0:50:03.047005 INFO: Resetting torch num_threads to 100
0:50:03.075543 PROGRESS: === Extracted 749006 precursors and 4027842 fragments ===
0:50:03.076032 INFO: === FDR correction performed with classifier version 6 ===
0:50:03.076695 PROGRESS: ============================= Precursor FDR =============================
0:50:03.076785 PROGRESS: Total precursors accumulated: 1,355
0:50:03.076845 PROGRESS: Target precursors: 1,342 (99.04%)
0:50:03.076897 PROGRESS: Decoy precursors: 13 (0.96%)
0:50:03.076946 PROGRESS: 
0:50:03.076993 PROGRESS: Precursor Summary:
0:50:03.078288 PROGRESS: Channel   0:	 0.050 FDR: 1,342; 0.010 FDR: 1,342; 0.001 FDR:   465
0:50:03.078375 PROGRESS: 
0:50:03.078430 PROGRESS: Protein Summary:
0:50:03.080052 PROGRESS: Channel   0:	 0.050 FDR: 1,138; 0.010 FDR: 1,138; 0.001 FDR:   414
0:50:03.080144 PROGRESS: =========================================================================
0:50:03.094177 INFO: Target number of precursors reached.
0:50:03.540349 INFO: fragments_df: keeping 5000 of 4027842 [sum(precursor_idx_mask)=32212 sum(mass_error_mask)=4027842 stop_rank=5000
0:50:03.956225 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:50:04.890779 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:50:05.540222 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:50:05.540700 INFO: Using score_cutoff 12.254903349781037 (fac=0.99, q=1)
0:50:05.541027 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:50:05.541104 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:50:05.541158 INFO: Updating optimization_manager: score_cutoff        : 12.202719629287719 -> 12.254903349781037
0:50:05.541217 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:50:05.694470 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:50:06.033481 INFO: === checking if optimization conditions were reached ===
0:50:06.036229 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
0:50:06.036389 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:50:06.036484 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:50:06.036558 INFO: ==============================================
0:50:06.036641 INFO: Starting optimization step 8.
0:50:06.036714 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:50:06.036794 INFO: Using rust extraction backend
0:50:06.036869 PROGRESS: Extracting batch of 250256 precursors
0:50:06.461773 INFO: === Search parameters used ===
0:50:06.462048 INFO: rt_error       : 805.6004638671875
0:50:06.462106 INFO: mobility_error : 0.1
0:50:06.462154 INFO: num_candidates : 3
0:50:06.462199 INFO: ms1_error      : 3
0:50:06.462242 INFO: ms2_error      : 10.0
0:50:06.462285 INFO: fwhm_rt        : 3.0
0:50:06.462326 INFO: quant_window   : 3
0:50:06.462368 INFO: ==============================================
0:50:08.947958 INFO: performing precursor FDR with 40 features
0:50:08.948077 INFO: Decoy channel: -1
0:50:08.948103 INFO: competitive: True
0:50:09.147054 INFO: Setting torch num_threads to 2 for FDR classification task
0:50:09.453583 INFO: Estimating optimal hyperparameters - samples: 599,235, batch_size: 2,454, learning_rate: 7.74e-04
0:50:09.454651 INFO: Using random state 713578 for train-test-split
0:50:22.242531 INFO: Test AUC: 0.602
0:50:22.242662 INFO: Train AUC: 0.616
0:50:22.242695 INFO: AUC difference: 2.30%
0:50:22.725138 INFO: Resetting torch num_threads to 100
0:50:22.786411 PROGRESS: === Extracted 749044 precursors and 4028516 fragments ===
0:50:22.786891 INFO: === FDR correction performed with classifier version 7 ===
0:50:22.787568 PROGRESS: ============================= Precursor FDR =============================
0:50:22.787665 PROGRESS: Total precursors accumulated: 1,318
0:50:22.787727 PROGRESS: Target precursors: 1,305 (99.01%)
0:50:22.787778 PROGRESS: Decoy precursors: 13 (0.99%)
0:50:22.787837 PROGRESS: 
0:50:22.787888 PROGRESS: Precursor Summary:
0:50:22.789193 PROGRESS: Channel   0:	 0.050 FDR: 1,305; 0.010 FDR: 1,305; 0.001 FDR:   454
0:50:22.789282 PROGRESS: 
0:50:22.789338 PROGRESS: Protein Summary:
0:50:22.790950 PROGRESS: Channel   0:	 0.050 FDR: 1,113; 0.010 FDR: 1,113; 0.001 FDR:   405
0:50:22.791039 PROGRESS: =========================================================================
0:50:22.805657 INFO: Target number of precursors reached.
0:50:23.250882 INFO: fragments_df: keeping 5000 of 4028516 [sum(precursor_idx_mask)=31444 sum(mass_error_mask)=4028516 stop_rank=5000
0:50:23.827688 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:50:24.029653 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:50:24.676458 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:50:24.676918 INFO: Using score_cutoff 12.544683614730836 (fac=0.99, q=1)
0:50:24.677226 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:50:24.677299 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:50:24.677351 INFO: Updating optimization_manager: score_cutoff        : 12.254903349781037 -> 12.544683614730836
0:50:24.677402 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:50:24.829167 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:50:25.171620 INFO: === checking if optimization conditions were reached ===
0:50:25.174256 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:50:25.174383 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:50:25.174462 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:50:25.174537 INFO: ==============================================
0:50:25.174618 INFO: Starting optimization step 9.
0:50:25.174685 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:50:25.174760 INFO: Using rust extraction backend
0:50:25.174829 PROGRESS: Extracting batch of 250256 precursors
0:50:25.599737 INFO: === Search parameters used ===
0:50:25.600019 INFO: rt_error       : 805.6004638671875
0:50:25.600074 INFO: mobility_error : 0.1
0:50:25.600119 INFO: num_candidates : 3
0:50:25.600160 INFO: ms1_error      : 3
0:50:25.600199 INFO: ms2_error      : 10.0
0:50:25.600237 INFO: fwhm_rt        : 3.0
0:50:25.600274 INFO: quant_window   : 3
0:50:25.600311 INFO: ==============================================
0:50:28.103726 INFO: performing precursor FDR with 40 features
0:50:28.103846 INFO: Decoy channel: -1
0:50:28.103872 INFO: competitive: True
0:50:28.293288 INFO: Setting torch num_threads to 2 for FDR classification task
0:50:28.580302 INFO: Estimating optimal hyperparameters - samples: 599,215, batch_size: 2,454, learning_rate: 7.74e-04
0:50:28.581423 INFO: Using random state 540814 for train-test-split
0:50:41.316615 INFO: Test AUC: 0.609
0:50:41.316738 INFO: Train AUC: 0.620
0:50:41.316770 INFO: AUC difference: 1.88%
0:50:41.789057 INFO: Resetting torch num_threads to 100
0:50:41.818841 PROGRESS: === Extracted 749019 precursors and 4027753 fragments ===
0:50:41.819368 INFO: === FDR correction performed with classifier version 8 ===
0:50:41.820057 PROGRESS: ============================= Precursor FDR =============================
0:50:41.820148 PROGRESS: Total precursors accumulated: 1,272
0:50:41.820208 PROGRESS: Target precursors: 1,260 (99.06%)
0:50:41.820270 PROGRESS: Decoy precursors: 12 (0.94%)
0:50:41.820319 PROGRESS: 
0:50:41.820364 PROGRESS: Precursor Summary:
0:50:41.821615 PROGRESS: Channel   0:	 0.050 FDR: 1,260; 0.010 FDR: 1,260; 0.001 FDR:   234
0:50:41.821699 PROGRESS: 
0:50:41.821755 PROGRESS: Protein Summary:
0:50:41.823344 PROGRESS: Channel   0:	 0.050 FDR: 1,089; 0.010 FDR: 1,089; 0.001 FDR:   220
0:50:41.823436 PROGRESS: =========================================================================
0:50:41.841044 INFO: Target number of precursors reached.
0:50:42.282656 INFO: fragments_df: keeping 5000 of 4027753 [sum(precursor_idx_mask)=30140 sum(mass_error_mask)=4027753 stop_rank=5000
0:50:42.721394 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:50:42.914090 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:50:43.566907 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:50:43.567371 INFO: Using score_cutoff 11.046774459457398 (fac=0.99, q=1)
0:50:43.567704 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:50:43.567782 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:50:43.567837 INFO: Updating optimization_manager: score_cutoff        : 12.544683614730836 -> 11.046774459457398
0:50:43.567890 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:50:43.720988 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:50:44.057061 INFO: === checking if optimization conditions were reached ===
0:50:44.059290 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:50:44.059400 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:50:44.059467 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:50:44.059525 INFO: ==============================================
0:50:44.059589 INFO: Starting optimization step 10.
0:50:44.059647 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:50:44.059707 INFO: Using rust extraction backend
0:50:44.059763 PROGRESS: Extracting batch of 250256 precursors
0:50:44.485729 INFO: === Search parameters used ===
0:50:44.486005 INFO: rt_error       : 805.6004638671875
0:50:44.486064 INFO: mobility_error : 0.1
0:50:44.486113 INFO: num_candidates : 3
0:50:44.486157 INFO: ms1_error      : 3
0:50:44.486199 INFO: ms2_error      : 10.0
0:50:44.486240 INFO: fwhm_rt        : 3.0
0:50:44.486280 INFO: quant_window   : 3
0:50:44.486321 INFO: ==============================================
0:50:46.991469 INFO: performing precursor FDR with 40 features
0:50:46.991590 INFO: Decoy channel: -1
0:50:46.991616 INFO: competitive: True
0:50:47.187668 INFO: Setting torch num_threads to 2 for FDR classification task
0:50:47.494756 INFO: Estimating optimal hyperparameters - samples: 599,235, batch_size: 2,454, learning_rate: 7.74e-04
0:50:47.495946 INFO: Using random state 972705 for train-test-split
0:51:00.324898 INFO: Test AUC: 0.607
0:51:00.325029 INFO: Train AUC: 0.623
0:51:00.325062 INFO: AUC difference: 2.56%
0:51:00.801186 INFO: Resetting torch num_threads to 100
0:51:00.831023 PROGRESS: === Extracted 749044 precursors and 4028053 fragments ===
0:51:00.831508 INFO: === FDR correction performed with classifier version 9 ===
0:51:00.832195 PROGRESS: ============================= Precursor FDR =============================
0:51:00.832284 PROGRESS: Total precursors accumulated: 1,467
0:51:00.832355 PROGRESS: Target precursors: 1,453 (99.05%)
0:51:00.832409 PROGRESS: Decoy precursors: 14 (0.95%)
0:51:00.832456 PROGRESS: 
0:51:00.832500 PROGRESS: Precursor Summary:
0:51:00.833810 PROGRESS: Channel   0:	 0.050 FDR: 1,453; 0.010 FDR: 1,453; 0.001 FDR:   540
0:51:00.833898 PROGRESS: 
0:51:00.833951 PROGRESS: Protein Summary:
0:51:00.835678 PROGRESS: Channel   0:	 0.050 FDR: 1,232; 0.010 FDR: 1,232; 0.001 FDR:   479
0:51:00.835775 PROGRESS: =========================================================================
0:51:00.849985 INFO: Target number of precursors reached.
0:51:01.285035 INFO: fragments_df: keeping 5000 of 4028053 [sum(precursor_idx_mask)=34668 sum(mass_error_mask)=4028053 stop_rank=5000
0:51:01.740541 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:51:01.944768 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:51:02.594422 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:51:02.594876 INFO: Using score_cutoff 11.731496034622193 (fac=0.99, q=1)
0:51:02.595186 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:51:02.595264 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:51:02.595317 INFO: Updating optimization_manager: score_cutoff        : 11.046774459457398 -> 11.731496034622193
0:51:02.595369 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:51:02.748610 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:51:03.087439 INFO: === checking if optimization conditions were reached ===
0:51:03.089658 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:51:03.089755 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:51:03.089820 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:51:03.089879 INFO: ==============================================
0:51:03.089943 INFO: Starting optimization step 11.
0:51:03.089997 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:51:03.090054 INFO: Using rust extraction backend
0:51:03.090108 PROGRESS: Extracting batch of 250256 precursors
0:51:03.512882 INFO: === Search parameters used ===
0:51:03.513182 INFO: rt_error       : 805.6004638671875
0:51:03.513244 INFO: mobility_error : 0.1
0:51:03.513295 INFO: num_candidates : 3
0:51:03.513342 INFO: ms1_error      : 3
0:51:03.513388 INFO: ms2_error      : 10.0
0:51:03.513432 INFO: fwhm_rt        : 3.0
0:51:03.513474 INFO: quant_window   : 3
0:51:03.513517 INFO: ==============================================
0:51:06.069317 INFO: performing precursor FDR with 40 features
0:51:06.069438 INFO: Decoy channel: -1
0:51:06.069464 INFO: competitive: True
0:51:06.260412 INFO: Setting torch num_threads to 2 for FDR classification task
0:51:06.565591 INFO: Estimating optimal hyperparameters - samples: 599,199, batch_size: 2,454, learning_rate: 7.74e-04
0:51:06.566774 INFO: Using random state 506571 for train-test-split
0:51:19.252038 INFO: Test AUC: 0.610
0:51:19.252208 INFO: Train AUC: 0.624
0:51:19.252243 INFO: AUC difference: 2.28%
0:51:19.726367 INFO: Resetting torch num_threads to 100
0:51:19.756501 PROGRESS: === Extracted 748999 precursors and 4027254 fragments ===
0:51:19.756995 INFO: === FDR correction performed with classifier version 10 ===
0:51:19.757665 PROGRESS: ============================= Precursor FDR =============================
0:51:19.757765 PROGRESS: Total precursors accumulated: 1,540
0:51:19.757830 PROGRESS: Target precursors: 1,525 (99.03%)
0:51:19.757888 PROGRESS: Decoy precursors: 15 (0.97%)
0:51:19.757940 PROGRESS: 
0:51:19.757985 PROGRESS: Precursor Summary:
0:51:19.759276 PROGRESS: Channel   0:	 0.050 FDR: 1,525; 0.010 FDR: 1,525; 0.001 FDR:   357
0:51:19.759367 PROGRESS: 
0:51:19.759420 PROGRESS: Protein Summary:
0:51:19.761071 PROGRESS: Channel   0:	 0.050 FDR: 1,298; 0.010 FDR: 1,298; 0.001 FDR:   324
0:51:19.761157 PROGRESS: =========================================================================
0:51:19.775568 INFO: Target number of precursors reached.
0:51:20.224505 INFO: fragments_df: keeping 5000 of 4027254 [sum(precursor_idx_mask)=35530 sum(mass_error_mask)=4027254 stop_rank=5000
0:51:20.640191 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:51:20.850369 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:51:21.500387 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:51:21.500845 INFO: Using score_cutoff 9.106418154144286 (fac=0.99, q=1)
0:51:21.501151 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:51:21.501227 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:51:21.501280 INFO: Updating optimization_manager: score_cutoff        : 11.731496034622193 -> 9.106418154144286
0:51:21.501334 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:51:21.652905 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:51:21.998250 INFO: === checking if optimization conditions were reached ===
0:51:22.000434 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:51:22.000539 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:51:22.000604 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:51:22.000661 INFO: ==============================================
0:51:22.000727 PROGRESS: Optimization finished for ms2_error.
0:51:22.399750 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:51:22.551734 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:51:22.896814 INFO: Starting optimization step 0.
0:51:22.897089 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:51:22.897167 INFO: Using rust extraction backend
0:51:22.897227 PROGRESS: Extracting batch of 250256 precursors
0:51:23.318947 INFO: === Search parameters used ===
0:51:23.319230 INFO: rt_error       : 805.6004638671875
0:51:23.319289 INFO: mobility_error : 0.1
0:51:23.319334 INFO: num_candidates : 3
0:51:23.319376 INFO: ms1_error      : 3
0:51:23.319417 INFO: ms2_error      : 10.0
0:51:23.319456 INFO: fwhm_rt        : 3.0
0:51:23.319496 INFO: quant_window   : 3
0:51:23.319551 INFO: ==============================================
0:51:25.873129 INFO: performing precursor FDR with 40 features
0:51:25.873259 INFO: Decoy channel: -1
0:51:25.873286 INFO: competitive: True
0:51:26.063092 INFO: Setting torch num_threads to 2 for FDR classification task
0:51:26.355021 INFO: Estimating optimal hyperparameters - samples: 599,228, batch_size: 2,454, learning_rate: 7.74e-04
0:51:26.356209 INFO: Using random state 704905 for train-test-split
0:51:38.873400 INFO: Test AUC: 0.612
0:51:38.873564 INFO: Train AUC: 0.627
0:51:38.873597 INFO: AUC difference: 2.44%
0:51:39.350906 INFO: Resetting torch num_threads to 100
0:51:39.382719 PROGRESS: === Extracted 749036 precursors and 4028425 fragments ===
0:51:39.383209 INFO: === FDR correction performed with classifier version 11 ===
0:51:39.383898 PROGRESS: ============================= Precursor FDR =============================
0:51:39.383988 PROGRESS: Total precursors accumulated: 1,457
0:51:39.384048 PROGRESS: Target precursors: 1,443 (99.04%)
0:51:39.384100 PROGRESS: Decoy precursors: 14 (0.96%)
0:51:39.384146 PROGRESS: 
0:51:39.384189 PROGRESS: Precursor Summary:
0:51:39.385478 PROGRESS: Channel   0:	 0.050 FDR: 1,443; 0.010 FDR: 1,443; 0.001 FDR:   506
0:51:39.385566 PROGRESS: 
0:51:39.385620 PROGRESS: Protein Summary:
0:51:39.387270 PROGRESS: Channel   0:	 0.050 FDR: 1,226; 0.010 FDR: 1,226; 0.001 FDR:   449
0:51:39.387362 PROGRESS: =========================================================================
0:51:39.402541 INFO: Target number of precursors reached.
0:51:39.847199 INFO: fragments_df: keeping 5000 of 4028425 [sum(precursor_idx_mask)=34704 sum(mass_error_mask)=4028425 stop_rank=5000
0:51:40.287944 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:51:40.497584 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:51:41.154272 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:51:41.154732 INFO: Using score_cutoff 12.348147065734864 (fac=0.99, q=1)
0:51:41.155048 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:51:41.155126 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:51:41.155197 INFO: Updating optimization_manager: score_cutoff        : 9.106418154144286 -> 12.348147065734864
0:51:41.155251 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:51:41.306938 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:51:41.647237 INFO: === checking if optimization conditions were reached ===
0:51:41.647518 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:51:41.650143 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 771.4885817563406
0:51:41.650244 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 771.4886.
0:51:41.650310 INFO: ==============================================
0:51:41.650385 INFO: Starting optimization step 1.
0:51:41.650445 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:51:41.650509 INFO: Using rust extraction backend
0:51:41.650568 PROGRESS: Extracting batch of 250256 precursors
0:51:42.079157 INFO: === Search parameters used ===
0:51:42.079442 INFO: rt_error       : 771.4885817563406
0:51:42.079501 INFO: mobility_error : 0.1
0:51:42.079550 INFO: num_candidates : 3
0:51:42.079609 INFO: ms1_error      : 3
0:51:42.079650 INFO: ms2_error      : 10.0
0:51:42.079695 INFO: fwhm_rt        : 3.0
0:51:42.079738 INFO: quant_window   : 3
0:51:42.079777 INFO: ==============================================
0:51:44.639942 INFO: performing precursor FDR with 40 features
0:51:44.640063 INFO: Decoy channel: -1
0:51:44.640087 INFO: competitive: True
0:51:44.837116 INFO: Setting torch num_threads to 2 for FDR classification task
0:51:45.142669 INFO: Estimating optimal hyperparameters - samples: 599,196, batch_size: 2,454, learning_rate: 7.74e-04
0:51:45.143848 INFO: Using random state 704905 for train-test-split
0:51:57.833718 INFO: Test AUC: 0.614
0:51:57.833850 INFO: Train AUC: 0.627
0:51:57.833902 INFO: AUC difference: 2.17%
0:51:58.319822 INFO: Resetting torch num_threads to 100
0:51:58.381792 PROGRESS: === Extracted 748996 precursors and 4027073 fragments ===
0:51:58.382277 INFO: === FDR correction performed with classifier version 11 ===
0:51:58.382932 PROGRESS: ============================= Precursor FDR =============================
0:51:58.383026 PROGRESS: Total precursors accumulated: 1,448
0:51:58.383087 PROGRESS: Target precursors: 1,434 (99.03%)
0:51:58.383141 PROGRESS: Decoy precursors: 14 (0.97%)
0:51:58.383207 PROGRESS: 
0:51:58.383255 PROGRESS: Precursor Summary:
0:51:58.384547 PROGRESS: Channel   0:	 0.050 FDR: 1,434; 0.010 FDR: 1,434; 0.001 FDR:   465
0:51:58.384636 PROGRESS: 
0:51:58.384693 PROGRESS: Protein Summary:
0:51:58.386356 PROGRESS: Channel   0:	 0.050 FDR: 1,219; 0.010 FDR: 1,219; 0.001 FDR:   410
0:51:58.386447 PROGRESS: =========================================================================
0:51:58.400955 INFO: Target number of precursors reached.
0:51:58.840347 INFO: fragments_df: keeping 5000 of 4027073 [sum(precursor_idx_mask)=34343 sum(mass_error_mask)=4027073 stop_rank=5000
0:51:59.315308 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:51:59.517587 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:52:00.172062 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:52:00.172523 INFO: Using score_cutoff 11.527496578502655 (fac=0.99, q=1)
0:52:00.172837 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:52:00.172913 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:52:00.172969 INFO: Updating optimization_manager: score_cutoff        : 12.348147065734864 -> 11.527496578502655
0:52:00.173024 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:52:00.325320 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:52:00.657342 INFO: === checking if optimization conditions were reached ===
0:52:00.657627 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:52:00.660456 INFO: Updating optimization_manager: rt_error            : 771.4885817563406 -> 686.5248040886815
0:52:00.660591 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 686.5248.
0:52:00.660659 INFO: ==============================================
0:52:00.660735 INFO: Starting optimization step 2.
0:52:00.660795 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:52:00.660862 INFO: Using rust extraction backend
0:52:00.660921 PROGRESS: Extracting batch of 250256 precursors
0:52:01.085826 INFO: === Search parameters used ===
0:52:01.086104 INFO: rt_error       : 686.5248040886815
0:52:01.086161 INFO: mobility_error : 0.1
0:52:01.086210 INFO: num_candidates : 3
0:52:01.086270 INFO: ms1_error      : 3
0:52:01.086320 INFO: ms2_error      : 10.0
0:52:01.086364 INFO: fwhm_rt        : 3.0
0:52:01.086406 INFO: quant_window   : 3
0:52:01.086448 INFO: ==============================================
0:52:03.559656 INFO: performing precursor FDR with 40 features
0:52:03.559780 INFO: Decoy channel: -1
0:52:03.559807 INFO: competitive: True
0:52:03.748057 INFO: Setting torch num_threads to 2 for FDR classification task
0:52:04.047490 INFO: Estimating optimal hyperparameters - samples: 599,142, batch_size: 2,454, learning_rate: 7.74e-04
0:52:04.048620 INFO: Using random state 704905 for train-test-split
0:52:16.317769 INFO: Test AUC: 0.613
0:52:16.317910 INFO: Train AUC: 0.627
0:52:16.317944 INFO: AUC difference: 2.21%
0:52:16.789390 INFO: Resetting torch num_threads to 100
0:52:16.819674 PROGRESS: === Extracted 748928 precursors and 4022731 fragments ===
0:52:16.820181 INFO: === FDR correction performed with classifier version 11 ===
0:52:16.820842 PROGRESS: ============================= Precursor FDR =============================
0:52:16.820931 PROGRESS: Total precursors accumulated: 1,532
0:52:16.820991 PROGRESS: Target precursors: 1,517 (99.02%)
0:52:16.821041 PROGRESS: Decoy precursors: 15 (0.98%)
0:52:16.821087 PROGRESS: 
0:52:16.821132 PROGRESS: Precursor Summary:
0:52:16.822431 PROGRESS: Channel   0:	 0.050 FDR: 1,517; 0.010 FDR: 1,517; 0.001 FDR:   606
0:52:16.822519 PROGRESS: 
0:52:16.822572 PROGRESS: Protein Summary:
0:52:16.824264 PROGRESS: Channel   0:	 0.050 FDR: 1,308; 0.010 FDR: 1,308; 0.001 FDR:   535
0:52:16.824359 PROGRESS: =========================================================================
0:52:16.838667 INFO: Target number of precursors reached.
0:52:17.285878 INFO: fragments_df: keeping 5000 of 4022731 [sum(precursor_idx_mask)=34685 sum(mass_error_mask)=4022731 stop_rank=5000
0:52:17.703051 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:52:17.909107 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:52:18.561246 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:52:18.561707 INFO: Using score_cutoff 8.853355975341797 (fac=0.99, q=1)
0:52:18.562021 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:52:18.562099 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:52:18.562154 INFO: Updating optimization_manager: score_cutoff        : 11.527496578502655 -> 8.853355975341797
0:52:18.562218 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:52:18.713344 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:52:19.043752 INFO: === checking if optimization conditions were reached ===
0:52:19.044030 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:52:19.046935 INFO: Updating optimization_manager: rt_error            : 686.5248040886815 -> 858.0731638307932
0:52:19.047043 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 858.0732.
0:52:19.047109 INFO: ==============================================
0:52:19.047198 INFO: Starting optimization step 3.
0:52:19.047262 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:52:19.047329 INFO: Using rust extraction backend
0:52:19.047387 PROGRESS: Extracting batch of 250256 precursors
0:52:19.468518 INFO: === Search parameters used ===
0:52:19.468794 INFO: rt_error       : 858.0731638307932
0:52:19.468870 INFO: mobility_error : 0.1
0:52:19.468924 INFO: num_candidates : 3
0:52:19.468970 INFO: ms1_error      : 3
0:52:19.469016 INFO: ms2_error      : 10.0
0:52:19.469058 INFO: fwhm_rt        : 3.0
0:52:19.469100 INFO: quant_window   : 3
0:52:19.469140 INFO: ==============================================
0:52:22.078294 INFO: performing precursor FDR with 40 features
0:52:22.078418 INFO: Decoy channel: -1
0:52:22.078445 INFO: competitive: True
0:52:22.267270 INFO: Setting torch num_threads to 2 for FDR classification task
0:52:22.559452 INFO: Estimating optimal hyperparameters - samples: 599,227, batch_size: 2,454, learning_rate: 7.74e-04
0:52:22.560463 INFO: Using random state 704905 for train-test-split
0:52:34.969902 INFO: Test AUC: 0.614
0:52:34.970032 INFO: Train AUC: 0.626
0:52:34.970064 INFO: AUC difference: 1.97%
0:52:35.448755 INFO: Resetting torch num_threads to 100
0:52:35.479033 PROGRESS: === Extracted 749034 precursors and 4027411 fragments ===
0:52:35.479539 INFO: === FDR correction performed with classifier version 11 ===
0:52:35.480204 PROGRESS: ============================= Precursor FDR =============================
0:52:35.480295 PROGRESS: Total precursors accumulated: 1,440
0:52:35.480369 PROGRESS: Target precursors: 1,426 (99.03%)
0:52:35.480421 PROGRESS: Decoy precursors: 14 (0.97%)
0:52:35.480469 PROGRESS: 
0:52:35.480514 PROGRESS: Precursor Summary:
0:52:35.481823 PROGRESS: Channel   0:	 0.050 FDR: 1,426; 0.010 FDR: 1,426; 0.001 FDR:   551
0:52:35.481911 PROGRESS: 
0:52:35.481966 PROGRESS: Protein Summary:
0:52:35.483635 PROGRESS: Channel   0:	 0.050 FDR: 1,222; 0.010 FDR: 1,222; 0.001 FDR:   485
0:52:35.483728 PROGRESS: =========================================================================
0:52:35.499180 INFO: Target number of precursors reached.
0:52:35.943919 INFO: fragments_df: keeping 5000 of 4027411 [sum(precursor_idx_mask)=33396 sum(mass_error_mask)=4027411 stop_rank=5000
0:52:36.379625 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:52:36.582901 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:52:37.233454 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:52:37.233916 INFO: Using score_cutoff 9.09075183391571 (fac=0.99, q=1)
0:52:37.234226 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:52:37.234303 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:52:37.234358 INFO: Updating optimization_manager: score_cutoff        : 8.853355975341797 -> 9.09075183391571
0:52:37.234411 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:52:37.386520 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:52:37.731385 INFO: === checking if optimization conditions were reached ===
0:52:37.731659 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:52:37.734448 INFO: Updating optimization_manager: rt_error            : 858.0731638307932 -> 987.2599129709839
0:52:37.734559 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 987.2599.
0:52:37.734624 INFO: ==============================================
0:52:37.734693 INFO: Starting optimization step 4.
0:52:37.734750 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:52:37.734811 INFO: Using rust extraction backend
0:52:37.734867 PROGRESS: Extracting batch of 250256 precursors
0:52:38.156493 INFO: === Search parameters used ===
0:52:38.156767 INFO: rt_error       : 987.2599129709839
0:52:38.156825 INFO: mobility_error : 0.1
0:52:38.156873 INFO: num_candidates : 3
0:52:38.156916 INFO: ms1_error      : 3
0:52:38.156975 INFO: ms2_error      : 10.0
0:52:38.157022 INFO: fwhm_rt        : 3.0
0:52:38.157062 INFO: quant_window   : 3
0:52:38.157100 INFO: ==============================================
0:52:40.743086 INFO: performing precursor FDR with 40 features
0:52:40.743234 INFO: Decoy channel: -1
0:52:40.743261 INFO: competitive: True
0:52:40.943539 INFO: Setting torch num_threads to 2 for FDR classification task
0:52:41.255399 INFO: Estimating optimal hyperparameters - samples: 599,179, batch_size: 2,454, learning_rate: 7.74e-04
0:52:41.256563 INFO: Using random state 704905 for train-test-split
0:52:57.326651 INFO: Test AUC: 0.613
0:52:57.326788 INFO: Train AUC: 0.627
0:52:57.326823 INFO: AUC difference: 2.38%
0:52:57.804564 INFO: Resetting torch num_threads to 100
0:52:57.831285 PROGRESS: === Extracted 748974 precursors and 4027098 fragments ===
0:52:57.831773 INFO: === FDR correction performed with classifier version 11 ===
0:52:57.832453 PROGRESS: ============================= Precursor FDR =============================
0:52:57.832547 PROGRESS: Total precursors accumulated: 1,581
0:52:57.832607 PROGRESS: Target precursors: 1,566 (99.05%)
0:52:57.832657 PROGRESS: Decoy precursors: 15 (0.95%)
0:52:57.832704 PROGRESS: 
0:52:57.832749 PROGRESS: Precursor Summary:
0:52:57.834095 PROGRESS: Channel   0:	 0.050 FDR: 1,566; 0.010 FDR: 1,566; 0.001 FDR:   425
0:52:57.834186 PROGRESS: 
0:52:57.834243 PROGRESS: Protein Summary:
0:52:57.835957 PROGRESS: Channel   0:	 0.050 FDR: 1,345; 0.010 FDR: 1,345; 0.001 FDR:   383
0:52:57.836065 PROGRESS: =========================================================================
0:52:57.850780 INFO: Target number of precursors reached.
0:52:58.300425 INFO: fragments_df: keeping 5000 of 4027098 [sum(precursor_idx_mask)=35994 sum(mass_error_mask)=4027098 stop_rank=5000
0:52:58.724743 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:52:58.955930 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:52:59.605024 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:52:59.605485 INFO: Using score_cutoff 8.240734013557434 (fac=0.99, q=1)
0:52:59.605789 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:52:59.605866 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:52:59.605922 INFO: Updating optimization_manager: score_cutoff        : 9.09075183391571 -> 8.240734013557434
0:52:59.605978 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:52:59.757483 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:53:00.116896 INFO: === checking if optimization conditions were reached ===
0:53:00.117172 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:53:00.120113 INFO: Updating optimization_manager: rt_error            : 987.2599129709839 -> 895.6013928577445
0:53:00.120217 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 895.6014.
0:53:00.120281 INFO: ==============================================
0:53:00.120349 INFO: Starting optimization step 5.
0:53:00.120407 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:53:00.120486 INFO: Using rust extraction backend
0:53:00.120542 PROGRESS: Extracting batch of 250256 precursors
0:53:00.541306 INFO: === Search parameters used ===
0:53:00.541575 INFO: rt_error       : 895.6013928577445
0:53:00.541629 INFO: mobility_error : 0.1
0:53:00.541675 INFO: num_candidates : 3
0:53:00.541717 INFO: ms1_error      : 3
0:53:00.541757 INFO: ms2_error      : 10.0
0:53:00.541796 INFO: fwhm_rt        : 3.0
0:53:00.541834 INFO: quant_window   : 3
0:53:00.541871 INFO: ==============================================
0:53:03.073158 INFO: performing precursor FDR with 40 features
0:53:03.073280 INFO: Decoy channel: -1
0:53:03.073306 INFO: competitive: True
0:53:03.258508 INFO: Setting torch num_threads to 2 for FDR classification task
0:53:03.558925 INFO: Estimating optimal hyperparameters - samples: 599,211, batch_size: 2,454, learning_rate: 7.74e-04
0:53:03.559964 INFO: Using random state 704905 for train-test-split
0:53:16.042540 INFO: Test AUC: 0.615
0:53:16.042671 INFO: Train AUC: 0.627
0:53:16.042703 INFO: AUC difference: 1.79%
0:53:16.520658 INFO: Resetting torch num_threads to 100
0:53:16.549614 PROGRESS: === Extracted 749014 precursors and 4027490 fragments ===
0:53:16.550092 INFO: === FDR correction performed with classifier version 11 ===
0:53:16.550745 PROGRESS: ============================= Precursor FDR =============================
0:53:16.550839 PROGRESS: Total precursors accumulated: 1,447
0:53:16.550901 PROGRESS: Target precursors: 1,433 (99.03%)
0:53:16.550954 PROGRESS: Decoy precursors: 14 (0.97%)
0:53:16.551013 PROGRESS: 
0:53:16.551061 PROGRESS: Precursor Summary:
0:53:16.552394 PROGRESS: Channel   0:	 0.050 FDR: 1,433; 0.010 FDR: 1,433; 0.001 FDR:   709
0:53:16.552490 PROGRESS: 
0:53:16.552547 PROGRESS: Protein Summary:
0:53:16.554241 PROGRESS: Channel   0:	 0.050 FDR: 1,233; 0.010 FDR: 1,233; 0.001 FDR:   625
0:53:16.554331 PROGRESS: =========================================================================
0:53:16.568219 INFO: Target number of precursors reached.
0:53:17.024611 INFO: fragments_df: keeping 5000 of 4027490 [sum(precursor_idx_mask)=32840 sum(mass_error_mask)=4027490 stop_rank=5000
0:53:17.432952 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:53:17.635529 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:53:18.286244 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:53:18.286711 INFO: Using score_cutoff 8.359194142913818 (fac=0.99, q=1)
0:53:18.287015 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:53:18.287104 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:53:18.287170 INFO: Updating optimization_manager: score_cutoff        : 8.240734013557434 -> 8.359194142913818
0:53:18.287227 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:53:18.439004 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:53:18.791459 INFO: === checking if optimization conditions were reached ===
0:53:18.791751 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
0:53:18.794577 INFO: Updating optimization_manager: rt_error            : 895.6013928577445 -> 899.1947364475939
0:53:18.794680 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 899.1947.
0:53:18.794756 INFO: ==============================================
0:53:18.794829 INFO: Starting optimization step 6.
0:53:18.794884 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:53:18.794943 INFO: Using rust extraction backend
0:53:18.794997 PROGRESS: Extracting batch of 250256 precursors
0:53:19.215687 INFO: === Search parameters used ===
0:53:19.215957 INFO: rt_error       : 899.1947364475939
0:53:19.216010 INFO: mobility_error : 0.1
0:53:19.216056 INFO: num_candidates : 3
0:53:19.216097 INFO: ms1_error      : 3
0:53:19.216137 INFO: ms2_error      : 10.0
0:53:19.216177 INFO: fwhm_rt        : 3.0
0:53:19.216217 INFO: quant_window   : 3
0:53:19.216256 INFO: ==============================================
0:53:21.736821 INFO: performing precursor FDR with 40 features
0:53:21.736948 INFO: Decoy channel: -1
0:53:21.736974 INFO: competitive: True
0:53:21.922834 INFO: Setting torch num_threads to 2 for FDR classification task
0:53:22.209843 INFO: Estimating optimal hyperparameters - samples: 599,212, batch_size: 2,454, learning_rate: 7.74e-04
0:53:22.210892 INFO: Using random state 704905 for train-test-split
0:53:36.520657 INFO: Test AUC: 0.613
0:53:36.520821 INFO: Train AUC: 0.628
0:53:36.520855 INFO: AUC difference: 2.42%
0:53:36.992434 INFO: Resetting torch num_threads to 100
0:53:37.018305 PROGRESS: === Extracted 749016 precursors and 4027195 fragments ===
0:53:37.018812 INFO: === FDR correction performed with classifier version 11 ===
0:53:37.019526 PROGRESS: ============================= Precursor FDR =============================
0:53:37.019622 PROGRESS: Total precursors accumulated: 1,620
0:53:37.019685 PROGRESS: Target precursors: 1,604 (99.01%)
0:53:37.019737 PROGRESS: Decoy precursors: 16 (0.99%)
0:53:37.019785 PROGRESS: 
0:53:37.019830 PROGRESS: Precursor Summary:
0:53:37.021147 PROGRESS: Channel   0:	 0.050 FDR: 1,604; 0.010 FDR: 1,604; 0.001 FDR:   485
0:53:37.021248 PROGRESS: 
0:53:37.021303 PROGRESS: Protein Summary:
0:53:37.023009 PROGRESS: Channel   0:	 0.050 FDR: 1,359; 0.010 FDR: 1,359; 0.001 FDR:   429
0:53:37.023102 PROGRESS: =========================================================================
0:53:37.037201 INFO: Target number of precursors reached.
0:53:37.473772 INFO: fragments_df: keeping 5000 of 4027195 [sum(precursor_idx_mask)=37470 sum(mass_error_mask)=4027195 stop_rank=5000
0:53:37.896680 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:53:38.114762 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:53:38.766471 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:53:38.767001 INFO: Using score_cutoff 9.23255122346878 (fac=0.99, q=1)
0:53:38.767338 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:53:38.767422 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:53:38.767477 INFO: Updating optimization_manager: score_cutoff        : 8.359194142913818 -> 9.23255122346878
0:53:38.767536 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:53:38.919954 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:53:39.253389 INFO: === checking if optimization conditions were reached ===
0:53:39.253676 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
0:53:39.254664 INFO: Updating optimization_manager: rt_error            : 899.1947364475939 -> 899.1947364475939
0:53:39.254791 INFO: Updating optimization_manager: classifier_version  : 11 -> 18
0:53:39.254902 INFO: Updating optimization_manager: score_cutoff        : 9.23255122346878 -> 9.23255122346878
0:53:39.254992 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:53:39.255075 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:53:39.255175 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 899.1947 found after 7 searches.
0:53:39.255244 INFO: ==============================================
0:53:39.255323 PROGRESS: Optimization finished for rt_error.
0:53:39.651494 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:53:39.804051 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:53:40.138660 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:53:40.138929 PROGRESS: ==============================================
0:53:40.139004 PROGRESS: ms2_error      : 10.0000
0:53:40.139060 PROGRESS: rt_error       : 899.1947
0:53:40.139104 PROGRESS: ==============================================
0:53:40.144796 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:53:47.851852 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:54:04.862263 INFO: Using rust extraction backend
0:54:04.862820 PROGRESS: Extracting batch of 11997144 precursors
0:54:20.959480 INFO: === Search parameters used ===
0:54:20.960032 INFO: rt_error       : 899.1947364475939
0:54:20.960109 INFO: mobility_error : 0.1
0:54:20.960165 INFO: num_candidates : 3
0:54:20.960212 INFO: ms1_error      : 3
0:54:20.960254 INFO: ms2_error      : 10.0
0:54:20.960294 INFO: fwhm_rt        : 3.0
0:54:20.960334 INFO: quant_window   : 3
0:54:20.960374 INFO: ==============================================
0:54:53.963155 INFO: Removed 5476097 precursors with score below cutoff 9.23255122346878
0:55:17.593205 INFO: performing precursor FDR with 40 features
0:55:17.593442 INFO: Decoy channel: -1
0:55:17.593473 INFO: competitive: True
0:55:20.795217 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:33.050341 INFO: Estimating optimal hyperparameters - samples: 24,412,029, batch_size: 4,096, learning_rate: 1.00e-03
0:55:33.123938 INFO: Using random state 437218 for train-test-split
1:11:03.173412 INFO: Test AUC: 0.622
1:11:03.173948 INFO: Train AUC: 0.622
1:11:03.174024 INFO: AUC difference: 0.01%
1:11:13.490949 INFO: Resetting torch num_threads to 100
1:11:18.298844 PROGRESS: ============================= Precursor FDR =============================
1:11:18.299467 PROGRESS: Total precursors accumulated: 93,586
1:11:18.300073 PROGRESS: Target precursors: 92,660 (99.01%)
1:11:18.300148 PROGRESS: Decoy precursors: 926 (0.99%)
1:11:18.300207 PROGRESS: 
1:11:18.300254 PROGRESS: Precursor Summary:
1:11:18.372363 PROGRESS: Channel   0:	 0.050 FDR: 92,660; 0.010 FDR: 92,660; 0.001 FDR: 47,019
1:11:18.372914 PROGRESS: 
1:11:18.372984 PROGRESS: Protein Summary:
1:11:18.479347 PROGRESS: Channel   0:	 0.050 FDR: 14,005; 0.010 FDR: 14,005; 0.001 FDR: 8,220
1:11:18.479907 PROGRESS: =========================================================================
1:11:18.847090 PROGRESS: === Transfer learning quantification ===
1:11:18.847636 INFO: creating library for charged fragment types: ['b', 'y']
1:11:23.106114 INFO: Calibrating library
1:11:23.106671 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:11:23.171057 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:11:24.046077 INFO: quantifying 93,586 precursors with 4,081,964 fragments
1:11:24.046635 INFO: Using rust extraction backend
1:11:26.457157 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/psm.parquet
1:11:26.829377 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.parquet
1:11:27.502500 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.transfer.parquet
1:11:29.047518 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:11:30.880421 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 
1:11:30.881039 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant
1:11:30.881277 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/figures
1:11:30.881661 INFO: Initializing TimingManager
1:11:30.883365 INFO: Initializing RawFileManager
1:12:07.786456 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.
1:12:07.802665 INFO: Determining DIA cycle
1:12:07.821385 INFO: Found cycle with start 0.00 min and length 300.
1:12:08.807387 INFO: RT (min)            : 0.0 - 26.9
1:12:08.807591 INFO: RT duration (sec)   : 1611.2
1:12:08.807626 INFO: RT duration (min)   : 26.9
1:12:08.807652 INFO: Cycle len (scans)   : 300
1:12:08.807674 INFO: Cycle len (sec)     : 1.65
1:12:08.807696 INFO: Number of cycles    : 977
1:12:08.807718 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:12:08.807772 INFO: Creating DIA data object took: 37.924174785614014
1:12:11.728472 INFO: Creating DIA data NG object took: 2.920456886291504
1:12:16.922026 INFO: Initializing CalibrationManager
1:12:16.922635 INFO: Setting up calibration estimators ..
1:12:16.922716 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:12:16.922815 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'}' ..
1:12:16.922948 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:12:16.923009 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:12:16.923076 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}}' ..
1:12:16.923136 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:12:16.923209 INFO: Done setting up calibration estimators.
1:12:16.924016 INFO: Initializing OptimizationManager
1:12:16.924251 INFO: initial parameter: ms1_error = 3
1:12:16.924310 INFO: initial parameter: ms2_error = 10
1:12:16.924367 INFO: initial parameter: rt_error = 805.5982666015625
1:12:16.924414 INFO: initial parameter: mobility_error = 0.1
1:12:16.924464 INFO: initial parameter: num_candidates = 1
1:12:16.924507 INFO: initial parameter: fwhm_rt = 5
1:12:16.924554 INFO: initial parameter: fwhm_mobility = 0.01
1:12:16.924596 INFO: initial parameter: score_cutoff = 0
1:12:16.924637 INFO: initial parameter: classifier_version = -1
1:12:16.924729 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:12:16.925336 INFO: FDRManager: loading saved state not requested, will be initialized.
1:12:16.925382 INFO: Initializing FDRManager
1:12:16.925449 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
1:12:22.227382 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
1:12:25.939198 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
1:12:25.940215 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
1:12:25.940398 PROGRESS: Starting initial search for precursors.
1:12:25.940528 INFO: Starting optimization step 0.
1:12:25.940608 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:12:25.940683 INFO: Using rust extraction backend
1:12:25.940768 PROGRESS: Extracting batch of 1963 precursors
1:12:25.956086 INFO: === Search parameters used ===
1:12:25.956686 INFO: rt_error       : 805.5982666015625
1:12:25.956747 INFO: mobility_error : 0.1
1:12:25.956803 INFO: num_candidates : 1
1:12:25.956850 INFO: ms1_error      : 3
1:12:25.956892 INFO: ms2_error      : 10
1:12:25.956932 INFO: fwhm_rt        : 5
1:12:25.956973 INFO: quant_window   : 3
1:12:25.957014 INFO: ==============================================
1:12:26.103501 INFO: performing precursor FDR with 40 features
1:12:26.103947 INFO: Decoy channel: -1
1:12:26.104095 INFO: competitive: True
1:12:26.116657 INFO: Setting torch num_threads to 2 for FDR classification task
1:12:26.132311 INFO: Estimating optimal hyperparameters - samples: 1,566, batch_size: 128, learning_rate: 1.77e-04
1:12:26.139558 INFO: Using random state 161349 for train-test-split
1:12:26.446067 INFO: Test AUC: 0.518
1:12:26.446317 INFO: Train AUC: 0.564
1:12:26.446350 INFO: AUC difference: 8.12%
1:12:26.446375 WARNING: AUC difference > 5%. This may indicate overfitting.
1:12:26.865984 INFO: Resetting torch num_threads to 100
1:12:26.871228 PROGRESS: === Extracted 1958 precursors and 11016 fragments ===
1:12:26.872366 INFO: === FDR correction performed with classifier version -1 ===
1:12:26.873731 PROGRESS: ============================= Precursor FDR =============================
1:12:26.873988 PROGRESS: Total precursors accumulated: 11
1:12:26.874082 PROGRESS: Target precursors: 11 (100.00%)
1:12:26.874141 PROGRESS: Decoy precursors: 0 (0.00%)
1:12:26.874189 PROGRESS: 
1:12:26.874245 PROGRESS: Precursor Summary:
1:12:26.876156 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
1:12:26.876353 PROGRESS: 
1:12:26.876417 PROGRESS: Protein Summary:
1:12:26.878159 PROGRESS: Channel   0:	 0.050 FDR:    11; 0.010 FDR:    11; 0.001 FDR:    11
1:12:26.878337 PROGRESS: =========================================================================
1:12:26.879212 INFO: Target number of precursors not reached yet.
1:12:26.996326 INFO: Starting optimization step 1.
1:12:26.997024 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:12:26.997176 INFO: Using rust extraction backend
1:12:26.997279 PROGRESS: Extracting batch of 3911 precursors
1:12:27.018513 INFO: === Search parameters used ===
1:12:27.019068 INFO: rt_error       : 805.5982666015625
1:12:27.019125 INFO: mobility_error : 0.1
1:12:27.019220 INFO: num_candidates : 1
1:12:27.019266 INFO: ms1_error      : 3
1:12:27.019308 INFO: ms2_error      : 10
1:12:27.019350 INFO: fwhm_rt        : 5
1:12:27.019390 INFO: quant_window   : 3
1:12:27.019428 INFO: ==============================================
1:12:27.107322 INFO: performing precursor FDR with 40 features
1:12:27.107538 INFO: Decoy channel: -1
1:12:27.107566 INFO: competitive: True
1:12:27.114461 INFO: Setting torch num_threads to 2 for FDR classification task
1:12:27.118428 INFO: Estimating optimal hyperparameters - samples: 4,688, batch_size: 128, learning_rate: 1.77e-04
1:12:27.118644 INFO: Using random state 661597 for train-test-split
1:12:27.739630 INFO: Test AUC: 0.530
1:12:27.739933 INFO: Train AUC: 0.586
1:12:27.739970 INFO: AUC difference: 9.59%
1:12:27.739996 WARNING: AUC difference > 5%. This may indicate overfitting.
1:12:28.175421 INFO: Resetting torch num_threads to 100
1:12:28.184110 PROGRESS: === Extracted 5860 precursors and 33057 fragments ===
1:12:28.185304 INFO: === FDR correction performed with classifier version -1 ===
1:12:28.186425 PROGRESS: ============================= Precursor FDR =============================
1:12:28.186551 PROGRESS: Total precursors accumulated: 19
1:12:28.186621 PROGRESS: Target precursors: 19 (100.00%)
1:12:28.186675 PROGRESS: Decoy precursors: 0 (0.00%)
1:12:28.186726 PROGRESS: 
1:12:28.186813 PROGRESS: Precursor Summary:
1:12:28.188107 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
1:12:28.188210 PROGRESS: 
1:12:28.188265 PROGRESS: Protein Summary:
1:12:28.189626 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
1:12:28.189720 PROGRESS: =========================================================================
1:12:28.191252 INFO: Target number of precursors not reached yet.
1:12:28.324537 INFO: Starting optimization step 2.
1:12:28.325094 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:12:28.325234 INFO: Using rust extraction backend
1:12:28.325314 PROGRESS: Extracting batch of 7891 precursors
1:12:28.361729 INFO: === Search parameters used ===
1:12:28.362364 INFO: rt_error       : 805.5982666015625
1:12:28.362469 INFO: mobility_error : 0.1
1:12:28.362528 INFO: num_candidates : 1
1:12:28.362577 INFO: ms1_error      : 3
1:12:28.362624 INFO: ms2_error      : 10
1:12:28.362670 INFO: fwhm_rt        : 5
1:12:28.362720 INFO: quant_window   : 3
1:12:28.362761 INFO: ==============================================
1:12:28.567468 INFO: performing precursor FDR with 40 features
1:12:28.567770 INFO: Decoy channel: -1
1:12:28.567806 INFO: competitive: True
1:12:28.596551 INFO: Setting torch num_threads to 2 for FDR classification task
1:12:28.609165 INFO: Estimating optimal hyperparameters - samples: 10,983, batch_size: 128, learning_rate: 1.77e-04
1:12:28.609516 INFO: Using random state 34563 for train-test-split
1:12:29.978885 INFO: Test AUC: 0.559
1:12:29.979170 INFO: Train AUC: 0.591
1:12:29.979221 INFO: AUC difference: 5.54%
1:12:29.979247 WARNING: AUC difference > 5%. This may indicate overfitting.
1:12:30.402787 INFO: Resetting torch num_threads to 100
1:12:30.416517 PROGRESS: === Extracted 13729 precursors and 77515 fragments ===
1:12:30.417701 INFO: === FDR correction performed with classifier version -1 ===
1:12:30.418735 PROGRESS: ============================= Precursor FDR =============================
1:12:30.418848 PROGRESS: Total precursors accumulated: 67
1:12:30.418909 PROGRESS: Target precursors: 67 (100.00%)
1:12:30.418963 PROGRESS: Decoy precursors: 0 (0.00%)
1:12:30.419010 PROGRESS: 
1:12:30.419054 PROGRESS: Precursor Summary:
1:12:30.420317 PROGRESS: Channel   0:	 0.050 FDR:    67; 0.010 FDR:    67; 0.001 FDR:    67
1:12:30.420438 PROGRESS: 
1:12:30.420495 PROGRESS: Protein Summary:
1:12:30.421850 PROGRESS: Channel   0:	 0.050 FDR:    66; 0.010 FDR:    66; 0.001 FDR:    66
1:12:30.421945 PROGRESS: =========================================================================
1:12:30.423680 INFO: Target number of precursors not reached yet.
1:12:30.593153 INFO: Starting optimization step 3.
1:12:30.593648 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:12:30.593758 INFO: Using rust extraction backend
1:12:30.593845 PROGRESS: Extracting batch of 15777 precursors
1:12:30.663297 INFO: === Search parameters used ===
1:12:30.663934 INFO: rt_error       : 805.5982666015625
1:12:30.664055 INFO: mobility_error : 0.1
1:12:30.664106 INFO: num_candidates : 1
1:12:30.664156 INFO: ms1_error      : 3
1:12:30.664202 INFO: ms2_error      : 10
1:12:30.664269 INFO: fwhm_rt        : 5
1:12:30.664326 INFO: quant_window   : 3
1:12:30.664370 INFO: ==============================================
1:12:31.010686 INFO: performing precursor FDR with 40 features
1:12:31.010914 INFO: Decoy channel: -1
1:12:31.010946 INFO: competitive: True
1:12:31.060577 INFO: Setting torch num_threads to 2 for FDR classification task
1:12:31.089528 INFO: Estimating optimal hyperparameters - samples: 23,576, batch_size: 128, learning_rate: 1.77e-04
1:12:31.089967 INFO: Using random state 824126 for train-test-split
1:12:34.078958 INFO: Test AUC: 0.581
1:12:34.079229 INFO: Train AUC: 0.609
1:12:34.079280 INFO: AUC difference: 4.56%
1:12:34.543616 INFO: Resetting torch num_threads to 100
1:12:34.576636 PROGRESS: === Extracted 29471 precursors and 166454 fragments ===
1:12:34.578114 INFO: === FDR correction performed with classifier version -1 ===
1:12:34.579997 PROGRESS: ============================= Precursor FDR =============================
1:12:34.580342 PROGRESS: Total precursors accumulated: 85
1:12:34.580449 PROGRESS: Target precursors: 85 (100.00%)
1:12:34.580513 PROGRESS: Decoy precursors: 0 (0.00%)
1:12:34.580563 PROGRESS: 
1:12:34.580611 PROGRESS: Precursor Summary:
1:12:34.583055 PROGRESS: Channel   0:	 0.050 FDR:    85; 0.010 FDR:    85; 0.001 FDR:    85
1:12:34.583303 PROGRESS: 
1:12:34.583395 PROGRESS: Protein Summary:
1:12:34.586212 PROGRESS: Channel   0:	 0.050 FDR:    84; 0.010 FDR:    84; 0.001 FDR:    84
1:12:34.586479 PROGRESS: =========================================================================
1:12:34.590687 INFO: Target number of precursors not reached yet.
1:12:34.833380 INFO: Starting optimization step 4.
1:12:34.833949 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:12:34.834080 INFO: Using rust extraction backend
1:12:34.834166 PROGRESS: Extracting batch of 31516 precursors
1:12:34.976075 INFO: === Search parameters used ===
1:12:34.976706 INFO: rt_error       : 805.5982666015625
1:12:34.976814 INFO: mobility_error : 0.1
1:12:34.976870 INFO: num_candidates : 1
1:12:34.976917 INFO: ms1_error      : 3
1:12:34.976958 INFO: ms2_error      : 10
1:12:34.977000 INFO: fwhm_rt        : 5
1:12:34.977042 INFO: quant_window   : 3
1:12:34.977099 INFO: ==============================================
1:12:35.371020 INFO: performing precursor FDR with 40 features
1:12:35.371298 INFO: Decoy channel: -1
1:12:35.371333 INFO: competitive: True
1:12:35.457726 INFO: Setting torch num_threads to 2 for FDR classification task
1:12:35.507134 INFO: Estimating optimal hyperparameters - samples: 48,733, batch_size: 199, learning_rate: 2.20e-04
1:12:35.507651 INFO: Using random state 58109 for train-test-split
1:12:39.975187 INFO: Test AUC: 0.580
1:12:39.975468 INFO: Train AUC: 0.609
1:12:39.975504 INFO: AUC difference: 4.82%
1:12:40.373547 INFO: Resetting torch num_threads to 100
1:12:40.423006 PROGRESS: === Extracted 60917 precursors and 343454 fragments ===
1:12:40.424422 INFO: === FDR correction performed with classifier version -1 ===
1:12:40.426257 PROGRESS: ============================= Precursor FDR =============================
1:12:40.426567 PROGRESS: Total precursors accumulated: 226
1:12:40.426659 PROGRESS: Target precursors: 224 (99.12%)
1:12:40.426718 PROGRESS: Decoy precursors: 2 (0.88%)
1:12:40.426770 PROGRESS: 
1:12:40.426823 PROGRESS: Precursor Summary:
1:12:40.429320 PROGRESS: Channel   0:	 0.050 FDR:   224; 0.010 FDR:   224; 0.001 FDR:   162
1:12:40.429554 PROGRESS: 
1:12:40.429615 PROGRESS: Protein Summary:
1:12:40.431293 PROGRESS: Channel   0:	 0.050 FDR:   213; 0.010 FDR:   213; 0.001 FDR:   155
1:12:40.431414 PROGRESS: =========================================================================
1:12:40.435750 INFO: Target number of precursors not reached yet.
1:12:40.809995 INFO: Starting optimization step 5.
1:12:40.810595 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:12:40.810789 INFO: Using rust extraction backend
1:12:40.810902 PROGRESS: Extracting batch of 63010 precursors
1:12:41.135356 INFO: === Search parameters used ===
1:12:41.135989 INFO: rt_error       : 805.5982666015625
1:12:41.136050 INFO: mobility_error : 0.1
1:12:41.136102 INFO: num_candidates : 1
1:12:41.136149 INFO: ms1_error      : 3
1:12:41.136192 INFO: ms2_error      : 10
1:12:41.136237 INFO: fwhm_rt        : 5
1:12:41.136278 INFO: quant_window   : 3
1:12:41.136320 INFO: ==============================================
1:12:41.840796 INFO: performing precursor FDR with 40 features
1:12:41.841057 INFO: Decoy channel: -1
1:12:41.841122 INFO: competitive: True
1:12:41.996792 INFO: Setting torch num_threads to 2 for FDR classification task
1:12:42.118554 INFO: Estimating optimal hyperparameters - samples: 99,028, batch_size: 405, learning_rate: 3.14e-04
1:12:42.119457 INFO: Using random state 801353 for train-test-split
1:12:48.269163 INFO: Test AUC: 0.590
1:12:48.269459 INFO: Train AUC: 0.614
1:12:48.269495 INFO: AUC difference: 3.91%
1:12:48.692020 INFO: Resetting torch num_threads to 100
1:12:48.788497 PROGRESS: === Extracted 123786 precursors and 697383 fragments ===
1:12:48.789897 INFO: === FDR correction performed with classifier version -1 ===
1:12:48.791383 PROGRESS: ============================= Precursor FDR =============================
1:12:48.791525 PROGRESS: Total precursors accumulated: 616
1:12:48.791594 PROGRESS: Target precursors: 610 (99.03%)
1:12:48.791648 PROGRESS: Decoy precursors: 6 (0.97%)
1:12:48.791697 PROGRESS: 
1:12:48.791777 PROGRESS: Precursor Summary:
1:12:48.793587 PROGRESS: Channel   0:	 0.050 FDR:   610; 0.010 FDR:   610; 0.001 FDR:   434
1:12:48.793718 PROGRESS: 
1:12:48.793777 PROGRESS: Protein Summary:
1:12:48.795584 PROGRESS: Channel   0:	 0.050 FDR:   561; 0.010 FDR:   561; 0.001 FDR:   403
1:12:48.795702 PROGRESS: =========================================================================
1:12:48.803054 INFO: Target number of precursors not reached yet.
1:12:49.418867 INFO: Starting optimization step 6.
1:12:49.419527 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:12:49.419715 INFO: Using rust extraction backend
1:12:49.419863 PROGRESS: Extracting batch of 126188 precursors
1:12:49.924049 INFO: === Search parameters used ===
1:12:49.924672 INFO: rt_error       : 805.5982666015625
1:12:49.924783 INFO: mobility_error : 0.1
1:12:49.924838 INFO: num_candidates : 1
1:12:49.924885 INFO: ms1_error      : 3
1:12:49.924929 INFO: ms2_error      : 10
1:12:49.924970 INFO: fwhm_rt        : 5
1:12:49.925011 INFO: quant_window   : 3
1:12:49.925053 INFO: ==============================================
1:12:51.003237 INFO: performing precursor FDR with 40 features
1:12:51.003367 INFO: Decoy channel: -1
1:12:51.003394 INFO: competitive: True
1:12:51.130315 INFO: Setting torch num_threads to 2 for FDR classification task
1:12:51.228370 INFO: Estimating optimal hyperparameters - samples: 199,752, batch_size: 818, learning_rate: 4.47e-04
1:12:51.229670 INFO: Using random state 427362 for train-test-split
1:12:57.651854 INFO: Test AUC: 0.592
1:12:57.652020 INFO: Train AUC: 0.612
1:12:57.652052 INFO: AUC difference: 3.23%
1:12:57.982537 INFO: Resetting torch num_threads to 100
1:12:58.025596 PROGRESS: === Extracted 249690 precursors and 1405835 fragments ===
1:12:58.026338 INFO: === FDR correction performed with classifier version -1 ===
1:12:58.027190 PROGRESS: ============================= Precursor FDR =============================
1:12:58.027283 PROGRESS: Total precursors accumulated: 1,135
1:12:58.027343 PROGRESS: Target precursors: 1,124 (99.03%)
1:12:58.027391 PROGRESS: Decoy precursors: 11 (0.97%)
1:12:58.027436 PROGRESS: 
1:12:58.027478 PROGRESS: Precursor Summary:
1:12:58.028686 PROGRESS: Channel   0:	 0.050 FDR: 1,124; 0.010 FDR: 1,124; 0.001 FDR:     0
1:12:58.028778 PROGRESS: 
1:12:58.028835 PROGRESS: Protein Summary:
1:12:58.030304 PROGRESS: Channel   0:	 0.050 FDR:   957; 0.010 FDR:   957; 0.001 FDR:     0
1:12:58.030392 PROGRESS: =========================================================================
1:12:58.034682 INFO: Target number of precursors reached.
1:12:58.196271 INFO: fragments_df: keeping 5000 of 1405835 [sum(precursor_idx_mask)=12169 sum(mass_error_mask)=1405835 stop_rank=5000
1:12:58.680298 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:12:58.853056 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:12:59.502850 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:12:59.503319 INFO: Using score_cutoff 12.76836413784027 (fac=0.99, q=1)
1:12:59.503641 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:12:59.503721 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:12:59.503776 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.76836413784027
1:12:59.503841 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:12:59.655609 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:12:59.992981 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
1:12:59.993293 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:12:59.993435 INFO: Starting optimization step 7.
1:12:59.993510 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:12:59.993588 INFO: Using rust extraction backend
1:12:59.993660 PROGRESS: Extracting batch of 250256 precursors
1:13:00.416508 INFO: === Search parameters used ===
1:13:00.416785 INFO: rt_error       : 805.5982666015625
1:13:00.416842 INFO: mobility_error : 0.1
1:13:00.416890 INFO: num_candidates : 3
1:13:00.416934 INFO: ms1_error      : 3
1:13:00.416975 INFO: ms2_error      : 10
1:13:00.417017 INFO: fwhm_rt        : 3.0
1:13:00.417055 INFO: quant_window   : 3
1:13:00.417094 INFO: ==============================================
1:13:03.078994 INFO: performing precursor FDR with 40 features
1:13:03.079110 INFO: Decoy channel: -1
1:13:03.079136 INFO: competitive: True
1:13:03.261864 INFO: Setting torch num_threads to 2 for FDR classification task
1:13:03.551899 INFO: Estimating optimal hyperparameters - samples: 599,435, batch_size: 2,455, learning_rate: 7.74e-04
1:13:03.553040 INFO: Using random state 65552 for train-test-split
1:13:16.574155 INFO: Test AUC: 0.598
1:13:16.574281 INFO: Train AUC: 0.608
1:13:16.574315 INFO: AUC difference: 1.57%
1:13:17.058501 INFO: Resetting torch num_threads to 100
1:13:17.086899 PROGRESS: === Extracted 749294 precursors and 4052000 fragments ===
1:13:17.087401 INFO: === FDR correction performed with classifier version 6 ===
1:13:17.088063 PROGRESS: ============================= Precursor FDR =============================
1:13:17.088157 PROGRESS: Total precursors accumulated: 1,349
1:13:17.088231 PROGRESS: Target precursors: 1,336 (99.04%)
1:13:17.088286 PROGRESS: Decoy precursors: 13 (0.96%)
1:13:17.088334 PROGRESS: 
1:13:17.088380 PROGRESS: Precursor Summary:
1:13:17.089754 PROGRESS: Channel   0:	 0.050 FDR: 1,336; 0.010 FDR: 1,336; 0.001 FDR: 1,016
1:13:17.089844 PROGRESS: 
1:13:17.089901 PROGRESS: Protein Summary:
1:13:17.091612 PROGRESS: Channel   0:	 0.050 FDR: 1,122; 0.010 FDR: 1,122; 0.001 FDR:   867
1:13:17.091708 PROGRESS: =========================================================================
1:13:17.105680 INFO: Target number of precursors reached.
1:13:17.561781 INFO: fragments_df: keeping 5000 of 4052000 [sum(precursor_idx_mask)=32212 sum(mass_error_mask)=4052000 stop_rank=5000
1:13:17.976028 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:13:18.164351 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:13:18.817900 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:13:18.818341 INFO: Using score_cutoff 12.55049024963379 (fac=0.99, q=1)
1:13:18.818647 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:13:18.818724 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:13:18.818779 INFO: Updating optimization_manager: score_cutoff        : 12.76836413784027 -> 12.55049024963379
1:13:18.818833 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:13:18.969210 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:13:19.314883 INFO: === checking if optimization conditions were reached ===
1:13:19.317585 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
1:13:19.317761 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1:13:19.317844 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:13:19.317919 INFO: ==============================================
1:13:19.318001 INFO: Starting optimization step 8.
1:13:19.318070 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:13:19.318145 INFO: Using rust extraction backend
1:13:19.318216 PROGRESS: Extracting batch of 250256 precursors
1:13:19.737499 INFO: === Search parameters used ===
1:13:19.737767 INFO: rt_error       : 805.5982666015625
1:13:19.737822 INFO: mobility_error : 0.1
1:13:19.737870 INFO: num_candidates : 3
1:13:19.737913 INFO: ms1_error      : 3
1:13:19.737955 INFO: ms2_error      : 10.0
1:13:19.737996 INFO: fwhm_rt        : 3.0
1:13:19.738037 INFO: quant_window   : 3
1:13:19.738091 INFO: ==============================================
1:13:22.217857 INFO: performing precursor FDR with 40 features
1:13:22.217975 INFO: Decoy channel: -1
1:13:22.218000 INFO: competitive: True
1:13:22.397850 INFO: Setting torch num_threads to 2 for FDR classification task
1:13:22.683460 INFO: Estimating optimal hyperparameters - samples: 599,416, batch_size: 2,455, learning_rate: 7.74e-04
1:13:22.684571 INFO: Using random state 283020 for train-test-split
1:13:35.794381 INFO: Test AUC: 0.604
1:13:35.794533 INFO: Train AUC: 0.614
1:13:35.794567 INFO: AUC difference: 1.67%
1:13:36.275927 INFO: Resetting torch num_threads to 100
1:13:36.305630 PROGRESS: === Extracted 749270 precursors and 4051972 fragments ===
1:13:36.306126 INFO: === FDR correction performed with classifier version 7 ===
1:13:36.306775 PROGRESS: ============================= Precursor FDR =============================
1:13:36.306874 PROGRESS: Total precursors accumulated: 1,298
1:13:36.306937 PROGRESS: Target precursors: 1,286 (99.08%)
1:13:36.306987 PROGRESS: Decoy precursors: 12 (0.92%)
1:13:36.307034 PROGRESS: 
1:13:36.307079 PROGRESS: Precursor Summary:
1:13:36.308370 PROGRESS: Channel   0:	 0.050 FDR: 1,286; 0.010 FDR: 1,286; 0.001 FDR:   646
1:13:36.308461 PROGRESS: 
1:13:36.308518 PROGRESS: Protein Summary:
1:13:36.310118 PROGRESS: Channel   0:	 0.050 FDR: 1,071; 0.010 FDR: 1,071; 0.001 FDR:   561
1:13:36.310205 PROGRESS: =========================================================================
1:13:36.326341 INFO: Target number of precursors reached.
1:13:36.777076 INFO: fragments_df: keeping 5000 of 4051972 [sum(precursor_idx_mask)=31405 sum(mass_error_mask)=4051972 stop_rank=5000
1:13:37.191904 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:13:37.380509 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:13:38.034144 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:13:38.034595 INFO: Using score_cutoff 12.751779483318328 (fac=0.99, q=1)
1:13:38.034915 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:13:38.034992 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:13:38.035048 INFO: Updating optimization_manager: score_cutoff        : 12.55049024963379 -> 12.751779483318328
1:13:38.035108 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:13:38.188993 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:13:38.529856 INFO: === checking if optimization conditions were reached ===
1:13:38.532487 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:13:38.532606 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:13:38.532685 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:13:38.532756 INFO: ==============================================
1:13:38.532842 INFO: Starting optimization step 9.
1:13:38.532913 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:13:38.532991 INFO: Using rust extraction backend
1:13:38.533066 PROGRESS: Extracting batch of 250256 precursors
1:13:38.956591 INFO: === Search parameters used ===
1:13:38.956882 INFO: rt_error       : 805.5982666015625
1:13:38.956941 INFO: mobility_error : 0.1
1:13:38.956992 INFO: num_candidates : 3
1:13:38.957037 INFO: ms1_error      : 3
1:13:38.957080 INFO: ms2_error      : 10.0
1:13:38.957121 INFO: fwhm_rt        : 3.0
1:13:38.957161 INFO: quant_window   : 3
1:13:38.957201 INFO: ==============================================
1:13:41.470240 INFO: performing precursor FDR with 40 features
1:13:41.470366 INFO: Decoy channel: -1
1:13:41.470391 INFO: competitive: True
1:13:41.651921 INFO: Setting torch num_threads to 2 for FDR classification task
1:13:41.951318 INFO: Estimating optimal hyperparameters - samples: 599,425, batch_size: 2,455, learning_rate: 7.74e-04
1:13:41.952224 INFO: Using random state 71616 for train-test-split
1:13:54.978799 INFO: Test AUC: 0.607
1:13:54.978941 INFO: Train AUC: 0.617
1:13:54.978975 INFO: AUC difference: 1.63%
1:13:55.458958 INFO: Resetting torch num_threads to 100
1:13:55.488612 PROGRESS: === Extracted 749282 precursors and 4052172 fragments ===
1:13:55.489106 INFO: === FDR correction performed with classifier version 8 ===
1:13:55.489804 PROGRESS: ============================= Precursor FDR =============================
1:13:55.489894 PROGRESS: Total precursors accumulated: 1,455
1:13:55.489956 PROGRESS: Target precursors: 1,441 (99.04%)
1:13:55.490006 PROGRESS: Decoy precursors: 14 (0.96%)
1:13:55.490052 PROGRESS: 
1:13:55.490096 PROGRESS: Precursor Summary:
1:13:55.491459 PROGRESS: Channel   0:	 0.050 FDR: 1,441; 0.010 FDR: 1,441; 0.001 FDR:   784
1:13:55.491550 PROGRESS: 
1:13:55.491604 PROGRESS: Protein Summary:
1:13:55.493307 PROGRESS: Channel   0:	 0.050 FDR: 1,225; 0.010 FDR: 1,225; 0.001 FDR:   680
1:13:55.493395 PROGRESS: =========================================================================
1:13:55.514202 INFO: Target number of precursors reached.
1:13:55.956546 INFO: fragments_df: keeping 5000 of 4052172 [sum(precursor_idx_mask)=34084 sum(mass_error_mask)=4052172 stop_rank=5000
1:13:56.386360 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:13:56.581366 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:13:57.233996 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:13:57.234453 INFO: Using score_cutoff 9.727795160293578 (fac=0.99, q=1)
1:13:57.234759 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:13:57.234838 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:13:57.234900 INFO: Updating optimization_manager: score_cutoff        : 12.751779483318328 -> 9.727795160293578
1:13:57.234955 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:13:57.384015 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:13:57.715043 INFO: === checking if optimization conditions were reached ===
1:13:57.717677 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:13:57.717796 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:13:57.717875 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:13:57.717945 INFO: ==============================================
1:13:57.718028 INFO: Starting optimization step 10.
1:13:57.718102 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:13:57.718176 INFO: Using rust extraction backend
1:13:57.718249 PROGRESS: Extracting batch of 250256 precursors
1:13:58.139777 INFO: === Search parameters used ===
1:13:58.140042 INFO: rt_error       : 805.5982666015625
1:13:58.140101 INFO: mobility_error : 0.1
1:13:58.140156 INFO: num_candidates : 3
1:13:58.140202 INFO: ms1_error      : 3
1:13:58.140245 INFO: ms2_error      : 10.0
1:13:58.140286 INFO: fwhm_rt        : 3.0
1:13:58.140327 INFO: quant_window   : 3
1:13:58.140368 INFO: ==============================================
1:14:00.616556 INFO: performing precursor FDR with 40 features
1:14:00.616676 INFO: Decoy channel: -1
1:14:00.616703 INFO: competitive: True
1:14:00.806227 INFO: Setting torch num_threads to 2 for FDR classification task
1:14:01.100116 INFO: Estimating optimal hyperparameters - samples: 599,445, batch_size: 2,455, learning_rate: 7.74e-04
1:14:01.101029 INFO: Using random state 41831 for train-test-split
1:14:13.818709 INFO: Test AUC: 0.609
1:14:13.818870 INFO: Train AUC: 0.621
1:14:13.818904 INFO: AUC difference: 1.90%
1:14:15.261741 INFO: Resetting torch num_threads to 100
1:14:15.294779 PROGRESS: === Extracted 749307 precursors and 4052626 fragments ===
1:14:15.295304 INFO: === FDR correction performed with classifier version 9 ===
1:14:15.296042 PROGRESS: ============================= Precursor FDR =============================
1:14:15.296134 PROGRESS: Total precursors accumulated: 1,429
1:14:15.296197 PROGRESS: Target precursors: 1,415 (99.02%)
1:14:15.296250 PROGRESS: Decoy precursors: 14 (0.98%)
1:14:15.296298 PROGRESS: 
1:14:15.296346 PROGRESS: Precursor Summary:
1:14:15.297673 PROGRESS: Channel   0:	 0.050 FDR: 1,415; 0.010 FDR: 1,415; 0.001 FDR:   820
1:14:15.297776 PROGRESS: 
1:14:15.297832 PROGRESS: Protein Summary:
1:14:15.299562 PROGRESS: Channel   0:	 0.050 FDR: 1,201; 0.010 FDR: 1,201; 0.001 FDR:   711
1:14:15.299655 PROGRESS: =========================================================================
1:14:15.315340 INFO: Target number of precursors reached.
1:14:15.742440 INFO: fragments_df: keeping 5000 of 4052626 [sum(precursor_idx_mask)=33825 sum(mass_error_mask)=4052626 stop_rank=5000
1:14:16.173789 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:14:16.372801 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:14:17.026715 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:14:17.027228 INFO: Using score_cutoff 10.653940303802491 (fac=0.99, q=1)
1:14:17.027541 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:14:17.027632 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:14:17.027689 INFO: Updating optimization_manager: score_cutoff        : 9.727795160293578 -> 10.653940303802491
1:14:17.027747 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:14:17.179270 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:14:17.526325 INFO: === checking if optimization conditions were reached ===
1:14:17.529002 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:14:17.529168 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:14:17.529251 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:14:17.529325 INFO: ==============================================
1:14:17.529414 INFO: Starting optimization step 11.
1:14:17.529488 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:14:17.529562 INFO: Using rust extraction backend
1:14:17.529635 PROGRESS: Extracting batch of 250256 precursors
1:14:17.951890 INFO: === Search parameters used ===
1:14:17.952172 INFO: rt_error       : 805.5982666015625
1:14:17.952235 INFO: mobility_error : 0.1
1:14:17.952285 INFO: num_candidates : 3
1:14:17.952338 INFO: ms1_error      : 3
1:14:17.952386 INFO: ms2_error      : 10.0
1:14:17.952434 INFO: fwhm_rt        : 3.0
1:14:17.952479 INFO: quant_window   : 3
1:14:17.952533 INFO: ==============================================
1:14:20.502228 INFO: performing precursor FDR with 40 features
1:14:20.502350 INFO: Decoy channel: -1
1:14:20.502443 INFO: competitive: True
1:14:20.699292 INFO: Setting torch num_threads to 2 for FDR classification task
1:14:21.001731 INFO: Estimating optimal hyperparameters - samples: 599,431, batch_size: 2,455, learning_rate: 7.74e-04
1:14:21.002883 INFO: Using random state 725384 for train-test-split
1:14:33.570944 INFO: Test AUC: 0.612
1:14:33.571073 INFO: Train AUC: 0.623
1:14:33.571106 INFO: AUC difference: 1.85%
1:14:34.052160 INFO: Resetting torch num_threads to 100
1:14:34.081400 PROGRESS: === Extracted 749289 precursors and 4051753 fragments ===
1:14:34.081881 INFO: === FDR correction performed with classifier version 10 ===
1:14:34.082543 PROGRESS: ============================= Precursor FDR =============================
1:14:34.082634 PROGRESS: Total precursors accumulated: 1,449
1:14:34.082696 PROGRESS: Target precursors: 1,435 (99.03%)
1:14:34.082750 PROGRESS: Decoy precursors: 14 (0.97%)
1:14:34.082806 PROGRESS: 
1:14:34.082854 PROGRESS: Precursor Summary:
1:14:34.084219 PROGRESS: Channel   0:	 0.050 FDR: 1,435; 0.010 FDR: 1,435; 0.001 FDR:   883
1:14:34.084319 PROGRESS: 
1:14:34.084377 PROGRESS: Protein Summary:
1:14:34.086105 PROGRESS: Channel   0:	 0.050 FDR: 1,192; 0.010 FDR: 1,192; 0.001 FDR:   762
1:14:34.086202 PROGRESS: =========================================================================
1:14:34.099963 INFO: Target number of precursors reached.
1:14:34.557422 INFO: fragments_df: keeping 5000 of 4051753 [sum(precursor_idx_mask)=34565 sum(mass_error_mask)=4051753 stop_rank=5000
1:14:34.979752 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:14:35.180057 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:14:35.840237 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:14:35.840697 INFO: Using score_cutoff 12.277618214035034 (fac=0.99, q=1)
1:14:35.841007 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:14:35.841083 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:14:35.841141 INFO: Updating optimization_manager: score_cutoff        : 10.653940303802491 -> 12.277618214035034
1:14:35.841194 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:14:35.991393 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:14:36.315892 INFO: === checking if optimization conditions were reached ===
1:14:36.318053 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:14:36.318151 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:14:36.318216 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:14:36.318273 INFO: ==============================================
1:14:36.318337 PROGRESS: Optimization finished for ms2_error.
1:14:36.711792 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:14:36.862677 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:14:37.199737 INFO: Starting optimization step 0.
1:14:37.200053 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:14:37.200146 INFO: Using rust extraction backend
1:14:37.200223 PROGRESS: Extracting batch of 250256 precursors
1:14:37.623177 INFO: === Search parameters used ===
1:14:37.623446 INFO: rt_error       : 805.5982666015625
1:14:37.623505 INFO: mobility_error : 0.1
1:14:37.623565 INFO: num_candidates : 3
1:14:37.623609 INFO: ms1_error      : 3
1:14:37.623648 INFO: ms2_error      : 10.0
1:14:37.623686 INFO: fwhm_rt        : 3.0
1:14:37.623724 INFO: quant_window   : 3
1:14:37.623762 INFO: ==============================================
1:14:40.121837 INFO: performing precursor FDR with 40 features
1:14:40.121960 INFO: Decoy channel: -1
1:14:40.121987 INFO: competitive: True
1:14:40.310492 INFO: Setting torch num_threads to 2 for FDR classification task
1:14:40.605337 INFO: Estimating optimal hyperparameters - samples: 599,422, batch_size: 2,455, learning_rate: 7.74e-04
1:14:40.606497 INFO: Using random state 1739 for train-test-split
1:14:53.145434 INFO: Test AUC: 0.616
1:14:53.145558 INFO: Train AUC: 0.626
1:14:53.145592 INFO: AUC difference: 1.53%
1:14:53.614814 INFO: Resetting torch num_threads to 100
1:14:53.644643 PROGRESS: === Extracted 749278 precursors and 4051363 fragments ===
1:14:53.645118 INFO: === FDR correction performed with classifier version 11 ===
1:14:53.645797 PROGRESS: ============================= Precursor FDR =============================
1:14:53.645887 PROGRESS: Total precursors accumulated: 1,530
1:14:53.645947 PROGRESS: Target precursors: 1,515 (99.02%)
1:14:53.645999 PROGRESS: Decoy precursors: 15 (0.98%)
1:14:53.646047 PROGRESS: 
1:14:53.646093 PROGRESS: Precursor Summary:
1:14:53.647438 PROGRESS: Channel   0:	 0.050 FDR: 1,515; 0.010 FDR: 1,515; 0.001 FDR: 1,066
1:14:53.647535 PROGRESS: 
1:14:53.647590 PROGRESS: Protein Summary:
1:14:53.649347 PROGRESS: Channel   0:	 0.050 FDR: 1,270; 0.010 FDR: 1,270; 0.001 FDR:   916
1:14:53.649439 PROGRESS: =========================================================================
1:14:53.664680 INFO: Target number of precursors reached.
1:14:54.130674 INFO: fragments_df: keeping 5000 of 4051363 [sum(precursor_idx_mask)=36354 sum(mass_error_mask)=4051363 stop_rank=5000
1:14:54.537652 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:14:54.740621 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:14:55.387794 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:14:55.388259 INFO: Using score_cutoff 11.891784555244445 (fac=0.99, q=1)
1:14:55.388560 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:14:55.388639 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:14:55.388696 INFO: Updating optimization_manager: score_cutoff        : 12.277618214035034 -> 11.891784555244445
1:14:55.388752 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:14:55.539567 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:14:55.873997 INFO: === checking if optimization conditions were reached ===
1:14:55.874318 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:14:55.877438 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 410.41678789433155
1:14:55.877558 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 410.4168.
1:14:55.877652 INFO: ==============================================
1:14:55.877735 INFO: Starting optimization step 1.
1:14:55.877804 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:14:55.877878 INFO: Using rust extraction backend
1:14:55.877947 PROGRESS: Extracting batch of 250256 precursors
1:14:56.299714 INFO: === Search parameters used ===
1:14:56.300003 INFO: rt_error       : 410.41678789433155
1:14:56.300061 INFO: mobility_error : 0.1
1:14:56.300108 INFO: num_candidates : 3
1:14:56.300151 INFO: ms1_error      : 3
1:14:56.300189 INFO: ms2_error      : 10.0
1:14:56.300227 INFO: fwhm_rt        : 3.0
1:14:56.300265 INFO: quant_window   : 3
1:14:56.300301 INFO: ==============================================
1:14:58.643762 INFO: performing precursor FDR with 40 features
1:14:58.643878 INFO: Decoy channel: -1
1:14:58.643902 INFO: competitive: True
1:14:58.835259 INFO: Setting torch num_threads to 2 for FDR classification task
1:14:59.135153 INFO: Estimating optimal hyperparameters - samples: 597,701, batch_size: 2,448, learning_rate: 7.73e-04
1:14:59.136283 INFO: Using random state 1739 for train-test-split
1:15:11.298040 INFO: Test AUC: 0.609
1:15:11.298171 INFO: Train AUC: 0.622
1:15:11.298204 INFO: AUC difference: 2.12%
1:15:11.775169 INFO: Resetting torch num_threads to 100
1:15:11.807597 PROGRESS: === Extracted 747127 precursors and 3898691 fragments ===
1:15:11.808067 INFO: === FDR correction performed with classifier version 11 ===
1:15:11.808736 PROGRESS: ============================= Precursor FDR =============================
1:15:11.808826 PROGRESS: Total precursors accumulated: 1,469
1:15:11.808888 PROGRESS: Target precursors: 1,455 (99.05%)
1:15:11.808941 PROGRESS: Decoy precursors: 14 (0.95%)
1:15:11.808989 PROGRESS: 
1:15:11.809035 PROGRESS: Precursor Summary:
1:15:11.810359 PROGRESS: Channel   0:	 0.050 FDR: 1,455; 0.010 FDR: 1,455; 0.001 FDR: 1,042
1:15:11.810450 PROGRESS: 
1:15:11.810505 PROGRESS: Protein Summary:
1:15:11.812243 PROGRESS: Channel   0:	 0.050 FDR: 1,226; 0.010 FDR: 1,226; 0.001 FDR:   897
1:15:11.812340 PROGRESS: =========================================================================
1:15:11.826691 INFO: Target number of precursors reached.
1:15:12.265335 INFO: fragments_df: keeping 5000 of 3898691 [sum(precursor_idx_mask)=35018 sum(mass_error_mask)=3898691 stop_rank=5000
1:15:12.672528 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:15:12.869110 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:15:13.514681 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:15:13.515132 INFO: Using score_cutoff 12.225995679473876 (fac=0.99, q=1)
1:15:13.515458 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:15:13.515534 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:15:13.515587 INFO: Updating optimization_manager: score_cutoff        : 11.891784555244445 -> 12.225995679473876
1:15:13.515643 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:15:13.665173 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:15:13.986628 INFO: === checking if optimization conditions were reached ===
1:15:13.986923 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:15:13.989661 INFO: Updating optimization_manager: rt_error            : 410.41678789433155 -> 344.77253368598025
1:15:13.989770 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 344.7725.
1:15:13.989842 INFO: ==============================================
1:15:13.989911 INFO: Starting optimization step 2.
1:15:13.989971 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:15:13.990032 INFO: Using rust extraction backend
1:15:13.990092 PROGRESS: Extracting batch of 250256 precursors
1:15:14.408556 INFO: === Search parameters used ===
1:15:14.408828 INFO: rt_error       : 344.77253368598025
1:15:14.408885 INFO: mobility_error : 0.1
1:15:14.408933 INFO: num_candidates : 3
1:15:14.408977 INFO: ms1_error      : 3
1:15:14.409018 INFO: ms2_error      : 10.0
1:15:14.409058 INFO: fwhm_rt        : 3.0
1:15:14.409096 INFO: quant_window   : 3
1:15:14.409136 INFO: ==============================================
1:15:16.699869 INFO: performing precursor FDR with 40 features
1:15:16.699991 INFO: Decoy channel: -1
1:15:16.700017 INFO: competitive: True
1:15:16.895725 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:17.207236 INFO: Estimating optimal hyperparameters - samples: 596,929, batch_size: 2,445, learning_rate: 7.73e-04
1:15:17.208361 INFO: Using random state 1739 for train-test-split
1:15:29.932876 INFO: Test AUC: 0.604
1:15:29.933000 INFO: Train AUC: 0.618
1:15:29.933033 INFO: AUC difference: 2.20%
1:15:30.413817 INFO: Resetting torch num_threads to 100
1:15:30.443374 PROGRESS: === Extracted 746162 precursors and 3801127 fragments ===
1:15:30.443853 INFO: === FDR correction performed with classifier version 11 ===
1:15:30.444516 PROGRESS: ============================= Precursor FDR =============================
1:15:30.444604 PROGRESS: Total precursors accumulated: 1,531
1:15:30.444665 PROGRESS: Target precursors: 1,516 (99.02%)
1:15:30.444716 PROGRESS: Decoy precursors: 15 (0.98%)
1:15:30.444763 PROGRESS: 
1:15:30.444809 PROGRESS: Precursor Summary:
1:15:30.446154 PROGRESS: Channel   0:	 0.050 FDR: 1,516; 0.010 FDR: 1,516; 0.001 FDR: 1,031
1:15:30.446245 PROGRESS: 
1:15:30.446302 PROGRESS: Protein Summary:
1:15:30.448210 PROGRESS: Channel   0:	 0.050 FDR: 1,268; 0.010 FDR: 1,268; 0.001 FDR:   880
1:15:30.448316 PROGRESS: =========================================================================
1:15:30.462789 INFO: Target number of precursors reached.
1:15:30.888492 INFO: fragments_df: keeping 5000 of 3801127 [sum(precursor_idx_mask)=36190 sum(mass_error_mask)=3801127 stop_rank=5000
1:15:31.297280 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:15:31.495402 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:15:32.146791 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:15:32.147261 INFO: Using score_cutoff 11.855579504013061 (fac=0.99, q=1)
1:15:32.147576 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:15:32.147654 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:15:32.147717 INFO: Updating optimization_manager: score_cutoff        : 12.225995679473876 -> 11.855579504013061
1:15:32.147771 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:15:32.297614 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:15:32.632152 INFO: === checking if optimization conditions were reached ===
1:15:32.632461 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:15:32.635892 INFO: Updating optimization_manager: rt_error            : 344.77253368598025 -> 350.2592705968709
1:15:32.636011 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 350.2593.
1:15:32.636088 INFO: ==============================================
1:15:32.636174 INFO: Starting optimization step 3.
1:15:32.636257 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:15:32.636333 INFO: Using rust extraction backend
1:15:32.636403 PROGRESS: Extracting batch of 250256 precursors
1:15:33.056716 INFO: === Search parameters used ===
1:15:33.056983 INFO: rt_error       : 350.2592705968709
1:15:33.057040 INFO: mobility_error : 0.1
1:15:33.057087 INFO: num_candidates : 3
1:15:33.057130 INFO: ms1_error      : 3
1:15:33.057185 INFO: ms2_error      : 10.0
1:15:33.057225 INFO: fwhm_rt        : 3.0
1:15:33.057264 INFO: quant_window   : 3
1:15:33.057303 INFO: ==============================================
1:15:35.362132 INFO: performing precursor FDR with 40 features
1:15:35.362250 INFO: Decoy channel: -1
1:15:35.362279 INFO: competitive: True
1:15:35.555498 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:35.861964 INFO: Estimating optimal hyperparameters - samples: 597,024, batch_size: 2,445, learning_rate: 7.73e-04
1:15:35.863093 INFO: Using random state 1739 for train-test-split
1:15:48.580063 INFO: Test AUC: 0.605
1:15:48.580198 INFO: Train AUC: 0.617
1:15:48.580231 INFO: AUC difference: 1.89%
1:15:49.055355 INFO: Resetting torch num_threads to 100
1:15:49.084872 PROGRESS: === Extracted 746281 precursors and 3814566 fragments ===
1:15:49.085339 INFO: === FDR correction performed with classifier version 11 ===
1:15:49.086006 PROGRESS: ============================= Precursor FDR =============================
1:15:49.086097 PROGRESS: Total precursors accumulated: 1,519
1:15:49.086159 PROGRESS: Target precursors: 1,504 (99.01%)
1:15:49.086213 PROGRESS: Decoy precursors: 15 (0.99%)
1:15:49.086261 PROGRESS: 
1:15:49.086308 PROGRESS: Precursor Summary:
1:15:49.087700 PROGRESS: Channel   0:	 0.050 FDR: 1,504; 0.010 FDR: 1,504; 0.001 FDR: 1,120
1:15:49.087799 PROGRESS: 
1:15:49.087868 PROGRESS: Protein Summary:
1:15:49.089634 PROGRESS: Channel   0:	 0.050 FDR: 1,267; 0.010 FDR: 1,267; 0.001 FDR:   950
1:15:49.089726 PROGRESS: =========================================================================
1:15:49.108913 INFO: Target number of precursors reached.
1:15:49.513093 INFO: fragments_df: keeping 5000 of 3814566 [sum(precursor_idx_mask)=35981 sum(mass_error_mask)=3814566 stop_rank=5000
1:15:49.924610 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:15:50.122177 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:15:50.768880 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:15:50.769329 INFO: Using score_cutoff 11.963612096500396 (fac=0.99, q=1)
1:15:50.769632 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:15:50.769708 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:15:50.769761 INFO: Updating optimization_manager: score_cutoff        : 11.855579504013061 -> 11.963612096500396
1:15:50.769812 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:15:50.917703 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:15:51.238085 INFO: === checking if optimization conditions were reached ===
1:15:51.238351 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:15:51.241271 INFO: Updating optimization_manager: rt_error            : 350.2592705968709 -> 336.02994523013706
1:15:51.241408 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 336.0299.
1:15:51.241487 INFO: ==============================================
1:15:51.241561 INFO: Starting optimization step 4.
1:15:51.241620 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:15:51.241680 INFO: Using rust extraction backend
1:15:51.241736 PROGRESS: Extracting batch of 250256 precursors
1:15:51.660897 INFO: === Search parameters used ===
1:15:51.661174 INFO: rt_error       : 336.02994523013706
1:15:51.661231 INFO: mobility_error : 0.1
1:15:51.661280 INFO: num_candidates : 3
1:15:51.661325 INFO: ms1_error      : 3
1:15:51.661368 INFO: ms2_error      : 10.0
1:15:51.661408 INFO: fwhm_rt        : 3.0
1:15:51.661448 INFO: quant_window   : 3
1:15:51.661487 INFO: ==============================================
1:15:53.936535 INFO: performing precursor FDR with 40 features
1:15:53.936661 INFO: Decoy channel: -1
1:15:53.936687 INFO: competitive: True
1:15:54.130956 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:54.431390 INFO: Estimating optimal hyperparameters - samples: 596,808, batch_size: 2,444, learning_rate: 7.72e-04
1:15:54.432549 INFO: Using random state 1739 for train-test-split
1:16:06.709634 INFO: Test AUC: 0.605
1:16:06.709764 INFO: Train AUC: 0.618
1:16:06.709796 INFO: AUC difference: 2.22%
1:16:07.183395 INFO: Resetting torch num_threads to 100
1:16:07.208717 PROGRESS: === Extracted 746010 precursors and 3790266 fragments ===
1:16:07.209188 INFO: === FDR correction performed with classifier version 11 ===
1:16:07.209862 PROGRESS: ============================= Precursor FDR =============================
1:16:07.209951 PROGRESS: Total precursors accumulated: 1,598
1:16:07.210012 PROGRESS: Target precursors: 1,583 (99.06%)
1:16:07.210063 PROGRESS: Decoy precursors: 15 (0.94%)
1:16:07.210109 PROGRESS: 
1:16:07.210155 PROGRESS: Precursor Summary:
1:16:07.211515 PROGRESS: Channel   0:	 0.050 FDR: 1,583; 0.010 FDR: 1,583; 0.001 FDR:   919
1:16:07.211605 PROGRESS: 
1:16:07.211660 PROGRESS: Protein Summary:
1:16:07.213389 PROGRESS: Channel   0:	 0.050 FDR: 1,328; 0.010 FDR: 1,328; 0.001 FDR:   791
1:16:07.213477 PROGRESS: =========================================================================
1:16:07.227532 INFO: Target number of precursors reached.
1:16:07.640513 INFO: fragments_df: keeping 5000 of 3790266 [sum(precursor_idx_mask)=37654 sum(mass_error_mask)=3790266 stop_rank=5000
1:16:08.049549 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:16:08.256860 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:16:08.904761 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:16:08.905216 INFO: Using score_cutoff 12.038399603462219 (fac=0.99, q=1)
1:16:08.905520 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:16:08.905599 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:16:08.905655 INFO: Updating optimization_manager: score_cutoff        : 11.963612096500396 -> 12.038399603462219
1:16:08.905709 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:16:09.056095 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:16:09.391784 INFO: === checking if optimization conditions were reached ===
1:16:09.392100 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:16:09.393192 INFO: Updating optimization_manager: rt_error            : 336.02994523013706 -> 336.02994523013706
1:16:09.393357 INFO: Updating optimization_manager: classifier_version  : 11 -> 16
1:16:09.393476 INFO: Updating optimization_manager: score_cutoff        : 12.038399603462219 -> 12.038399603462219
1:16:09.393582 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:16:09.393686 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:16:09.393791 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 336.0299 found after 5 searches.
1:16:09.393864 INFO: ==============================================
1:16:09.393948 PROGRESS: Optimization finished for rt_error.
1:16:09.793545 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:16:09.944026 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:16:10.279345 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:16:10.279650 PROGRESS: ==============================================
1:16:10.279732 PROGRESS: ms2_error      : 10.0000
1:16:10.279800 PROGRESS: rt_error       : 336.0299
1:16:10.279858 PROGRESS: ==============================================
1:16:10.280690 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:16:17.888297 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:16:34.377540 INFO: Using rust extraction backend
1:16:34.377833 PROGRESS: Extracting batch of 11997144 precursors
1:16:50.322009 INFO: === Search parameters used ===
1:16:50.322299 INFO: rt_error       : 336.02994523013706
1:16:50.322365 INFO: mobility_error : 0.1
1:16:50.322417 INFO: num_candidates : 3
1:16:50.322462 INFO: ms1_error      : 3
1:16:50.322506 INFO: ms2_error      : 10.0
1:16:50.322550 INFO: fwhm_rt        : 3.0
1:16:50.322598 INFO: quant_window   : 3
1:16:50.322639 INFO: ==============================================
1:17:12.775915 INFO: Removed 14521664 precursors with score below cutoff 12.038399603462219
1:17:29.983263 INFO: performing precursor FDR with 40 features
1:17:29.983391 INFO: Decoy channel: -1
1:17:29.983419 INFO: competitive: True
1:17:32.267437 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:40.917164 INFO: Estimating optimal hyperparameters - samples: 17,158,755, batch_size: 4,096, learning_rate: 1.00e-03
1:17:40.969091 INFO: Using random state 973970 for train-test-split
1:23:11.562102 INFO: Test AUC: 0.615
1:23:11.562349 INFO: Train AUC: 0.616
1:23:11.562391 INFO: AUC difference: 0.10%
1:23:17.353136 INFO: Resetting torch num_threads to 100
1:23:19.226277 PROGRESS: ============================= Precursor FDR =============================
1:23:19.226586 PROGRESS: Total precursors accumulated: 91,985
1:23:19.226654 PROGRESS: Target precursors: 91,075 (99.01%)
1:23:19.226708 PROGRESS: Decoy precursors: 910 (0.99%)
1:23:19.226756 PROGRESS: 
1:23:19.226801 PROGRESS: Precursor Summary:
1:23:19.251309 PROGRESS: Channel   0:	 0.050 FDR: 91,075; 0.010 FDR: 91,075; 0.001 FDR: 61,360
1:23:19.251555 PROGRESS: 
1:23:19.251615 PROGRESS: Protein Summary:
1:23:19.286802 PROGRESS: Channel   0:	 0.050 FDR: 13,046; 0.010 FDR: 13,046; 0.001 FDR: 9,306
1:23:19.287044 PROGRESS: =========================================================================
1:23:19.416418 PROGRESS: === Transfer learning quantification ===
1:23:19.416706 INFO: creating library for charged fragment types: ['b', 'y']
1:23:20.758395 INFO: Calibrating library
1:23:20.758663 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:20.812751 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:21.381598 INFO: quantifying 91,985 precursors with 4,061,256 fragments
1:23:21.381865 INFO: Using rust extraction backend
1:23:22.295645 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/psm.parquet
1:23:22.452539 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.parquet
1:23:22.679482 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.transfer.parquet
1:23:23.171756 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:23:23.688633 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 
1:23:23.688783 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant
1:23:23.688864 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/figures
1:23:23.689013 INFO: Initializing TimingManager
1:23:23.689427 INFO: Initializing RawFileManager
1:23:33.746991 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.
1:23:33.755939 INFO: Determining DIA cycle
1:23:33.772188 INFO: Found cycle with start 0.00 min and length 300.
1:23:33.947571 INFO: RT (min)            : 0.0 - 26.9
1:23:33.947664 INFO: RT duration (sec)   : 1611.2
1:23:33.947692 INFO: RT duration (min)   : 26.9
1:23:33.947714 INFO: Cycle len (scans)   : 300
1:23:33.947735 INFO: Cycle len (sec)     : 1.65
1:23:33.947754 INFO: Number of cycles    : 977
1:23:33.947772 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:23:33.947797 INFO: Creating DIA data object took: 10.258283615112305
1:23:34.618120 INFO: Creating DIA data NG object took: 0.6702001094818115
1:23:35.807861 INFO: Initializing CalibrationManager
1:23:35.808169 INFO: Setting up calibration estimators ..
1:23:35.808230 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:23:35.808300 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'}' ..
1:23:35.808364 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:23:35.808414 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:23:35.808466 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}}' ..
1:23:35.808515 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:23:35.808559 INFO: Done setting up calibration estimators.
1:23:35.808759 INFO: Initializing OptimizationManager
1:23:35.808897 INFO: initial parameter: ms1_error = 3
1:23:35.808950 INFO: initial parameter: ms2_error = 10
1:23:35.808998 INFO: initial parameter: rt_error = 805.6002197265625
1:23:35.809041 INFO: initial parameter: mobility_error = 0.1
1:23:35.809082 INFO: initial parameter: num_candidates = 1
1:23:35.809129 INFO: initial parameter: fwhm_rt = 5
1:23:35.809169 INFO: initial parameter: fwhm_mobility = 0.01
1:23:35.809206 INFO: initial parameter: score_cutoff = 0
1:23:35.809244 INFO: initial parameter: classifier_version = -1
1:23:35.809308 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:23:35.809528 INFO: FDRManager: loading saved state not requested, will be initialized.
1:23:35.809559 INFO: Initializing FDRManager
1:23:35.809590 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
1:23:37.198572 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
1:23:38.075903 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
1:23:38.076304 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
1:23:38.076397 PROGRESS: Starting initial search for precursors.
1:23:38.076476 INFO: Starting optimization step 0.
1:23:38.076533 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:23:38.076583 INFO: Using rust extraction backend
1:23:38.076634 PROGRESS: Extracting batch of 1963 precursors
1:23:38.081435 INFO: === Search parameters used ===
1:23:38.081531 INFO: rt_error       : 805.6002197265625
1:23:38.081580 INFO: mobility_error : 0.1
1:23:38.081624 INFO: num_candidates : 1
1:23:38.081665 INFO: ms1_error      : 3
1:23:38.081704 INFO: ms2_error      : 10
1:23:38.081743 INFO: fwhm_rt        : 5
1:23:38.081781 INFO: quant_window   : 3
1:23:38.081818 INFO: ==============================================
1:23:38.112228 INFO: performing precursor FDR with 40 features
1:23:38.112300 INFO: Decoy channel: -1
1:23:38.112323 INFO: competitive: True
1:23:38.113626 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:38.115352 INFO: Estimating optimal hyperparameters - samples: 1,565, batch_size: 128, learning_rate: 1.77e-04
1:23:38.116164 INFO: Using random state 850110 for train-test-split
1:23:38.267866 INFO: Test AUC: 0.518
1:23:38.267946 INFO: Train AUC: 0.563
1:23:38.267973 INFO: AUC difference: 8.05%
1:23:38.267995 WARNING: AUC difference > 5%. This may indicate overfitting.
1:23:38.500208 INFO: Resetting torch num_threads to 100
1:23:38.501734 PROGRESS: === Extracted 1957 precursors and 10961 fragments ===
1:23:38.502088 INFO: === FDR correction performed with classifier version -1 ===
1:23:38.502546 PROGRESS: ============================= Precursor FDR =============================
1:23:38.502626 PROGRESS: Total precursors accumulated: 0
1:23:38.502682 PROGRESS: Target precursors: 0 (0.00%)
1:23:38.502730 PROGRESS: Decoy precursors: 0 (0.00%)
1:23:38.502773 PROGRESS: 
1:23:38.502817 PROGRESS: Precursor Summary:
1:23:38.502937 PROGRESS: 
1:23:38.502997 PROGRESS: Protein Summary:
1:23:38.503068 PROGRESS: =========================================================================
1:23:38.503259 INFO: Target number of precursors not reached yet.
1:23:38.588085 INFO: Starting optimization step 1.
1:23:38.588330 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:23:38.588413 INFO: Using rust extraction backend
1:23:38.588475 PROGRESS: Extracting batch of 3911 precursors
1:23:38.597146 INFO: === Search parameters used ===
1:23:38.597278 INFO: rt_error       : 805.6002197265625
1:23:38.597327 INFO: mobility_error : 0.1
1:23:38.597371 INFO: num_candidates : 1
1:23:38.597424 INFO: ms1_error      : 3
1:23:38.597463 INFO: ms2_error      : 10
1:23:38.597501 INFO: fwhm_rt        : 5
1:23:38.597539 INFO: quant_window   : 3
1:23:38.597577 INFO: ==============================================
1:23:38.643164 INFO: performing precursor FDR with 40 features
1:23:38.643253 INFO: Decoy channel: -1
1:23:38.643276 INFO: competitive: True
1:23:38.647624 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:38.649877 INFO: Estimating optimal hyperparameters - samples: 4,682, batch_size: 128, learning_rate: 1.77e-04
1:23:38.649955 INFO: Using random state 543145 for train-test-split
1:23:39.115270 INFO: Test AUC: 0.541
1:23:39.115382 INFO: Train AUC: 0.581
1:23:39.115411 INFO: AUC difference: 6.84%
1:23:39.115432 WARNING: AUC difference > 5%. This may indicate overfitting.
1:23:39.361550 INFO: Resetting torch num_threads to 100
1:23:39.364648 PROGRESS: === Extracted 5853 precursors and 32796 fragments ===
1:23:39.365027 INFO: === FDR correction performed with classifier version -1 ===
1:23:39.365518 PROGRESS: ============================= Precursor FDR =============================
1:23:39.365603 PROGRESS: Total precursors accumulated: 28
1:23:39.365660 PROGRESS: Target precursors: 28 (100.00%)
1:23:39.365709 PROGRESS: Decoy precursors: 0 (0.00%)
1:23:39.365753 PROGRESS: 
1:23:39.365795 PROGRESS: Precursor Summary:
1:23:39.366853 PROGRESS: Channel   0:	 0.050 FDR:    28; 0.010 FDR:    28; 0.001 FDR:    28
1:23:39.366934 PROGRESS: 
1:23:39.366993 PROGRESS: Protein Summary:
1:23:39.368196 PROGRESS: Channel   0:	 0.050 FDR:    28; 0.010 FDR:    28; 0.001 FDR:    28
1:23:39.368284 PROGRESS: =========================================================================
1:23:39.368546 INFO: Target number of precursors not reached yet.
1:23:39.458577 INFO: Starting optimization step 2.
1:23:39.458812 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:23:39.458897 INFO: Using rust extraction backend
1:23:39.458959 PROGRESS: Extracting batch of 7891 precursors
1:23:39.473821 INFO: === Search parameters used ===
1:23:39.473960 INFO: rt_error       : 805.6002197265625
1:23:39.474009 INFO: mobility_error : 0.1
1:23:39.474052 INFO: num_candidates : 1
1:23:39.474094 INFO: ms1_error      : 3
1:23:39.474133 INFO: ms2_error      : 10
1:23:39.474172 INFO: fwhm_rt        : 5
1:23:39.474213 INFO: quant_window   : 3
1:23:39.474257 INFO: ==============================================
1:23:39.552703 INFO: performing precursor FDR with 40 features
1:23:39.552809 INFO: Decoy channel: -1
1:23:39.552833 INFO: competitive: True
1:23:39.559036 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:39.562595 INFO: Estimating optimal hyperparameters - samples: 10,978, batch_size: 128, learning_rate: 1.77e-04
1:23:39.562712 INFO: Using random state 143608 for train-test-split
1:23:40.657109 INFO: Test AUC: 0.551
1:23:40.657217 INFO: Train AUC: 0.596
1:23:40.657245 INFO: AUC difference: 7.52%
1:23:40.657280 WARNING: AUC difference > 5%. This may indicate overfitting.
1:23:40.899183 INFO: Resetting torch num_threads to 100
1:23:40.903447 PROGRESS: === Extracted 13723 precursors and 76970 fragments ===
1:23:40.903853 INFO: === FDR correction performed with classifier version -1 ===
1:23:40.904359 PROGRESS: ============================= Precursor FDR =============================
1:23:40.904444 PROGRESS: Total precursors accumulated: 68
1:23:40.904513 PROGRESS: Target precursors: 68 (100.00%)
1:23:40.904565 PROGRESS: Decoy precursors: 0 (0.00%)
1:23:40.904609 PROGRESS: 
1:23:40.904652 PROGRESS: Precursor Summary:
1:23:40.905711 PROGRESS: Channel   0:	 0.050 FDR:    68; 0.010 FDR:    68; 0.001 FDR:    68
1:23:40.905792 PROGRESS: 
1:23:40.905845 PROGRESS: Protein Summary:
1:23:40.907043 PROGRESS: Channel   0:	 0.050 FDR:    67; 0.010 FDR:    67; 0.001 FDR:    67
1:23:40.907124 PROGRESS: =========================================================================
1:23:40.907481 INFO: Target number of precursors not reached yet.
1:23:41.007872 INFO: Starting optimization step 3.
1:23:41.008116 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:23:41.008196 INFO: Using rust extraction backend
1:23:41.008256 PROGRESS: Extracting batch of 15777 precursors
1:23:41.036404 INFO: === Search parameters used ===
1:23:41.036592 INFO: rt_error       : 805.6002197265625
1:23:41.036646 INFO: mobility_error : 0.1
1:23:41.036694 INFO: num_candidates : 1
1:23:41.036740 INFO: ms1_error      : 3
1:23:41.036784 INFO: ms2_error      : 10
1:23:41.036827 INFO: fwhm_rt        : 5
1:23:41.036869 INFO: quant_window   : 3
1:23:41.036919 INFO: ==============================================
1:23:41.172342 INFO: performing precursor FDR with 40 features
1:23:41.172455 INFO: Decoy channel: -1
1:23:41.172481 INFO: competitive: True
1:23:41.185055 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:41.191998 INFO: Estimating optimal hyperparameters - samples: 23,571, batch_size: 128, learning_rate: 1.77e-04
1:23:41.192168 INFO: Using random state 214354 for train-test-split
1:23:43.572985 INFO: Test AUC: 0.582
1:23:43.573096 INFO: Train AUC: 0.608
1:23:43.573126 INFO: AUC difference: 4.23%
1:23:43.834995 INFO: Resetting torch num_threads to 100
1:23:43.841757 PROGRESS: === Extracted 29464 precursors and 165636 fragments ===
1:23:43.842275 INFO: === FDR correction performed with classifier version -1 ===
1:23:43.842792 PROGRESS: ============================= Precursor FDR =============================
1:23:43.842879 PROGRESS: Total precursors accumulated: 119
1:23:43.842939 PROGRESS: Target precursors: 118 (99.16%)
1:23:43.842989 PROGRESS: Decoy precursors: 1 (0.84%)
1:23:43.843035 PROGRESS: 
1:23:43.843081 PROGRESS: Precursor Summary:
1:23:43.844082 PROGRESS: Channel   0:	 0.050 FDR:   118; 0.010 FDR:   118; 0.001 FDR:   109
1:23:43.844171 PROGRESS: 
1:23:43.844227 PROGRESS: Protein Summary:
1:23:43.845365 PROGRESS: Channel   0:	 0.050 FDR:   117; 0.010 FDR:   117; 0.001 FDR:   108
1:23:43.845451 PROGRESS: =========================================================================
1:23:43.845966 INFO: Target number of precursors not reached yet.
1:23:43.964416 INFO: Starting optimization step 4.
1:23:43.964679 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:23:43.964761 INFO: Using rust extraction backend
1:23:43.964827 PROGRESS: Extracting batch of 31516 precursors
1:23:44.019190 INFO: === Search parameters used ===
1:23:44.019425 INFO: rt_error       : 805.6002197265625
1:23:44.019489 INFO: mobility_error : 0.1
1:23:44.019537 INFO: num_candidates : 1
1:23:44.019581 INFO: ms1_error      : 3
1:23:44.019623 INFO: ms2_error      : 10
1:23:44.019665 INFO: fwhm_rt        : 5
1:23:44.019706 INFO: quant_window   : 3
1:23:44.019748 INFO: ==============================================
1:23:44.241832 INFO: performing precursor FDR with 40 features
1:23:44.241949 INFO: Decoy channel: -1
1:23:44.241974 INFO: competitive: True
1:23:44.264832 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:44.278657 INFO: Estimating optimal hyperparameters - samples: 48,732, batch_size: 199, learning_rate: 2.20e-04
1:23:44.278873 INFO: Using random state 411825 for train-test-split
1:23:47.955032 INFO: Test AUC: 0.580
1:23:47.955157 INFO: Train AUC: 0.619
1:23:47.955191 INFO: AUC difference: 6.35%
1:23:47.955214 WARNING: AUC difference > 5%. This may indicate overfitting.
1:23:48.214705 INFO: Resetting torch num_threads to 100
1:23:48.225540 PROGRESS: === Extracted 60916 precursors and 341893 fragments ===
1:23:48.226046 INFO: === FDR correction performed with classifier version -1 ===
1:23:48.226579 PROGRESS: ============================= Precursor FDR =============================
1:23:48.226668 PROGRESS: Total precursors accumulated: 240
1:23:48.226727 PROGRESS: Target precursors: 238 (99.17%)
1:23:48.226778 PROGRESS: Decoy precursors: 2 (0.83%)
1:23:48.226825 PROGRESS: 
1:23:48.226871 PROGRESS: Precursor Summary:
1:23:48.227905 PROGRESS: Channel   0:	 0.050 FDR:   238; 0.010 FDR:   238; 0.001 FDR:   215
1:23:48.227994 PROGRESS: 
1:23:48.228050 PROGRESS: Protein Summary:
1:23:48.229219 PROGRESS: Channel   0:	 0.050 FDR:   227; 0.010 FDR:   227; 0.001 FDR:   205
1:23:48.229306 PROGRESS: =========================================================================
1:23:48.230168 INFO: Target number of precursors not reached yet.
1:23:48.390440 INFO: Starting optimization step 5.
1:23:48.390709 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:23:48.390793 INFO: Using rust extraction backend
1:23:48.390856 PROGRESS: Extracting batch of 63010 precursors
1:23:48.498619 INFO: === Search parameters used ===
1:23:48.498916 INFO: rt_error       : 805.6002197265625
1:23:48.498973 INFO: mobility_error : 0.1
1:23:48.499020 INFO: num_candidates : 1
1:23:48.499064 INFO: ms1_error      : 3
1:23:48.499106 INFO: ms2_error      : 10
1:23:48.499156 INFO: fwhm_rt        : 5
1:23:48.499202 INFO: quant_window   : 3
1:23:48.499242 INFO: ==============================================
1:23:48.878336 INFO: performing precursor FDR with 40 features
1:23:48.878458 INFO: Decoy channel: -1
1:23:48.878483 INFO: competitive: True
1:23:48.926313 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:48.957600 INFO: Estimating optimal hyperparameters - samples: 99,019, batch_size: 405, learning_rate: 3.14e-04
1:23:48.957920 INFO: Using random state 816275 for train-test-split
1:23:53.545641 INFO: Test AUC: 0.586
1:23:53.545764 INFO: Train AUC: 0.616
1:23:53.545796 INFO: AUC difference: 4.91%
1:23:53.822405 INFO: Resetting torch num_threads to 100
1:23:53.844101 PROGRESS: === Extracted 123774 precursors and 694207 fragments ===
1:23:53.844761 INFO: === FDR correction performed with classifier version -1 ===
1:23:53.845423 PROGRESS: ============================= Precursor FDR =============================
1:23:53.845515 PROGRESS: Total precursors accumulated: 544
1:23:53.845577 PROGRESS: Target precursors: 539 (99.08%)
1:23:53.845630 PROGRESS: Decoy precursors: 5 (0.92%)
1:23:53.845678 PROGRESS: 
1:23:53.845725 PROGRESS: Precursor Summary:
1:23:53.846843 PROGRESS: Channel   0:	 0.050 FDR:   539; 0.010 FDR:   539; 0.001 FDR:   389
1:23:53.846946 PROGRESS: 
1:23:53.847004 PROGRESS: Protein Summary:
1:23:53.848341 PROGRESS: Channel   0:	 0.050 FDR:   492; 0.010 FDR:   492; 0.001 FDR:   363
1:23:53.848435 PROGRESS: =========================================================================
1:23:53.850349 INFO: Target number of precursors not reached yet.
1:23:54.092687 INFO: Starting optimization step 6.
1:23:54.092959 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:23:54.093043 INFO: Using rust extraction backend
1:23:54.093108 PROGRESS: Extracting batch of 126188 precursors
1:23:54.306390 INFO: === Search parameters used ===
1:23:54.306666 INFO: rt_error       : 805.6002197265625
1:23:54.306723 INFO: mobility_error : 0.1
1:23:54.306772 INFO: num_candidates : 1
1:23:54.306817 INFO: ms1_error      : 3
1:23:54.306860 INFO: ms2_error      : 10
1:23:54.306904 INFO: fwhm_rt        : 5
1:23:54.306947 INFO: quant_window   : 3
1:23:54.306988 INFO: ==============================================
1:23:54.986529 INFO: performing precursor FDR with 40 features
1:23:54.986664 INFO: Decoy channel: -1
1:23:54.986691 INFO: competitive: True
1:23:55.087529 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:55.166952 INFO: Estimating optimal hyperparameters - samples: 199,741, batch_size: 818, learning_rate: 4.47e-04
1:23:55.167440 INFO: Using random state 483739 for train-test-split
1:24:01.535781 INFO: Test AUC: 0.595
1:24:01.535903 INFO: Train AUC: 0.613
1:24:01.535933 INFO: AUC difference: 2.89%
1:24:01.856237 INFO: Resetting torch num_threads to 100
1:24:01.909898 PROGRESS: === Extracted 249677 precursors and 1400347 fragments ===
1:24:01.910602 INFO: === FDR correction performed with classifier version -1 ===
1:24:01.912063 PROGRESS: ============================= Precursor FDR =============================
1:24:01.912167 PROGRESS: Total precursors accumulated: 1,405
1:24:01.912229 PROGRESS: Target precursors: 1,392 (99.07%)
1:24:01.912278 PROGRESS: Decoy precursors: 13 (0.93%)
1:24:01.912323 PROGRESS: 
1:24:01.912367 PROGRESS: Precursor Summary:
1:24:01.913761 PROGRESS: Channel   0:	 0.050 FDR: 1,392; 0.010 FDR: 1,392; 0.001 FDR: 1,107
1:24:01.913851 PROGRESS: 
1:24:01.913904 PROGRESS: Protein Summary:
1:24:01.915680 PROGRESS: Channel   0:	 0.050 FDR: 1,171; 0.010 FDR: 1,171; 0.001 FDR:   952
1:24:01.915775 PROGRESS: =========================================================================
1:24:01.920035 INFO: Target number of precursors reached.
1:24:02.083635 INFO: fragments_df: keeping 5000 of 1400347 [sum(precursor_idx_mask)=14585 sum(mass_error_mask)=1400347 stop_rank=5000
1:24:02.485450 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:24:02.677440 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:24:03.326924 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:24:03.327390 INFO: Using score_cutoff 12.268042723560333 (fac=0.99, q=1)
1:24:03.327709 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:24:03.327789 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:24:03.327847 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.268042723560333
1:24:03.327901 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:24:03.478263 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:24:03.826253 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
1:24:03.826540 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:24:03.826659 INFO: Starting optimization step 7.
1:24:03.826734 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:24:03.826817 INFO: Using rust extraction backend
1:24:03.826890 PROGRESS: Extracting batch of 250256 precursors
1:24:04.247821 INFO: === Search parameters used ===
1:24:04.248098 INFO: rt_error       : 805.6002197265625
1:24:04.248154 INFO: mobility_error : 0.1
1:24:04.248202 INFO: num_candidates : 3
1:24:04.248245 INFO: ms1_error      : 3
1:24:04.248288 INFO: ms2_error      : 10
1:24:04.248328 INFO: fwhm_rt        : 3.0
1:24:04.248368 INFO: quant_window   : 3
1:24:04.248409 INFO: ==============================================
1:24:06.800127 INFO: performing precursor FDR with 40 features
1:24:06.800242 INFO: Decoy channel: -1
1:24:06.800268 INFO: competitive: True
1:24:06.994938 INFO: Setting torch num_threads to 2 for FDR classification task
1:24:07.299471 INFO: Estimating optimal hyperparameters - samples: 599,395, batch_size: 2,455, learning_rate: 7.74e-04
1:24:07.300606 INFO: Using random state 523497 for train-test-split
1:24:20.416033 INFO: Test AUC: 0.595
1:24:20.416162 INFO: Train AUC: 0.608
1:24:20.416196 INFO: AUC difference: 2.11%
1:24:20.904728 INFO: Resetting torch num_threads to 100
1:24:20.967919 PROGRESS: === Extracted 749244 precursors and 4036540 fragments ===
1:24:20.968416 INFO: === FDR correction performed with classifier version 6 ===
1:24:20.969195 PROGRESS: ============================= Precursor FDR =============================
1:24:20.969295 PROGRESS: Total precursors accumulated: 1,470
1:24:20.969355 PROGRESS: Target precursors: 1,456 (99.05%)
1:24:20.969416 PROGRESS: Decoy precursors: 14 (0.95%)
1:24:20.969465 PROGRESS: 
1:24:20.969510 PROGRESS: Precursor Summary:
1:24:20.970859 PROGRESS: Channel   0:	 0.050 FDR: 1,456; 0.010 FDR: 1,456; 0.001 FDR:   660
1:24:20.970948 PROGRESS: 
1:24:20.971002 PROGRESS: Protein Summary:
1:24:20.972760 PROGRESS: Channel   0:	 0.050 FDR: 1,209; 0.010 FDR: 1,209; 0.001 FDR:   581
1:24:20.972860 PROGRESS: =========================================================================
1:24:20.986984 INFO: Target number of precursors reached.
1:24:21.434788 INFO: fragments_df: keeping 5000 of 4036540 [sum(precursor_idx_mask)=34744 sum(mass_error_mask)=4036540 stop_rank=5000
1:24:21.891169 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:24:22.097340 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:24:22.745464 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:24:22.745952 INFO: Using score_cutoff 11.776136936187743 (fac=0.99, q=1)
1:24:22.746292 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:24:22.746366 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:24:22.746418 INFO: Updating optimization_manager: score_cutoff        : 12.268042723560333 -> 11.776136936187743
1:24:22.746475 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:24:22.896910 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:24:23.240715 INFO: === checking if optimization conditions were reached ===
1:24:23.243463 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
1:24:23.243632 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1:24:23.243711 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:24:23.243788 INFO: ==============================================
1:24:23.243870 INFO: Starting optimization step 8.
1:24:23.243942 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:24:23.244027 INFO: Using rust extraction backend
1:24:23.244106 PROGRESS: Extracting batch of 250256 precursors
1:24:23.664316 INFO: === Search parameters used ===
1:24:23.664591 INFO: rt_error       : 805.6002197265625
1:24:23.664648 INFO: mobility_error : 0.1
1:24:23.664695 INFO: num_candidates : 3
1:24:23.664740 INFO: ms1_error      : 3
1:24:23.664783 INFO: ms2_error      : 10.0
1:24:23.664825 INFO: fwhm_rt        : 3.0
1:24:23.664865 INFO: quant_window   : 3
1:24:23.664905 INFO: ==============================================
1:24:26.178239 INFO: performing precursor FDR with 40 features
1:24:26.178359 INFO: Decoy channel: -1
1:24:26.178384 INFO: competitive: True
1:24:26.382411 INFO: Setting torch num_threads to 2 for FDR classification task
1:24:26.693406 INFO: Estimating optimal hyperparameters - samples: 599,390, batch_size: 2,455, learning_rate: 7.74e-04
1:24:26.694550 INFO: Using random state 86197 for train-test-split
1:24:39.774520 INFO: Test AUC: 0.602
1:24:39.774647 INFO: Train AUC: 0.612
1:24:39.774680 INFO: AUC difference: 1.64%
1:24:40.260008 INFO: Resetting torch num_threads to 100
1:24:40.289256 PROGRESS: === Extracted 749238 precursors and 4036575 fragments ===
1:24:40.289732 INFO: === FDR correction performed with classifier version 7 ===
1:24:40.290415 PROGRESS: ============================= Precursor FDR =============================
1:24:40.290503 PROGRESS: Total precursors accumulated: 1,588
1:24:40.290574 PROGRESS: Target precursors: 1,573 (99.06%)
1:24:40.290628 PROGRESS: Decoy precursors: 15 (0.94%)
1:24:40.290675 PROGRESS: 
1:24:40.290719 PROGRESS: Precursor Summary:
1:24:40.292054 PROGRESS: Channel   0:	 0.050 FDR: 1,573; 0.010 FDR: 1,573; 0.001 FDR:   782
1:24:40.292146 PROGRESS: 
1:24:40.292201 PROGRESS: Protein Summary:
1:24:40.293940 PROGRESS: Channel   0:	 0.050 FDR: 1,304; 0.010 FDR: 1,304; 0.001 FDR:   679
1:24:40.294034 PROGRESS: =========================================================================
1:24:40.308142 INFO: Target number of precursors reached.
1:24:40.757649 INFO: fragments_df: keeping 5000 of 4036575 [sum(precursor_idx_mask)=37570 sum(mass_error_mask)=4036575 stop_rank=5000
1:24:41.279960 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:24:41.498542 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:24:42.154049 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:24:42.154510 INFO: Using score_cutoff 11.815652265930176 (fac=0.99, q=1)
1:24:42.154814 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:24:42.154904 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:24:42.154958 INFO: Updating optimization_manager: score_cutoff        : 11.776136936187743 -> 11.815652265930176
1:24:42.155010 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:24:42.304476 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:24:42.638895 INFO: === checking if optimization conditions were reached ===
1:24:42.641535 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:24:42.641653 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:24:42.641732 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:24:42.641808 INFO: ==============================================
1:24:42.641886 INFO: Starting optimization step 9.
1:24:42.641953 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:24:42.642025 INFO: Using rust extraction backend
1:24:42.642097 PROGRESS: Extracting batch of 250256 precursors
1:24:43.064601 INFO: === Search parameters used ===
1:24:43.064868 INFO: rt_error       : 805.6002197265625
1:24:43.064923 INFO: mobility_error : 0.1
1:24:43.064970 INFO: num_candidates : 3
1:24:43.065011 INFO: ms1_error      : 3
1:24:43.065052 INFO: ms2_error      : 10.0
1:24:43.065092 INFO: fwhm_rt        : 3.0
1:24:43.065131 INFO: quant_window   : 3
1:24:43.065171 INFO: ==============================================
1:24:45.526357 INFO: performing precursor FDR with 40 features
1:24:45.526476 INFO: Decoy channel: -1
1:24:45.526502 INFO: competitive: True
1:24:45.711914 INFO: Setting torch num_threads to 2 for FDR classification task
1:24:46.004682 INFO: Estimating optimal hyperparameters - samples: 599,380, batch_size: 2,455, learning_rate: 7.74e-04
1:24:46.005706 INFO: Using random state 510138 for train-test-split
1:24:59.170608 INFO: Test AUC: 0.604
1:24:59.170738 INFO: Train AUC: 0.618
1:24:59.170769 INFO: AUC difference: 2.24%
1:24:59.649395 INFO: Resetting torch num_threads to 100
1:24:59.679382 PROGRESS: === Extracted 749225 precursors and 4035835 fragments ===
1:24:59.679855 INFO: === FDR correction performed with classifier version 8 ===
1:24:59.680530 PROGRESS: ============================= Precursor FDR =============================
1:24:59.680631 PROGRESS: Total precursors accumulated: 1,542
1:24:59.680692 PROGRESS: Target precursors: 1,527 (99.03%)
1:24:59.680743 PROGRESS: Decoy precursors: 15 (0.97%)
1:24:59.680790 PROGRESS: 
1:24:59.680834 PROGRESS: Precursor Summary:
1:24:59.682225 PROGRESS: Channel   0:	 0.050 FDR: 1,527; 0.010 FDR: 1,527; 0.001 FDR:   794
1:24:59.682313 PROGRESS: 
1:24:59.682375 PROGRESS: Protein Summary:
1:24:59.684108 PROGRESS: Channel   0:	 0.050 FDR: 1,263; 0.010 FDR: 1,263; 0.001 FDR:   687
1:24:59.684198 PROGRESS: =========================================================================
1:24:59.698420 INFO: Target number of precursors reached.
1:25:00.125230 INFO: fragments_df: keeping 5000 of 4035835 [sum(precursor_idx_mask)=36355 sum(mass_error_mask)=4035835 stop_rank=5000
1:25:00.537026 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:25:00.744682 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:25:01.392227 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:25:01.392669 INFO: Using score_cutoff 11.38460321674347 (fac=0.99, q=1)
1:25:01.392965 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:25:01.393039 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:25:01.393093 INFO: Updating optimization_manager: score_cutoff        : 11.815652265930176 -> 11.38460321674347
1:25:01.393145 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:01.543125 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:01.875141 INFO: === checking if optimization conditions were reached ===
1:25:01.877743 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:25:01.877872 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:25:01.877950 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:25:01.878025 INFO: ==============================================
1:25:01.878105 INFO: Starting optimization step 10.
1:25:01.878173 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:25:01.878245 INFO: Using rust extraction backend
1:25:01.878314 PROGRESS: Extracting batch of 250256 precursors
1:25:02.299053 INFO: === Search parameters used ===
1:25:02.299350 INFO: rt_error       : 805.6002197265625
1:25:02.299407 INFO: mobility_error : 0.1
1:25:02.299455 INFO: num_candidates : 3
1:25:02.299499 INFO: ms1_error      : 3
1:25:02.299542 INFO: ms2_error      : 10.0
1:25:02.299584 INFO: fwhm_rt        : 3.0
1:25:02.299624 INFO: quant_window   : 3
1:25:02.299664 INFO: ==============================================
1:25:04.710573 INFO: performing precursor FDR with 40 features
1:25:04.710701 INFO: Decoy channel: -1
1:25:04.710730 INFO: competitive: True
1:25:04.905499 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:05.214706 INFO: Estimating optimal hyperparameters - samples: 599,402, batch_size: 2,455, learning_rate: 7.74e-04
1:25:05.215850 INFO: Using random state 633192 for train-test-split
1:25:18.156466 INFO: Test AUC: 0.606
1:25:18.156597 INFO: Train AUC: 0.621
1:25:18.156631 INFO: AUC difference: 2.41%
1:25:18.635224 INFO: Resetting torch num_threads to 100
1:25:18.661120 PROGRESS: === Extracted 749253 precursors and 4036902 fragments ===
1:25:18.661582 INFO: === FDR correction performed with classifier version 9 ===
1:25:18.662250 PROGRESS: ============================= Precursor FDR =============================
1:25:18.662338 PROGRESS: Total precursors accumulated: 1,602
1:25:18.662398 PROGRESS: Target precursors: 1,587 (99.06%)
1:25:18.662449 PROGRESS: Decoy precursors: 15 (0.94%)
1:25:18.662496 PROGRESS: 
1:25:18.662542 PROGRESS: Precursor Summary:
1:25:18.663872 PROGRESS: Channel   0:	 0.050 FDR: 1,587; 0.010 FDR: 1,587; 0.001 FDR:   793
1:25:18.663963 PROGRESS: 
1:25:18.664017 PROGRESS: Protein Summary:
1:25:18.665716 PROGRESS: Channel   0:	 0.050 FDR: 1,310; 0.010 FDR: 1,310; 0.001 FDR:   691
1:25:18.665804 PROGRESS: =========================================================================
1:25:18.678763 INFO: Target number of precursors reached.
1:25:19.126544 INFO: fragments_df: keeping 5000 of 4036902 [sum(precursor_idx_mask)=37718 sum(mass_error_mask)=4036902 stop_rank=5000
1:25:19.538454 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:25:19.755069 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:25:20.399736 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:25:20.400185 INFO: Using score_cutoff 11.526123169898986 (fac=0.99, q=1)
1:25:20.400489 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:25:20.400567 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:25:20.400622 INFO: Updating optimization_manager: score_cutoff        : 11.38460321674347 -> 11.526123169898986
1:25:20.400682 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:20.549515 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:20.896637 INFO: === checking if optimization conditions were reached ===
1:25:20.899271 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:25:20.899390 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:25:20.899471 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:25:20.899541 INFO: ==============================================
1:25:20.899620 INFO: Starting optimization step 11.
1:25:20.899689 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:25:20.899762 INFO: Using rust extraction backend
1:25:20.899831 PROGRESS: Extracting batch of 250256 precursors
1:25:21.318352 INFO: === Search parameters used ===
1:25:21.318615 INFO: rt_error       : 805.6002197265625
1:25:21.318669 INFO: mobility_error : 0.1
1:25:21.318740 INFO: num_candidates : 3
1:25:21.318784 INFO: ms1_error      : 3
1:25:21.318825 INFO: ms2_error      : 10.0
1:25:21.318866 INFO: fwhm_rt        : 3.0
1:25:21.318905 INFO: quant_window   : 3
1:25:21.318945 INFO: ==============================================
1:25:23.785471 INFO: performing precursor FDR with 40 features
1:25:23.785594 INFO: Decoy channel: -1
1:25:23.785620 INFO: competitive: True
1:25:23.974441 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:24.260051 INFO: Estimating optimal hyperparameters - samples: 599,400, batch_size: 2,455, learning_rate: 7.74e-04
1:25:24.261194 INFO: Using random state 758210 for train-test-split
1:25:36.890828 INFO: Test AUC: 0.610
1:25:36.890961 INFO: Train AUC: 0.622
1:25:36.890995 INFO: AUC difference: 1.90%
1:25:37.370445 INFO: Resetting torch num_threads to 100
1:25:37.406642 PROGRESS: === Extracted 749250 precursors and 4037176 fragments ===
1:25:37.407158 INFO: === FDR correction performed with classifier version 10 ===
1:25:37.407878 PROGRESS: ============================= Precursor FDR =============================
1:25:37.407967 PROGRESS: Total precursors accumulated: 1,573
1:25:37.408027 PROGRESS: Target precursors: 1,558 (99.05%)
1:25:37.408078 PROGRESS: Decoy precursors: 15 (0.95%)
1:25:37.408124 PROGRESS: 
1:25:37.408169 PROGRESS: Precursor Summary:
1:25:37.409532 PROGRESS: Channel   0:	 0.050 FDR: 1,558; 0.010 FDR: 1,558; 0.001 FDR:   910
1:25:37.409623 PROGRESS: 
1:25:37.409681 PROGRESS: Protein Summary:
1:25:37.411440 PROGRESS: Channel   0:	 0.050 FDR: 1,293; 0.010 FDR: 1,293; 0.001 FDR:   779
1:25:37.411532 PROGRESS: =========================================================================
1:25:37.425948 INFO: Target number of precursors reached.
1:25:37.880505 INFO: fragments_df: keeping 5000 of 4037176 [sum(precursor_idx_mask)=36819 sum(mass_error_mask)=4037176 stop_rank=5000
1:25:38.288131 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:25:38.497001 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:25:39.143838 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:25:39.144285 INFO: Using score_cutoff 10.63966918287277 (fac=0.99, q=1)
1:25:39.144593 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:25:39.144672 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:25:39.144735 INFO: Updating optimization_manager: score_cutoff        : 11.526123169898986 -> 10.63966918287277
1:25:39.144791 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:39.293410 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:39.639017 INFO: === checking if optimization conditions were reached ===
1:25:39.641640 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:25:39.641745 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:25:39.641812 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:25:39.641881 INFO: ==============================================
1:25:39.641949 PROGRESS: Optimization finished for ms2_error.
1:25:40.033955 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:25:40.182445 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:25:40.528789 INFO: Starting optimization step 0.
1:25:40.529092 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:25:40.529187 INFO: Using rust extraction backend
1:25:40.529265 PROGRESS: Extracting batch of 250256 precursors
1:25:40.949310 INFO: === Search parameters used ===
1:25:40.949595 INFO: rt_error       : 805.6002197265625
1:25:40.949655 INFO: mobility_error : 0.1
1:25:40.949703 INFO: num_candidates : 3
1:25:40.949746 INFO: ms1_error      : 3
1:25:40.949799 INFO: ms2_error      : 10.0
1:25:40.949841 INFO: fwhm_rt        : 3.0
1:25:40.949887 INFO: quant_window   : 3
1:25:40.949925 INFO: ==============================================
1:25:43.507451 INFO: performing precursor FDR with 40 features
1:25:43.507571 INFO: Decoy channel: -1
1:25:43.507596 INFO: competitive: True
1:25:43.690529 INFO: Setting torch num_threads to 2 for FDR classification task
1:25:43.977924 INFO: Estimating optimal hyperparameters - samples: 599,397, batch_size: 2,455, learning_rate: 7.74e-04
1:25:43.978946 INFO: Using random state 790729 for train-test-split
1:25:57.863070 INFO: Test AUC: 0.611
1:25:57.863220 INFO: Train AUC: 0.625
1:25:57.863255 INFO: AUC difference: 2.23%
1:25:58.342482 INFO: Resetting torch num_threads to 100
1:25:58.368750 PROGRESS: === Extracted 749247 precursors and 4037146 fragments ===
1:25:58.369224 INFO: === FDR correction performed with classifier version 11 ===
1:25:58.369880 PROGRESS: ============================= Precursor FDR =============================
1:25:58.369968 PROGRESS: Total precursors accumulated: 1,602
1:25:58.370027 PROGRESS: Target precursors: 1,587 (99.06%)
1:25:58.370078 PROGRESS: Decoy precursors: 15 (0.94%)
1:25:58.370130 PROGRESS: 
1:25:58.370177 PROGRESS: Precursor Summary:
1:25:58.371556 PROGRESS: Channel   0:	 0.050 FDR: 1,587; 0.010 FDR: 1,587; 0.001 FDR: 1,128
1:25:58.371648 PROGRESS: 
1:25:58.371704 PROGRESS: Protein Summary:
1:25:58.373511 PROGRESS: Channel   0:	 0.050 FDR: 1,313; 0.010 FDR: 1,313; 0.001 FDR:   953
1:25:58.373601 PROGRESS: =========================================================================
1:25:58.388873 INFO: Target number of precursors reached.
1:25:58.828589 INFO: fragments_df: keeping 5000 of 4037146 [sum(precursor_idx_mask)=37763 sum(mass_error_mask)=4037146 stop_rank=5000
1:25:59.245722 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:25:59.456793 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:26:00.107395 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:26:00.107865 INFO: Using score_cutoff 11.572620038223267 (fac=0.99, q=1)
1:26:00.108179 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:26:00.108257 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:26:00.108313 INFO: Updating optimization_manager: score_cutoff        : 10.63966918287277 -> 11.572620038223267
1:26:00.108372 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:26:00.258717 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:26:00.591920 INFO: === checking if optimization conditions were reached ===
1:26:00.592227 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:26:00.595532 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 598.7610385931778
1:26:00.595690 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 598.7610.
1:26:00.595770 INFO: ==============================================
1:26:00.595856 INFO: Starting optimization step 1.
1:26:00.595927 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:26:00.596003 INFO: Using rust extraction backend
1:26:00.596073 PROGRESS: Extracting batch of 250256 precursors
1:26:01.022192 INFO: === Search parameters used ===
1:26:01.022430 INFO: rt_error       : 598.7610385931778
1:26:01.022492 INFO: mobility_error : 0.1
1:26:01.022554 INFO: num_candidates : 3
1:26:01.022601 INFO: ms1_error      : 3
1:26:01.022644 INFO: ms2_error      : 10.0
1:26:01.022687 INFO: fwhm_rt        : 3.0
1:26:01.022728 INFO: quant_window   : 3
1:26:01.022768 INFO: ==============================================
1:26:03.543782 INFO: performing precursor FDR with 40 features
1:26:03.543904 INFO: Decoy channel: -1
1:26:03.543931 INFO: competitive: True
1:26:03.739457 INFO: Setting torch num_threads to 2 for FDR classification task
1:26:04.050344 INFO: Estimating optimal hyperparameters - samples: 599,123, batch_size: 2,454, learning_rate: 7.74e-04
1:26:04.051493 INFO: Using random state 790729 for train-test-split
1:26:16.793754 INFO: Test AUC: 0.610
1:26:16.793882 INFO: Train AUC: 0.624
1:26:16.793915 INFO: AUC difference: 2.16%
1:26:17.265808 INFO: Resetting torch num_threads to 100
1:26:17.291915 PROGRESS: === Extracted 748904 precursors and 4015428 fragments ===
1:26:17.292373 INFO: === FDR correction performed with classifier version 11 ===
1:26:17.293054 PROGRESS: ============================= Precursor FDR =============================
1:26:17.293142 PROGRESS: Total precursors accumulated: 1,635
1:26:17.293200 PROGRESS: Target precursors: 1,619 (99.02%)
1:26:17.293249 PROGRESS: Decoy precursors: 16 (0.98%)
1:26:17.293296 PROGRESS: 
1:26:17.293340 PROGRESS: Precursor Summary:
1:26:17.294688 PROGRESS: Channel   0:	 0.050 FDR: 1,619; 0.010 FDR: 1,619; 0.001 FDR: 1,054
1:26:17.294777 PROGRESS: 
1:26:17.294832 PROGRESS: Protein Summary:
1:26:17.296605 PROGRESS: Channel   0:	 0.050 FDR: 1,337; 0.010 FDR: 1,337; 0.001 FDR:   902
1:26:17.296699 PROGRESS: =========================================================================
1:26:17.311578 INFO: Target number of precursors reached.
1:26:17.729399 INFO: fragments_df: keeping 5000 of 4015428 [sum(precursor_idx_mask)=38518 sum(mass_error_mask)=4015428 stop_rank=5000
1:26:18.138340 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:26:18.349603 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:26:18.997440 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:26:18.997899 INFO: Using score_cutoff 11.88251895904541 (fac=0.99, q=1)
1:26:18.998218 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:26:18.998298 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:26:18.998352 INFO: Updating optimization_manager: score_cutoff        : 11.572620038223267 -> 11.88251895904541
1:26:18.998407 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:26:19.147113 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:26:19.475829 INFO: === checking if optimization conditions were reached ===
1:26:19.476135 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:26:19.479494 INFO: Updating optimization_manager: rt_error            : 598.7610385931778 -> 492.0035533067926
1:26:19.479617 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 492.0036.
1:26:19.479709 INFO: ==============================================
1:26:19.479797 INFO: Starting optimization step 2.
1:26:19.479867 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:26:19.479939 INFO: Using rust extraction backend
1:26:19.480007 PROGRESS: Extracting batch of 250256 precursors
1:26:19.899775 INFO: === Search parameters used ===
1:26:19.900049 INFO: rt_error       : 492.0035533067926
1:26:19.900107 INFO: mobility_error : 0.1
1:26:19.900154 INFO: num_candidates : 3
1:26:19.900198 INFO: ms1_error      : 3
1:26:19.900241 INFO: ms2_error      : 10.0
1:26:19.900282 INFO: fwhm_rt        : 3.0
1:26:19.900323 INFO: quant_window   : 3
1:26:19.900363 INFO: ==============================================
1:26:22.261400 INFO: performing precursor FDR with 40 features
1:26:22.261533 INFO: Decoy channel: -1
1:26:22.261559 INFO: competitive: True
1:26:22.444679 INFO: Setting torch num_threads to 2 for FDR classification task
1:26:22.730840 INFO: Estimating optimal hyperparameters - samples: 598,604, batch_size: 2,451, learning_rate: 7.74e-04
1:26:22.731991 INFO: Using random state 790729 for train-test-split
1:26:35.396100 INFO: Test AUC: 0.611
1:26:35.396289 INFO: Train AUC: 0.621
1:26:35.396324 INFO: AUC difference: 1.60%
1:26:35.877304 INFO: Resetting torch num_threads to 100
1:26:35.906501 PROGRESS: === Extracted 748255 precursors and 3971619 fragments ===
1:26:35.907012 INFO: === FDR correction performed with classifier version 11 ===
1:26:35.907735 PROGRESS: ============================= Precursor FDR =============================
1:26:35.907830 PROGRESS: Total precursors accumulated: 1,740
1:26:35.907892 PROGRESS: Target precursors: 1,723 (99.02%)
1:26:35.907944 PROGRESS: Decoy precursors: 17 (0.98%)
1:26:35.907991 PROGRESS: 
1:26:35.908044 PROGRESS: Precursor Summary:
1:26:35.909431 PROGRESS: Channel   0:	 0.050 FDR: 1,723; 0.010 FDR: 1,723; 0.001 FDR: 1,046
1:26:35.909523 PROGRESS: 
1:26:35.909578 PROGRESS: Protein Summary:
1:26:35.911398 PROGRESS: Channel   0:	 0.050 FDR: 1,413; 0.010 FDR: 1,413; 0.001 FDR:   889
1:26:35.911494 PROGRESS: =========================================================================
1:26:35.925430 INFO: Target number of precursors reached.
1:26:36.347725 INFO: fragments_df: keeping 5000 of 3971619 [sum(precursor_idx_mask)=40765 sum(mass_error_mask)=3971619 stop_rank=5000
1:26:36.777338 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:26:37.018153 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:26:37.679982 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:26:37.680438 INFO: Using score_cutoff 11.456647522544861 (fac=0.99, q=1)
1:26:37.680757 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:26:37.680833 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:26:37.680888 INFO: Updating optimization_manager: score_cutoff        : 11.88251895904541 -> 11.456647522544861
1:26:37.680940 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:26:37.831890 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:26:38.180258 INFO: === checking if optimization conditions were reached ===
1:26:38.180588 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:26:38.184159 INFO: Updating optimization_manager: rt_error            : 492.0035533067926 -> 557.749656408843
1:26:38.184278 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 557.7497.
1:26:38.184353 INFO: ==============================================
1:26:38.184437 INFO: Starting optimization step 3.
1:26:38.184504 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:26:38.184578 INFO: Using rust extraction backend
1:26:38.184652 PROGRESS: Extracting batch of 250256 precursors
1:26:38.606896 INFO: === Search parameters used ===
1:26:38.607184 INFO: rt_error       : 557.749656408843
1:26:38.607243 INFO: mobility_error : 0.1
1:26:38.607289 INFO: num_candidates : 3
1:26:38.607330 INFO: ms1_error      : 3
1:26:38.607370 INFO: ms2_error      : 10.0
1:26:38.607414 INFO: fwhm_rt        : 3.0
1:26:38.607453 INFO: quant_window   : 3
1:26:38.607493 INFO: ==============================================
1:26:40.955227 INFO: performing precursor FDR with 40 features
1:26:40.955353 INFO: Decoy channel: -1
1:26:40.955380 INFO: competitive: True
1:26:41.147092 INFO: Setting torch num_threads to 2 for FDR classification task
1:26:41.458985 INFO: Estimating optimal hyperparameters - samples: 598,963, batch_size: 2,453, learning_rate: 7.74e-04
1:26:41.459877 INFO: Using random state 790729 for train-test-split
1:26:54.286794 INFO: Test AUC: 0.610
1:26:54.286925 INFO: Train AUC: 0.623
1:26:54.286959 INFO: AUC difference: 1.99%
1:26:54.753256 INFO: Resetting torch num_threads to 100
1:26:54.779063 PROGRESS: === Extracted 748704 precursors and 4002596 fragments ===
1:26:54.779546 INFO: === FDR correction performed with classifier version 11 ===
1:26:54.780261 PROGRESS: ============================= Precursor FDR =============================
1:26:54.780365 PROGRESS: Total precursors accumulated: 1,688
1:26:54.780426 PROGRESS: Target precursors: 1,672 (99.05%)
1:26:54.780478 PROGRESS: Decoy precursors: 16 (0.95%)
1:26:54.780526 PROGRESS: 
1:26:54.780573 PROGRESS: Precursor Summary:
1:26:54.781994 PROGRESS: Channel   0:	 0.050 FDR: 1,672; 0.010 FDR: 1,672; 0.001 FDR: 1,157
1:26:54.782094 PROGRESS: 
1:26:54.782150 PROGRESS: Protein Summary:
1:26:54.784001 PROGRESS: Channel   0:	 0.050 FDR: 1,370; 0.010 FDR: 1,370; 0.001 FDR:   982
1:26:54.784113 PROGRESS: =========================================================================
1:26:54.797019 INFO: Target number of precursors reached.
1:26:55.235609 INFO: fragments_df: keeping 5000 of 4002596 [sum(precursor_idx_mask)=39596 sum(mass_error_mask)=4002596 stop_rank=5000
1:26:55.728595 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:26:55.952198 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:26:56.600206 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:26:56.600670 INFO: Using score_cutoff 11.481729792881012 (fac=0.99, q=1)
1:26:56.601001 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:26:56.601079 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:26:56.601141 INFO: Updating optimization_manager: score_cutoff        : 11.456647522544861 -> 11.481729792881012
1:26:56.601194 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:26:56.750360 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:26:57.079725 INFO: === checking if optimization conditions were reached ===
1:26:57.080050 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:26:57.083688 INFO: Updating optimization_manager: rt_error            : 557.749656408843 -> 556.726549788623
1:26:57.083850 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 556.7265.
1:26:57.083928 INFO: ==============================================
1:26:57.084014 INFO: Starting optimization step 4.
1:26:57.084143 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:26:57.084220 INFO: Using rust extraction backend
1:26:57.084289 PROGRESS: Extracting batch of 250256 precursors
1:26:57.507983 INFO: === Search parameters used ===
1:26:57.508268 INFO: rt_error       : 556.726549788623
1:26:57.508325 INFO: mobility_error : 0.1
1:26:57.508373 INFO: num_candidates : 3
1:26:57.508417 INFO: ms1_error      : 3
1:26:57.508457 INFO: ms2_error      : 10.0
1:26:57.508497 INFO: fwhm_rt        : 3.0
1:26:57.508535 INFO: quant_window   : 3
1:26:57.508572 INFO: ==============================================
1:26:59.915464 INFO: performing precursor FDR with 40 features
1:26:59.915582 INFO: Decoy channel: -1
1:26:59.915607 INFO: competitive: True
1:27:00.098901 INFO: Setting torch num_threads to 2 for FDR classification task
1:27:00.385316 INFO: Estimating optimal hyperparameters - samples: 598,957, batch_size: 2,453, learning_rate: 7.74e-04
1:27:00.386274 INFO: Using random state 790729 for train-test-split
1:27:12.980035 INFO: Test AUC: 0.608
1:27:12.980189 INFO: Train AUC: 0.621
1:27:12.980222 INFO: AUC difference: 2.23%
1:27:13.468499 INFO: Resetting torch num_threads to 100
1:27:13.502516 PROGRESS: === Extracted 748697 precursors and 4002307 fragments ===
1:27:13.503033 INFO: === FDR correction performed with classifier version 11 ===
1:27:13.503757 PROGRESS: ============================= Precursor FDR =============================
1:27:13.503852 PROGRESS: Total precursors accumulated: 1,738
1:27:13.503920 PROGRESS: Target precursors: 1,721 (99.02%)
1:27:13.503974 PROGRESS: Decoy precursors: 17 (0.98%)
1:27:13.504022 PROGRESS: 
1:27:13.504068 PROGRESS: Precursor Summary:
1:27:13.505450 PROGRESS: Channel   0:	 0.050 FDR: 1,721; 0.010 FDR: 1,721; 0.001 FDR: 1,006
1:27:13.505538 PROGRESS: 
1:27:13.505605 PROGRESS: Protein Summary:
1:27:13.507403 PROGRESS: Channel   0:	 0.050 FDR: 1,415; 0.010 FDR: 1,415; 0.001 FDR:   863
1:27:13.507497 PROGRESS: =========================================================================
1:27:13.521590 INFO: Target number of precursors reached.
1:27:13.955198 INFO: fragments_df: keeping 5000 of 4002307 [sum(precursor_idx_mask)=40545 sum(mass_error_mask)=4002307 stop_rank=5000
1:27:14.386620 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:27:14.613099 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:27:15.262382 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:27:15.262841 INFO: Using score_cutoff 11.285221464157106 (fac=0.99, q=1)
1:27:15.263186 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:27:15.263266 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:27:15.263319 INFO: Updating optimization_manager: score_cutoff        : 11.481729792881012 -> 11.285221464157106
1:27:15.263374 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:27:15.414199 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:27:15.753625 INFO: === checking if optimization conditions were reached ===
1:27:15.753896 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:27:15.754838 INFO: Updating optimization_manager: rt_error            : 556.726549788623 -> 492.0035533067926
1:27:15.754962 INFO: Updating optimization_manager: classifier_version  : 11 -> 14
1:27:15.755055 INFO: Updating optimization_manager: score_cutoff        : 11.285221464157106 -> 11.456647522544861
1:27:15.755167 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:27:15.755262 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:27:15.755350 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 492.0036 found after 5 searches.
1:27:15.755409 INFO: ==============================================
1:27:15.755480 PROGRESS: Optimization finished for rt_error.
1:27:16.152489 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:27:16.304846 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:27:16.639971 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:27:16.640239 PROGRESS: ==============================================
1:27:16.640320 PROGRESS: ms2_error      : 10.0000
1:27:16.640388 PROGRESS: rt_error       : 492.0036
1:27:16.640438 PROGRESS: ==============================================
1:27:16.641205 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:27:24.279331 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:27:40.696394 INFO: Using rust extraction backend
1:27:40.696836 PROGRESS: Extracting batch of 11997144 precursors
1:27:56.785961 INFO: === Search parameters used ===
1:27:56.786509 INFO: rt_error       : 492.0035533067926
1:27:56.786582 INFO: mobility_error : 0.1
1:27:56.786638 INFO: num_candidates : 3
1:27:56.786700 INFO: ms1_error      : 3
1:27:56.786748 INFO: ms2_error      : 10.0
1:27:56.786790 INFO: fwhm_rt        : 3.0
1:27:56.786831 INFO: quant_window   : 3
1:27:56.786870 INFO: ==============================================
1:28:22.192774 INFO: Removed 10886066 precursors with score below cutoff 11.456647522544861
1:28:42.212805 INFO: performing precursor FDR with 40 features
1:28:42.213042 INFO: Decoy channel: -1
1:28:42.213075 INFO: competitive: True
1:28:44.870456 INFO: Setting torch num_threads to 2 for FDR classification task
1:28:54.923350 INFO: Estimating optimal hyperparameters - samples: 20,081,822, batch_size: 4,096, learning_rate: 1.00e-03
1:28:54.985206 INFO: Using random state 839539 for train-test-split
1:35:11.409837 INFO: Test AUC: 0.619
1:35:11.410124 INFO: Train AUC: 0.620
1:35:11.410176 INFO: AUC difference: 0.09%
1:35:17.620223 INFO: Resetting torch num_threads to 100
1:35:19.667832 PROGRESS: ============================= Precursor FDR =============================
1:35:19.668161 PROGRESS: Total precursors accumulated: 92,021
1:35:19.668234 PROGRESS: Target precursors: 91,111 (99.01%)
1:35:19.668291 PROGRESS: Decoy precursors: 910 (0.99%)
1:35:19.668340 PROGRESS: 
1:35:19.668386 PROGRESS: Precursor Summary:
1:35:19.694703 PROGRESS: Channel   0:	 0.050 FDR: 91,111; 0.010 FDR: 91,111; 0.001 FDR: 55,351
1:35:19.694963 PROGRESS: 
1:35:19.695026 PROGRESS: Protein Summary:
1:35:19.729704 PROGRESS: Channel   0:	 0.050 FDR: 14,511; 0.010 FDR: 14,511; 0.001 FDR: 9,017
1:35:19.729962 PROGRESS: =========================================================================
1:35:19.867468 PROGRESS: === Transfer learning quantification ===
1:35:19.867767 INFO: creating library for charged fragment types: ['b', 'y']
1:35:21.425198 INFO: Calibrating library
1:35:21.425471 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:35:21.479076 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:35:22.036879 INFO: quantifying 92,021 precursors with 4,104,790 fragments
1:35:22.037147 INFO: Using rust extraction backend
1:35:23.002538 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/psm.parquet
1:35:23.182502 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.parquet
1:35:23.410982 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.transfer.parquet
1:35:23.929126 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:35:24.518440 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 
1:35:24.518723 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant
1:35:24.518815 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/figures
1:35:24.519029 INFO: Initializing TimingManager
1:35:24.519706 INFO: Initializing RawFileManager
1:35:37.577945 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.
1:35:37.586469 INFO: Determining DIA cycle
1:35:37.603010 INFO: Found cycle with start 0.00 min and length 300.
1:35:38.522853 INFO: RT (min)            : 0.0 - 26.9
1:35:38.522974 INFO: RT duration (sec)   : 1611.2
1:35:38.523005 INFO: RT duration (min)   : 26.9
1:35:38.523028 INFO: Cycle len (scans)   : 300
1:35:38.523049 INFO: Cycle len (sec)     : 1.65
1:35:38.523067 INFO: Number of cycles    : 978
1:35:38.523087 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:35:38.523139 INFO: Creating DIA data object took: 14.00332260131836
1:35:39.680379 INFO: Creating DIA data NG object took: 1.156973123550415
1:35:41.093208 INFO: Initializing CalibrationManager
1:35:41.093522 INFO: Setting up calibration estimators ..
1:35:41.093588 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:35:41.093690 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'}' ..
1:35:41.093789 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:35:41.093843 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:35:41.093906 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}}' ..
1:35:41.093965 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:35:41.094012 INFO: Done setting up calibration estimators.
1:35:41.094249 INFO: Initializing OptimizationManager
1:35:41.094399 INFO: initial parameter: ms1_error = 3
1:35:41.094454 INFO: initial parameter: ms2_error = 10
1:35:41.094502 INFO: initial parameter: rt_error = 805.611083984375
1:35:41.094551 INFO: initial parameter: mobility_error = 0.1
1:35:41.094594 INFO: initial parameter: num_candidates = 1
1:35:41.094636 INFO: initial parameter: fwhm_rt = 5
1:35:41.094679 INFO: initial parameter: fwhm_mobility = 0.01
1:35:41.094720 INFO: initial parameter: score_cutoff = 0
1:35:41.094761 INFO: initial parameter: classifier_version = -1
1:35:41.094844 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:35:41.095261 INFO: FDRManager: loading saved state not requested, will be initialized.
1:35:41.095303 INFO: Initializing FDRManager
1:35:41.095346 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
1:35:42.478331 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
1:35:43.350430 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
1:35:43.350870 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
1:35:43.350981 PROGRESS: Starting initial search for precursors.
1:35:43.351075 INFO: Starting optimization step 0.
1:35:43.351137 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:35:43.351215 INFO: Using rust extraction backend
1:35:43.351285 PROGRESS: Extracting batch of 1963 precursors
1:35:43.356096 INFO: === Search parameters used ===
1:35:43.356205 INFO: rt_error       : 805.611083984375
1:35:43.356260 INFO: mobility_error : 0.1
1:35:43.356306 INFO: num_candidates : 1
1:35:43.356349 INFO: ms1_error      : 3
1:35:43.356390 INFO: ms2_error      : 10
1:35:43.356432 INFO: fwhm_rt        : 5
1:35:43.356472 INFO: quant_window   : 3
1:35:43.356511 INFO: ==============================================
1:35:43.383769 INFO: performing precursor FDR with 40 features
1:35:43.383846 INFO: Decoy channel: -1
1:35:43.383869 INFO: competitive: True
1:35:43.385202 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:43.387332 INFO: Estimating optimal hyperparameters - samples: 1,566, batch_size: 128, learning_rate: 1.77e-04
1:35:43.388189 INFO: Using random state 803333 for train-test-split
1:35:43.539795 INFO: Test AUC: 0.503
1:35:43.539873 INFO: Train AUC: 0.569
1:35:43.539900 INFO: AUC difference: 11.51%
1:35:43.539921 WARNING: AUC difference > 5%. This may indicate overfitting.
1:35:43.781884 INFO: Resetting torch num_threads to 100
1:35:43.783485 PROGRESS: === Extracted 1958 precursors and 10959 fragments ===
1:35:43.783860 INFO: === FDR correction performed with classifier version -1 ===
1:35:43.784327 PROGRESS: ============================= Precursor FDR =============================
1:35:43.784405 PROGRESS: Total precursors accumulated: 0
1:35:43.784461 PROGRESS: Target precursors: 0 (0.00%)
1:35:43.784508 PROGRESS: Decoy precursors: 0 (0.00%)
1:35:43.784552 PROGRESS: 
1:35:43.784594 PROGRESS: Precursor Summary:
1:35:43.784704 PROGRESS: 
1:35:43.784761 PROGRESS: Protein Summary:
1:35:43.784832 PROGRESS: =========================================================================
1:35:43.785009 INFO: Target number of precursors not reached yet.
1:35:43.869034 INFO: Starting optimization step 1.
1:35:43.869267 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:35:43.869349 INFO: Using rust extraction backend
1:35:43.869408 PROGRESS: Extracting batch of 3911 precursors
1:35:43.877518 INFO: === Search parameters used ===
1:35:43.877640 INFO: rt_error       : 805.611083984375
1:35:43.877695 INFO: mobility_error : 0.1
1:35:43.877739 INFO: num_candidates : 1
1:35:43.877779 INFO: ms1_error      : 3
1:35:43.877820 INFO: ms2_error      : 10
1:35:43.877859 INFO: fwhm_rt        : 5
1:35:43.877899 INFO: quant_window   : 3
1:35:43.877939 INFO: ==============================================
1:35:43.924098 INFO: performing precursor FDR with 40 features
1:35:43.924222 INFO: Decoy channel: -1
1:35:43.924256 INFO: competitive: True
1:35:43.928888 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:43.931319 INFO: Estimating optimal hyperparameters - samples: 4,683, batch_size: 128, learning_rate: 1.77e-04
1:35:43.931417 INFO: Using random state 908544 for train-test-split
1:35:44.396945 INFO: Test AUC: 0.523
1:35:44.397063 INFO: Train AUC: 0.588
1:35:44.397093 INFO: AUC difference: 11.02%
1:35:44.397114 WARNING: AUC difference > 5%. This may indicate overfitting.
1:35:44.650865 INFO: Resetting torch num_threads to 100
1:35:44.653951 PROGRESS: === Extracted 5854 precursors and 32795 fragments ===
1:35:44.654360 INFO: === FDR correction performed with classifier version -1 ===
1:35:44.654864 PROGRESS: ============================= Precursor FDR =============================
1:35:44.654949 PROGRESS: Total precursors accumulated: 19
1:35:44.655005 PROGRESS: Target precursors: 19 (100.00%)
1:35:44.655053 PROGRESS: Decoy precursors: 0 (0.00%)
1:35:44.655096 PROGRESS: 
1:35:44.655138 PROGRESS: Precursor Summary:
1:35:44.656235 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
1:35:44.656315 PROGRESS: 
1:35:44.656373 PROGRESS: Protein Summary:
1:35:44.657553 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
1:35:44.657637 PROGRESS: =========================================================================
1:35:44.657900 INFO: Target number of precursors not reached yet.
1:35:44.749197 INFO: Starting optimization step 2.
1:35:44.749428 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:35:44.749520 INFO: Using rust extraction backend
1:35:44.749583 PROGRESS: Extracting batch of 7891 precursors
1:35:44.764493 INFO: === Search parameters used ===
1:35:44.764639 INFO: rt_error       : 805.611083984375
1:35:44.764690 INFO: mobility_error : 0.1
1:35:44.764734 INFO: num_candidates : 1
1:35:44.764775 INFO: ms1_error      : 3
1:35:44.764815 INFO: ms2_error      : 10
1:35:44.764855 INFO: fwhm_rt        : 5
1:35:44.764894 INFO: quant_window   : 3
1:35:44.764932 INFO: ==============================================
1:35:44.841854 INFO: performing precursor FDR with 40 features
1:35:44.841961 INFO: Decoy channel: -1
1:35:44.841986 INFO: competitive: True
1:35:44.848258 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:44.851826 INFO: Estimating optimal hyperparameters - samples: 10,971, batch_size: 128, learning_rate: 1.77e-04
1:35:44.851941 INFO: Using random state 652037 for train-test-split
1:35:45.958260 INFO: Test AUC: 0.545
1:35:45.958367 INFO: Train AUC: 0.590
1:35:45.958395 INFO: AUC difference: 7.63%
1:35:45.958416 WARNING: AUC difference > 5%. This may indicate overfitting.
1:35:46.207442 INFO: Resetting torch num_threads to 100
1:35:46.212592 PROGRESS: === Extracted 13714 precursors and 77018 fragments ===
1:35:46.212991 INFO: === FDR correction performed with classifier version -1 ===
1:35:46.213506 PROGRESS: ============================= Precursor FDR =============================
1:35:46.213588 PROGRESS: Total precursors accumulated: 53
1:35:46.213650 PROGRESS: Target precursors: 53 (100.00%)
1:35:46.213700 PROGRESS: Decoy precursors: 0 (0.00%)
1:35:46.213743 PROGRESS: 
1:35:46.213785 PROGRESS: Precursor Summary:
1:35:46.214850 PROGRESS: Channel   0:	 0.050 FDR:    53; 0.010 FDR:    53; 0.001 FDR:    53
1:35:46.214930 PROGRESS: 
1:35:46.214982 PROGRESS: Protein Summary:
1:35:46.216157 PROGRESS: Channel   0:	 0.050 FDR:    52; 0.010 FDR:    52; 0.001 FDR:    52
1:35:46.216244 PROGRESS: =========================================================================
1:35:46.216581 INFO: Target number of precursors not reached yet.
1:35:46.319281 INFO: Starting optimization step 3.
1:35:46.319528 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:35:46.319610 INFO: Using rust extraction backend
1:35:46.319674 PROGRESS: Extracting batch of 15777 precursors
1:35:46.347929 INFO: === Search parameters used ===
1:35:46.348109 INFO: rt_error       : 805.611083984375
1:35:46.348163 INFO: mobility_error : 0.1
1:35:46.348211 INFO: num_candidates : 1
1:35:46.348257 INFO: ms1_error      : 3
1:35:46.348301 INFO: ms2_error      : 10
1:35:46.348344 INFO: fwhm_rt        : 5
1:35:46.348386 INFO: quant_window   : 3
1:35:46.348440 INFO: ==============================================
1:35:46.482422 INFO: performing precursor FDR with 40 features
1:35:46.482532 INFO: Decoy channel: -1
1:35:46.482557 INFO: competitive: True
1:35:46.497730 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:46.504963 INFO: Estimating optimal hyperparameters - samples: 23,562, batch_size: 128, learning_rate: 1.77e-04
1:35:46.505131 INFO: Using random state 983660 for train-test-split
1:35:48.872163 INFO: Test AUC: 0.581
1:35:48.872276 INFO: Train AUC: 0.603
1:35:48.872307 INFO: AUC difference: 3.67%
1:35:49.133213 INFO: Resetting torch num_threads to 100
1:35:49.140099 PROGRESS: === Extracted 29453 precursors and 165478 fragments ===
1:35:49.140614 INFO: === FDR correction performed with classifier version -1 ===
1:35:49.141147 PROGRESS: ============================= Precursor FDR =============================
1:35:49.141246 PROGRESS: Total precursors accumulated: 106
1:35:49.141304 PROGRESS: Target precursors: 105 (99.06%)
1:35:49.141354 PROGRESS: Decoy precursors: 1 (0.94%)
1:35:49.141399 PROGRESS: 
1:35:49.141442 PROGRESS: Precursor Summary:
1:35:49.142436 PROGRESS: Channel   0:	 0.050 FDR:   105; 0.010 FDR:   105; 0.001 FDR:    66
1:35:49.142524 PROGRESS: 
1:35:49.142578 PROGRESS: Protein Summary:
1:35:49.143706 PROGRESS: Channel   0:	 0.050 FDR:   104; 0.010 FDR:   104; 0.001 FDR:    66
1:35:49.143798 PROGRESS: =========================================================================
1:35:49.144302 INFO: Target number of precursors not reached yet.
1:35:49.262661 INFO: Starting optimization step 4.
1:35:49.262923 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:35:49.263004 INFO: Using rust extraction backend
1:35:49.263081 PROGRESS: Extracting batch of 31516 precursors
1:35:49.317856 INFO: === Search parameters used ===
1:35:49.318081 INFO: rt_error       : 805.611083984375
1:35:49.318144 INFO: mobility_error : 0.1
1:35:49.318191 INFO: num_candidates : 1
1:35:49.318232 INFO: ms1_error      : 3
1:35:49.318272 INFO: ms2_error      : 10
1:35:49.318312 INFO: fwhm_rt        : 5
1:35:49.318354 INFO: quant_window   : 3
1:35:49.318395 INFO: ==============================================
1:35:49.540843 INFO: performing precursor FDR with 40 features
1:35:49.540957 INFO: Decoy channel: -1
1:35:49.540980 INFO: competitive: True
1:35:49.563911 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:49.579962 INFO: Estimating optimal hyperparameters - samples: 48,728, batch_size: 199, learning_rate: 2.20e-04
1:35:49.580176 INFO: Using random state 614649 for train-test-split
1:35:53.256269 INFO: Test AUC: 0.588
1:35:53.256387 INFO: Train AUC: 0.609
1:35:53.256417 INFO: AUC difference: 3.33%
1:35:53.522588 INFO: Resetting torch num_threads to 100
1:35:53.534034 PROGRESS: === Extracted 60911 precursors and 342210 fragments ===
1:35:53.534671 INFO: === FDR correction performed with classifier version -1 ===
1:35:53.535259 PROGRESS: ============================= Precursor FDR =============================
1:35:53.535354 PROGRESS: Total precursors accumulated: 116
1:35:53.535415 PROGRESS: Target precursors: 115 (99.14%)
1:35:53.535467 PROGRESS: Decoy precursors: 1 (0.86%)
1:35:53.535514 PROGRESS: 
1:35:53.535560 PROGRESS: Precursor Summary:
1:35:53.536555 PROGRESS: Channel   0:	 0.050 FDR:   115; 0.010 FDR:   115; 0.001 FDR:    89
1:35:53.536640 PROGRESS: 
1:35:53.536695 PROGRESS: Protein Summary:
1:35:53.537804 PROGRESS: Channel   0:	 0.050 FDR:   110; 0.010 FDR:   110; 0.001 FDR:    86
1:35:53.537893 PROGRESS: =========================================================================
1:35:53.538950 INFO: Target number of precursors not reached yet.
1:35:53.724315 INFO: Starting optimization step 5.
1:35:53.724588 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:35:53.724672 INFO: Using rust extraction backend
1:35:53.724738 PROGRESS: Extracting batch of 63010 precursors
1:35:53.832430 INFO: === Search parameters used ===
1:35:53.832698 INFO: rt_error       : 805.611083984375
1:35:53.832752 INFO: mobility_error : 0.1
1:35:53.832800 INFO: num_candidates : 1
1:35:53.832844 INFO: ms1_error      : 3
1:35:53.832890 INFO: ms2_error      : 10
1:35:53.832932 INFO: fwhm_rt        : 5
1:35:53.832974 INFO: quant_window   : 3
1:35:53.833016 INFO: ==============================================
1:35:54.207849 INFO: performing precursor FDR with 40 features
1:35:54.207959 INFO: Decoy channel: -1
1:35:54.207985 INFO: competitive: True
1:35:54.254583 INFO: Setting torch num_threads to 2 for FDR classification task
1:35:54.284863 INFO: Estimating optimal hyperparameters - samples: 99,014, batch_size: 405, learning_rate: 3.14e-04
1:35:54.285198 INFO: Using random state 800983 for train-test-split
1:35:58.912843 INFO: Test AUC: 0.588
1:35:58.912962 INFO: Train AUC: 0.613
1:35:58.912992 INFO: AUC difference: 4.15%
1:35:59.192685 INFO: Resetting torch num_threads to 100
1:35:59.213610 PROGRESS: === Extracted 123768 precursors and 694984 fragments ===
1:35:59.214237 INFO: === FDR correction performed with classifier version -1 ===
1:35:59.214918 PROGRESS: ============================= Precursor FDR =============================
1:35:59.215022 PROGRESS: Total precursors accumulated: 550
1:35:59.215084 PROGRESS: Target precursors: 545 (99.09%)
1:35:59.215134 PROGRESS: Decoy precursors: 5 (0.91%)
1:35:59.215204 PROGRESS: 
1:35:59.215252 PROGRESS: Precursor Summary:
1:35:59.216357 PROGRESS: Channel   0:	 0.050 FDR:   545; 0.010 FDR:   545; 0.001 FDR:     1
1:35:59.216460 PROGRESS: 
1:35:59.216518 PROGRESS: Protein Summary:
1:35:59.217789 PROGRESS: Channel   0:	 0.050 FDR:   502; 0.010 FDR:   502; 0.001 FDR:     1
1:35:59.217877 PROGRESS: =========================================================================
1:35:59.219642 INFO: Target number of precursors not reached yet.
1:35:59.475943 INFO: Starting optimization step 6.
1:35:59.476214 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:35:59.476294 INFO: Using rust extraction backend
1:35:59.476355 PROGRESS: Extracting batch of 126188 precursors
1:35:59.689591 INFO: === Search parameters used ===
1:35:59.689860 INFO: rt_error       : 805.611083984375
1:35:59.689914 INFO: mobility_error : 0.1
1:35:59.689962 INFO: num_candidates : 1
1:35:59.690009 INFO: ms1_error      : 3
1:35:59.690052 INFO: ms2_error      : 10
1:35:59.690092 INFO: fwhm_rt        : 5
1:35:59.690133 INFO: quant_window   : 3
1:35:59.690172 INFO: ==============================================
1:36:00.369401 INFO: performing precursor FDR with 40 features
1:36:00.369520 INFO: Decoy channel: -1
1:36:00.369545 INFO: competitive: True
1:36:00.470387 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:00.552275 INFO: Estimating optimal hyperparameters - samples: 199,720, batch_size: 818, learning_rate: 4.47e-04
1:36:00.553361 INFO: Using random state 98279 for train-test-split
1:36:06.970907 INFO: Test AUC: 0.591
1:36:06.971019 INFO: Train AUC: 0.612
1:36:06.971049 INFO: AUC difference: 3.34%
1:36:07.297810 INFO: Resetting torch num_threads to 100
1:36:07.342094 PROGRESS: === Extracted 249650 precursors and 1401249 fragments ===
1:36:07.342804 INFO: === FDR correction performed with classifier version -1 ===
1:36:07.343712 PROGRESS: ============================= Precursor FDR =============================
1:36:07.343806 PROGRESS: Total precursors accumulated: 1,339
1:36:07.343873 PROGRESS: Target precursors: 1,326 (99.03%)
1:36:07.343926 PROGRESS: Decoy precursors: 13 (0.97%)
1:36:07.343972 PROGRESS: 
1:36:07.344016 PROGRESS: Precursor Summary:
1:36:07.345284 PROGRESS: Channel   0:	 0.050 FDR: 1,326; 0.010 FDR: 1,326; 0.001 FDR:     0
1:36:07.345374 PROGRESS: 
1:36:07.345429 PROGRESS: Protein Summary:
1:36:07.346994 PROGRESS: Channel   0:	 0.050 FDR: 1,120; 0.010 FDR: 1,120; 0.001 FDR:     0
1:36:07.347087 PROGRESS: =========================================================================
1:36:07.351263 INFO: Target number of precursors reached.
1:36:07.517495 INFO: fragments_df: keeping 5000 of 1401249 [sum(precursor_idx_mask)=13893 sum(mass_error_mask)=1401249 stop_rank=5000
1:36:07.921394 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:08.112953 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:08.763460 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:36:08.763928 INFO: Using score_cutoff 11.700319526195527 (fac=0.99, q=1)
1:36:08.764269 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:36:08.764346 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:36:08.764400 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.700319526195527
1:36:08.764463 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:08.915261 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:09.270640 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
1:36:09.270951 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:36:09.271090 INFO: Starting optimization step 7.
1:36:09.271175 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:36:09.271258 INFO: Using rust extraction backend
1:36:09.271328 PROGRESS: Extracting batch of 250256 precursors
1:36:09.691504 INFO: === Search parameters used ===
1:36:09.691772 INFO: rt_error       : 805.611083984375
1:36:09.691825 INFO: mobility_error : 0.1
1:36:09.691869 INFO: num_candidates : 3
1:36:09.691912 INFO: ms1_error      : 3
1:36:09.691952 INFO: ms2_error      : 10
1:36:09.691991 INFO: fwhm_rt        : 3.0
1:36:09.692031 INFO: quant_window   : 3
1:36:09.692075 INFO: ==============================================
1:36:12.202395 INFO: performing precursor FDR with 40 features
1:36:12.202517 INFO: Decoy channel: -1
1:36:12.202542 INFO: competitive: True
1:36:12.395706 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:12.701829 INFO: Estimating optimal hyperparameters - samples: 599,399, batch_size: 2,455, learning_rate: 7.74e-04
1:36:12.702933 INFO: Using random state 963389 for train-test-split
1:36:25.990248 INFO: Test AUC: 0.597
1:36:25.990497 INFO: Train AUC: 0.609
1:36:25.990533 INFO: AUC difference: 1.89%
1:36:26.475725 INFO: Resetting torch num_threads to 100
1:36:26.508183 PROGRESS: === Extracted 749249 precursors and 4037767 fragments ===
1:36:26.508789 INFO: === FDR correction performed with classifier version 6 ===
1:36:26.509553 PROGRESS: ============================= Precursor FDR =============================
1:36:26.509658 PROGRESS: Total precursors accumulated: 1,466
1:36:26.509722 PROGRESS: Target precursors: 1,452 (99.05%)
1:36:26.509774 PROGRESS: Decoy precursors: 14 (0.95%)
1:36:26.509828 PROGRESS: 
1:36:26.509874 PROGRESS: Precursor Summary:
1:36:26.511283 PROGRESS: Channel   0:	 0.050 FDR: 1,452; 0.010 FDR: 1,452; 0.001 FDR:   813
1:36:26.511382 PROGRESS: 
1:36:26.511437 PROGRESS: Protein Summary:
1:36:26.513170 PROGRESS: Channel   0:	 0.050 FDR: 1,219; 0.010 FDR: 1,219; 0.001 FDR:   706
1:36:26.513261 PROGRESS: =========================================================================
1:36:26.527391 INFO: Target number of precursors reached.
1:36:26.974711 INFO: fragments_df: keeping 5000 of 4037767 [sum(precursor_idx_mask)=34879 sum(mass_error_mask)=4037767 stop_rank=5000
1:36:27.529464 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:27.735907 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:28.387461 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:28.387953 INFO: Using score_cutoff 12.165750336456298 (fac=0.99, q=1)
1:36:28.388302 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:28.388381 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:28.388438 INFO: Updating optimization_manager: score_cutoff        : 11.700319526195527 -> 12.165750336456298
1:36:28.388502 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:28.540041 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:28.872265 INFO: === checking if optimization conditions were reached ===
1:36:28.875004 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
1:36:28.875202 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1:36:28.875290 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:36:28.875362 INFO: ==============================================
1:36:28.875449 INFO: Starting optimization step 8.
1:36:28.875525 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:36:28.875616 INFO: Using rust extraction backend
1:36:28.875702 PROGRESS: Extracting batch of 250256 precursors
1:36:29.301193 INFO: === Search parameters used ===
1:36:29.301497 INFO: rt_error       : 805.611083984375
1:36:29.301554 INFO: mobility_error : 0.1
1:36:29.301604 INFO: num_candidates : 3
1:36:29.301649 INFO: ms1_error      : 3
1:36:29.301693 INFO: ms2_error      : 10.0
1:36:29.301735 INFO: fwhm_rt        : 3.0
1:36:29.301775 INFO: quant_window   : 3
1:36:29.301832 INFO: ==============================================
1:36:31.904459 INFO: performing precursor FDR with 40 features
1:36:31.904578 INFO: Decoy channel: -1
1:36:31.904603 INFO: competitive: True
1:36:32.103941 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:32.417819 INFO: Estimating optimal hyperparameters - samples: 599,414, batch_size: 2,455, learning_rate: 7.74e-04
1:36:32.418985 INFO: Using random state 993779 for train-test-split
1:36:45.737815 INFO: Test AUC: 0.601
1:36:45.738027 INFO: Train AUC: 0.613
1:36:45.738073 INFO: AUC difference: 2.01%
1:36:46.219880 INFO: Resetting torch num_threads to 100
1:36:46.251209 PROGRESS: === Extracted 749268 precursors and 4037373 fragments ===
1:36:46.251774 INFO: === FDR correction performed with classifier version 7 ===
1:36:46.252462 PROGRESS: ============================= Precursor FDR =============================
1:36:46.252551 PROGRESS: Total precursors accumulated: 1,449
1:36:46.252612 PROGRESS: Target precursors: 1,435 (99.03%)
1:36:46.252682 PROGRESS: Decoy precursors: 14 (0.97%)
1:36:46.252736 PROGRESS: 
1:36:46.252782 PROGRESS: Precursor Summary:
1:36:46.254154 PROGRESS: Channel   0:	 0.050 FDR: 1,435; 0.010 FDR: 1,435; 0.001 FDR:   883
1:36:46.254246 PROGRESS: 
1:36:46.254302 PROGRESS: Protein Summary:
1:36:46.256087 PROGRESS: Channel   0:	 0.050 FDR: 1,204; 0.010 FDR: 1,204; 0.001 FDR:   766
1:36:46.256186 PROGRESS: =========================================================================
1:36:46.271048 INFO: Target number of precursors reached.
1:36:46.723658 INFO: fragments_df: keeping 5000 of 4037373 [sum(precursor_idx_mask)=34484 sum(mass_error_mask)=4037373 stop_rank=5000
1:36:47.261092 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:47.464526 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:48.112704 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:48.113179 INFO: Using score_cutoff 11.955590222167968 (fac=0.99, q=1)
1:36:48.113534 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:48.113614 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:48.113670 INFO: Updating optimization_manager: score_cutoff        : 12.165750336456298 -> 11.955590222167968
1:36:48.113730 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:48.266695 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:48.623659 INFO: === checking if optimization conditions were reached ===
1:36:48.626400 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:36:48.626580 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:36:48.626662 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:36:48.626735 INFO: ==============================================
1:36:48.626822 INFO: Starting optimization step 9.
1:36:48.626896 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:36:48.626999 INFO: Using rust extraction backend
1:36:48.627092 PROGRESS: Extracting batch of 250256 precursors
1:36:49.052395 INFO: === Search parameters used ===
1:36:49.052673 INFO: rt_error       : 805.611083984375
1:36:49.052731 INFO: mobility_error : 0.1
1:36:49.052777 INFO: num_candidates : 3
1:36:49.052821 INFO: ms1_error      : 3
1:36:49.052862 INFO: ms2_error      : 10.0
1:36:49.052902 INFO: fwhm_rt        : 3.0
1:36:49.052940 INFO: quant_window   : 3
1:36:49.052978 INFO: ==============================================
1:36:51.633250 INFO: performing precursor FDR with 40 features
1:36:51.633377 INFO: Decoy channel: -1
1:36:51.633404 INFO: competitive: True
1:36:51.828220 INFO: Setting torch num_threads to 2 for FDR classification task
1:36:52.132215 INFO: Estimating optimal hyperparameters - samples: 599,399, batch_size: 2,455, learning_rate: 7.74e-04
1:36:52.134065 INFO: Using random state 792534 for train-test-split
1:37:05.167469 INFO: Test AUC: 0.605
1:37:05.167618 INFO: Train AUC: 0.618
1:37:05.167652 INFO: AUC difference: 2.07%
1:37:05.646842 INFO: Resetting torch num_threads to 100
1:37:05.677956 PROGRESS: === Extracted 749249 precursors and 4037058 fragments ===
1:37:05.678473 INFO: === FDR correction performed with classifier version 8 ===
1:37:05.679173 PROGRESS: ============================= Precursor FDR =============================
1:37:05.679276 PROGRESS: Total precursors accumulated: 1,547
1:37:05.679340 PROGRESS: Target precursors: 1,532 (99.03%)
1:37:05.679392 PROGRESS: Decoy precursors: 15 (0.97%)
1:37:05.679437 PROGRESS: 
1:37:05.679481 PROGRESS: Precursor Summary:
1:37:05.680865 PROGRESS: Channel   0:	 0.050 FDR: 1,532; 0.010 FDR: 1,532; 0.001 FDR: 1,060
1:37:05.680953 PROGRESS: 
1:37:05.681007 PROGRESS: Protein Summary:
1:37:05.682796 PROGRESS: Channel   0:	 0.050 FDR: 1,283; 0.010 FDR: 1,283; 0.001 FDR:   905
1:37:05.682893 PROGRESS: =========================================================================
1:37:05.697700 INFO: Target number of precursors reached.
1:37:06.146047 INFO: fragments_df: keeping 5000 of 4037058 [sum(precursor_idx_mask)=36497 sum(mass_error_mask)=4037058 stop_rank=5000
1:37:06.659439 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:37:06.869552 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:37:07.515941 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:37:07.516406 INFO: Using score_cutoff 11.649517626571654 (fac=0.99, q=1)
1:37:07.516732 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:37:07.516808 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:37:07.516862 INFO: Updating optimization_manager: score_cutoff        : 11.955590222167968 -> 11.649517626571654
1:37:07.516922 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:37:07.666111 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:37:08.010938 INFO: === checking if optimization conditions were reached ===
1:37:08.013618 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:37:08.013742 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:37:08.013823 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:37:08.013894 INFO: ==============================================
1:37:08.013978 INFO: Starting optimization step 10.
1:37:08.014049 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:37:08.014137 INFO: Using rust extraction backend
1:37:08.014218 PROGRESS: Extracting batch of 250256 precursors
1:37:08.434142 INFO: === Search parameters used ===
1:37:08.434414 INFO: rt_error       : 805.611083984375
1:37:08.434472 INFO: mobility_error : 0.1
1:37:08.434519 INFO: num_candidates : 3
1:37:08.434565 INFO: ms1_error      : 3
1:37:08.434608 INFO: ms2_error      : 10.0
1:37:08.434650 INFO: fwhm_rt        : 3.0
1:37:08.434691 INFO: quant_window   : 3
1:37:08.434731 INFO: ==============================================
1:37:10.895115 INFO: performing precursor FDR with 40 features
1:37:10.895257 INFO: Decoy channel: -1
1:37:10.895283 INFO: competitive: True
1:37:11.091243 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:11.394297 INFO: Estimating optimal hyperparameters - samples: 599,400, batch_size: 2,455, learning_rate: 7.74e-04
1:37:11.395260 INFO: Using random state 326313 for train-test-split
1:37:24.654010 INFO: Test AUC: 0.609
1:37:24.654180 INFO: Train AUC: 0.622
1:37:24.654212 INFO: AUC difference: 2.16%
1:37:25.134296 INFO: Resetting torch num_threads to 100
1:37:25.167440 PROGRESS: === Extracted 749250 precursors and 4036751 fragments ===
1:37:25.167944 INFO: === FDR correction performed with classifier version 9 ===
1:37:25.168665 PROGRESS: ============================= Precursor FDR =============================
1:37:25.168755 PROGRESS: Total precursors accumulated: 1,507
1:37:25.168813 PROGRESS: Target precursors: 1,493 (99.07%)
1:37:25.168864 PROGRESS: Decoy precursors: 14 (0.93%)
1:37:25.168911 PROGRESS: 
1:37:25.168955 PROGRESS: Precursor Summary:
1:37:25.170320 PROGRESS: Channel   0:	 0.050 FDR: 1,493; 0.010 FDR: 1,493; 0.001 FDR: 1,083
1:37:25.170413 PROGRESS: 
1:37:25.170466 PROGRESS: Protein Summary:
1:37:25.172276 PROGRESS: Channel   0:	 0.050 FDR: 1,254; 0.010 FDR: 1,254; 0.001 FDR:   924
1:37:25.172371 PROGRESS: =========================================================================
1:37:25.186906 INFO: Target number of precursors reached.
1:37:25.638604 INFO: fragments_df: keeping 5000 of 4036751 [sum(precursor_idx_mask)=35712 sum(mass_error_mask)=4036751 stop_rank=5000
1:37:26.058557 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:37:26.269333 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:37:26.916273 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:37:26.916792 INFO: Using score_cutoff 11.710470921707152 (fac=0.99, q=1)
1:37:26.917115 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:37:26.917192 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:37:26.917250 INFO: Updating optimization_manager: score_cutoff        : 11.649517626571654 -> 11.710470921707152
1:37:26.917316 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:37:27.069076 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:37:27.406416 INFO: === checking if optimization conditions were reached ===
1:37:27.409169 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:37:27.409348 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:37:27.409435 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:37:27.409509 INFO: ==============================================
1:37:27.409598 INFO: Starting optimization step 11.
1:37:27.409677 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:37:27.409776 INFO: Using rust extraction backend
1:37:27.409864 PROGRESS: Extracting batch of 250256 precursors
1:37:27.835775 INFO: === Search parameters used ===
1:37:27.836055 INFO: rt_error       : 805.611083984375
1:37:27.836113 INFO: mobility_error : 0.1
1:37:27.836164 INFO: num_candidates : 3
1:37:27.836220 INFO: ms1_error      : 3
1:37:27.836276 INFO: ms2_error      : 10.0
1:37:27.836321 INFO: fwhm_rt        : 3.0
1:37:27.836365 INFO: quant_window   : 3
1:37:27.836407 INFO: ==============================================
1:37:30.466818 INFO: performing precursor FDR with 40 features
1:37:30.466949 INFO: Decoy channel: -1
1:37:30.466975 INFO: competitive: True
1:37:30.669417 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:30.984362 INFO: Estimating optimal hyperparameters - samples: 599,404, batch_size: 2,455, learning_rate: 7.74e-04
1:37:30.985331 INFO: Using random state 182021 for train-test-split
1:37:47.206984 INFO: Test AUC: 0.610
1:37:47.207163 INFO: Train AUC: 0.624
1:37:47.207200 INFO: AUC difference: 2.15%
1:37:47.689617 INFO: Resetting torch num_threads to 100
1:37:47.721000 PROGRESS: === Extracted 749256 precursors and 4037331 fragments ===
1:37:47.721524 INFO: === FDR correction performed with classifier version 10 ===
1:37:47.722231 PROGRESS: ============================= Precursor FDR =============================
1:37:47.722321 PROGRESS: Total precursors accumulated: 1,534
1:37:47.722381 PROGRESS: Target precursors: 1,519 (99.02%)
1:37:47.722432 PROGRESS: Decoy precursors: 15 (0.98%)
1:37:47.722477 PROGRESS: 
1:37:47.722521 PROGRESS: Precursor Summary:
1:37:47.723930 PROGRESS: Channel   0:	 0.050 FDR: 1,519; 0.010 FDR: 1,519; 0.001 FDR: 1,133
1:37:47.724023 PROGRESS: 
1:37:47.724079 PROGRESS: Protein Summary:
1:37:47.725879 PROGRESS: Channel   0:	 0.050 FDR: 1,275; 0.010 FDR: 1,275; 0.001 FDR:   968
1:37:47.725971 PROGRESS: =========================================================================
1:37:47.741320 INFO: Target number of precursors reached.
1:37:48.177281 INFO: fragments_df: keeping 5000 of 4037331 [sum(precursor_idx_mask)=36162 sum(mass_error_mask)=4037331 stop_rank=5000
1:37:48.618972 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:37:48.827397 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:37:49.476290 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:37:49.476760 INFO: Using score_cutoff 11.654100092697142 (fac=0.99, q=1)
1:37:49.477072 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:37:49.477149 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:37:49.477215 INFO: Updating optimization_manager: score_cutoff        : 11.710470921707152 -> 11.654100092697142
1:37:49.477273 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:37:49.626494 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:37:49.956313 INFO: === checking if optimization conditions were reached ===
1:37:49.958513 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:37:49.958615 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:37:49.958682 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:37:49.958740 INFO: ==============================================
1:37:49.958813 PROGRESS: Optimization finished for ms2_error.
1:37:50.361666 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:37:50.511235 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:37:50.840914 INFO: Starting optimization step 0.
1:37:50.841172 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:37:50.841267 INFO: Using rust extraction backend
1:37:50.841342 PROGRESS: Extracting batch of 250256 precursors
1:37:51.261379 INFO: === Search parameters used ===
1:37:51.261644 INFO: rt_error       : 805.611083984375
1:37:51.261699 INFO: mobility_error : 0.1
1:37:51.261746 INFO: num_candidates : 3
1:37:51.261789 INFO: ms1_error      : 3
1:37:51.261842 INFO: ms2_error      : 10.0
1:37:51.261885 INFO: fwhm_rt        : 3.0
1:37:51.261926 INFO: quant_window   : 3
1:37:51.261966 INFO: ==============================================
1:37:53.790472 INFO: performing precursor FDR with 40 features
1:37:53.790610 INFO: Decoy channel: -1
1:37:53.790636 INFO: competitive: True
1:37:53.990491 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:54.295898 INFO: Estimating optimal hyperparameters - samples: 599,405, batch_size: 2,455, learning_rate: 7.74e-04
1:37:54.297149 INFO: Using random state 333962 for train-test-split
1:38:07.142904 INFO: Test AUC: 0.612
1:38:07.143036 INFO: Train AUC: 0.626
1:38:07.143068 INFO: AUC difference: 2.28%
1:38:07.621477 INFO: Resetting torch num_threads to 100
1:38:07.652260 PROGRESS: === Extracted 749257 precursors and 4037648 fragments ===
1:38:07.652737 INFO: === FDR correction performed with classifier version 11 ===
1:38:07.653400 PROGRESS: ============================= Precursor FDR =============================
1:38:07.653491 PROGRESS: Total precursors accumulated: 1,521
1:38:07.653553 PROGRESS: Target precursors: 1,506 (99.01%)
1:38:07.653614 PROGRESS: Decoy precursors: 15 (0.99%)
1:38:07.653668 PROGRESS: 
1:38:07.653717 PROGRESS: Precursor Summary:
1:38:07.655089 PROGRESS: Channel   0:	 0.050 FDR: 1,506; 0.010 FDR: 1,506; 0.001 FDR: 1,129
1:38:07.655193 PROGRESS: 
1:38:07.655255 PROGRESS: Protein Summary:
1:38:07.657014 PROGRESS: Channel   0:	 0.050 FDR: 1,264; 0.010 FDR: 1,264; 0.001 FDR:   960
1:38:07.657105 PROGRESS: =========================================================================
1:38:07.671870 INFO: Target number of precursors reached.
1:38:08.103360 INFO: fragments_df: keeping 5000 of 4037648 [sum(precursor_idx_mask)=35930 sum(mass_error_mask)=4037648 stop_rank=5000
1:38:08.530575 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:38:08.738426 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:38:09.382685 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:38:09.383142 INFO: Using score_cutoff 11.720005172252655 (fac=0.99, q=1)
1:38:09.383463 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:38:09.383539 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:38:09.383593 INFO: Updating optimization_manager: score_cutoff        : 11.654100092697142 -> 11.720005172252655
1:38:09.383648 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:38:09.534835 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:38:09.867718 INFO: === checking if optimization conditions were reached ===
1:38:09.867992 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:38:09.870697 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 747.4404547502842
1:38:09.870800 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 747.4405.
1:38:09.870866 INFO: ==============================================
1:38:09.870936 INFO: Starting optimization step 1.
1:38:09.870996 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:38:09.871060 INFO: Using rust extraction backend
1:38:09.871118 PROGRESS: Extracting batch of 250256 precursors
1:38:10.291684 INFO: === Search parameters used ===
1:38:10.291958 INFO: rt_error       : 747.4404547502842
1:38:10.292027 INFO: mobility_error : 0.1
1:38:10.292082 INFO: num_candidates : 3
1:38:10.292128 INFO: ms1_error      : 3
1:38:10.292170 INFO: ms2_error      : 10.0
1:38:10.292210 INFO: fwhm_rt        : 3.0
1:38:10.292254 INFO: quant_window   : 3
1:38:10.292296 INFO: ==============================================
1:38:12.817315 INFO: performing precursor FDR with 40 features
1:38:12.817434 INFO: Decoy channel: -1
1:38:12.817460 INFO: competitive: True
1:38:13.016153 INFO: Setting torch num_threads to 2 for FDR classification task
1:38:13.321553 INFO: Estimating optimal hyperparameters - samples: 599,372, batch_size: 2,455, learning_rate: 7.74e-04
1:38:13.322690 INFO: Using random state 333962 for train-test-split
1:38:26.098862 INFO: Test AUC: 0.611
1:38:26.098991 INFO: Train AUC: 0.624
1:38:26.099027 INFO: AUC difference: 2.12%
1:38:26.562153 INFO: Resetting torch num_threads to 100
1:38:26.593346 PROGRESS: === Extracted 749215 precursors and 4035288 fragments ===
1:38:26.593822 INFO: === FDR correction performed with classifier version 11 ===
1:38:26.594502 PROGRESS: ============================= Precursor FDR =============================
1:38:26.594593 PROGRESS: Total precursors accumulated: 1,534
1:38:26.594656 PROGRESS: Target precursors: 1,519 (99.02%)
1:38:26.594709 PROGRESS: Decoy precursors: 15 (0.98%)
1:38:26.594757 PROGRESS: 
1:38:26.594803 PROGRESS: Precursor Summary:
1:38:26.596176 PROGRESS: Channel   0:	 0.050 FDR: 1,519; 0.010 FDR: 1,519; 0.001 FDR: 1,153
1:38:26.596267 PROGRESS: 
1:38:26.596325 PROGRESS: Protein Summary:
1:38:26.598095 PROGRESS: Channel   0:	 0.050 FDR: 1,279; 0.010 FDR: 1,279; 0.001 FDR:   978
1:38:26.598185 PROGRESS: =========================================================================
1:38:26.613569 INFO: Target number of precursors reached.
1:38:27.057395 INFO: fragments_df: keeping 5000 of 4035288 [sum(precursor_idx_mask)=35814 sum(mass_error_mask)=4035288 stop_rank=5000
1:38:27.474703 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:38:27.681285 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:38:28.326323 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:38:28.326827 INFO: Using score_cutoff 10.625021879768372 (fac=0.99, q=1)
1:38:28.327137 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:38:28.327229 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:38:28.327284 INFO: Updating optimization_manager: score_cutoff        : 11.720005172252655 -> 10.625021879768372
1:38:28.327340 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:38:28.478738 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:38:28.816261 INFO: === checking if optimization conditions were reached ===
1:38:28.816573 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:38:28.819904 INFO: Updating optimization_manager: rt_error            : 747.4404547502842 -> 885.2060541310278
1:38:28.820030 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 885.2061.
1:38:28.820123 INFO: ==============================================
1:38:28.820207 INFO: Starting optimization step 2.
1:38:28.820284 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:38:28.820355 INFO: Using rust extraction backend
1:38:28.820425 PROGRESS: Extracting batch of 250256 precursors
1:38:29.241513 INFO: === Search parameters used ===
1:38:29.241797 INFO: rt_error       : 885.2060541310278
1:38:29.241855 INFO: mobility_error : 0.1
1:38:29.241904 INFO: num_candidates : 3
1:38:29.241949 INFO: ms1_error      : 3
1:38:29.241990 INFO: ms2_error      : 10.0
1:38:29.242029 INFO: fwhm_rt        : 3.0
1:38:29.242069 INFO: quant_window   : 3
1:38:29.242108 INFO: ==============================================
1:38:31.746307 INFO: performing precursor FDR with 40 features
1:38:31.746433 INFO: Decoy channel: -1
1:38:31.746459 INFO: competitive: True
1:38:31.946444 INFO: Setting torch num_threads to 2 for FDR classification task
1:38:32.259597 INFO: Estimating optimal hyperparameters - samples: 599,412, batch_size: 2,455, learning_rate: 7.74e-04
1:38:32.260728 INFO: Using random state 333962 for train-test-split
1:38:45.122222 INFO: Test AUC: 0.614
1:38:45.122413 INFO: Train AUC: 0.625
1:38:45.122450 INFO: AUC difference: 1.85%
1:38:45.603573 INFO: Resetting torch num_threads to 100
1:38:45.636061 PROGRESS: === Extracted 749265 precursors and 4038201 fragments ===
1:38:45.636581 INFO: === FDR correction performed with classifier version 11 ===
1:38:45.637289 PROGRESS: ============================= Precursor FDR =============================
1:38:45.637380 PROGRESS: Total precursors accumulated: 1,574
1:38:45.637441 PROGRESS: Target precursors: 1,559 (99.05%)
1:38:45.637499 PROGRESS: Decoy precursors: 15 (0.95%)
1:38:45.637547 PROGRESS: 
1:38:45.637592 PROGRESS: Precursor Summary:
1:38:45.638976 PROGRESS: Channel   0:	 0.050 FDR: 1,559; 0.010 FDR: 1,559; 0.001 FDR: 1,069
1:38:45.639063 PROGRESS: 
1:38:45.639120 PROGRESS: Protein Summary:
1:38:45.640921 PROGRESS: Channel   0:	 0.050 FDR: 1,305; 0.010 FDR: 1,305; 0.001 FDR:   915
1:38:45.641014 PROGRESS: =========================================================================
1:38:45.656240 INFO: Target number of precursors reached.
1:38:46.099945 INFO: fragments_df: keeping 5000 of 4038201 [sum(precursor_idx_mask)=37065 sum(mass_error_mask)=4038201 stop_rank=5000
1:38:46.525620 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:38:46.739136 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:38:47.389217 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:38:47.389697 INFO: Using score_cutoff 11.257675872802734 (fac=0.99, q=1)
1:38:47.390038 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:38:47.390119 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:38:47.390176 INFO: Updating optimization_manager: score_cutoff        : 10.625021879768372 -> 11.257675872802734
1:38:47.390231 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:38:47.543774 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:38:47.890194 INFO: === checking if optimization conditions were reached ===
1:38:47.890527 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:38:47.894082 INFO: Updating optimization_manager: rt_error            : 885.2060541310278 -> 742.4869167162378
1:38:47.894208 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 742.4869.
1:38:47.894286 INFO: ==============================================
1:38:47.894382 INFO: Starting optimization step 3.
1:38:47.894457 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:38:47.894537 INFO: Using rust extraction backend
1:38:47.894619 PROGRESS: Extracting batch of 250256 precursors
1:38:48.321270 INFO: === Search parameters used ===
1:38:48.321635 INFO: rt_error       : 742.4869167162378
1:38:48.321693 INFO: mobility_error : 0.1
1:38:48.321741 INFO: num_candidates : 3
1:38:48.321786 INFO: ms1_error      : 3
1:38:48.321840 INFO: ms2_error      : 10.0
1:38:48.321880 INFO: fwhm_rt        : 3.0
1:38:48.321920 INFO: quant_window   : 3
1:38:48.321959 INFO: ==============================================
1:38:50.813106 INFO: performing precursor FDR with 40 features
1:38:50.813224 INFO: Decoy channel: -1
1:38:50.813253 INFO: competitive: True
1:38:51.011041 INFO: Setting torch num_threads to 2 for FDR classification task
1:38:51.317878 INFO: Estimating optimal hyperparameters - samples: 599,367, batch_size: 2,455, learning_rate: 7.74e-04
1:38:51.318793 INFO: Using random state 333962 for train-test-split
1:39:04.188171 INFO: Test AUC: 0.610
1:39:04.188375 INFO: Train AUC: 0.626
1:39:04.188410 INFO: AUC difference: 2.47%
1:39:04.668056 INFO: Resetting torch num_threads to 100
1:39:04.699548 PROGRESS: === Extracted 749209 precursors and 4034749 fragments ===
1:39:04.700056 INFO: === FDR correction performed with classifier version 11 ===
1:39:04.700738 PROGRESS: ============================= Precursor FDR =============================
1:39:04.700829 PROGRESS: Total precursors accumulated: 1,486
1:39:04.700889 PROGRESS: Target precursors: 1,472 (99.06%)
1:39:04.700941 PROGRESS: Decoy precursors: 14 (0.94%)
1:39:04.700989 PROGRESS: 
1:39:04.701035 PROGRESS: Precursor Summary:
1:39:04.702321 PROGRESS: Channel   0:	 0.050 FDR: 1,472; 0.010 FDR: 1,472; 0.001 FDR:   352
1:39:04.702408 PROGRESS: 
1:39:04.702465 PROGRESS: Protein Summary:
1:39:04.704132 PROGRESS: Channel   0:	 0.050 FDR: 1,241; 0.010 FDR: 1,241; 0.001 FDR:   319
1:39:04.704237 PROGRESS: =========================================================================
1:39:04.722349 INFO: Target number of precursors reached.
1:39:05.213041 INFO: fragments_df: keeping 5000 of 4034749 [sum(precursor_idx_mask)=35187 sum(mass_error_mask)=4034749 stop_rank=5000
1:39:05.641374 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:39:05.846135 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:39:06.492129 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:39:06.492593 INFO: Using score_cutoff 11.765414582920075 (fac=0.99, q=1)
1:39:06.492929 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:39:06.493007 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:39:06.493066 INFO: Updating optimization_manager: score_cutoff        : 11.257675872802734 -> 11.765414582920075
1:39:06.493120 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:39:06.643429 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:39:06.984253 INFO: === checking if optimization conditions were reached ===
1:39:06.984557 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:39:06.988000 INFO: Updating optimization_manager: rt_error            : 742.4869167162378 -> 751.0098719789196
1:39:06.988127 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 751.0099.
1:39:06.988204 INFO: ==============================================
1:39:06.988289 INFO: Starting optimization step 4.
1:39:06.988372 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:39:06.988452 INFO: Using rust extraction backend
1:39:06.988523 PROGRESS: Extracting batch of 250256 precursors
1:39:07.411807 INFO: === Search parameters used ===
1:39:07.412139 INFO: rt_error       : 751.0098719789196
1:39:07.412197 INFO: mobility_error : 0.1
1:39:07.412246 INFO: num_candidates : 3
1:39:07.412296 INFO: ms1_error      : 3
1:39:07.412340 INFO: ms2_error      : 10.0
1:39:07.412381 INFO: fwhm_rt        : 3.0
1:39:07.412421 INFO: quant_window   : 3
1:39:07.412460 INFO: ==============================================
1:39:09.939098 INFO: performing precursor FDR with 40 features
1:39:09.939236 INFO: Decoy channel: -1
1:39:09.939262 INFO: competitive: True
1:39:10.134482 INFO: Setting torch num_threads to 2 for FDR classification task
1:39:10.437160 INFO: Estimating optimal hyperparameters - samples: 599,388, batch_size: 2,455, learning_rate: 7.74e-04
1:39:10.438314 INFO: Using random state 333962 for train-test-split
1:39:23.345376 INFO: Test AUC: 0.613
1:39:23.345507 INFO: Train AUC: 0.626
1:39:23.345540 INFO: AUC difference: 2.07%
1:39:25.238486 INFO: Resetting torch num_threads to 100
1:39:25.412857 PROGRESS: === Extracted 749235 precursors and 4036046 fragments ===
1:39:25.413333 INFO: === FDR correction performed with classifier version 11 ===
1:39:25.414026 PROGRESS: ============================= Precursor FDR =============================
1:39:25.414117 PROGRESS: Total precursors accumulated: 1,463
1:39:25.414177 PROGRESS: Target precursors: 1,449 (99.04%)
1:39:25.414227 PROGRESS: Decoy precursors: 14 (0.96%)
1:39:25.414273 PROGRESS: 
1:39:25.414318 PROGRESS: Precursor Summary:
1:39:25.415685 PROGRESS: Channel   0:	 0.050 FDR: 1,449; 0.010 FDR: 1,449; 0.001 FDR: 1,147
1:39:25.415778 PROGRESS: 
1:39:25.415843 PROGRESS: Protein Summary:
1:39:25.417577 PROGRESS: Channel   0:	 0.050 FDR: 1,224; 0.010 FDR: 1,224; 0.001 FDR:   975
1:39:25.417670 PROGRESS: =========================================================================
1:39:25.432328 INFO: Target number of precursors reached.
1:39:25.873156 INFO: fragments_df: keeping 5000 of 4036046 [sum(precursor_idx_mask)=34754 sum(mass_error_mask)=4036046 stop_rank=5000
1:39:26.344295 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:39:26.552072 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:39:27.200646 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:39:27.201122 INFO: Using score_cutoff 11.95649670753479 (fac=0.99, q=1)
1:39:27.201494 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:39:27.201571 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:39:27.201623 INFO: Updating optimization_manager: score_cutoff        : 11.765414582920075 -> 11.95649670753479
1:39:27.201682 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:39:27.353659 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:39:27.676411 INFO: === checking if optimization conditions were reached ===
1:39:27.676694 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:39:27.677968 INFO: Updating optimization_manager: rt_error            : 751.0098719789196 -> 885.2060541310278
1:39:27.678117 INFO: Updating optimization_manager: classifier_version  : 11 -> 14
1:39:27.678214 INFO: Updating optimization_manager: score_cutoff        : 11.95649670753479 -> 11.257675872802734
1:39:27.678314 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:39:27.678402 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:39:27.678493 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 885.2061 found after 5 searches.
1:39:27.678557 INFO: ==============================================
1:39:27.678643 PROGRESS: Optimization finished for rt_error.
1:39:28.073297 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:39:28.224453 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:39:28.548547 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:39:28.548811 PROGRESS: ==============================================
1:39:28.548883 PROGRESS: ms2_error      : 10.0000
1:39:28.548944 PROGRESS: rt_error       : 885.2061
1:39:28.548993 PROGRESS: ==============================================
1:39:28.549810 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:39:36.208231 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:39:52.857517 INFO: Using rust extraction backend
1:39:52.858121 PROGRESS: Extracting batch of 11997144 precursors
1:40:08.834943 INFO: === Search parameters used ===
1:40:08.835524 INFO: rt_error       : 885.2060541310278
1:40:08.835592 INFO: mobility_error : 0.1
1:40:08.835645 INFO: num_candidates : 3
1:40:08.835700 INFO: ms1_error      : 3
1:40:08.835744 INFO: ms2_error      : 10.0
1:40:08.835785 INFO: fwhm_rt        : 3.0
1:40:08.835835 INFO: quant_window   : 3
1:40:08.835878 INFO: ==============================================
1:40:40.306210 INFO: Removed 9638919 precursors with score below cutoff 11.257675872802734
1:41:01.204152 INFO: performing precursor FDR with 40 features
1:41:01.204427 INFO: Decoy channel: -1
1:41:01.204459 INFO: competitive: True
1:41:03.965218 INFO: Setting torch num_threads to 2 for FDR classification task
1:41:14.580653 INFO: Estimating optimal hyperparameters - samples: 21,081,791, batch_size: 4,096, learning_rate: 1.00e-03
1:41:14.645593 INFO: Using random state 198618 for train-test-split
1:48:03.263785 INFO: Test AUC: 0.621
1:48:03.264083 INFO: Train AUC: 0.621
1:48:03.264130 INFO: AUC difference: 0.10%
1:48:09.641360 INFO: Resetting torch num_threads to 100
1:48:11.737277 PROGRESS: ============================= Precursor FDR =============================
1:48:11.737618 PROGRESS: Total precursors accumulated: 93,039
1:48:11.737690 PROGRESS: Target precursors: 92,118 (99.01%)
1:48:11.737746 PROGRESS: Decoy precursors: 921 (0.99%)
1:48:11.737799 PROGRESS: 
1:48:11.737846 PROGRESS: Precursor Summary:
1:48:11.765941 PROGRESS: Channel   0:	 0.050 FDR: 92,118; 0.010 FDR: 92,118; 0.001 FDR: 62,264
1:48:11.766177 PROGRESS: 
1:48:11.766237 PROGRESS: Protein Summary:
1:48:11.803420 PROGRESS: Channel   0:	 0.050 FDR: 13,580; 0.010 FDR: 13,580; 0.001 FDR: 9,411
1:48:11.803665 PROGRESS: =========================================================================
1:48:11.946424 PROGRESS: === Transfer learning quantification ===
1:48:11.946718 INFO: creating library for charged fragment types: ['b', 'y']
1:48:12.309341 INFO: Calibrating library
1:48:12.309626 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:48:12.364673 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:48:12.908669 INFO: quantifying 93,039 precursors with 4,174,000 fragments
1:48:12.908978 INFO: Using rust extraction backend
1:48:13.846843 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/psm.parquet
1:48:14.012491 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.parquet
1:48:14.246660 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.transfer.parquet
1:48:14.740136 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:48:43.739930 PROGRESS: Processing search outputs
1:48:43.740227 PROGRESS: === Performing protein grouping and FDR ===
1:48:43.740292 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:48:43.830398 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:48:43.899778 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:48:43.954231 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:48:44.034849 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:48:44.103746 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:48:44.216118 INFO: Performing protein inference
1:48:45.695684 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
1:53:50.494513 INFO: Performing protein FDR
1:54:03.154302 INFO: Normalizing q-values using 20,217 targets and 3,928 decoys
1:54:03.161928 INFO: Test AUC: 0.847
1:54:03.162173 INFO: Train AUC: 0.854
1:54:03.162232 INFO: AUC difference: 0.76%
1:54:05.156435 INFO: ================ Protein FDR =================
1:54:05.156889 INFO: Unique protein groups in output
1:54:05.156929 INFO:   1% protein FDR: 10,243
1:54:05.156951 INFO: 
1:54:05.156976 INFO: Unique precursor in output
1:54:05.156996 INFO:   1% protein FDR: 132,119
1:54:05.157015 INFO: ================================================
1:54:05.383743 PROGRESS: Building search statistics
1:54:05.794040 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
1:54:05.794562 INFO: Initializing OptimizationManager
1:54:05.795093 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
1:54:05.795193 INFO: Initializing CalibrationManager
1:54:05.795713 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
1:54:05.795807 INFO: Initializing RawFileManager
1:54:05.879582 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
1:54:05.879972 INFO: Initializing OptimizationManager
1:54:05.880345 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
1:54:05.880425 INFO: Initializing CalibrationManager
1:54:05.880796 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
1:54:05.880883 INFO: Initializing RawFileManager
1:54:05.969629 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
1:54:05.970003 INFO: Initializing OptimizationManager
1:54:05.970354 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
1:54:05.970437 INFO: Initializing CalibrationManager
1:54:05.970832 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
1:54:05.970947 INFO: Initializing RawFileManager
1:54:06.054926 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
1:54:06.055332 INFO: Initializing OptimizationManager
1:54:06.055705 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
1:54:06.055788 INFO: Initializing CalibrationManager
1:54:06.056187 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
1:54:06.056297 INFO: Initializing RawFileManager
1:54:06.145040 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
1:54:06.145438 INFO: Initializing OptimizationManager
1:54:06.145799 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
1:54:06.145881 INFO: Initializing CalibrationManager
1:54:06.146297 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
1:54:06.146382 INFO: Initializing RawFileManager
1:54:06.233593 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
1:54:06.234018 INFO: Initializing OptimizationManager
1:54:06.234347 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
1:54:06.234431 INFO: Initializing CalibrationManager
1:54:06.234779 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
1:54:06.234874 INFO: Initializing RawFileManager
1:54:06.249612 INFO: Writing stat output to disk
1:54:06.249917 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/stat.tsv to disk
1:54:06.284425 PROGRESS: Building internal statistics
1:54:06.285280 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
1:54:06.285341 INFO: Initializing TimingManager
1:54:06.286237 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
1:54:06.286282 INFO: Initializing TimingManager
1:54:06.286545 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
1:54:06.286581 INFO: Initializing TimingManager
1:54:06.286822 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
1:54:06.286857 INFO: Initializing TimingManager
1:54:06.287097 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
1:54:06.287135 INFO: Initializing TimingManager
1:54:06.287428 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
1:54:06.287465 INFO: Initializing TimingManager
1:54:06.288373 INFO: Writing internal output to disk
1:54:06.288438 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/internal.tsv to disk
1:54:06.625596 INFO: Performing label free quantification
1:54:06.625892 INFO: Accumulating fragment data
1:54:06.626006 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
1:54:07.234780 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
1:54:11.516538 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:54:15.801073 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:54:20.256248 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:54:25.184721 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
1:54:31.549804 INFO: Performing label free quantification on the precursor level
1:54:31.550368 INFO: Filtering fragments by quality
1:54:32.799822 INFO: Performing label-free quantification with directlfq normalization
1:54:34.519547 INFO: Applying directLFQ normalization
1:54:36.583705 INFO: 132119 lfq-groups total
1:57:36.658846 INFO: using 100 processes
1:57:37.542096 INFO: lfq-object 0
1:57:37.806475 INFO: lfq-object 400
1:57:37.898773 INFO: lfq-object 700
1:57:37.951336 INFO: lfq-object 500
1:57:38.076802 INFO: lfq-object 1000
1:57:38.090203 INFO: lfq-object 600
1:57:38.100002 INFO: lfq-object 800
1:57:38.213715 INFO: lfq-object 1400
1:57:38.242212 INFO: lfq-object 900
1:57:38.360732 INFO: lfq-object 100
1:57:38.363855 INFO: lfq-object 1100
1:57:38.395123 INFO: lfq-object 1500
1:57:38.539242 INFO: lfq-object 1700
1:57:38.555315 INFO: lfq-object 1200
1:57:38.558467 INFO: lfq-object 1600
1:57:38.706741 INFO: lfq-object 1300
1:57:38.725966 INFO: lfq-object 1800
1:57:38.924538 INFO: lfq-object 2000
1:57:38.927877 INFO: lfq-object 1900
1:57:39.006998 INFO: lfq-object 200
1:57:39.075997 INFO: lfq-object 2100
1:57:39.217759 INFO: lfq-object 2200
1:57:39.360101 INFO: lfq-object 2300
1:57:39.573013 INFO: lfq-object 2400
1:57:39.681434 INFO: lfq-object 300
1:57:39.720512 INFO: lfq-object 2500
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1:57:55.499635 INFO: lfq-object 2700
1:57:55.527078 INFO: lfq-object 3000
1:57:55.719726 INFO: lfq-object 3400
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1:57:57.454575 INFO: lfq-object 4100
1:57:57.470425 INFO: lfq-object 4900
1:57:57.491281 INFO: lfq-object 4600
1:57:57.544786 INFO: lfq-object 5000
1:57:57.661207 INFO: lfq-object 5300
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1:57:59.426116 INFO: lfq-object 6500
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1:57:59.553267 INFO: lfq-object 6600
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1:57:59.776957 INFO: lfq-object 6900
1:57:59.905273 INFO: lfq-object 7000
1:58:00.181409 INFO: lfq-object 7300
1:58:00.368158 INFO: lfq-object 7400
1:58:00.472766 INFO: lfq-object 7700
1:58:00.521781 INFO: lfq-object 7500
1:58:00.633741 INFO: lfq-object 7100
1:58:00.678144 INFO: lfq-object 7600
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1:58:01.080585 INFO: lfq-object 8000
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1:58:02.091887 INFO: lfq-object 8700
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1:58:03.559988 INFO: lfq-object 8500
1:58:03.581812 INFO: lfq-object 10000
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2:09:19.973240 INFO: Performing label free quantification on the pg level
2:09:19.973687 INFO: Filtering fragments by quality
2:09:20.362432 INFO: Performing label-free quantification with directlfq normalization
2:09:20.557586 INFO: Applying directLFQ normalization
2:09:20.748693 INFO: 10243 lfq-groups total
2:10:14.105380 INFO: using 100 processes
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2:10:19.588741 INFO: lfq-object 9400
2:10:19.609828 INFO: lfq-object 9500
2:10:19.651422 INFO: lfq-object 9600
2:10:19.691450 INFO: lfq-object 9700
2:10:19.820848 INFO: lfq-object 9800
2:10:19.822710 INFO: lfq-object 9900
2:10:19.989670 INFO: lfq-object 10200
2:10:20.018955 INFO: lfq-object 10100
2:10:20.091321 INFO: lfq-object 10000
2:10:23.013285 INFO: Writing psm output to disk
2:10:23.104336 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/precursors.parquet to disk
2:10:23.919727 INFO: Writing precursor output to disk
2:10:23.928395 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/precursor.matrix.parquet to disk
2:10:24.032797 INFO: Writing peptide output to disk
2:10:24.037243 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/peptide.matrix.parquet to disk
2:10:24.120265 INFO: Writing pg output to disk
2:10:24.124136 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/pg.matrix.parquet to disk
2:10:24.197871 PROGRESS: Building MBR spectral library
2:10:24.198089 INFO: Running MbrLibraryBuilder
2:10:26.176942 INFO: MBR spectral library contains 132,119 precursors, 10,243 proteins
2:10:26.177084 INFO: Writing MBR spectral library to disk
2:10:27.117678 PROGRESS: ======== Building transfer library ========
2:10:36.742172 INFO: Performing quality control for transfer learning.
2:10:36.742660 INFO: Normalize by delta: True
2:10:36.742754 INFO: Precursor correlation cutoff: 0.5
2:10:36.742809 INFO: Fragment correlation cutoff: 0.75
2:11:47.453056 INFO: Built transfer library using 6 folders and 4 processes
2:11:47.837753 INFO: Modification                    Total      Unique   Total MS2  Unique MS2
2:11:47.838261 INFO: Carbamidomethyl@C              55,126      23,932      30,576      14,930
2:11:47.838356 INFO: Oxidation@M                    16,881       8,672       6,617       3,909
2:11:47.838425 INFO:                               256,831     109,179     157,123      75,052
2:11:47.838494 INFO: ------------------------- ------------------------------------------------
2:11:47.838965 INFO: Total                         326,180     140,360     193,376      93,290
2:11:47.839026 INFO: Writing transfer library to disk
2:11:49.767413 PROGRESS: Train PeptDeep Models
2:11:51.087655 INFO: Device set to cpu
2:12:05.933944 PROGRESS:  Model tested on all dataset with the following metrics:
2:12:05.934296 PROGRESS:  l1_loss                       : 0.0562
2:12:05.934345 PROGRESS:  r_square                      : 0.9713
2:12:05.934382 PROGRESS:  r                             : 0.9855
2:12:05.934416 PROGRESS:  slope                         : 0.8251
2:12:05.934448 PROGRESS:  intercept                     : 0.1144
2:12:05.934481 PROGRESS:  abs_error_95th_percentile     : 0.1047
2:12:05.934654 PROGRESS:  Fine-tuning RT model with the following settings:
2:12:05.934704 INFO:  Train fraction:      0.70     Train size:      228326    
2:12:05.934740 INFO:  Validation fraction: 0.20     Validation size: 65236     
2:12:05.934772 INFO:  Test fraction:       0.10     Test size:       32618     
2:12:40.281355 PROGRESS:  Epoch 0   Lr: 0.00004   Training loss: 0.0422   validation loss: 0.0304
2:13:13.017755 PROGRESS:  Epoch 1   Lr: 0.00006   Training loss: 0.0211   validation loss: 0.0148
2:13:47.293079 PROGRESS:  Epoch 2   Lr: 0.00008   Training loss: 0.0141   validation loss: 0.0119
2:14:21.349998 PROGRESS:  Epoch 3   Lr: 0.00010   Training loss: 0.0122   validation loss: 0.0109
2:14:53.152919 PROGRESS:  Epoch 4   Lr: 0.00012   Training loss: 0.0114   validation loss: 0.0102
2:15:29.113492 PROGRESS:  Epoch 5   Lr: 0.00012   Training loss: 0.0109   validation loss: 0.0097
2:16:01.355435 PROGRESS:  Epoch 6   Lr: 0.00012   Training loss: 0.0105   validation loss: 0.0094
2:16:36.404885 PROGRESS:  Epoch 7   Lr: 0.00012   Training loss: 0.0103   validation loss: 0.0093
2:17:08.081745 PROGRESS:  Epoch 8   Lr: 0.00012   Training loss: 0.0099   validation loss: 0.0092
2:17:41.926367 PROGRESS:  Epoch 9   Lr: 0.00012   Training loss: 0.0099   validation loss: 0.0089
2:18:14.691789 PROGRESS:  Epoch 10  Lr: 0.00012   Training loss: 0.0096   validation loss: 0.0090
2:18:47.494783 PROGRESS:  Epoch 11  Lr: 0.00012   Training loss: 0.0096   validation loss: 0.0088
2:19:20.127964 PROGRESS:  Epoch 12  Lr: 0.00012   Training loss: 0.0094   validation loss: 0.0087
2:20:00.685426 PROGRESS:  Epoch 13  Lr: 0.00012   Training loss: 0.0094   validation loss: 0.0088
2:20:33.040714 PROGRESS:  Epoch 14  Lr: 0.00012   Training loss: 0.0092   validation loss: 0.0085
2:21:06.279502 PROGRESS:  Epoch 15  Lr: 0.00012   Training loss: 0.0091   validation loss: 0.0084
2:21:38.687046 PROGRESS:  Epoch 16  Lr: 0.00012   Training loss: 0.0090   validation loss: 0.0083
2:22:09.482898 PROGRESS:  Epoch 17  Lr: 0.00012   Training loss: 0.0089   validation loss: 0.0085
2:22:41.637756 PROGRESS:  Epoch 18  Lr: 0.00012   Training loss: 0.0089   validation loss: 0.0082
2:23:12.321066 PROGRESS:  Epoch 19  Lr: 0.00012   Training loss: 0.0088   validation loss: 0.0082
2:23:45.669402 PROGRESS:  Epoch 20  Lr: 0.00012   Training loss: 0.0087   validation loss: 0.0081
2:24:17.852295 PROGRESS:  Epoch 21  Lr: 0.00012   Training loss: 0.0086   validation loss: 0.0081
2:24:53.625815 PROGRESS:  Epoch 22  Lr: 0.00012   Training loss: 0.0086   validation loss: 0.0084
2:25:24.051443 PROGRESS:  Epoch 23  Lr: 0.00012   Training loss: 0.0085   validation loss: 0.0079
2:25:56.347652 PROGRESS:  Epoch 24  Lr: 0.00012   Training loss: 0.0085   validation loss: 0.0080
2:26:26.332760 PROGRESS:  Epoch 25  Lr: 0.00012   Training loss: 0.0084   validation loss: 0.0079
2:26:58.912908 PROGRESS:  Epoch 26  Lr: 0.00012   Training loss: 0.0083   validation loss: 0.0081
2:27:29.482190 PROGRESS:  Epoch 27  Lr: 0.00012   Training loss: 0.0084   validation loss: 0.0079
2:28:01.909140 PROGRESS:  Epoch 28  Lr: 0.00012   Training loss: 0.0082   validation loss: 0.0081
2:28:34.263939 PROGRESS:  Epoch 29  Lr: 0.00012   Training loss: 0.0082   validation loss: 0.0078
2:30:28.551721 PROGRESS:  Epoch 30  Lr: 0.00012   Training loss: 0.0082   validation loss: 0.0077
2:31:00.973395 PROGRESS:  Epoch 31  Lr: 0.00012   Training loss: 0.0081   validation loss: 0.0077
2:31:32.111292 PROGRESS:  Epoch 32  Lr: 0.00012   Training loss: 0.0080   validation loss: 0.0079
2:32:05.004659 PROGRESS:  Epoch 33  Lr: 0.00012   Training loss: 0.0080   validation loss: 0.0077
2:32:36.246189 PROGRESS:  Epoch 34  Lr: 0.00012   Training loss: 0.0081   validation loss: 0.0077
2:33:09.719195 PROGRESS:  Epoch 35  Lr: 0.00012   Training loss: 0.0080   validation loss: 0.0080
2:33:42.130182 PROGRESS:  Epoch 36  Lr: 0.00012   Training loss: 0.0080   validation loss: 0.0077
2:34:14.742644 PROGRESS:  Epoch 37  Lr: 0.00012   Training loss: 0.0079   validation loss: 0.0076
2:34:45.845836 PROGRESS:  Epoch 38  Lr: 0.00012   Training loss: 0.0079   validation loss: 0.0076
2:35:19.540497 PROGRESS:  Epoch 39  Lr: 0.00012   Training loss: 0.0078   validation loss: 0.0078
2:35:52.384351 PROGRESS:  Epoch 40  Lr: 0.00012   Training loss: 0.0078   validation loss: 0.0075
2:36:24.670850 PROGRESS:  Epoch 41  Lr: 0.00012   Training loss: 0.0077   validation loss: 0.0075
2:36:58.394328 PROGRESS:  Epoch 42  Lr: 0.00012   Training loss: 0.0076   validation loss: 0.0076
2:37:30.316862 PROGRESS:  Epoch 43  Lr: 0.00012   Training loss: 0.0077   validation loss: 0.0075
2:38:03.139567 PROGRESS:  Epoch 44  Lr: 0.00012   Training loss: 0.0077   validation loss: 0.0075
2:38:34.900833 PROGRESS:  Epoch 45  Lr: 0.00012   Training loss: 0.0076   validation loss: 0.0075
2:39:07.755849 PROGRESS:  Epoch 46  Lr: 0.00012   Training loss: 0.0077   validation loss: 0.0075
2:39:43.127444 PROGRESS:  Epoch 47  Lr: 0.00012   Training loss: 0.0075   validation loss: 0.0075
2:40:16.263972 PROGRESS:  Epoch 48  Lr: 0.00012   Training loss: 0.0075   validation loss: 0.0074
2:40:48.887026 PROGRESS:  Epoch 49  Lr: 0.00012   Training loss: 0.0075   validation loss: 0.0075
2:41:20.377212 PROGRESS:  Epoch 50  Lr: 0.00012   Training loss: 0.0075   validation loss: 0.0074
2:41:21.926360 PROGRESS:  Model tested on test dataset with the following metrics:
2:41:21.926574 PROGRESS:  l1_loss                       : 0.0075
2:41:21.926617 PROGRESS:  r_square                      : 0.9895
2:41:21.926651 PROGRESS:  r                             : 0.9947
2:41:21.926681 PROGRESS:  slope                         : 0.9937
2:41:21.926712 PROGRESS:  intercept                     : 0.0039
2:41:21.926741 PROGRESS:  abs_error_95th_percentile     : 0.0205
2:41:31.122368 PROGRESS:  Model tested on all dataset with the following metrics:
2:41:31.122591 PROGRESS:  bce_loss                      : 0.0816
2:41:31.122630 PROGRESS:  precision                     : 0.9170
2:41:31.122658 PROGRESS:  recall                        : 0.9247
2:41:31.122970 PROGRESS:  Fine-tuning Charge model with following settings:
2:41:31.123004 INFO:  Train fraction:      0.70     Train size:      95178     
2:41:31.123030 INFO:  Validation fraction: 0.20     Validation size: 27193     
2:41:31.123051 INFO:  Test fraction:       0.10     Test size:       13597     
2:41:51.679067 PROGRESS:  Epoch 0   Lr: 0.00004   Training loss: 0.0734   validation loss: 0.0683
2:42:10.839369 PROGRESS:  Epoch 1   Lr: 0.00006   Training loss: 0.0614   validation loss: 0.0520
2:42:30.436782 PROGRESS:  Epoch 2   Lr: 0.00008   Training loss: 0.0524   validation loss: 0.0459
2:42:50.719915 PROGRESS:  Epoch 3   Lr: 0.00010   Training loss: 0.0454   validation loss: 0.0399
2:43:13.429733 PROGRESS:  Epoch 4   Lr: 0.00012   Training loss: 0.0459   validation loss: 0.0387
2:43:33.241872 PROGRESS:  Epoch 5   Lr: 0.00012   Training loss: 0.0437   validation loss: 0.0366
2:43:53.052668 PROGRESS:  Epoch 6   Lr: 0.00012   Training loss: 0.0376   validation loss: 0.0338
2:44:12.586369 PROGRESS:  Epoch 7   Lr: 0.00012   Training loss: 0.0372   validation loss: 0.0588
2:44:32.345702 PROGRESS:  Epoch 8   Lr: 0.00012   Training loss: 0.0389   validation loss: 0.0348
2:44:53.887780 PROGRESS:  Epoch 9   Lr: 0.00012   Training loss: 0.0387   validation loss: 0.0364
2:45:13.426618 PROGRESS:  Epoch 10  Lr: 0.00012   Training loss: 0.0344   validation loss: 0.0319
2:45:33.608368 PROGRESS:  Epoch 11  Lr: 0.00012   Training loss: 0.0331   validation loss: 0.0311
2:45:53.716464 PROGRESS:  Epoch 12  Lr: 0.00012   Training loss: 0.0333   validation loss: 0.0367
2:46:16.293314 PROGRESS:  Epoch 13  Lr: 0.00012   Training loss: 0.0343   validation loss: 0.0319
2:46:36.421374 PROGRESS:  Epoch 14  Lr: 0.00012   Training loss: 0.0340   validation loss: 0.0312
2:46:56.304933 PROGRESS:  Epoch 15  Lr: 0.00012   Training loss: 0.0324   validation loss: 0.0299
2:47:16.196635 PROGRESS:  Epoch 16  Lr: 0.00012   Training loss: 0.0330   validation loss: 0.0301
2:47:35.974628 PROGRESS:  Epoch 17  Lr: 0.00012   Training loss: 0.0330   validation loss: 0.0304
2:47:57.827939 PROGRESS:  Epoch 18  Lr: 0.00012   Training loss: 0.0318   validation loss: 0.0312
2:48:17.912900 PROGRESS:  Epoch 19  Lr: 0.00012   Training loss: 0.0316   validation loss: 0.0308
2:48:38.405013 PROGRESS:  Epoch 20  Lr: 0.00012   Training loss: 0.0330   validation loss: 0.0304
2:48:58.475641 PROGRESS:  Epoch 21  Lr: 0.00012   Training loss: 0.0295   validation loss: 0.0294
2:49:18.860974 PROGRESS:  Epoch 22  Lr: 0.00012   Training loss: 0.0308   validation loss: 0.0314
2:49:40.481142 PROGRESS:  Epoch 23  Lr: 0.00012   Training loss: 0.0315   validation loss: 0.0299
2:50:00.116859 PROGRESS:  Epoch 24  Lr: 0.00012   Training loss: 0.0302   validation loss: 0.0292
2:50:19.760141 PROGRESS:  Epoch 25  Lr: 0.00006   Training loss: 0.0298   validation loss: 0.0296
2:50:40.086770 PROGRESS:  Epoch 26  Lr: 0.00006   Training loss: 0.0295   validation loss: 0.0280
2:51:02.064942 PROGRESS:  Epoch 27  Lr: 0.00006   Training loss: 0.0285   validation loss: 0.0279
2:51:21.631923 PROGRESS:  Epoch 28  Lr: 0.00006   Training loss: 0.0284   validation loss: 0.0278
2:51:40.962428 PROGRESS:  Epoch 29  Lr: 0.00006   Training loss: 0.0278   validation loss: 0.0281
2:52:00.750047 PROGRESS:  Epoch 30  Lr: 0.00006   Training loss: 0.0283   validation loss: 0.0276
2:52:20.167302 PROGRESS:  Epoch 31  Lr: 0.00006   Training loss: 0.0281   validation loss: 0.0275
2:52:41.614287 PROGRESS:  Epoch 32  Lr: 0.00006   Training loss: 0.0275   validation loss: 0.0274
2:53:01.301915 PROGRESS:  Epoch 33  Lr: 0.00006   Training loss: 0.0275   validation loss: 0.0275
2:53:20.826215 PROGRESS:  Epoch 34  Lr: 0.00006   Training loss: 0.0275   validation loss: 0.0274
2:53:40.997800 PROGRESS:  Epoch 35  Lr: 0.00006   Training loss: 0.0274   validation loss: 0.0274
2:54:02.709060 PROGRESS:  Epoch 36  Lr: 0.00006   Training loss: 0.0275   validation loss: 0.0278
2:54:22.712558 PROGRESS:  Epoch 37  Lr: 0.00006   Training loss: 0.0277   validation loss: 0.0277
2:54:43.020738 PROGRESS:  Epoch 38  Lr: 0.00006   Training loss: 0.0273   validation loss: 0.0280
2:55:03.219312 PROGRESS:  Epoch 39  Lr: 0.00006   Training loss: 0.0281   validation loss: 0.0279
2:55:23.248147 PROGRESS:  Epoch 40  Lr: 0.00006   Training loss: 0.0275   validation loss: 0.0277
2:55:45.365924 PROGRESS:  Epoch 41  Lr: 0.00006   Training loss: 0.0284   validation loss: 0.0293
2:56:05.602603 PROGRESS:  Epoch 42  Lr: 0.00006   Training loss: 0.0270   validation loss: 0.0285
2:56:26.277781 PROGRESS:  Epoch 43  Lr: 0.00006   Training loss: 0.0281   validation loss: 0.0291
2:56:46.953154 PROGRESS:  Epoch 44  Lr: 0.00006   Training loss: 0.0266   validation loss: 0.0270
2:57:08.614386 PROGRESS:  Epoch 45  Lr: 0.00006   Training loss: 0.0265   validation loss: 0.0272
2:57:28.951901 PROGRESS:  Epoch 46  Lr: 0.00006   Training loss: 0.0266   validation loss: 0.0270
2:57:49.374778 PROGRESS:  Epoch 47  Lr: 0.00006   Training loss: 0.0262   validation loss: 0.0271
2:58:09.432538 PROGRESS:  Epoch 48  Lr: 0.00006   Training loss: 0.0273   validation loss: 0.0269
2:58:29.478330 PROGRESS:  Epoch 49  Lr: 0.00006   Training loss: 0.0270   validation loss: 0.0272
2:58:50.916245 PROGRESS:  Epoch 50  Lr: 0.00006   Training loss: 0.0263   validation loss: 0.0273
2:58:51.853130 PROGRESS:  Model tested on test dataset with the following metrics:
2:58:51.853342 PROGRESS:  bce_loss                      : 0.0285
2:58:51.853380 PROGRESS:  precision                     : 0.9299
2:58:51.853407 PROGRESS:  recall                        : 0.9637
2:59:55.212008 PROGRESS:  Model tested on validation dataset with the following metrics:
2:59:55.212214 PROGRESS:  l1_loss                       : 0.0575
2:59:55.212251 PROGRESS:  PCC-mean                      : 0.8550
2:59:55.212279 PROGRESS:  COS-mean                      : 0.8745
2:59:55.212303 PROGRESS:  SA-mean                       : 0.6776
2:59:55.212327 PROGRESS:  SPC-mean                      : 0.2555
2:59:55.215232 PROGRESS:  Fine-tuning MS2 model with the following settings:
2:59:55.215300 INFO:  Train fraction:      0.70     Train size:      228326    
2:59:55.215329 INFO:  Validation fraction: 0.20     Validation size: 65236     
2:59:55.215352 INFO:  Test fraction:       0.10     Test size:       32618     
3:01:35.880987 PROGRESS:  Epoch 0   Lr: 0.00004   Training loss: 0.0521   validation loss: 0.0488
3:03:16.280592 PROGRESS:  Epoch 1   Lr: 0.00006   Training loss: 0.0483   validation loss: 0.0492
3:04:58.355821 PROGRESS:  Epoch 2   Lr: 0.00008   Training loss: 0.0472   validation loss: 0.0494
3:06:39.468557 PROGRESS:  Epoch 3   Lr: 0.00010   Training loss: 0.0470   validation loss: 0.0485
3:08:21.506249 PROGRESS:  Epoch 4   Lr: 0.00012   Training loss: 0.0468   validation loss: 0.0511
3:10:02.871171 PROGRESS:  Epoch 5   Lr: 0.00012   Training loss: 0.0466   validation loss: 0.0501
3:11:42.622264 PROGRESS:  Epoch 6   Lr: 0.00012   Training loss: 0.0465   validation loss: 0.0506
3:13:23.164882 PROGRESS:  Epoch 7   Lr: 0.00012   Training loss: 0.0464   validation loss: 0.0467
3:15:04.858577 PROGRESS:  Epoch 8   Lr: 0.00012   Training loss: 0.0465   validation loss: 0.0515
3:16:45.007772 PROGRESS:  Epoch 9   Lr: 0.00012   Training loss: 0.0463   validation loss: 0.0499
3:18:25.048079 PROGRESS:  Epoch 10  Lr: 0.00012   Training loss: 0.0462   validation loss: 0.0486
3:20:06.658395 PROGRESS:  Epoch 11  Lr: 0.00012   Training loss: 0.0464   validation loss: 0.0502
3:21:47.717694 PROGRESS:  Epoch 12  Lr: 0.00012   Training loss: 0.0461   validation loss: 0.0502
3:23:27.241040 PROGRESS:  Epoch 13  Lr: 0.00012   Training loss: 0.0461   validation loss: 0.0497
3:25:09.026771 PROGRESS:  Epoch 14  Lr: 0.00012   Training loss: 0.0462   validation loss: 0.0500
3:26:51.105138 PROGRESS:  Epoch 15  Lr: 0.00012   Training loss: 0.0460   validation loss: 0.0527
3:30:19.788113 PROGRESS:  Epoch 16  Lr: 0.00012   Training loss: 0.0457   validation loss: 0.0510
3:31:59.681623 PROGRESS:  Epoch 17  Lr: 0.00012   Training loss: 0.0457   validation loss: 0.0484
3:33:40.025419 PROGRESS:  Epoch 18  Lr: 0.00012   Training loss: 0.0458   validation loss: 0.0515
3:35:21.391572 PROGRESS:  Epoch 19  Lr: 0.00012   Training loss: 0.0458   validation loss: 0.0468
3:37:03.355428 PROGRESS:  Epoch 20  Lr: 0.00012   Training loss: 0.0455   validation loss: 0.0500
3:38:44.622774 PROGRESS:  Epoch 21  Lr: 0.00012   Training loss: 0.0456   validation loss: 0.0489
3:40:26.102540 PROGRESS:  Epoch 22  Lr: 0.00012   Training loss: 0.0457   validation loss: 0.0500
3:42:07.885812 PROGRESS:  Epoch 23  Lr: 0.00012   Training loss: 0.0456   validation loss: 0.0514
3:43:48.886565 PROGRESS:  Epoch 24  Lr: 0.00012   Training loss: 0.0455   validation loss: 0.0494
3:45:31.228049 PROGRESS:  Epoch 25  Lr: 0.00012   Training loss: 0.0454   validation loss: 0.0511
3:47:15.857871 PROGRESS:  Epoch 26  Lr: 0.00012   Training loss: 0.0454   validation loss: 0.0490
3:48:56.033961 PROGRESS:  Epoch 27  Lr: 0.00012   Training loss: 0.0452   validation loss: 0.0494
3:50:36.502097 PROGRESS:  Epoch 28  Lr: 0.00012   Training loss: 0.0452   validation loss: 0.0488
3:52:16.767401 PROGRESS:  Epoch 29  Lr: 0.00012   Training loss: 0.0450   validation loss: 0.0497
3:53:57.389685 PROGRESS:  Epoch 30  Lr: 0.00012   Training loss: 0.0453   validation loss: 0.0477
3:55:39.836104 PROGRESS:  Epoch 31  Lr: 0.00012   Training loss: 0.0453   validation loss: 0.0504
3:55:43.425798 PROGRESS:  Model tested on test dataset with the following metrics:
3:55:43.425974 PROGRESS:  l1_loss                       : 0.0506
3:55:43.426010 PROGRESS:  PCC-mean                      : 0.8753
3:55:43.426037 PROGRESS:  COS-mean                      : 0.8904
3:55:43.426061 PROGRESS:  SA-mean                       : 0.6991
3:55:43.426085 PROGRESS:  SPC-mean                      : 0.3242
3:55:43.507528 INFO: Writing transfer learning stats output to disk
3:55:43.507633 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/stats.transfer.tsv to disk
3:55:44.161762 PROGRESS: =================== Search step 'transfer' finished ===================
3:55:46.535751 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 3.0, 'target_ms2_tolerance': 10.0}})
3:55:46.535861 INFO: =================== Running step 'library' ===================
3:55:46.536022 INFO: loading default config from /home/robbe/bin/alphadia/alphadia/constants/default.yaml
3:55:46.548676 INFO: loading additional config provided via CLI
3:55:46.548735 INFO: loading additional config provided via CLI parameters
3:55:46.549115 INFO: Updating config with 'user defined'
3:55:46.549180 INFO: Updating config with 'user defined (cli)'
3:55:46.549261 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/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1', 'general': {'thread_count': 100, 'mbr_step_enabled': True, 'transfer_step_enabled': True}, 'library_prediction': {'enabled': True, 'enzyme': 'trypsin/p', 'missed_cleavages': 1, 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M', 'max_var_mod_num': 1, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [380.0, 980.0], 'fragment_mz': [150.0, 2000.0]}, 'search': {'target_ms1_tolerance': 3, 'target_ms2_tolerance': 10, 'extraction_backend': 'rust'}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins'}, 'search_output': {'normalize_directlfq': True}, 'search_initial': {'ms1_tolerance': 3, 'ms2_tolerance': 10}}, {'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']}, {'quant_directory': None, 'general': {'save_mbr_library': True, 'save_library': False}, 'transfer_library': {'enabled': False}, 'transfer_learning': {'enabled': False}, 'library_prediction': {'peptdeep_model_path': '/home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/peptdeep.transfer', 'enabled': True}, 'search': {'target_ms1_tolerance': 3.0, 'target_ms2_tolerance': 10.0}, 'output_directory': '/home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library'}]
3:55:46.549479 INFO: Updating config with 'user defined'
3:55:46.549534 INFO: Updating config with 'user defined (cli)'
3:55:46.549554 INFO: Updating config with 'multistep search'
3:55:46.549601 INFO: ├──version: None
3:55:46.549625 INFO: ├──workflow_name: None
3:55:46.549651 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library [multistep search, default: None][0m
3:55:46.549672 INFO: ├──library_path: None
3:55:46.549690 INFO: ├──raw_paths:
3:55:46.549708 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
3:55:46.549725 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
3:55:46.549742 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
3:55:46.549760 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
3:55:46.549777 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
3:55:46.549794 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
3:55:46.549810 INFO: ├──fasta_paths:
3:55:46.549828 INFO: │   [32;20m- /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta [user defined, default: None][0m
3:55:46.549846 INFO: ├──quant_directory: None
3:55:46.549864 INFO: ├──general
3:55:46.549884 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
3:55:46.549903 INFO: │   [32;20m├──transfer_step_enabled: True [user defined, default: False][0m
3:55:46.549920 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
3:55:46.549938 INFO: │   ├──reuse_calibration: False
3:55:46.549956 INFO: │   ├──reuse_quant: False
3:55:46.549977 INFO: │   ├──log_level: INFO
3:55:46.549995 INFO: │   ├──use_gpu: True
3:55:46.550012 INFO: │   ├──save_figures: True
3:55:46.550030 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
3:55:46.550047 INFO: │   ├──save_flat_library: False
3:55:46.550064 INFO: │   ├──input_library_type: base
3:55:46.550081 INFO: │   ├──save_mbr_library: True
3:55:46.550098 INFO: │   ├──random_state: None
3:55:46.550116 INFO: │   └──fail_fast: False
3:55:46.550132 INFO: ├──library_loading
3:55:46.550150 INFO: │   └──drop_decoys: False
3:55:46.550166 INFO: ├──library_prediction
3:55:46.550184 INFO: │   [32;20m├──enabled: True [multistep search, default: False][0m
3:55:46.550201 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
3:55:46.550218 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
3:55:46.550236 INFO: │   [32;20m├──variable_modifications: Oxidation@M [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
3:55:46.550254 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
3:55:46.550271 INFO: │   ├──missed_cleavages: 1
3:55:46.550287 INFO: │   ├──precursor_len:
3:55:46.550304 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
3:55:46.550322 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
3:55:46.550338 INFO: │   ├──precursor_charge:
3:55:46.550354 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
3:55:46.550371 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
3:55:46.550388 INFO: │   ├──precursor_mz:
3:55:46.550406 INFO: │   │   [32;20m- 380.0 [user defined, default: 400][0m
3:55:46.550423 INFO: │   │   [32;20m- 980.0 [user defined, default: 1200][0m
3:55:46.550439 INFO: │   ├──fragment_mz:
3:55:46.550456 INFO: │   │   [32;20m- 150.0 [user defined, default: 200][0m
3:55:46.550473 INFO: │   │   - 2000.0
3:55:46.550490 INFO: │   ├──nce: 25.0
3:55:46.550507 INFO: │   ├──fragment_types:
3:55:46.550526 INFO: │   │   - b
3:55:46.550543 INFO: │   │   - y
3:55:46.550560 INFO: │   ├──max_fragment_charge: 2
3:55:46.550578 INFO: │   ├──instrument: Lumos
3:55:46.550596 INFO: │   [32;20m├──peptdeep_model_path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/peptdeep.transfer [multistep search, default: None][0m
3:55:46.550615 INFO: │   ├──peptdeep_model_type: generic
3:55:46.550633 INFO: │   ├──predict_charge: False
3:55:46.550652 INFO: │   └──min_charge_probability: 0.1
3:55:46.550669 INFO: ├──custom_modifications:
3:55:46.550688 INFO: │   ├──name: Dimethyl:d12@K
3:55:46.550706 INFO: │   └──composition: H(-2)2H(8)13C(2)
3:55:46.550723 INFO: │   ├──name: Dimethyl:d12@Any_N-term
3:55:46.550740 INFO: │   └──composition: H(-2)2H(8)13C(2)
3:55:46.550757 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
3:55:46.550775 INFO: │   └──composition: H(-2)2H(8)13C(2)
3:55:46.550793 INFO: │   ├──name: mTRAQ:d12@K
3:55:46.550810 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
3:55:46.550828 INFO: │   ├──name: mTRAQ:d12@Any_N-term
3:55:46.550845 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
3:55:46.550863 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
3:55:46.550879 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
3:55:46.550897 INFO: │   ├──name: Label:13C(12)@K
3:55:46.550914 INFO: │   └──composition: C(12)
3:55:46.550931 INFO: ├──search
3:55:46.550948 INFO: │   ├──extraction_backend: rust
3:55:46.550967 INFO: │   [32;20m├──target_ms1_tolerance: 3.0 [multistep search, default: 5][0m
3:55:46.550986 INFO: │   ├──target_ms2_tolerance: 10.0
3:55:46.551004 INFO: │   ├──target_rt_tolerance: 0.0
3:55:46.551022 INFO: │   ├──target_mobility_tolerance: 0.0
3:55:46.551043 INFO: │   ├──quant_window: 3
3:55:46.551062 INFO: │   ├──target_num_candidates: 3
3:55:46.551080 INFO: │   ├──channel_filter: 
3:55:46.551097 INFO: │   ├──compete_for_fragments: True
3:55:46.551114 INFO: │   ├──top_k_fragments_selection: 12
3:55:46.551131 INFO: │   ├──top_k_fragments_scoring: 12
3:55:46.551160 INFO: │   ├──min_fragment_intensity: 0.01
3:55:46.551180 INFO: │   ├──optimized_peak_group_score: False
3:55:46.551198 INFO: │   ├──exclude_shared_ions: True
3:55:46.551214 INFO: │   ├──quant_all: True
3:55:46.551232 INFO: │   └──experimental_xic: True
3:55:46.551249 INFO: ├──calibration
3:55:46.551266 INFO: │   ├──batch_size: 1000
3:55:46.551284 INFO: │   ├──optimization_lock_target: 1000
3:55:46.551301 INFO: │   ├──max_steps: 20
3:55:46.551318 INFO: │   ├──min_steps: 5
3:55:46.551335 INFO: │   ├──max_skips: 1
3:55:46.551352 INFO: │   ├──max_fragments: 5000
3:55:46.551371 INFO: │   └──min_correlation: 0.7
3:55:46.551387 INFO: ├──search_initial
3:55:46.551405 INFO: │   ├──num_candidates: 1
3:55:46.551424 INFO: │   [32;20m├──ms1_tolerance: 3 [user defined, default: 30][0m
3:55:46.551442 INFO: │   [32;20m├──ms2_tolerance: 10 [user defined, default: 30][0m
3:55:46.551459 INFO: │   ├──mobility_tolerance: 0.1
3:55:46.551477 INFO: │   └──rt_tolerance: 0.5
3:55:46.551494 INFO: ├──library_multiplexing
3:55:46.551511 INFO: │   ├──enabled: False
3:55:46.551528 INFO: │   ├──input_channel: 0
3:55:46.551545 INFO: │   └──multiplex_mapping:
3:55:46.551562 INFO: ├──multiplexing
3:55:46.551579 INFO: │   ├──enabled: False
3:55:46.551596 INFO: │   ├──target_channels: 4,8
3:55:46.551613 INFO: │   ├──decoy_channel: 12
3:55:46.551630 INFO: │   ├──reference_channel: 0
3:55:46.551646 INFO: │   └──competitive_scoring: True
3:55:46.551662 INFO: ├──fdr
3:55:46.551680 INFO: │   ├──fdr: 0.01
3:55:46.551699 INFO: │   ├──group_level: proteins
3:55:46.551716 INFO: │   ├──inference_strategy: heuristic
3:55:46.551733 INFO: │   ├──competitive_scoring: True
3:55:46.551750 INFO: │   ├──keep_decoys: False
3:55:46.551768 INFO: │   ├──keep_decoys_in_mbr_library: False
3:55:46.551785 INFO: │   ├──channel_wise_fdr: False
3:55:46.551803 INFO: │   └──enable_nn_hyperparameter_tuning: True
3:55:46.551819 INFO: ├──search_output
3:55:46.551837 INFO: │   ├──file_format: parquet
3:55:46.551854 INFO: │   ├──precursor_level_lfq: True
3:55:46.551871 INFO: │   ├──peptide_level_lfq: True
3:55:46.551888 INFO: │   ├──save_fragment_quant_matrix: False
3:55:46.551906 INFO: │   ├──min_k_fragments: 12
3:55:46.551923 INFO: │   ├──min_correlation: 0.9
3:55:46.551940 INFO: │   ├──num_samples_quadratic: 50
3:55:46.551957 INFO: │   ├──min_nonnan: 3
3:55:46.551975 INFO: │   ├──normalization_method: directlfq
3:55:46.551993 INFO: │   └──normalize_directlfq: True
3:55:46.552010 INFO: ├──optimization
3:55:46.552028 INFO: │   ├──order_of_optimization: None
3:55:46.552045 INFO: │   ├──ms2_error
3:55:46.552063 INFO: │   │   ├──targeted_update_percentile_range: 0.95
3:55:46.552082 INFO: │   │   ├──targeted_update_factor: 1.0
3:55:46.552100 INFO: │   │   ├──automatic_update_percentile_range: 0.99
3:55:46.552118 INFO: │   │   ├──automatic_update_factor: 1.1
3:55:46.552136 INFO: │   │   ├──try_narrower_values: True
3:55:46.552154 INFO: │   │   ├──maximal_decrease: 0.5
3:55:46.552171 INFO: │   │   ├──favour_narrower_optimum: False
3:55:46.552190 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
3:55:46.552207 INFO: │   ├──ms1_error
3:55:46.552225 INFO: │   │   ├──targeted_update_percentile_range: 0.95
3:55:46.552243 INFO: │   │   ├──targeted_update_factor: 1.0
3:55:46.552263 INFO: │   │   ├──automatic_update_percentile_range: 0.99
3:55:46.552283 INFO: │   │   ├──automatic_update_factor: 1.1
3:55:46.552300 INFO: │   │   ├──try_narrower_values: False
3:55:46.552318 INFO: │   │   ├──maximal_decrease: 0.2
3:55:46.552335 INFO: │   │   ├──favour_narrower_optimum: False
3:55:46.552352 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
3:55:46.552369 INFO: │   ├──mobility_error
3:55:46.552387 INFO: │   │   ├──targeted_update_percentile_range: 0.95
3:55:46.552405 INFO: │   │   ├──targeted_update_factor: 1.0
3:55:46.552423 INFO: │   │   ├──automatic_update_percentile_range: 0.99
3:55:46.552440 INFO: │   │   ├──automatic_update_factor: 1.1
3:55:46.552458 INFO: │   │   ├──try_narrower_values: False
3:55:46.552476 INFO: │   │   ├──maximal_decrease: 0.2
3:55:46.552493 INFO: │   │   ├──favour_narrower_optimum: False
3:55:46.552510 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
3:55:46.552527 INFO: │   └──rt_error
3:55:46.552545 INFO: │       ├──targeted_update_percentile_range: 0.95
3:55:46.552562 INFO: │       ├──targeted_update_factor: 1.0
3:55:46.552579 INFO: │       ├──automatic_update_percentile_range: 0.999
3:55:46.552597 INFO: │       ├──automatic_update_factor: 1.5
3:55:46.552614 INFO: │       ├──try_narrower_values: True
3:55:46.552631 INFO: │       ├──maximal_decrease: 0.1
3:55:46.552648 INFO: │       ├──favour_narrower_optimum: False
3:55:46.552665 INFO: │       └──maximum_decrease_from_maximum: 0.5
3:55:46.552682 INFO: ├──optimization_manager
3:55:46.552700 INFO: │   ├──fwhm_rt: 5
3:55:46.552718 INFO: │   ├──fwhm_mobility: 0.01
3:55:46.552736 INFO: │   └──score_cutoff: 0
3:55:46.552752 INFO: ├──transfer_library
3:55:46.552768 INFO: │   ├──enabled: False
3:55:46.552785 INFO: │   ├──fragment_types:
3:55:46.552802 INFO: │   │   - b
3:55:46.552821 INFO: │   │   - y
3:55:46.552838 INFO: │   ├──max_charge: 2
3:55:46.552855 INFO: │   ├──top_k_samples: 3
3:55:46.552872 INFO: │   ├──norm_delta_max: True
3:55:46.552890 INFO: │   ├──precursor_correlation_cutoff: 0.5
3:55:46.552908 INFO: │   └──fragment_correlation_ratio: 0.75
3:55:46.552924 INFO: └──transfer_learning
3:55:46.552942 INFO:     ├──enabled: False
3:55:46.552959 INFO:     ├──batch_size: 2000
3:55:46.552976 INFO:     ├──max_lr: 0.0001
3:55:46.552994 INFO:     ├──train_fraction: 0.7
3:55:46.553012 INFO:     ├──validation_fraction: 0.2
3:55:46.553029 INFO:     ├──test_fraction: 0.1
3:55:46.553046 INFO:     ├──test_interval: 1
3:55:46.553063 INFO:     ├──lr_patience: 3
3:55:46.553081 INFO:     ├──epochs: 51
3:55:46.553098 INFO:     ├──warmup_epochs: 5
3:55:46.553115 INFO:     ├──nce: 25
3:55:46.553133 INFO:     └──instrument: Lumos
3:55:46.558435 INFO: Registering 7 custom modifications
3:55:46.581811 INFO: Searching 6 files:
3:55:46.581896 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
3:55:46.581921 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
3:55:46.581940 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
3:55:46.581957 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
3:55:46.581974 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
3:55:46.581990 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
3:55:46.582006 INFO: Using 1 fasta files:
3:55:46.582024 INFO:   /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
3:55:46.582041 INFO: Using library: None
3:55:46.582057 INFO: Saving output to: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library
3:55:46.582085 PROGRESS: Loading spectral library
3:55:46.582116 PROGRESS: No library provided. Building library from fasta files.
3:55:46.582162 INFO: Running FastaDigest
3:55:46.582944 INFO: Digesting fasta file
3:55:56.157735 INFO: Adding modifications
3:57:57.345722 INFO: Removing non-canonical amino acids
3:58:04.334182 INFO: Fasta library contains 6,091,314 precursors
3:58:04.334379 PROGRESS: Predicting library properties.
3:58:04.334443 INFO: Running PeptDeepPrediction
3:58:04.334544 INFO: Device set to cpu
3:58:05.540916 INFO: Loading PeptDeep models of type generic
3:58:06.529192 INFO: Loading PeptDeep models from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/peptdeep.transfer
3:58:06.529332 INFO: Using external ms2 model: '/home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/peptdeep.transfer/ms2.pth'
3:58:06.558018 INFO: Using external rt model: '/home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/peptdeep.transfer/rt.pth'
3:58:06.562583 INFO: Using external ccs model: '/home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/peptdeep.transfer/ccs.pth'
3:58:06.567590 INFO: Using external charge model: '/home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/transfer/peptdeep.transfer/charge.pth'
3:58:06.576038 INFO: Predicting RT, MS2 and mobility
3:58:06.576143 INFO: Using multiprocessing with 100 processes ...
3:58:07.151870 INFO: Predicting rt,ms2,mobility ...
4:03:52.849875 INFO: Adding fragment mz information
4:03:53.152878 INFO: Adding fragment intensity information
4:03:53.454692 INFO: Adding precursor information
4:03:53.773045 INFO: Running PrecursorInitializer
4:03:53.800629 INFO: Running AnnotateFasta
4:04:22.097085 INFO: Running IsotopeGenerator
4:04:22.098240 WARNING: Multiprocessing not compatible with custom modifications yet, falling back to single process.
4:08:51.802376 INFO: Running RTNormalization
4:08:51.802745 WARNING: Input library already contains normalized RT information. Skipping RT normalization
4:08:51.803825 INFO: Saving library to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/speclib.hdf
4:09:26.721586 INFO: Running DecoyGenerator
4:11:54.130910 INFO: Running FlattenLibrary
4:12:13.776637 INFO: Running InitFlatColumns
4:12:13.915778 INFO: Running LogFlatLibraryStats
4:12:13.915927 INFO: ============ Library Stats ============
4:12:13.915963 INFO: Number of precursors: 12,150,378
4:12:15.317270 INFO: 	thereof targets:6,091,314
4:12:15.317423 INFO: 	thereof decoys: 6,059,064
4:12:15.400274 INFO: Number of elution groups: 6,091,314
4:12:15.400422 INFO: 	average size: 1.99
4:12:15.699472 INFO: Number of proteins: 117,993
4:12:15.733063 INFO: Number of channels: 1 ([0])
4:12:15.733252 INFO: Isotopes Distribution for 4 isotopes
4:12:15.733282 INFO: =======================================
4:12:15.752490 PROGRESS: =================== Starting Search Workflows for step library ===================
4:12:15.752686 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 
4:12:15.752758 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant
4:12:15.752840 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/figures
4:12:15.753034 INFO: Initializing TimingManager
4:12:15.753467 INFO: Initializing RawFileManager
4:12:27.002827 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.
4:12:27.010501 INFO: Determining DIA cycle
4:12:27.026876 INFO: Found cycle with start 0.00 min and length 300.
4:12:27.190086 INFO: RT (min)            : 0.0 - 26.9
4:12:27.190182 INFO: RT duration (sec)   : 1611.2
4:12:27.190210 INFO: RT duration (min)   : 26.9
4:12:27.190233 INFO: Cycle len (scans)   : 300
4:12:27.190253 INFO: Cycle len (sec)     : 1.65
4:12:27.190272 INFO: Number of cycles    : 977
4:12:27.190292 INFO: MS2 range (m/z)     : 380.4 - 980.7
4:12:27.190331 INFO: Creating DIA data object took: 11.436773777008057
4:12:27.877769 INFO: Creating DIA data NG object took: 0.6872894763946533
4:12:28.884336 INFO: Initializing CalibrationManager
4:12:28.884620 INFO: Setting up calibration estimators ..
4:12:28.884682 INFO: Found 1 estimator(s) in calibration group 'fragment'
4:12:28.884751 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
4:12:28.884819 INFO: Found 3 estimator(s) in calibration group 'precursor'
4:12:28.884871 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
4:12:28.884924 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
4:12:28.884974 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
4:12:28.885020 INFO: Done setting up calibration estimators.
4:12:28.885229 INFO: Initializing OptimizationManager
4:12:28.885390 INFO: initial parameter: ms1_error = 3
4:12:28.885444 INFO: initial parameter: ms2_error = 10
4:12:28.885493 INFO: initial parameter: rt_error = 805.5992431640625
4:12:28.885540 INFO: initial parameter: mobility_error = 0.1
4:12:28.885586 INFO: initial parameter: num_candidates = 1
4:12:28.885629 INFO: initial parameter: fwhm_rt = 5
4:12:28.885671 INFO: initial parameter: fwhm_mobility = 0.01
4:12:28.885713 INFO: initial parameter: score_cutoff = 0
4:12:28.885753 INFO: initial parameter: classifier_version = -1
4:12:28.885825 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
4:12:28.886068 INFO: FDRManager: loading saved state not requested, will be initialized.
4:12:28.886101 INFO: Initializing FDRManager
4:12:28.886141 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
4:12:30.274432 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
4:12:31.153325 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
4:12:31.153741 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
4:12:31.153842 PROGRESS: Starting initial search for precursors.
4:12:31.153929 INFO: Starting optimization step 0.
4:12:31.153993 PROGRESS: === Extracting elution groups 0 to 1000 ===
4:12:31.154054 INFO: Using rust extraction backend
4:12:31.154113 PROGRESS: Extracting batch of 1967 precursors
4:12:31.157812 INFO: === Search parameters used ===
4:12:31.157917 INFO: rt_error       : 805.5992431640625
4:12:31.157970 INFO: mobility_error : 0.1
4:12:31.158016 INFO: num_candidates : 1
4:12:31.158059 INFO: ms1_error      : 3
4:12:31.158102 INFO: ms2_error      : 10
4:12:31.158144 INFO: fwhm_rt        : 5
4:12:31.158185 INFO: quant_window   : 3
4:12:31.158226 INFO: ==============================================
4:12:31.185745 INFO: performing precursor FDR with 40 features
4:12:31.185812 INFO: Decoy channel: -1
4:12:31.185838 INFO: competitive: True
4:12:31.187508 INFO: Setting torch num_threads to 2 for FDR classification task
4:12:31.189357 INFO: Estimating optimal hyperparameters - samples: 1,514, batch_size: 128, learning_rate: 1.77e-04
4:12:31.190118 INFO: Using random state 631868 for train-test-split
4:12:31.362234 INFO: Test AUC: 0.535
4:12:31.362318 INFO: Train AUC: 0.563
4:12:31.362348 INFO: AUC difference: 4.98%
4:12:31.636675 INFO: Resetting torch num_threads to 100
4:12:31.638283 PROGRESS: === Extracted 1893 precursors and 6649 fragments ===
4:12:31.638644 INFO: === FDR correction performed with classifier version -1 ===
4:12:31.639130 PROGRESS: ============================= Precursor FDR =============================
4:12:31.639226 PROGRESS: Total precursors accumulated: 1
4:12:31.639286 PROGRESS: Target precursors: 1 (100.00%)
4:12:31.639337 PROGRESS: Decoy precursors: 0 (0.00%)
4:12:31.639385 PROGRESS: 
4:12:31.639431 PROGRESS: Precursor Summary:
4:12:31.640490 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
4:12:31.640576 PROGRESS: 
4:12:31.640632 PROGRESS: Protein Summary:
4:12:31.641788 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
4:12:31.641873 PROGRESS: =========================================================================
4:12:31.642088 INFO: Target number of precursors not reached yet.
4:12:31.725642 INFO: Starting optimization step 1.
4:12:31.725870 PROGRESS: === Extracting elution groups 1000 to 3000 ===
4:12:31.725954 INFO: Using rust extraction backend
4:12:31.726020 PROGRESS: Extracting batch of 3942 precursors
4:12:31.731636 INFO: === Search parameters used ===
4:12:31.731773 INFO: rt_error       : 805.5992431640625
4:12:31.731825 INFO: mobility_error : 0.1
4:12:31.731872 INFO: num_candidates : 1
4:12:31.731916 INFO: ms1_error      : 3
4:12:31.731958 INFO: ms2_error      : 10
4:12:31.732000 INFO: fwhm_rt        : 5
4:12:31.732042 INFO: quant_window   : 3
4:12:31.732084 INFO: ==============================================
4:12:31.772746 INFO: performing precursor FDR with 40 features
4:12:31.772836 INFO: Decoy channel: -1
4:12:31.772862 INFO: competitive: True
4:12:31.777672 INFO: Setting torch num_threads to 2 for FDR classification task
4:12:31.780339 INFO: Estimating optimal hyperparameters - samples: 4,571, batch_size: 128, learning_rate: 1.77e-04
4:12:31.780464 INFO: Using random state 308144 for train-test-split
4:12:32.336672 INFO: Test AUC: 0.509
4:12:32.336762 INFO: Train AUC: 0.557
4:12:32.336791 INFO: AUC difference: 8.68%
4:12:32.336812 WARNING: AUC difference > 5%. This may indicate overfitting.
4:12:32.583267 INFO: Resetting torch num_threads to 100
4:12:32.586386 PROGRESS: === Extracted 5714 precursors and 19586 fragments ===
4:12:32.586752 INFO: === FDR correction performed with classifier version -1 ===
4:12:32.587261 PROGRESS: ============================= Precursor FDR =============================
4:12:32.587348 PROGRESS: Total precursors accumulated: 5
4:12:32.587404 PROGRESS: Target precursors: 5 (100.00%)
4:12:32.587451 PROGRESS: Decoy precursors: 0 (0.00%)
4:12:32.587495 PROGRESS: 
4:12:32.587537 PROGRESS: Precursor Summary:
4:12:32.588599 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
4:12:32.588681 PROGRESS: 
4:12:32.588735 PROGRESS: Protein Summary:
4:12:32.589896 PROGRESS: Channel   0:	 0.050 FDR:     5; 0.010 FDR:     5; 0.001 FDR:     5
4:12:32.589977 PROGRESS: =========================================================================
4:12:32.590247 INFO: Target number of precursors not reached yet.
4:12:32.678708 INFO: Starting optimization step 2.
4:12:32.678937 PROGRESS: === Extracting elution groups 3000 to 7000 ===
4:12:32.679018 INFO: Using rust extraction backend
4:12:32.679077 PROGRESS: Extracting batch of 7891 precursors
4:12:32.688703 INFO: === Search parameters used ===
4:12:32.688835 INFO: rt_error       : 805.5992431640625
4:12:32.688885 INFO: mobility_error : 0.1
4:12:32.688928 INFO: num_candidates : 1
4:12:32.688968 INFO: ms1_error      : 3
4:12:32.689009 INFO: ms2_error      : 10
4:12:32.689048 INFO: fwhm_rt        : 5
4:12:32.689086 INFO: quant_window   : 3
4:12:32.689124 INFO: ==============================================
4:12:32.758290 INFO: performing precursor FDR with 40 features
4:12:32.758396 INFO: Decoy channel: -1
4:12:32.758419 INFO: competitive: True
4:12:32.769441 INFO: Setting torch num_threads to 2 for FDR classification task
4:12:32.775111 INFO: Estimating optimal hyperparameters - samples: 10,700, batch_size: 128, learning_rate: 1.77e-04
4:12:32.775253 INFO: Using random state 271183 for train-test-split
4:12:34.101105 INFO: Test AUC: 0.535
4:12:34.101209 INFO: Train AUC: 0.567
4:12:34.101237 INFO: AUC difference: 5.67%
4:12:34.101258 WARNING: AUC difference > 5%. This may indicate overfitting.
4:12:34.350662 INFO: Resetting torch num_threads to 100
4:12:34.355307 PROGRESS: === Extracted 13375 precursors and 46074 fragments ===
4:12:34.355712 INFO: === FDR correction performed with classifier version -1 ===
4:12:34.356233 PROGRESS: ============================= Precursor FDR =============================
4:12:34.356328 PROGRESS: Total precursors accumulated: 45
4:12:34.356387 PROGRESS: Target precursors: 45 (100.00%)
4:12:34.356437 PROGRESS: Decoy precursors: 0 (0.00%)
4:12:34.356481 PROGRESS: 
4:12:34.356524 PROGRESS: Precursor Summary:
4:12:34.357592 PROGRESS: Channel   0:	 0.050 FDR:    45; 0.010 FDR:    45; 0.001 FDR:    45
4:12:34.357678 PROGRESS: 
4:12:34.357734 PROGRESS: Protein Summary:
4:12:34.358903 PROGRESS: Channel   0:	 0.050 FDR:    45; 0.010 FDR:    45; 0.001 FDR:    45
4:12:34.358987 PROGRESS: =========================================================================
4:12:34.359345 INFO: Target number of precursors not reached yet.
4:12:34.457916 INFO: Starting optimization step 3.
4:12:34.458152 PROGRESS: === Extracting elution groups 7000 to 15000 ===
4:12:34.458233 INFO: Using rust extraction backend
4:12:34.458294 PROGRESS: Extracting batch of 15751 precursors
4:12:34.475809 INFO: === Search parameters used ===
4:12:34.475978 INFO: rt_error       : 805.5992431640625
4:12:34.476033 INFO: mobility_error : 0.1
4:12:34.476079 INFO: num_candidates : 1
4:12:34.476123 INFO: ms1_error      : 3
4:12:34.476164 INFO: ms2_error      : 10
4:12:34.476215 INFO: fwhm_rt        : 5
4:12:34.476260 INFO: quant_window   : 3
4:12:34.476302 INFO: ==============================================
4:12:34.593564 INFO: performing precursor FDR with 40 features
4:12:34.593677 INFO: Decoy channel: -1
4:12:34.593702 INFO: competitive: True
4:12:34.606042 INFO: Setting torch num_threads to 2 for FDR classification task
4:12:34.613188 INFO: Estimating optimal hyperparameters - samples: 22,918, batch_size: 128, learning_rate: 1.77e-04
4:12:34.613365 INFO: Using random state 855600 for train-test-split
4:12:37.424564 INFO: Test AUC: 0.548
4:12:37.424675 INFO: Train AUC: 0.574
4:12:37.424705 INFO: AUC difference: 4.55%
4:12:37.682057 INFO: Resetting torch num_threads to 100
4:12:37.688538 PROGRESS: === Extracted 28648 precursors and 98741 fragments ===
4:12:37.689018 INFO: === FDR correction performed with classifier version -1 ===
4:12:37.689528 PROGRESS: ============================= Precursor FDR =============================
4:12:37.689613 PROGRESS: Total precursors accumulated: 0
4:12:37.689670 PROGRESS: Target precursors: 0 (0.00%)
4:12:37.689719 PROGRESS: Decoy precursors: 0 (0.00%)
4:12:37.689761 PROGRESS: 
4:12:37.689803 PROGRESS: Precursor Summary:
4:12:37.689915 PROGRESS: 
4:12:37.689970 PROGRESS: Protein Summary:
4:12:37.690040 PROGRESS: =========================================================================
4:12:37.690507 INFO: Target number of precursors not reached yet.
4:12:37.804793 INFO: Starting optimization step 4.
4:12:37.805058 PROGRESS: === Extracting elution groups 15000 to 31000 ===
4:12:37.805138 INFO: Using rust extraction backend
4:12:37.805215 PROGRESS: Extracting batch of 31575 precursors
4:12:37.838860 INFO: === Search parameters used ===
4:12:37.839112 INFO: rt_error       : 805.5992431640625
4:12:37.839200 INFO: mobility_error : 0.1
4:12:37.839251 INFO: num_candidates : 1
4:12:37.839294 INFO: ms1_error      : 3
4:12:37.839334 INFO: ms2_error      : 10
4:12:37.839374 INFO: fwhm_rt        : 5
4:12:37.839414 INFO: quant_window   : 3
4:12:37.839452 INFO: ==============================================
4:12:38.047701 INFO: performing precursor FDR with 40 features
4:12:38.047811 INFO: Decoy channel: -1
4:12:38.047835 INFO: competitive: True
4:12:38.072155 INFO: Setting torch num_threads to 2 for FDR classification task
4:12:38.087347 INFO: Estimating optimal hyperparameters - samples: 47,475, batch_size: 194, learning_rate: 2.18e-04
4:12:38.087597 INFO: Using random state 68921 for train-test-split
4:12:42.596271 INFO: Test AUC: 0.556
4:12:42.596396 INFO: Train AUC: 0.580
4:12:42.596431 INFO: AUC difference: 4.20%
4:12:42.865945 INFO: Resetting torch num_threads to 100
4:12:42.877120 PROGRESS: === Extracted 59344 precursors and 205804 fragments ===
4:12:42.877775 INFO: === FDR correction performed with classifier version -1 ===
4:12:42.878342 PROGRESS: ============================= Precursor FDR =============================
4:12:42.878431 PROGRESS: Total precursors accumulated: 0
4:12:42.878497 PROGRESS: Target precursors: 0 (0.00%)
4:12:42.878549 PROGRESS: Decoy precursors: 0 (0.00%)
4:12:42.878599 PROGRESS: 
4:12:42.878646 PROGRESS: Precursor Summary:
4:12:42.878771 PROGRESS: 
4:12:42.878833 PROGRESS: Protein Summary:
4:12:42.878908 PROGRESS: =========================================================================
4:12:42.879781 INFO: Target number of precursors not reached yet.
4:12:43.029720 INFO: Starting optimization step 5.
4:12:43.029994 PROGRESS: === Extracting elution groups 31000 to 63000 ===
4:12:43.030087 INFO: Using rust extraction backend
4:12:43.030167 PROGRESS: Extracting batch of 63070 precursors
4:12:43.095065 INFO: === Search parameters used ===
4:12:43.095385 INFO: rt_error       : 805.5992431640625
4:12:43.095444 INFO: mobility_error : 0.1
4:12:43.095494 INFO: num_candidates : 1
4:12:43.095541 INFO: ms1_error      : 3
4:12:43.095586 INFO: ms2_error      : 10
4:12:43.095631 INFO: fwhm_rt        : 5
4:12:43.095673 INFO: quant_window   : 3
4:12:43.095714 INFO: ==============================================
4:12:43.443190 INFO: performing precursor FDR with 40 features
4:12:43.443310 INFO: Decoy channel: -1
4:12:43.443336 INFO: competitive: True
4:12:43.493655 INFO: Setting torch num_threads to 2 for FDR classification task
4:12:43.528111 INFO: Estimating optimal hyperparameters - samples: 96,474, batch_size: 395, learning_rate: 3.11e-04
4:12:43.528471 INFO: Using random state 876980 for train-test-split
4:12:48.285477 INFO: Test AUC: 0.555
4:12:48.285584 INFO: Train AUC: 0.584
4:12:48.285615 INFO: AUC difference: 5.07%
4:12:48.285639 WARNING: AUC difference > 5%. This may indicate overfitting.
4:12:48.573066 INFO: Resetting torch num_threads to 100
4:12:48.595558 PROGRESS: === Extracted 120593 precursors and 416331 fragments ===
4:12:48.596232 INFO: === FDR correction performed with classifier version -1 ===
4:12:48.596909 PROGRESS: ============================= Precursor FDR =============================
4:12:48.597024 PROGRESS: Total precursors accumulated: 526
4:12:48.597085 PROGRESS: Target precursors: 521 (99.05%)
4:12:48.597136 PROGRESS: Decoy precursors: 5 (0.95%)
4:12:48.597181 PROGRESS: 
4:12:48.597225 PROGRESS: Precursor Summary:
4:12:48.598346 PROGRESS: Channel   0:	 0.050 FDR:   521; 0.010 FDR:   521; 0.001 FDR:     0
4:12:48.598438 PROGRESS: 
4:12:48.598493 PROGRESS: Protein Summary:
4:12:48.599792 PROGRESS: Channel   0:	 0.050 FDR:   487; 0.010 FDR:   487; 0.001 FDR:     0
4:12:48.599899 PROGRESS: =========================================================================
4:12:48.601851 INFO: Target number of precursors not reached yet.
4:12:48.823830 INFO: Starting optimization step 6.
4:12:48.824113 PROGRESS: === Extracting elution groups 63000 to 127000 ===
4:12:48.824196 INFO: Using rust extraction backend
4:12:48.824269 PROGRESS: Extracting batch of 126133 precursors
4:12:48.952508 INFO: === Search parameters used ===
4:12:48.952828 INFO: rt_error       : 805.5992431640625
4:12:48.952884 INFO: mobility_error : 0.1
4:12:48.952932 INFO: num_candidates : 1
4:12:48.952977 INFO: ms1_error      : 3
4:12:48.953019 INFO: ms2_error      : 10
4:12:48.953059 INFO: fwhm_rt        : 5
4:12:48.953099 INFO: quant_window   : 3
4:12:48.953138 INFO: ==============================================
4:12:49.581574 INFO: performing precursor FDR with 40 features
4:12:49.581702 INFO: Decoy channel: -1
4:12:49.581729 INFO: competitive: True
4:12:49.686916 INFO: Setting torch num_threads to 2 for FDR classification task
4:12:49.789792 INFO: Estimating optimal hyperparameters - samples: 194,470, batch_size: 796, learning_rate: 4.41e-04
4:12:49.790339 INFO: Using random state 329408 for train-test-split
4:12:56.251063 INFO: Test AUC: 0.565
4:12:56.251219 INFO: Train AUC: 0.587
4:12:56.251252 INFO: AUC difference: 3.84%
4:12:56.582914 INFO: Resetting torch num_threads to 100
4:12:56.628106 PROGRESS: === Extracted 243088 precursors and 840902 fragments ===
4:12:56.628800 INFO: === FDR correction performed with classifier version -1 ===
4:12:56.629637 PROGRESS: ============================= Precursor FDR =============================
4:12:56.629729 PROGRESS: Total precursors accumulated: 1,217
4:12:56.629792 PROGRESS: Target precursors: 1,205 (99.01%)
4:12:56.629844 PROGRESS: Decoy precursors: 12 (0.99%)
4:12:56.629904 PROGRESS: 
4:12:56.629996 PROGRESS: Precursor Summary:
4:12:56.631299 PROGRESS: Channel   0:	 0.050 FDR: 1,205; 0.010 FDR: 1,205; 0.001 FDR:     3
4:12:56.631391 PROGRESS: 
4:12:56.631447 PROGRESS: Protein Summary:
4:12:56.633011 PROGRESS: Channel   0:	 0.050 FDR: 1,061; 0.010 FDR: 1,061; 0.001 FDR:     3
4:12:56.633102 PROGRESS: =========================================================================
4:12:56.636938 INFO: Target number of precursors reached.
4:12:56.739804 INFO: fragments_df: keeping 5000 of 840902 [sum(precursor_idx_mask)=11806 sum(mass_error_mask)=840902 stop_rank=5000
4:12:57.098403 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:12:57.317517 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:12:58.041520 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
4:12:58.041996 INFO: Using score_cutoff 12.169577568054198 (fac=0.99, q=1)
4:12:58.042351 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
4:12:58.042428 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
4:12:58.042482 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.169577568054198
4:12:58.042540 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:12:58.192194 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:12:58.388169 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
4:12:58.388485 PROGRESS: Required number of precursors found. Starting search parameter optimization.
4:12:58.388628 INFO: Starting optimization step 7.
4:12:58.388707 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:12:58.388791 INFO: Using rust extraction backend
4:12:58.388867 PROGRESS: Extracting batch of 250329 precursors
4:12:58.645855 INFO: === Search parameters used ===
4:12:58.646188 INFO: rt_error       : 805.5992431640625
4:12:58.646242 INFO: mobility_error : 0.1
4:12:58.646287 INFO: num_candidates : 3
4:12:58.646328 INFO: ms1_error      : 3
4:12:58.646368 INFO: ms2_error      : 10
4:12:58.646407 INFO: fwhm_rt        : 3.0
4:12:58.646447 INFO: quant_window   : 3
4:12:58.646485 INFO: ==============================================
4:13:00.931205 INFO: performing precursor FDR with 40 features
4:13:00.931326 INFO: Decoy channel: -1
4:13:00.931353 INFO: competitive: True
4:13:01.113833 INFO: Setting torch num_threads to 2 for FDR classification task
4:13:01.389645 INFO: Estimating optimal hyperparameters - samples: 578,965, batch_size: 2,371, learning_rate: 7.61e-04
4:13:01.390559 INFO: Using random state 263935 for train-test-split
4:13:14.568896 INFO: Test AUC: 0.566
4:13:14.569018 INFO: Train AUC: 0.580
4:13:14.569050 INFO: AUC difference: 2.40%
4:13:15.061556 INFO: Resetting torch num_threads to 100
4:13:15.112082 PROGRESS: === Extracted 723707 precursors and 2398728 fragments ===
4:13:15.112536 INFO: === FDR correction performed with classifier version 6 ===
4:13:15.113012 PROGRESS: ============================= Precursor FDR =============================
4:13:15.113098 PROGRESS: Total precursors accumulated: 0
4:13:15.113156 PROGRESS: Target precursors: 0 (0.00%)
4:13:15.113207 PROGRESS: Decoy precursors: 0 (0.00%)
4:13:15.113253 PROGRESS: 
4:13:15.113298 PROGRESS: Precursor Summary:
4:13:15.113450 PROGRESS: 
4:13:15.113537 PROGRESS: Protein Summary:
4:13:15.113658 PROGRESS: =========================================================================
4:13:15.127482 INFO: Target number of precursors not reached yet.
4:13:15.652173 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:13:15.807899 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:13:16.000737 INFO: === skipping optimization until target number of precursors are found ===
4:13:16.001094 INFO: Starting optimization step 8.
4:13:16.001191 PROGRESS: === Extracting elution groups 127000 to 255000 ===
4:13:16.001305 INFO: Using rust extraction backend
4:13:16.001388 PROGRESS: Extracting batch of 252185 precursors
4:13:16.259524 INFO: === Search parameters used ===
4:13:16.259857 INFO: rt_error       : 805.5992431640625
4:13:16.259922 INFO: mobility_error : 0.1
4:13:16.259971 INFO: num_candidates : 3
4:13:16.260015 INFO: ms1_error      : 3
4:13:16.260060 INFO: ms2_error      : 10
4:13:16.260101 INFO: fwhm_rt        : 3.0
4:13:16.260140 INFO: quant_window   : 3
4:13:16.260180 INFO: ==============================================
4:13:18.754467 INFO: performing precursor FDR with 40 features
4:13:18.754593 INFO: Decoy channel: -1
4:13:18.754622 INFO: competitive: True
4:13:19.334387 INFO: Setting torch num_threads to 2 for FDR classification task
4:13:19.949296 INFO: Estimating optimal hyperparameters - samples: 1,162,412, batch_size: 4,096, learning_rate: 1.00e-03
4:13:19.951652 INFO: Using random state 263935 for train-test-split
4:13:44.281488 INFO: Test AUC: 0.574
4:13:44.281668 INFO: Train AUC: 0.580
4:13:44.281706 INFO: AUC difference: 1.01%
4:13:45.004138 INFO: Resetting torch num_threads to 100
4:13:45.267825 PROGRESS: === Extracted 1453015 precursors and 4809337 fragments ===
4:13:45.268744 INFO: === FDR correction performed with classifier version 6 ===
4:13:45.270306 PROGRESS: ============================= Precursor FDR =============================
4:13:45.270400 PROGRESS: Total precursors accumulated: 3,196
4:13:45.270461 PROGRESS: Target precursors: 3,165 (99.03%)
4:13:45.270513 PROGRESS: Decoy precursors: 31 (0.97%)
4:13:45.270560 PROGRESS: 
4:13:45.270605 PROGRESS: Precursor Summary:
4:13:45.272589 PROGRESS: Channel   0:	 0.050 FDR: 3,165; 0.010 FDR: 3,165; 0.001 FDR: 1,709
4:13:45.272714 PROGRESS: 
4:13:45.272770 PROGRESS: Protein Summary:
4:13:45.275384 PROGRESS: Channel   0:	 0.050 FDR: 2,433; 0.010 FDR: 2,433; 0.001 FDR: 1,410
4:13:45.275493 PROGRESS: =========================================================================
4:13:45.292113 INFO: Target number of precursors reached.
4:13:45.855623 INFO: fragments_df: keeping 5000 of 4809337 [sum(precursor_idx_mask)=68253 sum(mass_error_mask)=4809337 stop_rank=5000
4:13:46.374800 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:13:46.843049 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:13:47.565456 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:13:47.565952 INFO: Using score_cutoff 11.359796889495849 (fac=0.99, q=1)
4:13:47.566300 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:13:47.566376 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:13:47.566427 INFO: Updating optimization_manager: score_cutoff        : 12.169577568054198 -> 11.359796889495849
4:13:47.566483 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:13:47.719062 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:13:47.929277 INFO: === checking if optimization conditions were reached ===
4:13:47.932080 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
4:13:47.932197 INFO: Updating optimization_manager: classifier_version  : 6 -> 8
4:13:47.932273 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
4:13:47.932342 INFO: ==============================================
4:13:47.932418 INFO: Starting optimization step 9.
4:13:47.932485 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:13:47.932558 INFO: Using rust extraction backend
4:13:47.932627 PROGRESS: Extracting batch of 250329 precursors
4:13:48.192936 INFO: === Search parameters used ===
4:13:48.193243 INFO: rt_error       : 805.5992431640625
4:13:48.193300 INFO: mobility_error : 0.1
4:13:48.193346 INFO: num_candidates : 3
4:13:48.193387 INFO: ms1_error      : 3
4:13:48.193425 INFO: ms2_error      : 10.0
4:13:48.193463 INFO: fwhm_rt        : 3.0
4:13:48.193500 INFO: quant_window   : 3
4:13:48.193537 INFO: ==============================================
4:13:50.469280 INFO: performing precursor FDR with 40 features
4:13:50.469409 INFO: Decoy channel: -1
4:13:50.469435 INFO: competitive: True
4:13:50.659296 INFO: Setting torch num_threads to 2 for FDR classification task
4:13:50.937754 INFO: Estimating optimal hyperparameters - samples: 578,960, batch_size: 2,371, learning_rate: 7.61e-04
4:13:50.938824 INFO: Using random state 495622 for train-test-split
4:14:04.277150 INFO: Test AUC: 0.575
4:14:04.277286 INFO: Train AUC: 0.587
4:14:04.277320 INFO: AUC difference: 1.97%
4:14:04.750474 INFO: Resetting torch num_threads to 100
4:14:04.776613 PROGRESS: === Extracted 723701 precursors and 2398569 fragments ===
4:14:04.777107 INFO: === FDR correction performed with classifier version 8 ===
4:14:04.777840 PROGRESS: ============================= Precursor FDR =============================
4:14:04.777937 PROGRESS: Total precursors accumulated: 1,597
4:14:04.777996 PROGRESS: Target precursors: 1,582 (99.06%)
4:14:04.778046 PROGRESS: Decoy precursors: 15 (0.94%)
4:14:04.778091 PROGRESS: 
4:14:04.778135 PROGRESS: Precursor Summary:
4:14:04.779475 PROGRESS: Channel   0:	 0.050 FDR: 1,582; 0.010 FDR: 1,582; 0.001 FDR:     0
4:14:04.779566 PROGRESS: 
4:14:04.779621 PROGRESS: Protein Summary:
4:14:04.781278 PROGRESS: Channel   0:	 0.050 FDR: 1,364; 0.010 FDR: 1,364; 0.001 FDR:     0
4:14:04.781367 PROGRESS: =========================================================================
4:14:04.794592 INFO: Target number of precursors reached.
4:14:05.060790 INFO: fragments_df: keeping 5000 of 2398569 [sum(precursor_idx_mask)=34047 sum(mass_error_mask)=2398569 stop_rank=5000
4:14:05.432234 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:14:05.684454 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:14:06.408858 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:14:06.409325 INFO: Using score_cutoff 11.393571116924285 (fac=0.99, q=1)
4:14:06.409636 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:14:06.409713 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:14:06.409786 INFO: Updating optimization_manager: score_cutoff        : 11.359796889495849 -> 11.393571116924285
4:14:06.409840 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:14:06.558034 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:14:06.770583 INFO: === checking if optimization conditions were reached ===
4:14:06.773356 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
4:14:06.773482 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
4:14:06.773559 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
4:14:06.773628 INFO: ==============================================
4:14:06.773705 INFO: Starting optimization step 10.
4:14:06.773775 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:14:06.773848 INFO: Using rust extraction backend
4:14:06.773920 PROGRESS: Extracting batch of 250329 precursors
4:14:07.026721 INFO: === Search parameters used ===
4:14:07.027031 INFO: rt_error       : 805.5992431640625
4:14:07.027086 INFO: mobility_error : 0.1
4:14:07.027130 INFO: num_candidates : 3
4:14:07.027183 INFO: ms1_error      : 3
4:14:07.027225 INFO: ms2_error      : 10.0
4:14:07.027264 INFO: fwhm_rt        : 3.0
4:14:07.027302 INFO: quant_window   : 3
4:14:07.027352 INFO: ==============================================
4:14:09.269593 INFO: performing precursor FDR with 40 features
4:14:09.269701 INFO: Decoy channel: -1
4:14:09.269726 INFO: competitive: True
4:14:09.457104 INFO: Setting torch num_threads to 2 for FDR classification task
4:14:09.735490 INFO: Estimating optimal hyperparameters - samples: 578,986, batch_size: 2,371, learning_rate: 7.61e-04
4:14:09.736561 INFO: Using random state 868440 for train-test-split
4:14:22.930613 INFO: Test AUC: 0.580
4:14:22.930758 INFO: Train AUC: 0.591
4:14:22.930791 INFO: AUC difference: 1.90%
4:14:23.415893 INFO: Resetting torch num_threads to 100
4:14:23.445338 PROGRESS: === Extracted 723733 precursors and 2398669 fragments ===
4:14:23.445831 INFO: === FDR correction performed with classifier version 9 ===
4:14:23.446594 PROGRESS: ============================= Precursor FDR =============================
4:14:23.446687 PROGRESS: Total precursors accumulated: 1,770
4:14:23.446746 PROGRESS: Target precursors: 1,753 (99.04%)
4:14:23.446797 PROGRESS: Decoy precursors: 17 (0.96%)
4:14:23.446843 PROGRESS: 
4:14:23.446889 PROGRESS: Precursor Summary:
4:14:23.448232 PROGRESS: Channel   0:	 0.050 FDR: 1,753; 0.010 FDR: 1,753; 0.001 FDR:     0
4:14:23.448328 PROGRESS: 
4:14:23.448383 PROGRESS: Protein Summary:
4:14:23.450109 PROGRESS: Channel   0:	 0.050 FDR: 1,502; 0.010 FDR: 1,502; 0.001 FDR:     0
4:14:23.450205 PROGRESS: =========================================================================
4:14:23.463440 INFO: Target number of precursors reached.
4:14:23.730951 INFO: fragments_df: keeping 5000 of 2398669 [sum(precursor_idx_mask)=37010 sum(mass_error_mask)=2398669 stop_rank=5000
4:14:24.149994 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:14:24.416825 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:14:25.141932 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:14:25.142417 INFO: Using score_cutoff 10.662197277832032 (fac=0.99, q=1)
4:14:25.142746 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:14:25.142830 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:14:25.142884 INFO: Updating optimization_manager: score_cutoff        : 11.393571116924285 -> 10.662197277832032
4:14:25.142937 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:14:25.294749 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:14:25.505367 INFO: === checking if optimization conditions were reached ===
4:14:25.508208 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
4:14:25.508333 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
4:14:25.508416 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
4:14:25.508489 INFO: ==============================================
4:14:25.508576 INFO: Starting optimization step 11.
4:14:25.508651 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:14:25.508733 INFO: Using rust extraction backend
4:14:25.508810 PROGRESS: Extracting batch of 250329 precursors
4:14:25.766622 INFO: === Search parameters used ===
4:14:25.766943 INFO: rt_error       : 805.5992431640625
4:14:25.767002 INFO: mobility_error : 0.1
4:14:25.767054 INFO: num_candidates : 3
4:14:25.767101 INFO: ms1_error      : 3
4:14:25.767154 INFO: ms2_error      : 10.0
4:14:25.767203 INFO: fwhm_rt        : 3.0
4:14:25.767259 INFO: quant_window   : 3
4:14:25.767304 INFO: ==============================================
4:14:28.048750 INFO: performing precursor FDR with 40 features
4:14:28.048875 INFO: Decoy channel: -1
4:14:28.048902 INFO: competitive: True
4:14:28.241297 INFO: Setting torch num_threads to 2 for FDR classification task
4:14:28.519873 INFO: Estimating optimal hyperparameters - samples: 578,993, batch_size: 2,371, learning_rate: 7.61e-04
4:14:28.521023 INFO: Using random state 115698 for train-test-split
4:14:41.477415 INFO: Test AUC: 0.582
4:14:41.477540 INFO: Train AUC: 0.594
4:14:41.477574 INFO: AUC difference: 1.88%
4:14:41.956906 INFO: Resetting torch num_threads to 100
4:14:41.984122 PROGRESS: === Extracted 723742 precursors and 2398288 fragments ===
4:14:41.984607 INFO: === FDR correction performed with classifier version 10 ===
4:14:41.985334 PROGRESS: ============================= Precursor FDR =============================
4:14:41.985425 PROGRESS: Total precursors accumulated: 1,637
4:14:41.985487 PROGRESS: Target precursors: 1,621 (99.02%)
4:14:41.985539 PROGRESS: Decoy precursors: 16 (0.98%)
4:14:41.985585 PROGRESS: 
4:14:41.985629 PROGRESS: Precursor Summary:
4:14:41.987028 PROGRESS: Channel   0:	 0.050 FDR: 1,621; 0.010 FDR: 1,621; 0.001 FDR:   462
4:14:41.987123 PROGRESS: 
4:14:41.987199 PROGRESS: Protein Summary:
4:14:41.988957 PROGRESS: Channel   0:	 0.050 FDR: 1,406; 0.010 FDR: 1,406; 0.001 FDR:   437
4:14:41.989053 PROGRESS: =========================================================================
4:14:42.002324 INFO: Target number of precursors reached.
4:14:42.268075 INFO: fragments_df: keeping 5000 of 2398288 [sum(precursor_idx_mask)=34590 sum(mass_error_mask)=2398288 stop_rank=5000
4:14:42.663460 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:14:42.913762 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:14:43.636116 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:14:43.636591 INFO: Using score_cutoff 10.657027633666992 (fac=0.99, q=1)
4:14:43.636898 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:14:43.636977 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:14:43.637031 INFO: Updating optimization_manager: score_cutoff        : 10.662197277832032 -> 10.657027633666992
4:14:43.637085 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:14:43.785660 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:14:44.001409 INFO: === checking if optimization conditions were reached ===
4:14:44.004151 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
4:14:44.004280 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
4:14:44.004360 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
4:14:44.004432 INFO: ==============================================
4:14:44.004518 INFO: Starting optimization step 12.
4:14:44.004591 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:14:44.004667 INFO: Using rust extraction backend
4:14:44.004745 PROGRESS: Extracting batch of 250329 precursors
4:14:44.259759 INFO: === Search parameters used ===
4:14:44.260069 INFO: rt_error       : 805.5992431640625
4:14:44.260126 INFO: mobility_error : 0.1
4:14:44.260173 INFO: num_candidates : 3
4:14:44.260216 INFO: ms1_error      : 3
4:14:44.260273 INFO: ms2_error      : 10.0
4:14:44.260318 INFO: fwhm_rt        : 3.0
4:14:44.260358 INFO: quant_window   : 3
4:14:44.260399 INFO: ==============================================
4:14:46.518246 INFO: performing precursor FDR with 40 features
4:14:46.518377 INFO: Decoy channel: -1
4:14:46.518404 INFO: competitive: True
4:14:46.706861 INFO: Setting torch num_threads to 2 for FDR classification task
4:14:46.983664 INFO: Estimating optimal hyperparameters - samples: 578,988, batch_size: 2,371, learning_rate: 7.61e-04
4:14:46.984734 INFO: Using random state 906300 for train-test-split
4:14:59.771537 INFO: Test AUC: 0.582
4:14:59.771662 INFO: Train AUC: 0.596
4:14:59.771695 INFO: AUC difference: 2.43%
4:15:00.245405 INFO: Resetting torch num_threads to 100
4:15:00.271949 PROGRESS: === Extracted 723735 precursors and 2398385 fragments ===
4:15:00.272420 INFO: === FDR correction performed with classifier version 11 ===
4:15:00.273136 PROGRESS: ============================= Precursor FDR =============================
4:15:00.273227 PROGRESS: Total precursors accumulated: 1,778
4:15:00.273289 PROGRESS: Target precursors: 1,761 (99.04%)
4:15:00.273342 PROGRESS: Decoy precursors: 17 (0.96%)
4:15:00.273398 PROGRESS: 
4:15:00.273449 PROGRESS: Precursor Summary:
4:15:00.274776 PROGRESS: Channel   0:	 0.050 FDR: 1,761; 0.010 FDR: 1,761; 0.001 FDR:     0
4:15:00.274868 PROGRESS: 
4:15:00.274925 PROGRESS: Protein Summary:
4:15:00.276637 PROGRESS: Channel   0:	 0.050 FDR: 1,527; 0.010 FDR: 1,527; 0.001 FDR:     0
4:15:00.276735 PROGRESS: =========================================================================
4:15:00.289809 INFO: Target number of precursors reached.
4:15:00.554880 INFO: fragments_df: keeping 5000 of 2398385 [sum(precursor_idx_mask)=36552 sum(mass_error_mask)=2398385 stop_rank=5000
4:15:00.922135 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:15:01.187278 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:15:01.906336 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:15:01.906804 INFO: Using score_cutoff 8.833779207229615 (fac=0.99, q=1)
4:15:01.907112 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:15:01.907200 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:15:01.907256 INFO: Updating optimization_manager: score_cutoff        : 10.657027633666992 -> 8.833779207229615
4:15:01.907310 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:15:02.055088 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:15:02.268937 INFO: === checking if optimization conditions were reached ===
4:15:02.271642 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
4:15:02.271763 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
4:15:02.271844 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
4:15:02.271918 INFO: ==============================================
4:15:02.272007 PROGRESS: Optimization finished for ms2_error.
4:15:02.633414 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:15:02.781305 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:15:02.993458 INFO: Starting optimization step 0.
4:15:02.993768 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:15:02.993864 INFO: Using rust extraction backend
4:15:02.993942 PROGRESS: Extracting batch of 250329 precursors
4:15:03.246803 INFO: === Search parameters used ===
4:15:03.247119 INFO: rt_error       : 805.5992431640625
4:15:03.247190 INFO: mobility_error : 0.1
4:15:03.247241 INFO: num_candidates : 3
4:15:03.247287 INFO: ms1_error      : 3
4:15:03.247330 INFO: ms2_error      : 10.0
4:15:03.247391 INFO: fwhm_rt        : 3.0
4:15:03.247433 INFO: quant_window   : 3
4:15:03.247474 INFO: ==============================================
4:15:05.473635 INFO: performing precursor FDR with 40 features
4:15:05.473754 INFO: Decoy channel: -1
4:15:05.473778 INFO: competitive: True
4:15:05.659713 INFO: Setting torch num_threads to 2 for FDR classification task
4:15:05.937327 INFO: Estimating optimal hyperparameters - samples: 578,968, batch_size: 2,371, learning_rate: 7.61e-04
4:15:05.938396 INFO: Using random state 320849 for train-test-split
4:15:18.353349 INFO: Test AUC: 0.584
4:15:18.353475 INFO: Train AUC: 0.599
4:15:18.353508 INFO: AUC difference: 2.43%
4:15:18.827242 INFO: Resetting torch num_threads to 100
4:15:18.853471 PROGRESS: === Extracted 723710 precursors and 2398507 fragments ===
4:15:18.853940 INFO: === FDR correction performed with classifier version 12 ===
4:15:18.854683 PROGRESS: ============================= Precursor FDR =============================
4:15:18.854776 PROGRESS: Total precursors accumulated: 1,711
4:15:18.854838 PROGRESS: Target precursors: 1,695 (99.06%)
4:15:18.854890 PROGRESS: Decoy precursors: 16 (0.94%)
4:15:18.854937 PROGRESS: 
4:15:18.854984 PROGRESS: Precursor Summary:
4:15:18.856320 PROGRESS: Channel   0:	 0.050 FDR: 1,695; 0.010 FDR: 1,695; 0.001 FDR:     0
4:15:18.856412 PROGRESS: 
4:15:18.856469 PROGRESS: Protein Summary:
4:15:18.858135 PROGRESS: Channel   0:	 0.050 FDR: 1,468; 0.010 FDR: 1,468; 0.001 FDR:     0
4:15:18.858225 PROGRESS: =========================================================================
4:15:18.871468 INFO: Target number of precursors reached.
4:15:19.135795 INFO: fragments_df: keeping 5000 of 2398507 [sum(precursor_idx_mask)=35600 sum(mass_error_mask)=2398507 stop_rank=5000
4:15:19.502833 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:15:19.760210 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:15:20.480458 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:15:20.480917 INFO: Using score_cutoff 9.53922815208435 (fac=0.99, q=1)
4:15:20.481217 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:15:20.481293 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:15:20.481347 INFO: Updating optimization_manager: score_cutoff        : 8.833779207229615 -> 9.53922815208435
4:15:20.481401 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:15:20.629541 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:15:20.839525 INFO: === checking if optimization conditions were reached ===
4:15:20.839850 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
4:15:20.843213 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 506.650941953578
4:15:20.843337 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 506.6509.
4:15:20.843444 INFO: ==============================================
4:15:20.843528 INFO: Starting optimization step 1.
4:15:20.843598 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:15:20.843677 INFO: Using rust extraction backend
4:15:20.843750 PROGRESS: Extracting batch of 250329 precursors
4:15:21.097208 INFO: === Search parameters used ===
4:15:21.097498 INFO: rt_error       : 506.650941953578
4:15:21.097555 INFO: mobility_error : 0.1
4:15:21.097603 INFO: num_candidates : 3
4:15:21.097647 INFO: ms1_error      : 3
4:15:21.097688 INFO: ms2_error      : 10.0
4:15:21.097728 INFO: fwhm_rt        : 3.0
4:15:21.097769 INFO: quant_window   : 3
4:15:21.097807 INFO: ==============================================
4:15:23.251701 INFO: performing precursor FDR with 40 features
4:15:23.251823 INFO: Decoy channel: -1
4:15:23.251848 INFO: competitive: True
4:15:23.434904 INFO: Setting torch num_threads to 2 for FDR classification task
4:15:23.711237 INFO: Estimating optimal hyperparameters - samples: 576,556, batch_size: 2,361, learning_rate: 7.59e-04
4:15:23.712297 INFO: Using random state 320849 for train-test-split
4:15:37.046672 INFO: Test AUC: 0.582
4:15:37.046802 INFO: Train AUC: 0.597
4:15:37.046835 INFO: AUC difference: 2.39%
4:15:37.522265 INFO: Resetting torch num_threads to 100
4:15:37.549272 PROGRESS: === Extracted 720695 precursors and 2352986 fragments ===
4:15:37.549758 INFO: === FDR correction performed with classifier version 12 ===
4:15:37.550520 PROGRESS: ============================= Precursor FDR =============================
4:15:37.550610 PROGRESS: Total precursors accumulated: 2,021
4:15:37.550672 PROGRESS: Target precursors: 2,001 (99.01%)
4:15:37.550725 PROGRESS: Decoy precursors: 20 (0.99%)
4:15:37.550771 PROGRESS: 
4:15:37.550817 PROGRESS: Precursor Summary:
4:15:37.552216 PROGRESS: Channel   0:	 0.050 FDR: 2,001; 0.010 FDR: 2,001; 0.001 FDR:     1
4:15:37.552310 PROGRESS: 
4:15:37.552370 PROGRESS: Protein Summary:
4:15:37.554157 PROGRESS: Channel   0:	 0.050 FDR: 1,710; 0.010 FDR: 1,710; 0.001 FDR:     1
4:15:37.554247 PROGRESS: =========================================================================
4:15:37.567916 INFO: Target number of precursors reached.
4:15:37.832207 INFO: fragments_df: keeping 5000 of 2352986 [sum(precursor_idx_mask)=41473 sum(mass_error_mask)=2352986 stop_rank=5000
4:15:38.199291 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:15:38.501991 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:15:39.224574 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:15:39.225028 INFO: Using score_cutoff 9.774652519226073 (fac=0.99, q=1)
4:15:39.225337 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:15:39.225418 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:15:39.225471 INFO: Updating optimization_manager: score_cutoff        : 9.53922815208435 -> 9.774652519226073
4:15:39.225525 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:15:39.373894 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:15:39.572528 INFO: === checking if optimization conditions were reached ===
4:15:39.572840 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
4:15:39.576515 INFO: Updating optimization_manager: rt_error            : 506.650941953578 -> 434.3118005163148
4:15:39.576638 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 434.3118.
4:15:39.576712 INFO: ==============================================
4:15:39.576792 INFO: Starting optimization step 2.
4:15:39.576869 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:15:39.576942 INFO: Using rust extraction backend
4:15:39.577010 PROGRESS: Extracting batch of 250329 precursors
4:15:39.831423 INFO: === Search parameters used ===
4:15:39.831725 INFO: rt_error       : 434.3118005163148
4:15:39.831783 INFO: mobility_error : 0.1
4:15:39.831832 INFO: num_candidates : 3
4:15:39.831878 INFO: ms1_error      : 3
4:15:39.831924 INFO: ms2_error      : 10.0
4:15:39.831968 INFO: fwhm_rt        : 3.0
4:15:39.832012 INFO: quant_window   : 3
4:15:39.832054 INFO: ==============================================
4:15:42.039676 INFO: performing precursor FDR with 40 features
4:15:42.039801 INFO: Decoy channel: -1
4:15:42.039828 INFO: competitive: True
4:15:42.233960 INFO: Setting torch num_threads to 2 for FDR classification task
4:15:42.522174 INFO: Estimating optimal hyperparameters - samples: 574,439, batch_size: 2,352, learning_rate: 7.58e-04
4:15:42.523352 INFO: Using random state 320849 for train-test-split
4:15:54.561275 INFO: Test AUC: 0.582
4:15:54.561400 INFO: Train AUC: 0.595
4:15:54.561433 INFO: AUC difference: 2.28%
4:15:55.036072 INFO: Resetting torch num_threads to 100
4:15:55.063366 PROGRESS: === Extracted 718049 precursors and 2312858 fragments ===
4:15:55.063854 INFO: === FDR correction performed with classifier version 12 ===
4:15:55.064708 PROGRESS: ============================= Precursor FDR =============================
4:15:55.064803 PROGRESS: Total precursors accumulated: 2,043
4:15:55.064864 PROGRESS: Target precursors: 2,023 (99.02%)
4:15:55.064914 PROGRESS: Decoy precursors: 20 (0.98%)
4:15:55.064962 PROGRESS: 
4:15:55.065008 PROGRESS: Precursor Summary:
4:15:55.066537 PROGRESS: Channel   0:	 0.050 FDR: 2,023; 0.010 FDR: 2,023; 0.001 FDR: 1,436
4:15:55.066639 PROGRESS: 
4:15:55.066695 PROGRESS: Protein Summary:
4:15:55.068755 PROGRESS: Channel   0:	 0.050 FDR: 1,722; 0.010 FDR: 1,722; 0.001 FDR: 1,250
4:15:55.068851 PROGRESS: =========================================================================
4:15:55.083016 INFO: Target number of precursors reached.
4:15:55.341792 INFO: fragments_df: keeping 5000 of 2312858 [sum(precursor_idx_mask)=41920 sum(mass_error_mask)=2312858 stop_rank=5000
4:15:55.577141 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:15:55.875349 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:15:56.590108 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:15:56.590583 INFO: Using score_cutoff 9.698589340782165 (fac=0.99, q=1)
4:15:56.590910 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:15:56.590989 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:15:56.591046 INFO: Updating optimization_manager: score_cutoff        : 9.774652519226073 -> 9.698589340782165
4:15:56.591112 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:15:56.665624 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:15:56.762246 INFO: === checking if optimization conditions were reached ===
4:15:56.762545 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
4:15:56.766318 INFO: Updating optimization_manager: rt_error            : 434.3118005163148 -> 411.64051212061094
4:15:56.766443 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 411.6405.
4:15:56.766546 INFO: ==============================================
4:15:56.766631 INFO: Starting optimization step 3.
4:15:56.766701 PROGRESS: === Extracting elution groups 0 to 63000 ===
4:15:56.766775 INFO: Using rust extraction backend
4:15:56.766846 PROGRESS: Extracting batch of 124196 precursors
4:15:56.896124 INFO: === Search parameters used ===
4:15:56.896429 INFO: rt_error       : 411.64051212061094
4:15:56.896486 INFO: mobility_error : 0.1
4:15:56.896533 INFO: num_candidates : 3
4:15:56.896577 INFO: ms1_error      : 3
4:15:56.896620 INFO: ms2_error      : 10.0
4:15:56.896662 INFO: fwhm_rt        : 3.0
4:15:56.896703 INFO: quant_window   : 3
4:15:56.896744 INFO: ==============================================
4:15:58.022052 INFO: performing precursor FDR with 40 features
4:15:58.022175 INFO: Decoy channel: -1
4:15:58.022200 INFO: competitive: True
4:15:58.119043 INFO: Setting torch num_threads to 2 for FDR classification task
4:15:58.252065 INFO: Estimating optimal hyperparameters - samples: 284,724, batch_size: 1,166, learning_rate: 5.34e-04
4:15:58.252698 INFO: Using random state 320849 for train-test-split
4:16:06.169955 INFO: Test AUC: 0.583
4:16:06.170130 INFO: Train AUC: 0.600
4:16:06.170163 INFO: AUC difference: 2.86%
4:16:06.539718 INFO: Resetting torch num_threads to 100
4:16:06.553123 PROGRESS: === Extracted 355905 precursors and 1138092 fragments ===
4:16:06.553587 INFO: === FDR correction performed with classifier version 12 ===
4:16:06.554187 PROGRESS: ============================= Precursor FDR =============================
4:16:06.554278 PROGRESS: Total precursors accumulated: 915
4:16:06.554338 PROGRESS: Target precursors: 906 (99.02%)
4:16:06.554390 PROGRESS: Decoy precursors: 9 (0.98%)
4:16:06.554437 PROGRESS: 
4:16:06.554483 PROGRESS: Precursor Summary:
4:16:06.555717 PROGRESS: Channel   0:	 0.050 FDR:   906; 0.010 FDR:   906; 0.001 FDR:   469
4:16:06.555809 PROGRESS: 
4:16:06.555864 PROGRESS: Protein Summary:
4:16:06.557359 PROGRESS: Channel   0:	 0.050 FDR:   843; 0.010 FDR:   843; 0.001 FDR:   445
4:16:06.557451 PROGRESS: =========================================================================
4:16:06.563184 INFO: Target number of precursors not reached yet.
4:16:06.786353 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:16:06.861970 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:16:06.962671 INFO: === skipping optimization until target number of precursors are found ===
4:16:06.962973 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
4:16:06.963109 INFO: Starting optimization step 4.
4:16:06.963198 PROGRESS: === Extracting elution groups 63000 to 127000 ===
4:16:06.963280 INFO: Using rust extraction backend
4:16:06.963351 PROGRESS: Extracting batch of 126133 precursors
4:16:07.095653 INFO: === Search parameters used ===
4:16:07.095987 INFO: rt_error       : 411.64051212061094
4:16:07.096048 INFO: mobility_error : 0.1
4:16:07.096095 INFO: num_candidates : 3
4:16:07.096138 INFO: ms1_error      : 3
4:16:07.096179 INFO: ms2_error      : 10.0
4:16:07.096230 INFO: fwhm_rt        : 3.0
4:16:07.096272 INFO: quant_window   : 3
4:16:07.096309 INFO: ==============================================
4:16:08.319871 INFO: performing precursor FDR with 40 features
4:16:08.319993 INFO: Decoy channel: -1
4:16:08.320017 INFO: competitive: True
4:16:08.587167 INFO: Setting torch num_threads to 2 for FDR classification task
4:16:08.864651 INFO: Estimating optimal hyperparameters - samples: 573,587, batch_size: 2,349, learning_rate: 7.57e-04
4:16:08.865747 INFO: Using random state 320849 for train-test-split
4:16:22.060617 INFO: Test AUC: 0.579
4:16:22.060854 INFO: Train AUC: 0.594
4:16:22.060894 INFO: AUC difference: 2.48%
4:16:22.544280 INFO: Resetting torch num_threads to 100
4:16:22.722703 PROGRESS: === Extracted 716984 precursors and 2297227 fragments ===
4:16:22.723500 INFO: === FDR correction performed with classifier version 12 ===
4:16:22.724609 PROGRESS: ============================= Precursor FDR =============================
4:16:22.724710 PROGRESS: Total precursors accumulated: 1,939
4:16:22.724774 PROGRESS: Target precursors: 1,920 (99.02%)
4:16:22.724827 PROGRESS: Decoy precursors: 19 (0.98%)
4:16:22.724878 PROGRESS: 
4:16:22.724925 PROGRESS: Precursor Summary:
4:16:22.726500 PROGRESS: Channel   0:	 0.050 FDR: 1,920; 0.010 FDR: 1,920; 0.001 FDR: 1,087
4:16:22.726598 PROGRESS: 
4:16:22.726655 PROGRESS: Protein Summary:
4:16:22.728648 PROGRESS: Channel   0:	 0.050 FDR: 1,635; 0.010 FDR: 1,635; 0.001 FDR:   961
4:16:22.728748 PROGRESS: =========================================================================
4:16:22.742338 INFO: Target number of precursors reached.
4:16:23.009198 INFO: fragments_df: keeping 5000 of 2297227 [sum(precursor_idx_mask)=39630 sum(mass_error_mask)=2297227 stop_rank=5000
4:16:23.479675 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:16:23.771810 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:16:24.487103 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:16:24.487602 INFO: Using score_cutoff 9.646873534870148 (fac=0.99, q=1)
4:16:24.487944 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:16:24.488023 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:16:24.488078 INFO: Updating optimization_manager: score_cutoff        : 9.698589340782165 -> 9.646873534870148
4:16:24.488136 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:16:24.637653 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:16:24.848309 INFO: === checking if optimization conditions were reached ===
4:16:24.848664 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
4:16:24.852794 INFO: Updating optimization_manager: rt_error            : 411.64051212061094 -> 499.76799017043845
4:16:24.852923 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 499.7680.
4:16:24.852998 INFO: ==============================================
4:16:24.853083 INFO: Starting optimization step 5.
4:16:24.853156 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:16:24.853242 INFO: Using rust extraction backend
4:16:24.853318 PROGRESS: Extracting batch of 250329 precursors
4:16:25.110398 INFO: === Search parameters used ===
4:16:25.110686 INFO: rt_error       : 499.76799017043845
4:16:25.110758 INFO: mobility_error : 0.1
4:16:25.110805 INFO: num_candidates : 3
4:16:25.110856 INFO: ms1_error      : 3
4:16:25.110899 INFO: ms2_error      : 10.0
4:16:25.110939 INFO: fwhm_rt        : 3.0
4:16:25.110979 INFO: quant_window   : 3
4:16:25.111017 INFO: ==============================================
4:16:27.310052 INFO: performing precursor FDR with 40 features
4:16:27.310173 INFO: Decoy channel: -1
4:16:27.310199 INFO: competitive: True
4:16:27.506448 INFO: Setting torch num_threads to 2 for FDR classification task
4:16:27.785677 INFO: Estimating optimal hyperparameters - samples: 576,285, batch_size: 2,360, learning_rate: 7.59e-04
4:16:27.786835 INFO: Using random state 320849 for train-test-split
4:16:40.452825 INFO: Test AUC: 0.584
4:16:40.452973 INFO: Train AUC: 0.596
4:16:40.453005 INFO: AUC difference: 2.02%
4:16:40.932666 INFO: Resetting torch num_threads to 100
4:16:40.961618 PROGRESS: === Extracted 720357 precursors and 2347568 fragments ===
4:16:40.962107 INFO: === FDR correction performed with classifier version 12 ===
4:16:40.962941 PROGRESS: ============================= Precursor FDR =============================
4:16:40.963033 PROGRESS: Total precursors accumulated: 2,054
4:16:40.963092 PROGRESS: Target precursors: 2,034 (99.03%)
4:16:40.963142 PROGRESS: Decoy precursors: 20 (0.97%)
4:16:40.963217 PROGRESS: 
4:16:40.963263 PROGRESS: Precursor Summary:
4:16:40.964830 PROGRESS: Channel   0:	 0.050 FDR: 2,034; 0.010 FDR: 2,034; 0.001 FDR: 1,492
4:16:40.964928 PROGRESS: 
4:16:40.964986 PROGRESS: Protein Summary:
4:16:40.967072 PROGRESS: Channel   0:	 0.050 FDR: 1,751; 0.010 FDR: 1,751; 0.001 FDR: 1,303
4:16:40.967188 PROGRESS: =========================================================================
4:16:40.980694 INFO: Target number of precursors reached.
4:16:41.244953 INFO: fragments_df: keeping 5000 of 2347568 [sum(precursor_idx_mask)=41069 sum(mass_error_mask)=2347568 stop_rank=5000
4:16:41.507892 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:16:41.807200 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:16:42.524396 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:16:42.524869 INFO: Using score_cutoff 5.584209752368927 (fac=0.99, q=1)
4:16:42.525194 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:16:42.525273 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:16:42.525337 INFO: Updating optimization_manager: score_cutoff        : 9.646873534870148 -> 5.584209752368927
4:16:42.525399 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:16:42.599254 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:16:42.698805 INFO: === checking if optimization conditions were reached ===
4:16:42.699110 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
4:16:42.702770 INFO: Updating optimization_manager: rt_error            : 499.76799017043845 -> 544.7784428191203
4:16:42.702910 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 544.7784.
4:16:42.702989 INFO: ==============================================
4:16:42.703082 INFO: Starting optimization step 6.
4:16:42.703165 PROGRESS: === Extracting elution groups 0 to 63000 ===
4:16:42.703252 INFO: Using rust extraction backend
4:16:42.703328 PROGRESS: Extracting batch of 124196 precursors
4:16:42.833934 INFO: === Search parameters used ===
4:16:42.834234 INFO: rt_error       : 544.7784428191203
4:16:42.834304 INFO: mobility_error : 0.1
4:16:42.834353 INFO: num_candidates : 3
4:16:42.834397 INFO: ms1_error      : 3
4:16:42.834439 INFO: ms2_error      : 10.0
4:16:42.834481 INFO: fwhm_rt        : 3.0
4:16:42.834520 INFO: quant_window   : 3
4:16:42.834561 INFO: ==============================================
4:16:43.989928 INFO: performing precursor FDR with 40 features
4:16:43.990083 INFO: Decoy channel: -1
4:16:43.990109 INFO: competitive: True
4:16:44.081471 INFO: Setting torch num_threads to 2 for FDR classification task
4:16:44.211846 INFO: Estimating optimal hyperparameters - samples: 286,520, batch_size: 1,173, learning_rate: 5.35e-04
4:16:44.212385 INFO: Using random state 320849 for train-test-split
4:16:52.106038 INFO: Test AUC: 0.586
4:16:52.106195 INFO: Train AUC: 0.602
4:16:52.106229 INFO: AUC difference: 2.54%
4:16:52.471217 INFO: Resetting torch num_threads to 100
4:16:52.486203 PROGRESS: === Extracted 358151 precursors and 1173539 fragments ===
4:16:52.486670 INFO: === FDR correction performed with classifier version 12 ===
4:16:52.487257 PROGRESS: ============================= Precursor FDR =============================
4:16:52.487349 PROGRESS: Total precursors accumulated: 834
4:16:52.487409 PROGRESS: Target precursors: 826 (99.04%)
4:16:52.487463 PROGRESS: Decoy precursors: 8 (0.96%)
4:16:52.487510 PROGRESS: 
4:16:52.487557 PROGRESS: Precursor Summary:
4:16:52.488665 PROGRESS: Channel   0:	 0.050 FDR:   826; 0.010 FDR:   826; 0.001 FDR:     4
4:16:52.488754 PROGRESS: 
4:16:52.488810 PROGRESS: Protein Summary:
4:16:52.490164 PROGRESS: Channel   0:	 0.050 FDR:   772; 0.010 FDR:   772; 0.001 FDR:     4
4:16:52.490254 PROGRESS: =========================================================================
4:16:52.496095 INFO: Target number of precursors not reached yet.
4:16:52.723097 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:16:52.798527 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:16:52.900290 INFO: === skipping optimization until target number of precursors are found ===
4:16:52.900591 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
4:16:52.900743 INFO: Starting optimization step 7.
4:16:52.900821 PROGRESS: === Extracting elution groups 63000 to 127000 ===
4:16:52.900907 INFO: Using rust extraction backend
4:16:52.900979 PROGRESS: Extracting batch of 126133 precursors
4:16:53.034782 INFO: === Search parameters used ===
4:16:53.035091 INFO: rt_error       : 544.7784428191203
4:16:53.035157 INFO: mobility_error : 0.1
4:16:53.035210 INFO: num_candidates : 3
4:16:53.035254 INFO: ms1_error      : 3
4:16:53.035295 INFO: ms2_error      : 10.0
4:16:53.035336 INFO: fwhm_rt        : 3.0
4:16:53.035377 INFO: quant_window   : 3
4:16:53.035417 INFO: ==============================================
4:16:54.296019 INFO: performing precursor FDR with 40 features
4:16:54.296142 INFO: Decoy channel: -1
4:16:54.296169 INFO: competitive: True
4:16:54.563025 INFO: Setting torch num_threads to 2 for FDR classification task
4:16:54.840454 INFO: Estimating optimal hyperparameters - samples: 577,383, batch_size: 2,364, learning_rate: 7.60e-04
4:16:54.841380 INFO: Using random state 320849 for train-test-split
4:17:07.294141 INFO: Test AUC: 0.581
4:17:07.294275 INFO: Train AUC: 0.598
4:17:07.294311 INFO: AUC difference: 2.86%
4:17:07.768595 INFO: Resetting torch num_threads to 100
4:17:07.864857 PROGRESS: === Extracted 721729 precursors and 2368096 fragments ===
4:17:07.865579 INFO: === FDR correction performed with classifier version 12 ===
4:17:07.866674 PROGRESS: ============================= Precursor FDR =============================
4:17:07.866767 PROGRESS: Total precursors accumulated: 1,949
4:17:07.866830 PROGRESS: Target precursors: 1,930 (99.03%)
4:17:07.866894 PROGRESS: Decoy precursors: 19 (0.97%)
4:17:07.866944 PROGRESS: 
4:17:07.866992 PROGRESS: Precursor Summary:
4:17:07.868585 PROGRESS: Channel   0:	 0.050 FDR: 1,930; 0.010 FDR: 1,930; 0.001 FDR: 1,037
4:17:07.868692 PROGRESS: 
4:17:07.868751 PROGRESS: Protein Summary:
4:17:07.870720 PROGRESS: Channel   0:	 0.050 FDR: 1,664; 0.010 FDR: 1,664; 0.001 FDR:   930
4:17:07.870822 PROGRESS: =========================================================================
4:17:07.879807 INFO: Target number of precursors reached.
4:17:08.155430 INFO: fragments_df: keeping 5000 of 2368096 [sum(precursor_idx_mask)=39610 sum(mass_error_mask)=2368096 stop_rank=5000
4:17:08.517507 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:17:08.800317 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:17:09.512221 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:17:09.512684 INFO: Using score_cutoff 8.667150387382506 (fac=0.99, q=1)
4:17:09.513000 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:17:09.513079 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:17:09.513140 INFO: Updating optimization_manager: score_cutoff        : 5.584209752368927 -> 8.667150387382506
4:17:09.513196 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:17:09.659492 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:17:09.860588 INFO: === checking if optimization conditions were reached ===
4:17:09.860903 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
4:17:09.864550 INFO: Updating optimization_manager: rt_error            : 544.7784428191203 -> 570.6155852994065
4:17:09.864672 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 570.6156.
4:17:09.864749 INFO: ==============================================
4:17:09.864833 INFO: Starting optimization step 8.
4:17:09.864904 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:17:09.864979 INFO: Using rust extraction backend
4:17:09.865051 PROGRESS: Extracting batch of 250329 precursors
4:17:10.117514 INFO: === Search parameters used ===
4:17:10.117803 INFO: rt_error       : 570.6155852994065
4:17:10.117860 INFO: mobility_error : 0.1
4:17:10.117908 INFO: num_candidates : 3
4:17:10.117951 INFO: ms1_error      : 3
4:17:10.117993 INFO: ms2_error      : 10.0
4:17:10.118040 INFO: fwhm_rt        : 3.0
4:17:10.118082 INFO: quant_window   : 3
4:17:10.118121 INFO: ==============================================
4:17:12.374887 INFO: performing precursor FDR with 40 features
4:17:12.375009 INFO: Decoy channel: -1
4:17:12.375035 INFO: competitive: True
4:17:12.590088 INFO: Setting torch num_threads to 2 for FDR classification task
4:17:12.868363 INFO: Estimating optimal hyperparameters - samples: 577,780, batch_size: 2,366, learning_rate: 7.60e-04
4:17:12.869488 INFO: Using random state 320849 for train-test-split
4:17:25.933329 INFO: Test AUC: 0.586
4:17:25.933558 INFO: Train AUC: 0.598
4:17:25.933595 INFO: AUC difference: 2.03%
4:17:26.417193 INFO: Resetting torch num_threads to 100
4:17:26.446375 PROGRESS: === Extracted 722226 precursors and 2376098 fragments ===
4:17:26.446908 INFO: === FDR correction performed with classifier version 12 ===
4:17:26.447725 PROGRESS: ============================= Precursor FDR =============================
4:17:26.447832 PROGRESS: Total precursors accumulated: 1,865
4:17:26.447893 PROGRESS: Target precursors: 1,847 (99.03%)
4:17:26.447943 PROGRESS: Decoy precursors: 18 (0.97%)
4:17:26.447990 PROGRESS: 
4:17:26.448036 PROGRESS: Precursor Summary:
4:17:26.449376 PROGRESS: Channel   0:	 0.050 FDR: 1,847; 0.010 FDR: 1,847; 0.001 FDR:     1
4:17:26.449464 PROGRESS: 
4:17:26.449518 PROGRESS: Protein Summary:
4:17:26.451228 PROGRESS: Channel   0:	 0.050 FDR: 1,581; 0.010 FDR: 1,581; 0.001 FDR:     1
4:17:26.451321 PROGRESS: =========================================================================
4:17:26.465321 INFO: Target number of precursors reached.
4:17:26.728288 INFO: fragments_df: keeping 5000 of 2376098 [sum(precursor_idx_mask)=38805 sum(mass_error_mask)=2376098 stop_rank=5000
4:17:27.157732 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:17:29.315214 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:17:30.059217 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:17:30.059672 INFO: Using score_cutoff 9.557120559883117 (fac=0.99, q=1)
4:17:30.059984 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:17:30.060062 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:17:30.060117 INFO: Updating optimization_manager: score_cutoff        : 8.667150387382506 -> 9.557120559883117
4:17:30.060182 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:17:30.216009 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:17:30.423370 INFO: === checking if optimization conditions were reached ===
4:17:30.423678 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
4:17:30.424855 INFO: Updating optimization_manager: rt_error            : 570.6155852994065 -> 499.76799017043845
4:17:30.425014 INFO: Updating optimization_manager: classifier_version  : 12 -> 18
4:17:30.425130 INFO: Updating optimization_manager: score_cutoff        : 9.557120559883117 -> 5.584209752368927
4:17:30.425235 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:17:30.425335 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:17:30.425456 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 499.7680 found after 7 searches.
4:17:30.425528 INFO: ==============================================
4:17:30.425611 PROGRESS: Optimization finished for rt_error.
4:17:30.691662 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:17:30.765938 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:17:30.872738 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
4:17:30.873027 PROGRESS: ==============================================
4:17:30.873109 PROGRESS: ms2_error      : 10.0000
4:17:30.873172 PROGRESS: rt_error       : 499.7680
4:17:30.873227 PROGRESS: ==============================================
4:17:30.874311 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:17:38.323036 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:17:47.643695 INFO: Using rust extraction backend
4:17:47.644046 PROGRESS: Extracting batch of 11997144 precursors
4:17:57.902889 INFO: === Search parameters used ===
4:17:57.903186 INFO: rt_error       : 499.76799017043845
4:17:57.903253 INFO: mobility_error : 0.1
4:17:57.903306 INFO: num_candidates : 3
4:17:57.903361 INFO: ms1_error      : 3
4:17:57.903409 INFO: ms2_error      : 10.0
4:17:57.903453 INFO: fwhm_rt        : 3.0
4:17:57.903496 INFO: quant_window   : 3
4:17:57.903538 INFO: ==============================================
4:18:19.765988 INFO: Removed 2337033 precursors with score below cutoff 5.584209752368927
4:18:44.641180 INFO: performing precursor FDR with 40 features
4:18:44.641378 INFO: Decoy channel: -1
4:18:44.641409 INFO: competitive: True
4:18:48.147310 INFO: Setting torch num_threads to 2 for FDR classification task
4:19:02.076387 INFO: Estimating optimal hyperparameters - samples: 26,691,063, batch_size: 4,096, learning_rate: 1.00e-03
4:19:02.156607 INFO: Using random state 563187 for train-test-split
4:28:41.419782 INFO: Test AUC: 0.591
4:28:41.420566 INFO: Train AUC: 0.591
4:28:41.420732 INFO: AUC difference: 0.08%
4:28:50.809779 INFO: Resetting torch num_threads to 100
4:28:54.451401 PROGRESS: ============================= Precursor FDR =============================
4:28:54.451915 PROGRESS: Total precursors accumulated: 97,606
4:28:54.451991 PROGRESS: Target precursors: 96,640 (99.01%)
4:28:54.452045 PROGRESS: Decoy precursors: 966 (0.99%)
4:28:54.452095 PROGRESS: 
4:28:54.452142 PROGRESS: Precursor Summary:
4:28:54.485941 PROGRESS: Channel   0:	 0.050 FDR: 96,640; 0.010 FDR: 96,640; 0.001 FDR:     2
4:28:54.486272 PROGRESS: 
4:28:54.486355 PROGRESS: Protein Summary:
4:28:54.525875 PROGRESS: Channel   0:	 0.050 FDR: 13,673; 0.010 FDR: 13,673; 0.001 FDR:     2
4:28:54.526217 PROGRESS: =========================================================================
4:28:54.734460 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/psm.parquet
4:28:54.928531 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.parquet
4:28:55.167089 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
4:28:56.016915 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 
4:28:56.017358 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant
4:28:56.017521 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/figures
4:28:56.017793 INFO: Initializing TimingManager
4:28:56.019232 INFO: Initializing RawFileManager
4:29:24.241518 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.
4:29:24.257450 INFO: Determining DIA cycle
4:29:24.277166 INFO: Found cycle with start 0.00 min and length 300.
4:29:24.954326 INFO: RT (min)            : 0.0 - 26.9
4:29:24.954597 INFO: RT duration (sec)   : 1611.2
4:29:24.954628 INFO: RT duration (min)   : 26.9
4:29:24.954654 INFO: Cycle len (scans)   : 300
4:29:24.954675 INFO: Cycle len (sec)     : 1.65
4:29:24.954696 INFO: Number of cycles    : 978
4:29:24.954717 INFO: MS2 range (m/z)     : 380.4 - 980.7
4:29:24.954767 INFO: Creating DIA data object took: 28.935424327850342
4:29:26.927638 INFO: Creating DIA data NG object took: 1.972445011138916
4:29:30.845239 INFO: Initializing CalibrationManager
4:29:30.846090 INFO: Setting up calibration estimators ..
4:29:30.846175 INFO: Found 1 estimator(s) in calibration group 'fragment'
4:29:30.846352 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
4:29:30.846533 INFO: Found 3 estimator(s) in calibration group 'precursor'
4:29:30.846615 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
4:29:30.846714 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
4:29:30.846794 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
4:29:30.846858 INFO: Done setting up calibration estimators.
4:29:30.848287 INFO: Initializing OptimizationManager
4:29:30.848703 INFO: initial parameter: ms1_error = 3
4:29:30.848770 INFO: initial parameter: ms2_error = 10
4:29:30.848844 INFO: initial parameter: rt_error = 805.6019897460938
4:29:30.848897 INFO: initial parameter: mobility_error = 0.1
4:29:30.848942 INFO: initial parameter: num_candidates = 1
4:29:30.848984 INFO: initial parameter: fwhm_rt = 5
4:29:30.849030 INFO: initial parameter: fwhm_mobility = 0.01
4:29:30.849073 INFO: initial parameter: score_cutoff = 0
4:29:30.849118 INFO: initial parameter: classifier_version = -1
4:29:30.849235 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
4:29:30.850454 INFO: FDRManager: loading saved state not requested, will be initialized.
4:29:30.850532 INFO: Initializing FDRManager
4:29:30.850637 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
4:29:35.481497 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
4:29:38.924385 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
4:29:38.927914 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
4:29:38.928890 PROGRESS: Starting initial search for precursors.
4:29:38.929664 INFO: Starting optimization step 0.
4:29:38.930231 PROGRESS: === Extracting elution groups 0 to 1000 ===
4:29:38.930748 INFO: Using rust extraction backend
4:29:38.931267 PROGRESS: Extracting batch of 1967 precursors
4:29:38.955619 INFO: === Search parameters used ===
4:29:38.956883 INFO: rt_error       : 805.6019897460938
4:29:38.957050 INFO: mobility_error : 0.1
4:29:38.957184 INFO: num_candidates : 1
4:29:38.957251 INFO: ms1_error      : 3
4:29:38.957310 INFO: ms2_error      : 10
4:29:38.957365 INFO: fwhm_rt        : 5
4:29:38.957414 INFO: quant_window   : 3
4:29:38.957466 INFO: ==============================================
4:29:39.055854 INFO: performing precursor FDR with 40 features
4:29:39.056192 INFO: Decoy channel: -1
4:29:39.056231 INFO: competitive: True
4:29:39.063929 INFO: Setting torch num_threads to 2 for FDR classification task
4:29:39.075058 INFO: Estimating optimal hyperparameters - samples: 1,518, batch_size: 128, learning_rate: 1.77e-04
4:29:39.079106 INFO: Using random state 768627 for train-test-split
4:29:39.395842 INFO: Test AUC: 0.466
4:29:39.396039 INFO: Train AUC: 0.529
4:29:39.396074 INFO: AUC difference: 11.90%
4:29:39.396100 WARNING: AUC difference > 5%. This may indicate overfitting.
4:29:39.864775 INFO: Resetting torch num_threads to 100
4:29:39.870607 PROGRESS: === Extracted 1898 precursors and 6658 fragments ===
4:29:39.871991 INFO: === FDR correction performed with classifier version -1 ===
4:29:39.872950 PROGRESS: ============================= Precursor FDR =============================
4:29:39.873103 PROGRESS: Total precursors accumulated: 4
4:29:39.873185 PROGRESS: Target precursors: 4 (100.00%)
4:29:39.873241 PROGRESS: Decoy precursors: 0 (0.00%)
4:29:39.873289 PROGRESS: 
4:29:39.873334 PROGRESS: Precursor Summary:
4:29:39.874649 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
4:29:39.874780 PROGRESS: 
4:29:39.874837 PROGRESS: Protein Summary:
4:29:39.876268 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
4:29:39.876401 PROGRESS: =========================================================================
4:29:39.877868 INFO: Target number of precursors not reached yet.
4:29:39.992449 INFO: Starting optimization step 1.
4:29:39.993291 PROGRESS: === Extracting elution groups 1000 to 3000 ===
4:29:39.993451 INFO: Using rust extraction backend
4:29:39.993555 PROGRESS: Extracting batch of 3942 precursors
4:29:40.008130 INFO: === Search parameters used ===
4:29:40.009015 INFO: rt_error       : 805.6019897460938
4:29:40.009080 INFO: mobility_error : 0.1
4:29:40.009147 INFO: num_candidates : 1
4:29:40.009198 INFO: ms1_error      : 3
4:29:40.009244 INFO: ms2_error      : 10
4:29:40.009288 INFO: fwhm_rt        : 5
4:29:40.009330 INFO: quant_window   : 3
4:29:40.009375 INFO: ==============================================
4:29:40.151619 INFO: performing precursor FDR with 40 features
4:29:40.151894 INFO: Decoy channel: -1
4:29:40.151923 INFO: competitive: True
4:29:40.168583 INFO: Setting torch num_threads to 2 for FDR classification task
4:29:40.175019 INFO: Estimating optimal hyperparameters - samples: 4,564, batch_size: 128, learning_rate: 1.77e-04
4:29:40.175538 INFO: Using random state 164353 for train-test-split
4:29:40.676268 INFO: Test AUC: 0.542
4:29:40.676872 INFO: Train AUC: 0.529
4:29:40.676927 INFO: AUC difference: 2.48%
4:29:41.202142 INFO: Resetting torch num_threads to 100
4:29:41.225932 PROGRESS: === Extracted 5705 precursors and 19517 fragments ===
4:29:41.227921 INFO: === FDR correction performed with classifier version -1 ===
4:29:41.230301 PROGRESS: ============================= Precursor FDR =============================
4:29:41.230545 PROGRESS: Total precursors accumulated: 21
4:29:41.230644 PROGRESS: Target precursors: 21 (100.00%)
4:29:41.230713 PROGRESS: Decoy precursors: 0 (0.00%)
4:29:41.230772 PROGRESS: 
4:29:41.230832 PROGRESS: Precursor Summary:
4:29:41.232695 PROGRESS: Channel   0:	 0.050 FDR:    21; 0.010 FDR:    21; 0.001 FDR:    21
4:29:41.232822 PROGRESS: 
4:29:41.232880 PROGRESS: Protein Summary:
4:29:41.234278 PROGRESS: Channel   0:	 0.050 FDR:    21; 0.010 FDR:    21; 0.001 FDR:    21
4:29:41.234392 PROGRESS: =========================================================================
4:29:41.237055 INFO: Target number of precursors not reached yet.
4:29:41.416667 INFO: Starting optimization step 2.
4:29:41.418180 PROGRESS: === Extracting elution groups 3000 to 7000 ===
4:29:41.418595 INFO: Using rust extraction backend
4:29:41.418795 PROGRESS: Extracting batch of 7891 precursors
4:29:41.455975 INFO: === Search parameters used ===
4:29:41.457156 INFO: rt_error       : 805.6019897460938
4:29:41.457236 INFO: mobility_error : 0.1
4:29:41.457295 INFO: num_candidates : 1
4:29:41.457348 INFO: ms1_error      : 3
4:29:41.457400 INFO: ms2_error      : 10
4:29:41.457447 INFO: fwhm_rt        : 5
4:29:41.457504 INFO: quant_window   : 3
4:29:41.457556 INFO: ==============================================
4:29:41.777490 INFO: performing precursor FDR with 40 features
4:29:41.777780 INFO: Decoy channel: -1
4:29:41.777808 INFO: competitive: True
4:29:41.816113 INFO: Setting torch num_threads to 2 for FDR classification task
4:29:41.842024 INFO: Estimating optimal hyperparameters - samples: 10,682, batch_size: 128, learning_rate: 1.77e-04
4:29:41.843073 INFO: Using random state 742732 for train-test-split
4:29:43.036212 INFO: Test AUC: 0.527
4:29:43.037080 INFO: Train AUC: 0.563
4:29:43.037134 INFO: AUC difference: 6.45%
4:29:43.037187 WARNING: AUC difference > 5%. This may indicate overfitting.
4:29:43.600513 INFO: Resetting torch num_threads to 100
4:29:43.635446 PROGRESS: === Extracted 13353 precursors and 45889 fragments ===
4:29:43.637985 INFO: === FDR correction performed with classifier version -1 ===
4:29:43.640448 PROGRESS: ============================= Precursor FDR =============================
4:29:43.640801 PROGRESS: Total precursors accumulated: 65
4:29:43.640892 PROGRESS: Target precursors: 65 (100.00%)
4:29:43.640956 PROGRESS: Decoy precursors: 0 (0.00%)
4:29:43.641010 PROGRESS: 
4:29:43.641064 PROGRESS: Precursor Summary:
4:29:43.643111 PROGRESS: Channel   0:	 0.050 FDR:    65; 0.010 FDR:    65; 0.001 FDR:    65
4:29:43.643277 PROGRESS: 
4:29:43.643342 PROGRESS: Protein Summary:
4:29:43.645183 PROGRESS: Channel   0:	 0.050 FDR:    65; 0.010 FDR:    65; 0.001 FDR:    65
4:29:43.645297 PROGRESS: =========================================================================
4:29:43.649544 INFO: Target number of precursors not reached yet.
4:29:43.879681 INFO: Starting optimization step 3.
4:29:43.880589 PROGRESS: === Extracting elution groups 7000 to 15000 ===
4:29:43.880742 INFO: Using rust extraction backend
4:29:43.880844 PROGRESS: Extracting batch of 15751 precursors
4:29:43.948349 INFO: === Search parameters used ===
4:29:43.949394 INFO: rt_error       : 805.6019897460938
4:29:43.949468 INFO: mobility_error : 0.1
4:29:43.949526 INFO: num_candidates : 1
4:29:43.949579 INFO: ms1_error      : 3
4:29:43.949633 INFO: ms2_error      : 10
4:29:43.949748 INFO: fwhm_rt        : 5
4:29:43.949794 INFO: quant_window   : 3
4:29:43.949844 INFO: ==============================================
4:29:44.473207 INFO: performing precursor FDR with 40 features
4:29:44.473503 INFO: Decoy channel: -1
4:29:44.473535 INFO: competitive: True
4:29:44.553757 INFO: Setting torch num_threads to 2 for FDR classification task
4:29:44.597362 INFO: Estimating optimal hyperparameters - samples: 22,926, batch_size: 128, learning_rate: 1.77e-04
4:29:44.598227 INFO: Using random state 575905 for train-test-split
4:29:46.935987 INFO: Test AUC: 0.552
4:29:46.936596 INFO: Train AUC: 0.571
4:29:46.936660 INFO: AUC difference: 3.23%
4:29:47.412424 INFO: Resetting torch num_threads to 100
4:29:47.456547 PROGRESS: === Extracted 28658 precursors and 98294 fragments ===
4:29:47.458777 INFO: === FDR correction performed with classifier version -1 ===
4:29:47.460213 PROGRESS: ============================= Precursor FDR =============================
4:29:47.460373 PROGRESS: Total precursors accumulated: 117
4:29:47.460455 PROGRESS: Target precursors: 116 (99.15%)
4:29:47.460516 PROGRESS: Decoy precursors: 1 (0.85%)
4:29:47.460572 PROGRESS: 
4:29:47.460622 PROGRESS: Precursor Summary:
4:29:47.462044 PROGRESS: Channel   0:	 0.050 FDR:   116; 0.010 FDR:   116; 0.001 FDR:    80
4:29:47.462164 PROGRESS: 
4:29:47.462225 PROGRESS: Protein Summary:
4:29:47.464089 PROGRESS: Channel   0:	 0.050 FDR:   114; 0.010 FDR:   114; 0.001 FDR:    79
4:29:47.464238 PROGRESS: =========================================================================
4:29:47.469229 INFO: Target number of precursors not reached yet.
4:29:47.756999 INFO: Starting optimization step 4.
4:29:47.757876 PROGRESS: === Extracting elution groups 15000 to 31000 ===
4:29:47.758023 INFO: Using rust extraction backend
4:29:47.758123 PROGRESS: Extracting batch of 31575 precursors
4:29:47.840793 INFO: === Search parameters used ===
4:29:47.841968 INFO: rt_error       : 805.6019897460938
4:29:47.842032 INFO: mobility_error : 0.1
4:29:47.842091 INFO: num_candidates : 1
4:29:47.842139 INFO: ms1_error      : 3
4:29:47.842188 INFO: ms2_error      : 10
4:29:47.842241 INFO: fwhm_rt        : 5
4:29:47.842286 INFO: quant_window   : 3
4:29:47.842344 INFO: ==============================================
4:29:48.824304 INFO: performing precursor FDR with 40 features
4:29:48.824740 INFO: Decoy channel: -1
4:29:48.824770 INFO: competitive: True
4:29:48.998689 INFO: Setting torch num_threads to 2 for FDR classification task
4:29:49.110434 INFO: Estimating optimal hyperparameters - samples: 47,486, batch_size: 194, learning_rate: 2.18e-04
4:29:49.111621 INFO: Using random state 898498 for train-test-split
4:29:52.832895 INFO: Test AUC: 0.551
4:29:52.833754 INFO: Train AUC: 0.578
4:29:52.833832 INFO: AUC difference: 4.65%
4:29:53.382863 INFO: Resetting torch num_threads to 100
4:29:53.484311 PROGRESS: === Extracted 59358 precursors and 204667 fragments ===
4:29:53.486657 INFO: === FDR correction performed with classifier version -1 ===
4:29:53.490645 PROGRESS: ============================= Precursor FDR =============================
4:29:53.490919 PROGRESS: Total precursors accumulated: 268
4:29:53.490997 PROGRESS: Target precursors: 266 (99.25%)
4:29:53.491055 PROGRESS: Decoy precursors: 2 (0.75%)
4:29:53.491105 PROGRESS: 
4:29:53.491168 PROGRESS: Precursor Summary:
4:29:53.492824 PROGRESS: Channel   0:	 0.050 FDR:   266; 0.010 FDR:   266; 0.001 FDR:   236
4:29:53.492965 PROGRESS: 
4:29:53.493024 PROGRESS: Protein Summary:
4:29:53.494737 PROGRESS: Channel   0:	 0.050 FDR:   255; 0.010 FDR:   255; 0.001 FDR:   227
4:29:53.494875 PROGRESS: =========================================================================
4:29:53.509772 INFO: Target number of precursors not reached yet.
4:29:54.142949 INFO: Starting optimization step 5.
4:29:54.144578 PROGRESS: === Extracting elution groups 31000 to 63000 ===
4:29:54.144767 INFO: Using rust extraction backend
4:29:54.144926 PROGRESS: Extracting batch of 63070 precursors
4:29:54.412318 INFO: === Search parameters used ===
4:29:54.414405 INFO: rt_error       : 805.6019897460938
4:29:54.414485 INFO: mobility_error : 0.1
4:29:54.414563 INFO: num_candidates : 1
4:29:54.414625 INFO: ms1_error      : 3
4:29:54.414695 INFO: ms2_error      : 10
4:29:54.414786 INFO: fwhm_rt        : 5
4:29:54.414859 INFO: quant_window   : 3
4:29:54.414914 INFO: ==============================================
4:29:56.195482 INFO: performing precursor FDR with 40 features
4:29:56.195894 INFO: Decoy channel: -1
4:29:56.195937 INFO: competitive: True
4:29:56.497172 INFO: Setting torch num_threads to 2 for FDR classification task
4:29:56.730101 INFO: Estimating optimal hyperparameters - samples: 96,508, batch_size: 395, learning_rate: 3.11e-04
4:29:56.732816 INFO: Using random state 304387 for train-test-split
4:30:02.040216 INFO: Test AUC: 0.563
4:30:02.040737 INFO: Train AUC: 0.582
4:30:02.040807 INFO: AUC difference: 3.26%
4:30:02.503097 INFO: Resetting torch num_threads to 100
4:30:02.623256 PROGRESS: === Extracted 120635 precursors and 414323 fragments ===
4:30:02.625390 INFO: === FDR correction performed with classifier version -1 ===
4:30:02.627433 PROGRESS: ============================= Precursor FDR =============================
4:30:02.627683 PROGRESS: Total precursors accumulated: 644
4:30:02.627760 PROGRESS: Target precursors: 638 (99.07%)
4:30:02.627815 PROGRESS: Decoy precursors: 6 (0.93%)
4:30:02.627865 PROGRESS: 
4:30:02.627944 PROGRESS: Precursor Summary:
4:30:02.630235 PROGRESS: Channel   0:	 0.050 FDR:   638; 0.010 FDR:   638; 0.001 FDR:    74
4:30:02.630447 PROGRESS: 
4:30:02.630509 PROGRESS: Protein Summary:
4:30:02.632510 PROGRESS: Channel   0:	 0.050 FDR:   596; 0.010 FDR:   596; 0.001 FDR:    74
4:30:02.632687 PROGRESS: =========================================================================
4:30:02.644155 INFO: Target number of precursors not reached yet.
4:30:03.247328 INFO: Starting optimization step 6.
4:30:03.248270 PROGRESS: === Extracting elution groups 63000 to 127000 ===
4:30:03.248500 INFO: Using rust extraction backend
4:30:03.248630 PROGRESS: Extracting batch of 126133 precursors
4:30:03.605011 INFO: === Search parameters used ===
4:30:03.606012 INFO: rt_error       : 805.6019897460938
4:30:03.606162 INFO: mobility_error : 0.1
4:30:03.606228 INFO: num_candidates : 1
4:30:03.606277 INFO: ms1_error      : 3
4:30:03.606321 INFO: ms2_error      : 10
4:30:03.606362 INFO: fwhm_rt        : 5
4:30:03.606405 INFO: quant_window   : 3
4:30:03.606445 INFO: ==============================================
4:30:06.337660 INFO: performing precursor FDR with 40 features
4:30:06.338037 INFO: Decoy channel: -1
4:30:06.338069 INFO: competitive: True
4:30:06.872189 INFO: Setting torch num_threads to 2 for FDR classification task
4:30:07.770918 INFO: Estimating optimal hyperparameters - samples: 194,539, batch_size: 796, learning_rate: 4.41e-04
4:30:07.774753 INFO: Using random state 858633 for train-test-split
4:30:24.561543 INFO: Test AUC: 0.563
4:30:24.561977 INFO: Train AUC: 0.581
4:30:24.562048 INFO: AUC difference: 3.14%
4:30:25.120684 INFO: Resetting torch num_threads to 100
4:30:25.335742 PROGRESS: === Extracted 243174 precursors and 835558 fragments ===
4:30:25.338282 INFO: === FDR correction performed with classifier version -1 ===
4:30:25.341269 PROGRESS: ============================= Precursor FDR =============================
4:30:25.341502 PROGRESS: Total precursors accumulated: 1,329
4:30:25.341569 PROGRESS: Target precursors: 1,316 (99.02%)
4:30:25.341624 PROGRESS: Decoy precursors: 13 (0.98%)
4:30:25.341673 PROGRESS: 
4:30:25.341721 PROGRESS: Precursor Summary:
4:30:25.344332 PROGRESS: Channel   0:	 0.050 FDR: 1,316; 0.010 FDR: 1,316; 0.001 FDR:     0
4:30:25.344543 PROGRESS: 
4:30:25.344604 PROGRESS: Protein Summary:
4:30:25.346713 PROGRESS: Channel   0:	 0.050 FDR: 1,151; 0.010 FDR: 1,151; 0.001 FDR:     0
4:30:25.346837 PROGRESS: =========================================================================
4:30:25.365448 INFO: Target number of precursors reached.
4:30:25.506391 INFO: fragments_df: keeping 5000 of 835558 [sum(precursor_idx_mask)=12558 sum(mass_error_mask)=835558 stop_rank=5000
4:30:26.594338 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:30:27.130251 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:30:28.142396 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
4:30:28.144535 INFO: Using score_cutoff 11.465142032146453 (fac=0.99, q=1)
4:30:28.145454 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
4:30:28.145557 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
4:30:28.145621 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.465142032146453
4:30:28.145764 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:30:28.363606 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:30:28.780763 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
4:30:28.781960 PROGRESS: Required number of precursors found. Starting search parameter optimization.
4:30:28.782386 INFO: Starting optimization step 7.
4:30:28.782526 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:30:28.782715 INFO: Using rust extraction backend
4:30:28.782876 PROGRESS: Extracting batch of 250329 precursors
4:30:29.766048 INFO: === Search parameters used ===
4:30:29.767041 INFO: rt_error       : 805.6019897460938
4:30:29.767106 INFO: mobility_error : 0.1
4:30:29.767175 INFO: num_candidates : 3
4:30:29.767248 INFO: ms1_error      : 3
4:30:29.767318 INFO: ms2_error      : 10
4:30:29.767452 INFO: fwhm_rt        : 3.0
4:30:29.767508 INFO: quant_window   : 3
4:30:29.767570 INFO: ==============================================
4:30:38.639001 INFO: performing precursor FDR with 40 features
4:30:38.639415 INFO: Decoy channel: -1
4:30:38.639451 INFO: competitive: True
4:30:39.495906 INFO: Setting torch num_threads to 2 for FDR classification task
4:30:40.730503 INFO: Estimating optimal hyperparameters - samples: 579,024, batch_size: 2,371, learning_rate: 7.61e-04
4:30:40.736531 INFO: Using random state 684207 for train-test-split
4:31:17.132023 INFO: Test AUC: 0.571
4:31:17.132698 INFO: Train AUC: 0.577
4:31:17.132753 INFO: AUC difference: 0.95%
4:31:18.015085 INFO: Resetting torch num_threads to 100
4:31:18.144656 PROGRESS: === Extracted 723781 precursors and 2385873 fragments ===
4:31:18.146585 INFO: === FDR correction performed with classifier version 6 ===
4:31:18.150510 PROGRESS: ============================= Precursor FDR =============================
4:31:18.151211 PROGRESS: Total precursors accumulated: 1,516
4:31:18.151320 PROGRESS: Target precursors: 1,501 (99.01%)
4:31:18.151377 PROGRESS: Decoy precursors: 15 (0.99%)
4:31:18.151428 PROGRESS: 
4:31:18.151492 PROGRESS: Precursor Summary:
4:31:18.156632 PROGRESS: Channel   0:	 0.050 FDR: 1,501; 0.010 FDR: 1,501; 0.001 FDR:   266
4:31:18.157433 PROGRESS: 
4:31:18.157508 PROGRESS: Protein Summary:
4:31:18.162277 PROGRESS: Channel   0:	 0.050 FDR: 1,313; 0.010 FDR: 1,313; 0.001 FDR:   257
4:31:18.163002 PROGRESS: =========================================================================
4:31:18.221695 INFO: Target number of precursors reached.
4:31:18.535575 INFO: fragments_df: keeping 5000 of 2385873 [sum(precursor_idx_mask)=32590 sum(mass_error_mask)=2385873 stop_rank=5000
4:31:19.841917 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:31:20.381100 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:31:21.291926 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:31:21.293588 INFO: Using score_cutoff 11.819563865661621 (fac=0.99, q=1)
4:31:21.294369 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:31:21.294462 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:31:21.294517 INFO: Updating optimization_manager: score_cutoff        : 11.465142032146453 -> 11.819563865661621
4:31:21.294610 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:31:21.521956 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:31:21.932484 INFO: === checking if optimization conditions were reached ===
4:31:21.942839 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
4:31:21.944032 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
4:31:21.944227 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
4:31:21.944346 INFO: ==============================================
4:31:21.944536 INFO: Starting optimization step 8.
4:31:21.944702 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:31:21.944944 INFO: Using rust extraction backend
4:31:21.945194 PROGRESS: Extracting batch of 250329 precursors
4:31:22.708764 INFO: === Search parameters used ===
4:31:22.709723 INFO: rt_error       : 805.6019897460938
4:31:22.709790 INFO: mobility_error : 0.1
4:31:22.709855 INFO: num_candidates : 3
4:31:22.709912 INFO: ms1_error      : 3
4:31:22.709959 INFO: ms2_error      : 10.0
4:31:22.710005 INFO: fwhm_rt        : 3.0
4:31:22.710046 INFO: quant_window   : 3
4:31:22.710086 INFO: ==============================================
4:31:31.471816 INFO: performing precursor FDR with 40 features
4:31:31.472231 INFO: Decoy channel: -1
4:31:31.472266 INFO: competitive: True
4:31:32.411168 INFO: Setting torch num_threads to 2 for FDR classification task
4:31:33.583479 INFO: Estimating optimal hyperparameters - samples: 579,000, batch_size: 2,371, learning_rate: 7.61e-04
4:31:33.595794 INFO: Using random state 126490 for train-test-split
4:32:08.836452 INFO: Test AUC: 0.569
4:32:08.837141 INFO: Train AUC: 0.579
4:32:08.837195 INFO: AUC difference: 1.74%
4:32:09.613957 INFO: Resetting torch num_threads to 100
4:32:09.769764 PROGRESS: === Extracted 723751 precursors and 2385759 fragments ===
4:32:09.771472 INFO: === FDR correction performed with classifier version 7 ===
4:32:09.774179 PROGRESS: ============================= Precursor FDR =============================
4:32:09.774411 PROGRESS: Total precursors accumulated: 1,641
4:32:09.774483 PROGRESS: Target precursors: 1,625 (99.02%)
4:32:09.774534 PROGRESS: Decoy precursors: 16 (0.98%)
4:32:09.774583 PROGRESS: 
4:32:09.774628 PROGRESS: Precursor Summary:
4:32:09.777005 PROGRESS: Channel   0:	 0.050 FDR: 1,625; 0.010 FDR: 1,625; 0.001 FDR:     0
4:32:09.777213 PROGRESS: 
4:32:09.777270 PROGRESS: Protein Summary:
4:32:09.779660 PROGRESS: Channel   0:	 0.050 FDR: 1,409; 0.010 FDR: 1,409; 0.001 FDR:     0
4:32:09.779862 PROGRESS: =========================================================================
4:32:09.842224 INFO: Target number of precursors reached.
4:32:10.151829 INFO: fragments_df: keeping 5000 of 2385759 [sum(precursor_idx_mask)=34722 sum(mass_error_mask)=2385759 stop_rank=5000
4:32:11.370779 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:32:12.000664 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:32:13.271482 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:32:13.273071 INFO: Using score_cutoff 10.55726356201172 (fac=0.99, q=1)
4:32:13.273846 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:32:13.273948 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:32:13.274007 INFO: Updating optimization_manager: score_cutoff        : 11.819563865661621 -> 10.55726356201172
4:32:13.274120 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:32:13.523115 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:32:13.951179 INFO: === checking if optimization conditions were reached ===
4:32:13.960217 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
4:32:13.961242 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
4:32:13.961452 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
4:32:13.961625 INFO: ==============================================
4:32:13.961807 INFO: Starting optimization step 9.
4:32:13.961927 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:32:13.962095 INFO: Using rust extraction backend
4:32:13.962270 PROGRESS: Extracting batch of 250329 precursors
4:32:14.703378 INFO: === Search parameters used ===
4:32:14.704754 INFO: rt_error       : 805.6019897460938
4:32:14.704835 INFO: mobility_error : 0.1
4:32:14.704895 INFO: num_candidates : 3
4:32:14.704952 INFO: ms1_error      : 3
4:32:14.704998 INFO: ms2_error      : 10.0
4:32:14.705045 INFO: fwhm_rt        : 3.0
4:32:14.705095 INFO: quant_window   : 3
4:32:14.705140 INFO: ==============================================
4:32:20.993199 INFO: performing precursor FDR with 40 features
4:32:20.993599 INFO: Decoy channel: -1
4:32:20.993639 INFO: competitive: True
4:32:21.840836 INFO: Setting torch num_threads to 2 for FDR classification task
4:32:23.026389 INFO: Estimating optimal hyperparameters - samples: 578,992, batch_size: 2,371, learning_rate: 7.61e-04
4:32:23.037294 INFO: Using random state 179185 for train-test-split
4:32:57.352544 INFO: Test AUC: 0.577
4:32:57.353109 INFO: Train AUC: 0.590
4:32:57.353161 INFO: AUC difference: 2.17%
4:32:58.239200 INFO: Resetting torch num_threads to 100
4:32:58.362022 PROGRESS: === Extracted 723740 precursors and 2385603 fragments ===
4:32:58.363703 INFO: === FDR correction performed with classifier version 8 ===
4:32:58.366333 PROGRESS: ============================= Precursor FDR =============================
4:32:58.366555 PROGRESS: Total precursors accumulated: 1,647
4:32:58.366630 PROGRESS: Target precursors: 1,631 (99.03%)
4:32:58.366692 PROGRESS: Decoy precursors: 16 (0.97%)
4:32:58.366744 PROGRESS: 
4:32:58.366794 PROGRESS: Precursor Summary:
4:32:58.369213 PROGRESS: Channel   0:	 0.050 FDR: 1,631; 0.010 FDR: 1,631; 0.001 FDR:     0
4:32:58.369396 PROGRESS: 
4:32:58.369455 PROGRESS: Protein Summary:
4:32:58.371732 PROGRESS: Channel   0:	 0.050 FDR: 1,412; 0.010 FDR: 1,412; 0.001 FDR:     0
4:32:58.371942 PROGRESS: =========================================================================
4:32:58.427560 INFO: Target number of precursors reached.
4:32:58.726994 INFO: fragments_df: keeping 5000 of 2385603 [sum(precursor_idx_mask)=34958 sum(mass_error_mask)=2385603 stop_rank=5000
4:32:59.947297 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:33:00.425460 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:33:01.342745 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:33:01.344302 INFO: Using score_cutoff 10.91774461555481 (fac=0.99, q=1)
4:33:01.345029 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:33:01.345129 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:33:01.345224 INFO: Updating optimization_manager: score_cutoff        : 10.55726356201172 -> 10.91774461555481
4:33:01.345317 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:33:01.541874 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:33:01.938161 INFO: === checking if optimization conditions were reached ===
4:33:01.946677 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
4:33:01.947426 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
4:33:01.947684 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
4:33:01.947827 INFO: ==============================================
4:33:01.948028 INFO: Starting optimization step 10.
4:33:01.948185 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:33:01.948431 INFO: Using rust extraction backend
4:33:01.948695 PROGRESS: Extracting batch of 250329 precursors
4:33:02.956669 INFO: === Search parameters used ===
4:33:02.957764 INFO: rt_error       : 805.6019897460938
4:33:02.957847 INFO: mobility_error : 0.1
4:33:02.957920 INFO: num_candidates : 3
4:33:02.957971 INFO: ms1_error      : 3
4:33:02.958017 INFO: ms2_error      : 10.0
4:33:02.958061 INFO: fwhm_rt        : 3.0
4:33:02.958106 INFO: quant_window   : 3
4:33:02.958149 INFO: ==============================================
4:33:09.649967 INFO: performing precursor FDR with 40 features
4:33:09.650521 INFO: Decoy channel: -1
4:33:09.650561 INFO: competitive: True
4:33:10.423542 INFO: Setting torch num_threads to 2 for FDR classification task
4:33:11.606735 INFO: Estimating optimal hyperparameters - samples: 578,969, batch_size: 2,371, learning_rate: 7.61e-04
4:33:11.622203 INFO: Using random state 863928 for train-test-split
4:33:48.738325 INFO: Test AUC: 0.579
4:33:48.738909 INFO: Train AUC: 0.592
4:33:48.738975 INFO: AUC difference: 2.15%
4:33:49.587034 INFO: Resetting torch num_threads to 100
4:33:49.692355 PROGRESS: === Extracted 723712 precursors and 2385326 fragments ===
4:33:49.693967 INFO: === FDR correction performed with classifier version 9 ===
4:33:49.696690 PROGRESS: ============================= Precursor FDR =============================
4:33:49.696942 PROGRESS: Total precursors accumulated: 1,577
4:33:49.697017 PROGRESS: Target precursors: 1,562 (99.05%)
4:33:49.697074 PROGRESS: Decoy precursors: 15 (0.95%)
4:33:49.697127 PROGRESS: 
4:33:49.697178 PROGRESS: Precursor Summary:
4:33:49.700046 PROGRESS: Channel   0:	 0.050 FDR: 1,562; 0.010 FDR: 1,562; 0.001 FDR: 1,143
4:33:49.700317 PROGRESS: 
4:33:49.700391 PROGRESS: Protein Summary:
4:33:49.703191 PROGRESS: Channel   0:	 0.050 FDR: 1,358; 0.010 FDR: 1,358; 0.001 FDR: 1,014
4:33:49.703454 PROGRESS: =========================================================================
4:33:49.770704 INFO: Target number of precursors reached.
4:33:50.084466 INFO: fragments_df: keeping 5000 of 2385326 [sum(precursor_idx_mask)=33682 sum(mass_error_mask)=2385326 stop_rank=5000
4:33:51.285969 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:33:51.772521 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:33:52.813239 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:33:52.816036 INFO: Using score_cutoff 11.815969363975524 (fac=0.99, q=1)
4:33:52.817662 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:33:52.817860 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:33:52.817921 INFO: Updating optimization_manager: score_cutoff        : 10.91774461555481 -> 11.815969363975524
4:33:52.818044 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:33:53.067830 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:33:53.397143 INFO: === checking if optimization conditions were reached ===
4:33:53.404878 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
4:33:53.405433 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
4:33:53.405658 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
4:33:53.405810 INFO: ==============================================
4:33:53.405985 INFO: Starting optimization step 11.
4:33:53.406161 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:33:53.406343 INFO: Using rust extraction backend
4:33:53.406505 PROGRESS: Extracting batch of 250329 precursors
4:33:54.222387 INFO: === Search parameters used ===
4:33:54.223879 INFO: rt_error       : 805.6019897460938
4:33:54.224097 INFO: mobility_error : 0.1
4:33:54.224168 INFO: num_candidates : 3
4:33:54.224227 INFO: ms1_error      : 3
4:33:54.224284 INFO: ms2_error      : 10.0
4:33:54.224338 INFO: fwhm_rt        : 3.0
4:33:54.224386 INFO: quant_window   : 3
4:33:54.224494 INFO: ==============================================
4:33:59.681907 INFO: performing precursor FDR with 40 features
4:33:59.682146 INFO: Decoy channel: -1
4:33:59.682176 INFO: competitive: True
4:34:00.064684 INFO: Setting torch num_threads to 2 for FDR classification task
4:34:00.834062 INFO: Estimating optimal hyperparameters - samples: 578,947, batch_size: 2,371, learning_rate: 7.61e-04
4:34:00.839931 INFO: Using random state 550592 for train-test-split
4:34:19.425450 INFO: Test AUC: 0.583
4:34:19.425930 INFO: Train AUC: 0.597
4:34:19.425984 INFO: AUC difference: 2.36%
4:34:20.271260 INFO: Resetting torch num_threads to 100
4:34:20.394948 PROGRESS: === Extracted 723684 precursors and 2385584 fragments ===
4:34:20.396648 INFO: === FDR correction performed with classifier version 10 ===
4:34:20.399576 PROGRESS: ============================= Precursor FDR =============================
4:34:20.399783 PROGRESS: Total precursors accumulated: 1,825
4:34:20.399858 PROGRESS: Target precursors: 1,807 (99.01%)
4:34:20.399914 PROGRESS: Decoy precursors: 18 (0.99%)
4:34:20.399965 PROGRESS: 
4:34:20.400025 PROGRESS: Precursor Summary:
4:34:20.403032 PROGRESS: Channel   0:	 0.050 FDR: 1,807; 0.010 FDR: 1,807; 0.001 FDR: 1,067
4:34:20.403279 PROGRESS: 
4:34:20.403345 PROGRESS: Protein Summary:
4:34:20.406097 PROGRESS: Channel   0:	 0.050 FDR: 1,560; 0.010 FDR: 1,560; 0.001 FDR:   949
4:34:20.406311 PROGRESS: =========================================================================
4:34:20.464337 INFO: Target number of precursors reached.
4:34:20.779978 INFO: fragments_df: keeping 5000 of 2385584 [sum(precursor_idx_mask)=37949 sum(mass_error_mask)=2385584 stop_rank=5000
4:34:22.021155 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:34:22.588309 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:34:23.504543 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:34:23.505581 INFO: Using score_cutoff 9.821944445800781 (fac=0.99, q=1)
4:34:23.506113 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:34:23.506192 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:34:23.506247 INFO: Updating optimization_manager: score_cutoff        : 11.815969363975524 -> 9.821944445800781
4:34:23.506314 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:34:23.703948 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:34:24.055640 INFO: === checking if optimization conditions were reached ===
4:34:24.065094 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
4:34:24.066093 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
4:34:24.066286 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
4:34:24.066421 INFO: ==============================================
4:34:24.066736 PROGRESS: Optimization finished for ms2_error.
4:34:25.224204 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:34:25.440275 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:34:25.761498 INFO: Starting optimization step 0.
4:34:25.762427 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:34:25.762744 INFO: Using rust extraction backend
4:34:25.762962 PROGRESS: Extracting batch of 250329 precursors
4:34:26.679206 INFO: === Search parameters used ===
4:34:26.680572 INFO: rt_error       : 805.6019897460938
4:34:26.680709 INFO: mobility_error : 0.1
4:34:26.680812 INFO: num_candidates : 3
4:34:26.680868 INFO: ms1_error      : 3
4:34:26.680915 INFO: ms2_error      : 10.0
4:34:26.680960 INFO: fwhm_rt        : 3.0
4:34:26.681005 INFO: quant_window   : 3
4:34:26.681048 INFO: ==============================================
4:34:35.834232 INFO: performing precursor FDR with 40 features
4:34:35.834645 INFO: Decoy channel: -1
4:34:35.834677 INFO: competitive: True
4:34:36.767487 INFO: Setting torch num_threads to 2 for FDR classification task
4:34:37.952849 INFO: Estimating optimal hyperparameters - samples: 578,934, batch_size: 2,371, learning_rate: 7.61e-04
4:34:37.959135 INFO: Using random state 451542 for train-test-split
4:35:14.223623 INFO: Test AUC: 0.586
4:35:14.224186 INFO: Train AUC: 0.599
4:35:14.224263 INFO: AUC difference: 2.19%
4:35:15.104723 INFO: Resetting torch num_threads to 100
4:35:15.194272 PROGRESS: === Extracted 723668 precursors and 2385278 fragments ===
4:35:15.195939 INFO: === FDR correction performed with classifier version 11 ===
4:35:15.198911 PROGRESS: ============================= Precursor FDR =============================
4:35:15.199181 PROGRESS: Total precursors accumulated: 1,942
4:35:15.199277 PROGRESS: Target precursors: 1,923 (99.02%)
4:35:15.199335 PROGRESS: Decoy precursors: 19 (0.98%)
4:35:15.199384 PROGRESS: 
4:35:15.199436 PROGRESS: Precursor Summary:
4:35:15.202316 PROGRESS: Channel   0:	 0.050 FDR: 1,923; 0.010 FDR: 1,923; 0.001 FDR: 1,136
4:35:15.202578 PROGRESS: 
4:35:15.202675 PROGRESS: Protein Summary:
4:35:15.205524 PROGRESS: Channel   0:	 0.050 FDR: 1,654; 0.010 FDR: 1,654; 0.001 FDR: 1,014
4:35:15.205739 PROGRESS: =========================================================================
4:35:15.264209 INFO: Target number of precursors reached.
4:35:15.582383 INFO: fragments_df: keeping 5000 of 2385278 [sum(precursor_idx_mask)=40412 sum(mass_error_mask)=2385278 stop_rank=5000
4:35:16.799915 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:35:17.690292 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:35:18.663295 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:35:18.665108 INFO: Using score_cutoff 9.240853034591675 (fac=0.99, q=1)
4:35:18.666075 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:35:18.666181 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:35:18.666250 INFO: Updating optimization_manager: score_cutoff        : 9.821944445800781 -> 9.240853034591675
4:35:18.666338 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:35:18.925097 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:35:19.345242 INFO: === checking if optimization conditions were reached ===
4:35:19.347215 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
4:35:19.357971 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 846.6585420478211
4:35:19.358735 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 846.6585.
4:35:19.358992 INFO: ==============================================
4:35:19.359237 INFO: Starting optimization step 1.
4:35:19.359413 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:35:19.359637 INFO: Using rust extraction backend
4:35:19.359792 PROGRESS: Extracting batch of 250329 precursors
4:35:20.125431 INFO: === Search parameters used ===
4:35:20.126428 INFO: rt_error       : 846.6585420478211
4:35:20.126506 INFO: mobility_error : 0.1
4:35:20.126556 INFO: num_candidates : 3
4:35:20.126606 INFO: ms1_error      : 3
4:35:20.126650 INFO: ms2_error      : 10.0
4:35:20.126694 INFO: fwhm_rt        : 3.0
4:35:20.126733 INFO: quant_window   : 3
4:35:20.126776 INFO: ==============================================
4:35:25.134127 INFO: performing precursor FDR with 40 features
4:35:25.134392 INFO: Decoy channel: -1
4:35:25.134425 INFO: competitive: True
4:35:25.634724 INFO: Setting torch num_threads to 2 for FDR classification task
4:35:26.786155 INFO: Estimating optimal hyperparameters - samples: 579,020, batch_size: 2,371, learning_rate: 7.61e-04
4:35:26.795732 INFO: Using random state 451542 for train-test-split
4:36:08.165665 INFO: Test AUC: 0.584
4:36:08.166097 INFO: Train AUC: 0.600
4:36:08.166149 INFO: AUC difference: 2.65%
4:36:08.961421 INFO: Resetting torch num_threads to 100
4:36:09.064050 PROGRESS: === Extracted 723776 precursors and 2385980 fragments ===
4:36:09.065805 INFO: === FDR correction performed with classifier version 11 ===
4:36:09.069091 PROGRESS: ============================= Precursor FDR =============================
4:36:09.069330 PROGRESS: Total precursors accumulated: 1,971
4:36:09.069404 PROGRESS: Target precursors: 1,952 (99.04%)
4:36:09.069463 PROGRESS: Decoy precursors: 19 (0.96%)
4:36:09.069515 PROGRESS: 
4:36:09.069583 PROGRESS: Precursor Summary:
4:36:09.073023 PROGRESS: Channel   0:	 0.050 FDR: 1,952; 0.010 FDR: 1,952; 0.001 FDR: 1,258
4:36:09.073224 PROGRESS: 
4:36:09.073287 PROGRESS: Protein Summary:
4:36:09.076321 PROGRESS: Channel   0:	 0.050 FDR: 1,674; 0.010 FDR: 1,674; 0.001 FDR: 1,103
4:36:09.076505 PROGRESS: =========================================================================
4:36:09.136337 INFO: Target number of precursors reached.
4:36:09.444888 INFO: fragments_df: keeping 5000 of 2385980 [sum(precursor_idx_mask)=40287 sum(mass_error_mask)=2385980 stop_rank=5000
4:36:10.641115 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:36:11.144312 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:36:12.133273 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:36:12.134525 INFO: Using score_cutoff 8.63518097333908 (fac=0.99, q=1)
4:36:12.135136 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:36:12.135247 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:36:12.135306 INFO: Updating optimization_manager: score_cutoff        : 9.240853034591675 -> 8.63518097333908
4:36:12.135386 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:36:12.350817 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:36:12.753091 INFO: === checking if optimization conditions were reached ===
4:36:12.754030 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
4:36:12.763703 INFO: Updating optimization_manager: rt_error            : 846.6585420478211 -> 689.5854443282686
4:36:12.764644 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 689.5854.
4:36:12.764801 INFO: ==============================================
4:36:12.764952 INFO: Starting optimization step 2.
4:36:12.765082 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:36:12.765241 INFO: Using rust extraction backend
4:36:12.765377 PROGRESS: Extracting batch of 250329 precursors
4:36:13.643679 INFO: === Search parameters used ===
4:36:13.644736 INFO: rt_error       : 689.5854443282686
4:36:13.644871 INFO: mobility_error : 0.1
4:36:13.644940 INFO: num_candidates : 3
4:36:13.644990 INFO: ms1_error      : 3
4:36:13.645072 INFO: ms2_error      : 10.0
4:36:13.645119 INFO: fwhm_rt        : 3.0
4:36:13.645159 INFO: quant_window   : 3
4:36:13.645202 INFO: ==============================================
4:36:20.889221 INFO: performing precursor FDR with 40 features
4:36:20.889567 INFO: Decoy channel: -1
4:36:20.889598 INFO: competitive: True
4:36:21.732000 INFO: Setting torch num_threads to 2 for FDR classification task
4:36:22.955052 INFO: Estimating optimal hyperparameters - samples: 578,565, batch_size: 2,369, learning_rate: 7.61e-04
4:36:22.969653 INFO: Using random state 451542 for train-test-split
4:36:59.629142 INFO: Test AUC: 0.582
4:36:59.629658 INFO: Train AUC: 0.598
4:36:59.629751 INFO: AUC difference: 2.62%
4:37:00.515522 INFO: Resetting torch num_threads to 100
4:37:00.609752 PROGRESS: === Extracted 723207 precursors and 2380744 fragments ===
4:37:00.611634 INFO: === FDR correction performed with classifier version 11 ===
4:37:00.614444 PROGRESS: ============================= Precursor FDR =============================
4:37:00.614658 PROGRESS: Total precursors accumulated: 1,852
4:37:00.614733 PROGRESS: Target precursors: 1,834 (99.03%)
4:37:00.614793 PROGRESS: Decoy precursors: 18 (0.97%)
4:37:00.614843 PROGRESS: 
4:37:00.614893 PROGRESS: Precursor Summary:
4:37:00.618381 PROGRESS: Channel   0:	 0.050 FDR: 1,834; 0.010 FDR: 1,834; 0.001 FDR: 1,269
4:37:00.618672 PROGRESS: 
4:37:00.618738 PROGRESS: Protein Summary:
4:37:00.621689 PROGRESS: Channel   0:	 0.050 FDR: 1,581; 0.010 FDR: 1,581; 0.001 FDR: 1,114
4:37:00.621963 PROGRESS: =========================================================================
4:37:00.683001 INFO: Target number of precursors reached.
4:37:00.976154 INFO: fragments_df: keeping 5000 of 2380744 [sum(precursor_idx_mask)=38145 sum(mass_error_mask)=2380744 stop_rank=5000
4:37:02.186033 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:37:03.370352 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:37:04.283323 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:37:04.284795 INFO: Using score_cutoff 9.18510578956604 (fac=0.99, q=1)
4:37:04.285457 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:37:04.285545 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:37:04.285603 INFO: Updating optimization_manager: score_cutoff        : 8.63518097333908 -> 9.18510578956604
4:37:04.285665 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:37:04.528320 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:37:04.948084 INFO: === checking if optimization conditions were reached ===
4:37:04.949397 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
4:37:04.959481 INFO: Updating optimization_manager: rt_error            : 689.5854443282686 -> 285.2838912703302
4:37:04.960276 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 285.2839.
4:37:04.960444 INFO: ==============================================
4:37:04.960594 INFO: Starting optimization step 3.
4:37:04.960725 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:37:04.961053 INFO: Using rust extraction backend
4:37:04.961224 PROGRESS: Extracting batch of 250329 precursors
4:37:05.882161 INFO: === Search parameters used ===
4:37:05.883366 INFO: rt_error       : 285.2838912703302
4:37:05.883573 INFO: mobility_error : 0.1
4:37:05.883633 INFO: num_candidates : 3
4:37:05.883689 INFO: ms1_error      : 3
4:37:05.883739 INFO: ms2_error      : 10.0
4:37:05.883785 INFO: fwhm_rt        : 3.0
4:37:05.883827 INFO: quant_window   : 3
4:37:05.883869 INFO: ==============================================
4:37:13.867582 INFO: performing precursor FDR with 40 features
4:37:13.867928 INFO: Decoy channel: -1
4:37:13.867958 INFO: competitive: True
4:37:14.672039 INFO: Setting torch num_threads to 2 for FDR classification task
4:37:16.108063 INFO: Estimating optimal hyperparameters - samples: 563,929, batch_size: 2,309, learning_rate: 7.51e-04
4:37:16.121968 INFO: Using random state 451542 for train-test-split
4:37:45.279397 INFO: Test AUC: 0.577
4:37:45.279743 INFO: Train AUC: 0.591
4:37:45.279804 INFO: AUC difference: 2.36%
4:37:46.146162 INFO: Resetting torch num_threads to 100
4:37:46.242244 PROGRESS: === Extracted 704912 precursors and 2141087 fragments ===
4:37:46.243779 INFO: === FDR correction performed with classifier version 11 ===
4:37:46.246706 PROGRESS: ============================= Precursor FDR =============================
4:37:46.246952 PROGRESS: Total precursors accumulated: 1,874
4:37:46.247035 PROGRESS: Target precursors: 1,856 (99.04%)
4:37:46.247101 PROGRESS: Decoy precursors: 18 (0.96%)
4:37:46.247184 PROGRESS: 
4:37:46.247248 PROGRESS: Precursor Summary:
4:37:46.250202 PROGRESS: Channel   0:	 0.050 FDR: 1,856; 0.010 FDR: 1,856; 0.001 FDR: 1,137
4:37:46.250459 PROGRESS: 
4:37:46.250548 PROGRESS: Protein Summary:
4:37:46.253340 PROGRESS: Channel   0:	 0.050 FDR: 1,594; 0.010 FDR: 1,594; 0.001 FDR: 1,024
4:37:46.253570 PROGRESS: =========================================================================
4:37:46.316189 INFO: Target number of precursors reached.
4:37:46.591383 INFO: fragments_df: keeping 5000 of 2141087 [sum(precursor_idx_mask)=39182 sum(mass_error_mask)=2141087 stop_rank=5000
4:37:47.795663 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:37:48.270234 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:37:49.229561 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:37:49.231628 INFO: Using score_cutoff 9.749067004680635 (fac=0.99, q=1)
4:37:49.232339 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:37:49.232469 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:37:49.232529 INFO: Updating optimization_manager: score_cutoff        : 9.18510578956604 -> 9.749067004680635
4:37:49.232612 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:37:49.462995 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:37:49.929417 INFO: === checking if optimization conditions were reached ===
4:37:49.930426 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
4:37:49.940975 INFO: Updating optimization_manager: rt_error            : 285.2838912703302 -> 265.5549691667706
4:37:49.942240 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 265.5550.
4:37:49.942408 INFO: ==============================================
4:37:49.942656 INFO: Starting optimization step 4.
4:37:49.942793 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:37:49.943002 INFO: Using rust extraction backend
4:37:49.943196 PROGRESS: Extracting batch of 250329 precursors
4:37:50.728703 INFO: === Search parameters used ===
4:37:50.729713 INFO: rt_error       : 265.5549691667706
4:37:50.729822 INFO: mobility_error : 0.1
4:37:50.729875 INFO: num_candidates : 3
4:37:50.729921 INFO: ms1_error      : 3
4:37:50.729964 INFO: ms2_error      : 10.0
4:37:50.730009 INFO: fwhm_rt        : 3.0
4:37:50.730089 INFO: quant_window   : 3
4:37:50.730132 INFO: ==============================================
4:37:58.850755 INFO: performing precursor FDR with 40 features
4:37:58.851113 INFO: Decoy channel: -1
4:37:58.851156 INFO: competitive: True
4:37:59.798735 INFO: Setting torch num_threads to 2 for FDR classification task
4:38:00.916839 INFO: Estimating optimal hyperparameters - samples: 562,294, batch_size: 2,303, learning_rate: 7.50e-04
4:38:00.927984 INFO: Using random state 451542 for train-test-split
4:38:22.412068 INFO: Test AUC: 0.577
4:38:22.412684 INFO: Train AUC: 0.591
4:38:22.412749 INFO: AUC difference: 2.45%
4:38:23.328479 INFO: Resetting torch num_threads to 100
4:38:23.430893 PROGRESS: === Extracted 702868 precursors and 2115359 fragments ===
4:38:23.432717 INFO: === FDR correction performed with classifier version 11 ===
4:38:23.435018 PROGRESS: ============================= Precursor FDR =============================
4:38:23.435303 PROGRESS: Total precursors accumulated: 1,543
4:38:23.435441 PROGRESS: Target precursors: 1,528 (99.03%)
4:38:23.435504 PROGRESS: Decoy precursors: 15 (0.97%)
4:38:23.435559 PROGRESS: 
4:38:23.435607 PROGRESS: Precursor Summary:
4:38:23.437682 PROGRESS: Channel   0:	 0.050 FDR: 1,528; 0.010 FDR: 1,528; 0.001 FDR:    20
4:38:23.437826 PROGRESS: 
4:38:23.437887 PROGRESS: Protein Summary:
4:38:23.440109 PROGRESS: Channel   0:	 0.050 FDR: 1,342; 0.010 FDR: 1,342; 0.001 FDR:    20
4:38:23.440256 PROGRESS: =========================================================================
4:38:23.502570 INFO: Target number of precursors reached.
4:38:23.789355 INFO: fragments_df: keeping 5000 of 2115359 [sum(precursor_idx_mask)=32189 sum(mass_error_mask)=2115359 stop_rank=5000
4:38:25.027703 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:38:25.598932 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:38:26.608063 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:38:26.609512 INFO: Using score_cutoff 10.596539911651611 (fac=0.99, q=1)
4:38:26.610194 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:38:26.610282 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:38:26.610338 INFO: Updating optimization_manager: score_cutoff        : 9.749067004680635 -> 10.596539911651611
4:38:26.610416 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:38:26.816010 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:38:27.260029 INFO: === checking if optimization conditions were reached ===
4:38:27.260895 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
4:38:27.264821 INFO: Updating optimization_manager: rt_error            : 265.5549691667706 -> 846.6585420478211
4:38:27.265591 INFO: Updating optimization_manager: classifier_version  : 11 -> 13
4:38:27.265896 INFO: Updating optimization_manager: score_cutoff        : 10.596539911651611 -> 8.63518097333908
4:38:27.266138 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:38:27.266309 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:38:27.266549 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 846.6585 found after 5 searches.
4:38:27.266677 INFO: ==============================================
4:38:27.266861 PROGRESS: Optimization finished for rt_error.
4:38:28.432152 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:38:28.661350 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:38:29.118610 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
4:38:29.119563 PROGRESS: ==============================================
4:38:29.119713 PROGRESS: ms2_error      : 10.0000
4:38:29.119805 PROGRESS: rt_error       : 846.6585
4:38:29.119872 PROGRESS: ==============================================
4:38:29.125173 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:38:39.932615 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:38:57.545669 INFO: Using rust extraction backend
4:38:57.546933 PROGRESS: Extracting batch of 11997144 precursors
4:39:27.699175 INFO: === Search parameters used ===
4:39:27.700507 INFO: rt_error       : 846.6585420478211
4:39:27.700613 INFO: mobility_error : 0.1
4:39:27.700679 INFO: num_candidates : 3
4:39:27.700738 INFO: ms1_error      : 3
4:39:27.700792 INFO: ms2_error      : 10.0
4:39:27.700837 INFO: fwhm_rt        : 3.0
4:39:27.700881 INFO: quant_window   : 3
4:39:27.700923 INFO: ==============================================
4:40:54.582437 INFO: Removed 11216859 precursors with score below cutoff 8.63518097333908
4:41:27.865390 INFO: performing precursor FDR with 40 features
4:41:27.866088 INFO: Decoy channel: -1
4:41:27.866134 INFO: competitive: True
4:41:36.729990 INFO: Setting torch num_threads to 2 for FDR classification task
4:42:07.662239 INFO: Estimating optimal hyperparameters - samples: 19,662,088, batch_size: 4,096, learning_rate: 1.00e-03
4:42:07.865878 INFO: Using random state 249528 for train-test-split
4:54:34.046056 INFO: Test AUC: 0.597
4:54:34.046338 INFO: Train AUC: 0.598
4:54:34.046384 INFO: AUC difference: 0.11%
4:54:39.530874 INFO: Resetting torch num_threads to 100
4:54:41.666194 PROGRESS: ============================= Precursor FDR =============================
4:54:41.666631 PROGRESS: Total precursors accumulated: 100,153
4:54:41.666704 PROGRESS: Target precursors: 99,162 (99.01%)
4:54:41.666759 PROGRESS: Decoy precursors: 991 (0.99%)
4:54:41.666810 PROGRESS: 
4:54:41.666857 PROGRESS: Precursor Summary:
4:54:41.698333 PROGRESS: Channel   0:	 0.050 FDR: 99,162; 0.010 FDR: 99,162; 0.001 FDR: 66,750
4:54:41.698603 PROGRESS: 
4:54:41.698663 PROGRESS: Protein Summary:
4:54:41.739293 PROGRESS: Channel   0:	 0.050 FDR: 15,572; 0.010 FDR: 15,572; 0.001 FDR: 10,330
4:54:41.739552 PROGRESS: =========================================================================
4:54:41.864240 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/psm.parquet
4:54:42.053436 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.parquet
4:54:42.271660 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
4:54:42.782160 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 
4:54:42.782330 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant
4:54:42.782421 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/figures
4:54:42.782605 INFO: Initializing TimingManager
4:54:42.783082 INFO: Initializing RawFileManager
4:54:54.075424 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.
4:54:54.083602 INFO: Determining DIA cycle
4:54:54.100000 INFO: Found cycle with start 0.00 min and length 300.
4:54:54.267231 INFO: RT (min)            : 0.0 - 26.9
4:54:54.267365 INFO: RT duration (sec)   : 1611.2
4:54:54.267396 INFO: RT duration (min)   : 26.9
4:54:54.267424 INFO: Cycle len (scans)   : 300
4:54:54.267445 INFO: Cycle len (sec)     : 1.65
4:54:54.267466 INFO: Number of cycles    : 977
4:54:54.267486 INFO: MS2 range (m/z)     : 380.4 - 980.7
4:54:54.267523 INFO: Creating DIA data object took: 11.48432731628418
4:54:55.533823 INFO: Creating DIA data NG object took: 1.2661159038543701
4:54:56.861562 INFO: Initializing CalibrationManager
4:54:56.861925 INFO: Setting up calibration estimators ..
4:54:56.861994 INFO: Found 1 estimator(s) in calibration group 'fragment'
4:54:56.862090 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
4:54:56.862179 INFO: Found 3 estimator(s) in calibration group 'precursor'
4:54:56.862236 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
4:54:56.862298 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
4:54:56.862351 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
4:54:56.862398 INFO: Done setting up calibration estimators.
4:54:56.862703 INFO: Initializing OptimizationManager
4:54:56.862880 INFO: initial parameter: ms1_error = 3
4:54:56.862944 INFO: initial parameter: ms2_error = 10
4:54:56.862993 INFO: initial parameter: rt_error = 805.6004638671875
4:54:56.863045 INFO: initial parameter: mobility_error = 0.1
4:54:56.863087 INFO: initial parameter: num_candidates = 1
4:54:56.863130 INFO: initial parameter: fwhm_rt = 5
4:54:56.863194 INFO: initial parameter: fwhm_mobility = 0.01
4:54:56.863235 INFO: initial parameter: score_cutoff = 0
4:54:56.863281 INFO: initial parameter: classifier_version = -1
4:54:56.863356 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
4:54:56.863708 INFO: FDRManager: loading saved state not requested, will be initialized.
4:54:56.863743 INFO: Initializing FDRManager
4:54:56.863783 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
4:54:58.178932 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
4:54:59.063734 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
4:54:59.064171 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
4:54:59.064289 PROGRESS: Starting initial search for precursors.
4:54:59.064379 INFO: Starting optimization step 0.
4:54:59.064441 PROGRESS: === Extracting elution groups 0 to 1000 ===
4:54:59.064503 INFO: Using rust extraction backend
4:54:59.064566 PROGRESS: Extracting batch of 1967 precursors
4:54:59.068167 INFO: === Search parameters used ===
4:54:59.068269 INFO: rt_error       : 805.6004638671875
4:54:59.068317 INFO: mobility_error : 0.1
4:54:59.068360 INFO: num_candidates : 1
4:54:59.068400 INFO: ms1_error      : 3
4:54:59.068440 INFO: ms2_error      : 10
4:54:59.068479 INFO: fwhm_rt        : 5
4:54:59.068516 INFO: quant_window   : 3
4:54:59.068554 INFO: ==============================================
4:54:59.098783 INFO: performing precursor FDR with 40 features
4:54:59.098858 INFO: Decoy channel: -1
4:54:59.098884 INFO: competitive: True
4:54:59.100240 INFO: Setting torch num_threads to 2 for FDR classification task
4:54:59.102391 INFO: Estimating optimal hyperparameters - samples: 1,521, batch_size: 128, learning_rate: 1.77e-04
4:54:59.103248 INFO: Using random state 894661 for train-test-split
4:54:59.251419 INFO: Test AUC: 0.467
4:54:59.251503 INFO: Train AUC: 0.553
4:54:59.251532 INFO: AUC difference: 15.47%
4:54:59.251555 WARNING: AUC difference > 5%. This may indicate overfitting.
4:54:59.491714 INFO: Resetting torch num_threads to 100
4:54:59.493500 PROGRESS: === Extracted 1902 precursors and 6665 fragments ===
4:54:59.493873 INFO: === FDR correction performed with classifier version -1 ===
4:54:59.494403 PROGRESS: ============================= Precursor FDR =============================
4:54:59.494490 PROGRESS: Total precursors accumulated: 547
4:54:59.494552 PROGRESS: Target precursors: 542 (99.09%)
4:54:59.494606 PROGRESS: Decoy precursors: 5 (0.91%)
4:54:59.494654 PROGRESS: 
4:54:59.494700 PROGRESS: Precursor Summary:
4:54:59.495839 PROGRESS: Channel   0:	 0.050 FDR:   542; 0.010 FDR:   542; 0.001 FDR:   542
4:54:59.495932 PROGRESS: 
4:54:59.495988 PROGRESS: Protein Summary:
4:54:59.497347 PROGRESS: Channel   0:	 0.050 FDR:   529; 0.010 FDR:   529; 0.001 FDR:   529
4:54:59.497438 PROGRESS: =========================================================================
4:54:59.497671 INFO: Target number of precursors not reached yet.
4:54:59.580880 INFO: Starting optimization step 1.
4:54:59.581113 PROGRESS: === Extracting elution groups 1000 to 3000 ===
4:54:59.581196 INFO: Using rust extraction backend
4:54:59.581259 PROGRESS: Extracting batch of 3942 precursors
4:54:59.586684 INFO: === Search parameters used ===
4:54:59.586808 INFO: rt_error       : 805.6004638671875
4:54:59.586861 INFO: mobility_error : 0.1
4:54:59.586907 INFO: num_candidates : 1
4:54:59.586951 INFO: ms1_error      : 3
4:54:59.586992 INFO: ms2_error      : 10
4:54:59.587034 INFO: fwhm_rt        : 5
4:54:59.587074 INFO: quant_window   : 3
4:54:59.587115 INFO: ==============================================
4:54:59.629286 INFO: performing precursor FDR with 40 features
4:54:59.629382 INFO: Decoy channel: -1
4:54:59.629410 INFO: competitive: True
4:54:59.634451 INFO: Setting torch num_threads to 2 for FDR classification task
4:54:59.637235 INFO: Estimating optimal hyperparameters - samples: 4,588, batch_size: 128, learning_rate: 1.77e-04
4:54:59.637321 INFO: Using random state 688254 for train-test-split
4:55:00.105690 INFO: Test AUC: 0.517
4:55:00.105788 INFO: Train AUC: 0.541
4:55:00.105815 INFO: AUC difference: 4.47%
4:55:00.352016 INFO: Resetting torch num_threads to 100
4:55:00.355097 PROGRESS: === Extracted 5736 precursors and 19678 fragments ===
4:55:00.355499 INFO: === FDR correction performed with classifier version -1 ===
4:55:00.355976 PROGRESS: ============================= Precursor FDR =============================
4:55:00.356057 PROGRESS: Total precursors accumulated: 0
4:55:00.356114 PROGRESS: Target precursors: 0 (0.00%)
4:55:00.356161 PROGRESS: Decoy precursors: 0 (0.00%)
4:55:00.356205 PROGRESS: 
4:55:00.356247 PROGRESS: Precursor Summary:
4:55:00.356363 PROGRESS: 
4:55:00.356423 PROGRESS: Protein Summary:
4:55:00.356495 PROGRESS: =========================================================================
4:55:00.356783 INFO: Target number of precursors not reached yet.
4:55:00.444514 INFO: Starting optimization step 2.
4:55:00.444749 PROGRESS: === Extracting elution groups 3000 to 7000 ===
4:55:00.444832 INFO: Using rust extraction backend
4:55:00.444891 PROGRESS: Extracting batch of 7891 precursors
4:55:00.454345 INFO: === Search parameters used ===
4:55:00.454482 INFO: rt_error       : 805.6004638671875
4:55:00.454533 INFO: mobility_error : 0.1
4:55:00.454577 INFO: num_candidates : 1
4:55:00.454619 INFO: ms1_error      : 3
4:55:00.454659 INFO: ms2_error      : 10
4:55:00.454698 INFO: fwhm_rt        : 5
4:55:00.454736 INFO: quant_window   : 3
4:55:00.454775 INFO: ==============================================
4:55:00.520414 INFO: performing precursor FDR with 40 features
4:55:00.520520 INFO: Decoy channel: -1
4:55:00.520544 INFO: competitive: True
4:55:00.528034 INFO: Setting torch num_threads to 2 for FDR classification task
4:55:00.532440 INFO: Estimating optimal hyperparameters - samples: 10,728, batch_size: 128, learning_rate: 1.77e-04
4:55:00.532567 INFO: Using random state 55213 for train-test-split
4:55:01.636683 INFO: Test AUC: 0.532
4:55:01.636799 INFO: Train AUC: 0.560
4:55:01.636830 INFO: AUC difference: 5.00%
4:55:01.636852 WARNING: AUC difference > 5%. This may indicate overfitting.
4:55:01.887557 INFO: Resetting torch num_threads to 100
4:55:01.892138 PROGRESS: === Extracted 13411 precursors and 46236 fragments ===
4:55:01.892548 INFO: === FDR correction performed with classifier version -1 ===
4:55:01.893077 PROGRESS: ============================= Precursor FDR =============================
4:55:01.893163 PROGRESS: Total precursors accumulated: 21
4:55:01.893228 PROGRESS: Target precursors: 21 (100.00%)
4:55:01.893278 PROGRESS: Decoy precursors: 0 (0.00%)
4:55:01.893321 PROGRESS: 
4:55:01.893364 PROGRESS: Precursor Summary:
4:55:01.894448 PROGRESS: Channel   0:	 0.050 FDR:    21; 0.010 FDR:    21; 0.001 FDR:    21
4:55:01.894533 PROGRESS: 
4:55:01.894587 PROGRESS: Protein Summary:
4:55:01.895808 PROGRESS: Channel   0:	 0.050 FDR:    21; 0.010 FDR:    21; 0.001 FDR:    21
4:55:01.895914 PROGRESS: =========================================================================
4:55:01.896281 INFO: Target number of precursors not reached yet.
4:55:01.993239 INFO: Starting optimization step 3.
4:55:01.993481 PROGRESS: === Extracting elution groups 7000 to 15000 ===
4:55:01.993562 INFO: Using rust extraction backend
4:55:01.993621 PROGRESS: Extracting batch of 15751 precursors
4:55:02.010976 INFO: === Search parameters used ===
4:55:02.011141 INFO: rt_error       : 805.6004638671875
4:55:02.011212 INFO: mobility_error : 0.1
4:55:02.011258 INFO: num_candidates : 1
4:55:02.011300 INFO: ms1_error      : 3
4:55:02.011340 INFO: ms2_error      : 10
4:55:02.011379 INFO: fwhm_rt        : 5
4:55:02.011418 INFO: quant_window   : 3
4:55:02.011468 INFO: ==============================================
4:55:02.125164 INFO: performing precursor FDR with 40 features
4:55:02.125281 INFO: Decoy channel: -1
4:55:02.125318 INFO: competitive: True
4:55:02.137683 INFO: Setting torch num_threads to 2 for FDR classification task
4:55:02.145550 INFO: Estimating optimal hyperparameters - samples: 22,983, batch_size: 128, learning_rate: 1.77e-04
4:55:02.145743 INFO: Using random state 963550 for train-test-split
4:55:04.594370 INFO: Test AUC: 0.558
4:55:04.594467 INFO: Train AUC: 0.571
4:55:04.594500 INFO: AUC difference: 2.36%
4:55:04.849716 INFO: Resetting torch num_threads to 100
4:55:04.856195 PROGRESS: === Extracted 28729 precursors and 99457 fragments ===
4:55:04.856686 INFO: === FDR correction performed with classifier version -1 ===
4:55:04.857200 PROGRESS: ============================= Precursor FDR =============================
4:55:04.857287 PROGRESS: Total precursors accumulated: 0
4:55:04.857348 PROGRESS: Target precursors: 0 (0.00%)
4:55:04.857401 PROGRESS: Decoy precursors: 0 (0.00%)
4:55:04.857449 PROGRESS: 
4:55:04.857496 PROGRESS: Precursor Summary:
4:55:04.857615 PROGRESS: 
4:55:04.857679 PROGRESS: Protein Summary:
4:55:04.857757 PROGRESS: =========================================================================
4:55:04.858245 INFO: Target number of precursors not reached yet.
4:55:04.972367 INFO: Starting optimization step 4.
4:55:04.972652 PROGRESS: === Extracting elution groups 15000 to 31000 ===
4:55:04.972737 INFO: Using rust extraction backend
4:55:04.972802 PROGRESS: Extracting batch of 31575 precursors
4:55:05.006454 INFO: === Search parameters used ===
4:55:05.006694 INFO: rt_error       : 805.6004638671875
4:55:05.006751 INFO: mobility_error : 0.1
4:55:05.006800 INFO: num_candidates : 1
4:55:05.006849 INFO: ms1_error      : 3
4:55:05.006906 INFO: ms2_error      : 10
4:55:05.006960 INFO: fwhm_rt        : 5
4:55:05.007002 INFO: quant_window   : 3
4:55:05.007043 INFO: ==============================================
4:55:05.202098 INFO: performing precursor FDR with 40 features
4:55:05.202229 INFO: Decoy channel: -1
4:55:05.202270 INFO: competitive: True
4:55:05.228697 INFO: Setting torch num_threads to 2 for FDR classification task
4:55:05.243489 INFO: Estimating optimal hyperparameters - samples: 47,550, batch_size: 194, learning_rate: 2.18e-04
4:55:05.243723 INFO: Using random state 73269 for train-test-split
4:55:09.030036 INFO: Test AUC: 0.552
4:55:09.030136 INFO: Train AUC: 0.583
4:55:09.030166 INFO: AUC difference: 5.31%
4:55:09.030190 WARNING: AUC difference > 5%. This may indicate overfitting.
4:55:09.308049 INFO: Resetting torch num_threads to 100
4:55:09.320798 PROGRESS: === Extracted 59438 precursors and 206138 fragments ===
4:55:09.321449 INFO: === FDR correction performed with classifier version -1 ===
4:55:09.322069 PROGRESS: ============================= Precursor FDR =============================
4:55:09.322158 PROGRESS: Total precursors accumulated: 0
4:55:09.322218 PROGRESS: Target precursors: 0 (0.00%)
4:55:09.322268 PROGRESS: Decoy precursors: 0 (0.00%)
4:55:09.322313 PROGRESS: 
4:55:09.322356 PROGRESS: Precursor Summary:
4:55:09.322483 PROGRESS: 
4:55:09.322546 PROGRESS: Protein Summary:
4:55:09.322623 PROGRESS: =========================================================================
4:55:09.323751 INFO: Target number of precursors not reached yet.
4:55:09.478541 INFO: Starting optimization step 5.
4:55:09.478803 PROGRESS: === Extracting elution groups 31000 to 63000 ===
4:55:09.478891 INFO: Using rust extraction backend
4:55:09.478957 PROGRESS: Extracting batch of 63070 precursors
4:55:09.544997 INFO: === Search parameters used ===
4:55:09.545297 INFO: rt_error       : 805.6004638671875
4:55:09.545359 INFO: mobility_error : 0.1
4:55:09.545407 INFO: num_candidates : 1
4:55:09.545450 INFO: ms1_error      : 3
4:55:09.545491 INFO: ms2_error      : 10
4:55:09.545532 INFO: fwhm_rt        : 5
4:55:09.545571 INFO: quant_window   : 3
4:55:09.545611 INFO: ==============================================
4:55:09.900817 INFO: performing precursor FDR with 40 features
4:55:09.900937 INFO: Decoy channel: -1
4:55:09.900963 INFO: competitive: True
4:55:09.961096 INFO: Setting torch num_threads to 2 for FDR classification task
4:55:09.999923 INFO: Estimating optimal hyperparameters - samples: 96,612, batch_size: 395, learning_rate: 3.11e-04
4:55:10.000261 INFO: Using random state 444275 for train-test-split
4:55:14.773139 INFO: Test AUC: 0.560
4:55:14.773258 INFO: Train AUC: 0.585
4:55:14.773290 INFO: AUC difference: 4.21%
4:55:15.058950 INFO: Resetting torch num_threads to 100
4:55:15.088945 PROGRESS: === Extracted 120766 precursors and 417054 fragments ===
4:55:15.089613 INFO: === FDR correction performed with classifier version -1 ===
4:55:15.090281 PROGRESS: ============================= Precursor FDR =============================
4:55:15.090374 PROGRESS: Total precursors accumulated: 530
4:55:15.090437 PROGRESS: Target precursors: 525 (99.06%)
4:55:15.090490 PROGRESS: Decoy precursors: 5 (0.94%)
4:55:15.090537 PROGRESS: 
4:55:15.090584 PROGRESS: Precursor Summary:
4:55:15.091683 PROGRESS: Channel   0:	 0.050 FDR:   525; 0.010 FDR:   525; 0.001 FDR:     0
4:55:15.091776 PROGRESS: 
4:55:15.091832 PROGRESS: Protein Summary:
4:55:15.093103 PROGRESS: Channel   0:	 0.050 FDR:   492; 0.010 FDR:   492; 0.001 FDR:     0
4:55:15.093194 PROGRESS: =========================================================================
4:55:15.095463 INFO: Target number of precursors not reached yet.
4:55:15.352095 INFO: Starting optimization step 6.
4:55:15.352339 PROGRESS: === Extracting elution groups 63000 to 127000 ===
4:55:15.352423 INFO: Using rust extraction backend
4:55:15.352486 PROGRESS: Extracting batch of 126133 precursors
4:55:15.481322 INFO: === Search parameters used ===
4:55:15.481590 INFO: rt_error       : 805.6004638671875
4:55:15.481648 INFO: mobility_error : 0.1
4:55:15.481698 INFO: num_candidates : 1
4:55:15.481742 INFO: ms1_error      : 3
4:55:15.481784 INFO: ms2_error      : 10
4:55:15.481827 INFO: fwhm_rt        : 5
4:55:15.481869 INFO: quant_window   : 3
4:55:15.481917 INFO: ==============================================
4:55:16.110456 INFO: performing precursor FDR with 40 features
4:55:16.110596 INFO: Decoy channel: -1
4:55:16.110624 INFO: competitive: True
4:55:16.216681 INFO: Setting torch num_threads to 2 for FDR classification task
4:55:16.310625 INFO: Estimating optimal hyperparameters - samples: 194,660, batch_size: 797, learning_rate: 4.41e-04
4:55:16.311069 INFO: Using random state 132477 for train-test-split
4:55:22.803214 INFO: Test AUC: 0.565
4:55:22.803334 INFO: Train AUC: 0.585
4:55:22.803365 INFO: AUC difference: 3.37%
4:55:23.134085 INFO: Resetting torch num_threads to 100
4:55:23.186450 PROGRESS: === Extracted 243325 precursors and 841464 fragments ===
4:55:23.187156 INFO: === FDR correction performed with classifier version -1 ===
4:55:23.187927 PROGRESS: ============================= Precursor FDR =============================
4:55:23.188019 PROGRESS: Total precursors accumulated: 850
4:55:23.188093 PROGRESS: Target precursors: 842 (99.06%)
4:55:23.188145 PROGRESS: Decoy precursors: 8 (0.94%)
4:55:23.188191 PROGRESS: 
4:55:23.188235 PROGRESS: Precursor Summary:
4:55:23.189378 PROGRESS: Channel   0:	 0.050 FDR:   842; 0.010 FDR:   842; 0.001 FDR:     0
4:55:23.189473 PROGRESS: 
4:55:23.189529 PROGRESS: Protein Summary:
4:55:23.190909 PROGRESS: Channel   0:	 0.050 FDR:   769; 0.010 FDR:   769; 0.001 FDR:     0
4:55:23.190995 PROGRESS: =========================================================================
4:55:23.195279 INFO: Target number of precursors not reached yet.
4:55:23.558864 INFO: Starting optimization step 7.
4:55:23.559168 PROGRESS: === Extracting elution groups 127000 to 255000 ===
4:55:23.559258 INFO: Using rust extraction backend
4:55:23.559325 PROGRESS: Extracting batch of 252185 precursors
4:55:23.814935 INFO: === Search parameters used ===
4:55:23.815230 INFO: rt_error       : 805.6004638671875
4:55:23.815289 INFO: mobility_error : 0.1
4:55:23.815336 INFO: num_candidates : 1
4:55:23.815382 INFO: ms1_error      : 3
4:55:23.815426 INFO: ms2_error      : 10
4:55:23.815470 INFO: fwhm_rt        : 5
4:55:23.815511 INFO: quant_window   : 3
4:55:23.815552 INFO: ==============================================
4:55:24.968353 INFO: performing precursor FDR with 40 features
4:55:24.968493 INFO: Decoy channel: -1
4:55:24.968520 INFO: competitive: True
4:55:25.160926 INFO: Setting torch num_threads to 2 for FDR classification task
4:55:25.346931 INFO: Estimating optimal hyperparameters - samples: 390,670, batch_size: 1,600, learning_rate: 6.25e-04
4:55:25.347538 INFO: Using random state 372759 for train-test-split
4:55:35.083990 INFO: Test AUC: 0.571
4:55:35.084131 INFO: Train AUC: 0.584
4:55:35.084166 INFO: AUC difference: 2.33%
4:55:35.485126 INFO: Resetting torch num_threads to 100
4:55:35.573703 PROGRESS: === Extracted 488338 precursors and 1686023 fragments ===
4:55:35.574454 INFO: === FDR correction performed with classifier version -1 ===
4:55:35.575589 PROGRESS: ============================= Precursor FDR =============================
4:55:35.575697 PROGRESS: Total precursors accumulated: 2,532
4:55:35.575762 PROGRESS: Target precursors: 2,507 (99.01%)
4:55:35.575814 PROGRESS: Decoy precursors: 25 (0.99%)
4:55:35.575859 PROGRESS: 
4:55:35.575903 PROGRESS: Precursor Summary:
4:55:35.577407 PROGRESS: Channel   0:	 0.050 FDR: 2,507; 0.010 FDR: 2,507; 0.001 FDR:     0
4:55:35.577497 PROGRESS: 
4:55:35.577552 PROGRESS: Protein Summary:
4:55:35.579521 PROGRESS: Channel   0:	 0.050 FDR: 1,983; 0.010 FDR: 1,983; 0.001 FDR:     0
4:55:35.579616 PROGRESS: =========================================================================
4:55:35.587079 INFO: Target number of precursors reached.
4:55:35.784678 INFO: fragments_df: keeping 5000 of 1686023 [sum(precursor_idx_mask)=24262 sum(mass_error_mask)=1686023 stop_rank=5000
4:55:36.152244 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:55:36.464225 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:55:37.112825 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
4:55:37.113468 INFO: Using score_cutoff 11.74547767353058 (fac=0.99, q=1)
4:55:37.113835 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
4:55:37.113917 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
4:55:37.113972 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.74547767353058
4:55:37.114035 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:55:37.264863 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:55:37.458546 INFO: Updating optimization_manager: classifier_version  : -1 -> 7
4:55:37.458812 PROGRESS: Required number of precursors found. Starting search parameter optimization.
4:55:37.458912 INFO: Starting optimization step 8.
4:55:37.458976 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:55:37.459048 INFO: Using rust extraction backend
4:55:37.459113 PROGRESS: Extracting batch of 250329 precursors
4:55:37.710351 INFO: === Search parameters used ===
4:55:37.710648 INFO: rt_error       : 805.6004638671875
4:55:37.710705 INFO: mobility_error : 0.1
4:55:37.710755 INFO: num_candidates : 3
4:55:37.710801 INFO: ms1_error      : 3
4:55:37.710844 INFO: ms2_error      : 10
4:55:37.710887 INFO: fwhm_rt        : 3.0
4:55:37.710929 INFO: quant_window   : 3
4:55:37.710971 INFO: ==============================================
4:55:40.012643 INFO: performing precursor FDR with 40 features
4:55:40.012767 INFO: Decoy channel: -1
4:55:40.012793 INFO: competitive: True
4:55:40.202413 INFO: Setting torch num_threads to 2 for FDR classification task
4:55:40.488383 INFO: Estimating optimal hyperparameters - samples: 579,028, batch_size: 2,371, learning_rate: 7.61e-04
4:55:40.489589 INFO: Using random state 962807 for train-test-split
4:55:53.158190 INFO: Test AUC: 0.570
4:55:53.158318 INFO: Train AUC: 0.582
4:55:53.158350 INFO: AUC difference: 2.00%
4:55:53.623890 INFO: Resetting torch num_threads to 100
4:55:53.655978 PROGRESS: === Extracted 723786 precursors and 2396231 fragments ===
4:55:53.656471 INFO: === FDR correction performed with classifier version 7 ===
4:55:53.657228 PROGRESS: ============================= Precursor FDR =============================
4:55:53.657328 PROGRESS: Total precursors accumulated: 1,426
4:55:53.657387 PROGRESS: Target precursors: 1,412 (99.02%)
4:55:53.657444 PROGRESS: Decoy precursors: 14 (0.98%)
4:55:53.657490 PROGRESS: 
4:55:53.657533 PROGRESS: Precursor Summary:
4:55:53.658761 PROGRESS: Channel   0:	 0.050 FDR: 1,412; 0.010 FDR: 1,412; 0.001 FDR:     0
4:55:53.658845 PROGRESS: 
4:55:53.658899 PROGRESS: Protein Summary:
4:55:53.660484 PROGRESS: Channel   0:	 0.050 FDR: 1,226; 0.010 FDR: 1,226; 0.001 FDR:     0
4:55:53.660581 PROGRESS: =========================================================================
4:55:53.674849 INFO: Target number of precursors reached.
4:55:53.942574 INFO: fragments_df: keeping 5000 of 2396231 [sum(precursor_idx_mask)=30622 sum(mass_error_mask)=2396231 stop_rank=5000
4:55:54.403457 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:55:54.601161 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:55:55.249715 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:55:55.250178 INFO: Using score_cutoff 11.83363306388855 (fac=0.99, q=1)
4:55:55.250490 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:55:55.250563 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:55:55.250615 INFO: Updating optimization_manager: score_cutoff        : 11.74547767353058 -> 11.83363306388855
4:55:55.250664 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:55:55.399373 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:55:55.581224 INFO: === checking if optimization conditions were reached ===
4:55:55.583487 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
4:55:55.583595 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
4:55:55.583659 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
4:55:55.583715 INFO: ==============================================
4:55:55.583780 INFO: Starting optimization step 9.
4:55:55.583835 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:55:55.583892 INFO: Using rust extraction backend
4:55:55.583945 PROGRESS: Extracting batch of 250329 precursors
4:55:55.840142 INFO: === Search parameters used ===
4:55:55.840464 INFO: rt_error       : 805.6004638671875
4:55:55.840521 INFO: mobility_error : 0.1
4:55:55.840567 INFO: num_candidates : 3
4:55:55.840608 INFO: ms1_error      : 3
4:55:55.840648 INFO: ms2_error      : 10.0
4:55:55.840692 INFO: fwhm_rt        : 3.0
4:55:55.840736 INFO: quant_window   : 3
4:55:55.840775 INFO: ==============================================
4:55:58.094741 INFO: performing precursor FDR with 40 features
4:55:58.094880 INFO: Decoy channel: -1
4:55:58.094907 INFO: competitive: True
4:55:58.286429 INFO: Setting torch num_threads to 2 for FDR classification task
4:55:58.579761 INFO: Estimating optimal hyperparameters - samples: 578,984, batch_size: 2,371, learning_rate: 7.61e-04
4:55:58.580694 INFO: Using random state 330587 for train-test-split
4:56:11.396848 INFO: Test AUC: 0.578
4:56:11.396982 INFO: Train AUC: 0.586
4:56:11.397017 INFO: AUC difference: 1.40%
4:56:11.853737 INFO: Resetting torch num_threads to 100
4:56:11.883375 PROGRESS: === Extracted 723731 precursors and 2395816 fragments ===
4:56:11.883857 INFO: === FDR correction performed with classifier version 8 ===
4:56:11.884544 PROGRESS: ============================= Precursor FDR =============================
4:56:11.884638 PROGRESS: Total precursors accumulated: 1,425
4:56:11.884715 PROGRESS: Target precursors: 1,411 (99.02%)
4:56:11.884774 PROGRESS: Decoy precursors: 14 (0.98%)
4:56:11.884821 PROGRESS: 
4:56:11.884864 PROGRESS: Precursor Summary:
4:56:11.886112 PROGRESS: Channel   0:	 0.050 FDR: 1,411; 0.010 FDR: 1,411; 0.001 FDR:     0
4:56:11.886197 PROGRESS: 
4:56:11.886249 PROGRESS: Protein Summary:
4:56:11.887838 PROGRESS: Channel   0:	 0.050 FDR: 1,226; 0.010 FDR: 1,226; 0.001 FDR:     0
4:56:11.887929 PROGRESS: =========================================================================
4:56:11.901868 INFO: Target number of precursors reached.
4:56:12.174465 INFO: fragments_df: keeping 5000 of 2395816 [sum(precursor_idx_mask)=30746 sum(mass_error_mask)=2395816 stop_rank=5000
4:56:12.636398 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:56:12.862954 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:56:13.581766 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:56:13.582249 INFO: Using score_cutoff 11.246177410125732 (fac=0.99, q=1)
4:56:13.582585 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:56:13.582664 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:56:13.582720 INFO: Updating optimization_manager: score_cutoff        : 11.83363306388855 -> 11.246177410125732
4:56:13.582778 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:56:13.730097 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:56:13.909388 INFO: === checking if optimization conditions were reached ===
4:56:13.911679 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
4:56:13.911784 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
4:56:13.911849 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
4:56:13.911909 INFO: ==============================================
4:56:13.911975 INFO: Starting optimization step 10.
4:56:13.912034 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:56:13.912099 INFO: Using rust extraction backend
4:56:13.912158 PROGRESS: Extracting batch of 250329 precursors
4:56:14.169225 INFO: === Search parameters used ===
4:56:14.169522 INFO: rt_error       : 805.6004638671875
4:56:14.169579 INFO: mobility_error : 0.1
4:56:14.169626 INFO: num_candidates : 3
4:56:14.169669 INFO: ms1_error      : 3
4:56:14.169711 INFO: ms2_error      : 10.0
4:56:14.169752 INFO: fwhm_rt        : 3.0
4:56:14.169792 INFO: quant_window   : 3
4:56:14.169832 INFO: ==============================================
4:56:16.491111 INFO: performing precursor FDR with 40 features
4:56:16.491258 INFO: Decoy channel: -1
4:56:16.491285 INFO: competitive: True
4:56:16.688278 INFO: Setting torch num_threads to 2 for FDR classification task
4:56:16.983407 INFO: Estimating optimal hyperparameters - samples: 579,006, batch_size: 2,371, learning_rate: 7.61e-04
4:56:16.984465 INFO: Using random state 630489 for train-test-split
4:56:29.622327 INFO: Test AUC: 0.579
4:56:29.622451 INFO: Train AUC: 0.592
4:56:29.622492 INFO: AUC difference: 2.23%
4:56:30.092279 INFO: Resetting torch num_threads to 100
4:56:30.149662 PROGRESS: === Extracted 723758 precursors and 2396062 fragments ===
4:56:30.150150 INFO: === FDR correction performed with classifier version 9 ===
4:56:30.150949 PROGRESS: ============================= Precursor FDR =============================
4:56:30.151049 PROGRESS: Total precursors accumulated: 1,344
4:56:30.151113 PROGRESS: Target precursors: 1,331 (99.03%)
4:56:30.151181 PROGRESS: Decoy precursors: 13 (0.97%)
4:56:30.151232 PROGRESS: 
4:56:30.151277 PROGRESS: Precursor Summary:
4:56:30.152504 PROGRESS: Channel   0:	 0.050 FDR: 1,331; 0.010 FDR: 1,331; 0.001 FDR:     0
4:56:30.152594 PROGRESS: 
4:56:30.152655 PROGRESS: Protein Summary:
4:56:30.154195 PROGRESS: Channel   0:	 0.050 FDR: 1,162; 0.010 FDR: 1,162; 0.001 FDR:     0
4:56:30.154285 PROGRESS: =========================================================================
4:56:30.168799 INFO: Target number of precursors reached.
4:56:30.443414 INFO: fragments_df: keeping 5000 of 2396062 [sum(precursor_idx_mask)=28870 sum(mass_error_mask)=2396062 stop_rank=5000
4:56:30.979788 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:56:31.197976 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:56:31.916435 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:56:31.916900 INFO: Using score_cutoff 10.367077886581422 (fac=0.99, q=1)
4:56:31.917206 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:56:31.917283 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:56:31.917347 INFO: Updating optimization_manager: score_cutoff        : 11.246177410125732 -> 10.367077886581422
4:56:31.917400 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:56:32.065851 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:56:32.248442 INFO: === checking if optimization conditions were reached ===
4:56:32.250631 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
4:56:32.250731 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
4:56:32.250793 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
4:56:32.250857 INFO: ==============================================
4:56:32.250927 INFO: Starting optimization step 11.
4:56:32.250987 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:56:32.251050 INFO: Using rust extraction backend
4:56:32.251112 PROGRESS: Extracting batch of 250329 precursors
4:56:32.508374 INFO: === Search parameters used ===
4:56:32.508670 INFO: rt_error       : 805.6004638671875
4:56:32.508726 INFO: mobility_error : 0.1
4:56:32.508772 INFO: num_candidates : 3
4:56:32.508816 INFO: ms1_error      : 3
4:56:32.508858 INFO: ms2_error      : 10.0
4:56:32.508897 INFO: fwhm_rt        : 3.0
4:56:32.508936 INFO: quant_window   : 3
4:56:32.508976 INFO: ==============================================
4:56:34.836606 INFO: performing precursor FDR with 40 features
4:56:34.836732 INFO: Decoy channel: -1
4:56:34.836759 INFO: competitive: True
4:56:35.031034 INFO: Setting torch num_threads to 2 for FDR classification task
4:56:35.326379 INFO: Estimating optimal hyperparameters - samples: 579,008, batch_size: 2,371, learning_rate: 7.61e-04
4:56:35.327813 INFO: Using random state 221011 for train-test-split
4:56:48.179290 INFO: Test AUC: 0.581
4:56:48.179414 INFO: Train AUC: 0.595
4:56:48.179446 INFO: AUC difference: 2.38%
4:56:48.650120 INFO: Resetting torch num_threads to 100
4:56:48.679702 PROGRESS: === Extracted 723760 precursors and 2396054 fragments ===
4:56:48.680200 INFO: === FDR correction performed with classifier version 10 ===
4:56:48.680946 PROGRESS: ============================= Precursor FDR =============================
4:56:48.681034 PROGRESS: Total precursors accumulated: 1,453
4:56:48.681093 PROGRESS: Target precursors: 1,439 (99.04%)
4:56:48.681143 PROGRESS: Decoy precursors: 14 (0.96%)
4:56:48.681188 PROGRESS: 
4:56:48.681232 PROGRESS: Precursor Summary:
4:56:48.682474 PROGRESS: Channel   0:	 0.050 FDR: 1,439; 0.010 FDR: 1,439; 0.001 FDR:     0
4:56:48.682562 PROGRESS: 
4:56:48.682616 PROGRESS: Protein Summary:
4:56:48.684201 PROGRESS: Channel   0:	 0.050 FDR: 1,251; 0.010 FDR: 1,251; 0.001 FDR:     0
4:56:48.684300 PROGRESS: =========================================================================
4:56:48.698403 INFO: Target number of precursors reached.
4:56:48.967054 INFO: fragments_df: keeping 5000 of 2396054 [sum(precursor_idx_mask)=31292 sum(mass_error_mask)=2396054 stop_rank=5000
4:56:49.338282 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:56:49.552348 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:56:50.200709 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:56:50.201174 INFO: Using score_cutoff 11.208186522674561 (fac=0.99, q=1)
4:56:50.201484 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:56:50.201565 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:56:50.201630 INFO: Updating optimization_manager: score_cutoff        : 10.367077886581422 -> 11.208186522674561
4:56:50.201687 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:56:50.350237 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:56:50.535679 INFO: === checking if optimization conditions were reached ===
4:56:50.537902 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
4:56:50.538007 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
4:56:50.538072 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
4:56:50.538151 INFO: ==============================================
4:56:50.538219 INFO: Starting optimization step 12.
4:56:50.538276 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:56:50.538336 INFO: Using rust extraction backend
4:56:50.538392 PROGRESS: Extracting batch of 250329 precursors
4:56:50.788945 INFO: === Search parameters used ===
4:56:50.789229 INFO: rt_error       : 805.6004638671875
4:56:50.789285 INFO: mobility_error : 0.1
4:56:50.789334 INFO: num_candidates : 3
4:56:50.789379 INFO: ms1_error      : 3
4:56:50.789421 INFO: ms2_error      : 10.0
4:56:50.789461 INFO: fwhm_rt        : 3.0
4:56:50.789501 INFO: quant_window   : 3
4:56:50.789541 INFO: ==============================================
4:56:53.034697 INFO: performing precursor FDR with 40 features
4:56:53.034827 INFO: Decoy channel: -1
4:56:53.034853 INFO: competitive: True
4:56:53.231373 INFO: Setting torch num_threads to 2 for FDR classification task
4:56:53.524131 INFO: Estimating optimal hyperparameters - samples: 578,990, batch_size: 2,371, learning_rate: 7.61e-04
4:56:53.525183 INFO: Using random state 825099 for train-test-split
4:57:06.159173 INFO: Test AUC: 0.581
4:57:06.159302 INFO: Train AUC: 0.597
4:57:06.159335 INFO: AUC difference: 2.57%
4:57:06.625695 INFO: Resetting torch num_threads to 100
4:57:06.654789 PROGRESS: === Extracted 723738 precursors and 2395563 fragments ===
4:57:06.655282 INFO: === FDR correction performed with classifier version 11 ===
4:57:06.655958 PROGRESS: ============================= Precursor FDR =============================
4:57:06.656049 PROGRESS: Total precursors accumulated: 1,415
4:57:06.656109 PROGRESS: Target precursors: 1,401 (99.01%)
4:57:06.656160 PROGRESS: Decoy precursors: 14 (0.99%)
4:57:06.656206 PROGRESS: 
4:57:06.656250 PROGRESS: Precursor Summary:
4:57:06.657485 PROGRESS: Channel   0:	 0.050 FDR: 1,401; 0.010 FDR: 1,401; 0.001 FDR:     0
4:57:06.657574 PROGRESS: 
4:57:06.657630 PROGRESS: Protein Summary:
4:57:06.659206 PROGRESS: Channel   0:	 0.050 FDR: 1,215; 0.010 FDR: 1,215; 0.001 FDR:     0
4:57:06.659304 PROGRESS: =========================================================================
4:57:06.672987 INFO: Target number of precursors reached.
4:57:06.938177 INFO: fragments_df: keeping 5000 of 2395563 [sum(precursor_idx_mask)=30757 sum(mass_error_mask)=2395563 stop_rank=5000
4:57:07.303216 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:57:07.511471 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:57:08.160580 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:57:08.161037 INFO: Using score_cutoff 11.322336645126343 (fac=0.99, q=1)
4:57:08.161342 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:57:08.161427 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:57:08.161483 INFO: Updating optimization_manager: score_cutoff        : 11.208186522674561 -> 11.322336645126343
4:57:08.161535 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:57:08.309230 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:57:08.494329 INFO: === checking if optimization conditions were reached ===
4:57:08.496578 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
4:57:08.496685 INFO: Updating optimization_manager: classifier_version  : 11 -> 12
4:57:08.496751 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
4:57:08.496810 INFO: ==============================================
4:57:08.496888 PROGRESS: Optimization finished for ms2_error.
4:57:08.849112 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:57:08.997169 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:57:09.181648 INFO: Starting optimization step 0.
4:57:09.181909 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:57:09.181987 INFO: Using rust extraction backend
4:57:09.182050 PROGRESS: Extracting batch of 250329 precursors
4:57:09.432406 INFO: === Search parameters used ===
4:57:09.432681 INFO: rt_error       : 805.6004638671875
4:57:09.432760 INFO: mobility_error : 0.1
4:57:09.432808 INFO: num_candidates : 3
4:57:09.432856 INFO: ms1_error      : 3
4:57:09.432899 INFO: ms2_error      : 10.0
4:57:09.432938 INFO: fwhm_rt        : 3.0
4:57:09.432977 INFO: quant_window   : 3
4:57:09.433016 INFO: ==============================================
4:57:13.668809 INFO: performing precursor FDR with 40 features
4:57:13.668942 INFO: Decoy channel: -1
4:57:13.668970 INFO: competitive: True
4:57:13.859580 INFO: Setting torch num_threads to 2 for FDR classification task
4:57:14.153821 INFO: Estimating optimal hyperparameters - samples: 578,994, batch_size: 2,371, learning_rate: 7.61e-04
4:57:14.154911 INFO: Using random state 759730 for train-test-split
4:57:27.563362 INFO: Test AUC: 0.586
4:57:27.563511 INFO: Train AUC: 0.599
4:57:27.563545 INFO: AUC difference: 2.10%
4:57:28.032889 INFO: Resetting torch num_threads to 100
4:57:28.064453 PROGRESS: === Extracted 723743 precursors and 2395905 fragments ===
4:57:28.064950 INFO: === FDR correction performed with classifier version 12 ===
4:57:28.065758 PROGRESS: ============================= Precursor FDR =============================
4:57:28.065849 PROGRESS: Total precursors accumulated: 1,351
4:57:28.065909 PROGRESS: Target precursors: 1,338 (99.04%)
4:57:28.065961 PROGRESS: Decoy precursors: 13 (0.96%)
4:57:28.066009 PROGRESS: 
4:57:28.066055 PROGRESS: Precursor Summary:
4:57:28.067336 PROGRESS: Channel   0:	 0.050 FDR: 1,338; 0.010 FDR: 1,338; 0.001 FDR:     0
4:57:28.067431 PROGRESS: 
4:57:28.067487 PROGRESS: Protein Summary:
4:57:28.069069 PROGRESS: Channel   0:	 0.050 FDR: 1,176; 0.010 FDR: 1,176; 0.001 FDR:     0
4:57:28.069159 PROGRESS: =========================================================================
4:57:28.083476 INFO: Target number of precursors reached.
4:57:28.358927 INFO: fragments_df: keeping 5000 of 2395905 [sum(precursor_idx_mask)=29535 sum(mass_error_mask)=2395905 stop_rank=5000
4:57:28.785243 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:57:28.979867 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:57:29.632530 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:57:29.632998 INFO: Using score_cutoff 10.802097383594514 (fac=0.99, q=1)
4:57:29.633325 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:57:29.633405 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:57:29.633461 INFO: Updating optimization_manager: score_cutoff        : 11.322336645126343 -> 10.802097383594514
4:57:29.633515 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:57:29.779486 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:57:29.965375 INFO: === checking if optimization conditions were reached ===
4:57:29.965651 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
4:57:29.968252 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 520.2137180628195
4:57:29.968373 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 520.2137.
4:57:29.968436 INFO: ==============================================
4:57:29.968505 INFO: Starting optimization step 1.
4:57:29.968563 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:57:29.968628 INFO: Using rust extraction backend
4:57:29.968685 PROGRESS: Extracting batch of 250329 precursors
4:57:30.226583 INFO: === Search parameters used ===
4:57:30.226874 INFO: rt_error       : 520.2137180628195
4:57:30.226943 INFO: mobility_error : 0.1
4:57:30.226992 INFO: num_candidates : 3
4:57:30.227038 INFO: ms1_error      : 3
4:57:30.227081 INFO: ms2_error      : 10.0
4:57:30.227123 INFO: fwhm_rt        : 3.0
4:57:30.227177 INFO: quant_window   : 3
4:57:30.227221 INFO: ==============================================
4:57:32.489559 INFO: performing precursor FDR with 40 features
4:57:32.489681 INFO: Decoy channel: -1
4:57:32.489708 INFO: competitive: True
4:57:32.682632 INFO: Setting torch num_threads to 2 for FDR classification task
4:57:32.981667 INFO: Estimating optimal hyperparameters - samples: 577,164, batch_size: 2,364, learning_rate: 7.60e-04
4:57:32.982812 INFO: Using random state 759730 for train-test-split
4:57:46.203160 INFO: Test AUC: 0.581
4:57:46.203331 INFO: Train AUC: 0.598
4:57:46.203373 INFO: AUC difference: 2.80%
4:57:46.866068 INFO: Resetting torch num_threads to 100
4:57:46.914403 PROGRESS: === Extracted 721456 precursors and 2365410 fragments ===
4:57:46.915071 INFO: === FDR correction performed with classifier version 12 ===
4:57:46.916324 PROGRESS: ============================= Precursor FDR =============================
4:57:46.916472 PROGRESS: Total precursors accumulated: 1,468
4:57:46.916547 PROGRESS: Target precursors: 1,454 (99.05%)
4:57:46.916618 PROGRESS: Decoy precursors: 14 (0.95%)
4:57:46.916680 PROGRESS: 
4:57:46.916739 PROGRESS: Precursor Summary:
4:57:46.918747 PROGRESS: Channel   0:	 0.050 FDR: 1,454; 0.010 FDR: 1,454; 0.001 FDR:     0
4:57:46.918899 PROGRESS: 
4:57:46.918967 PROGRESS: Protein Summary:
4:57:46.921427 PROGRESS: Channel   0:	 0.050 FDR: 1,265; 0.010 FDR: 1,265; 0.001 FDR:     0
4:57:46.921577 PROGRESS: =========================================================================
4:57:46.948609 INFO: Target number of precursors reached.
4:57:47.356133 INFO: fragments_df: keeping 5000 of 2365410 [sum(precursor_idx_mask)=31717 sum(mass_error_mask)=2365410 stop_rank=5000
4:57:47.906624 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:57:48.419105 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:57:49.681438 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:57:49.682079 INFO: Using score_cutoff 10.247386479091645 (fac=0.99, q=1)
4:57:49.682500 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:57:49.682592 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:57:49.682666 INFO: Updating optimization_manager: score_cutoff        : 10.802097383594514 -> 10.247386479091645
4:57:49.682730 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:57:49.846100 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:57:50.082298 INFO: === checking if optimization conditions were reached ===
4:57:50.082619 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
4:57:50.086001 INFO: Updating optimization_manager: rt_error            : 520.2137180628195 -> 507.1553988309362
4:57:50.086154 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 507.1554.
4:57:50.086230 INFO: ==============================================
4:57:50.086319 INFO: Starting optimization step 2.
4:57:50.086389 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:57:50.086468 INFO: Using rust extraction backend
4:57:50.086538 PROGRESS: Extracting batch of 250329 precursors
4:57:50.349910 INFO: === Search parameters used ===
4:57:50.350232 INFO: rt_error       : 507.1553988309362
4:57:50.350300 INFO: mobility_error : 0.1
4:57:50.350355 INFO: num_candidates : 3
4:57:50.350408 INFO: ms1_error      : 3
4:57:50.350460 INFO: ms2_error      : 10.0
4:57:50.350510 INFO: fwhm_rt        : 3.0
4:57:50.350561 INFO: quant_window   : 3
4:57:50.350614 INFO: ==============================================
4:57:53.880739 INFO: performing precursor FDR with 40 features
4:57:53.880877 INFO: Decoy channel: -1
4:57:53.880909 INFO: competitive: True
4:57:54.137344 INFO: Setting torch num_threads to 2 for FDR classification task
4:57:54.560453 INFO: Estimating optimal hyperparameters - samples: 576,896, batch_size: 2,362, learning_rate: 7.59e-04
4:57:54.561717 INFO: Using random state 759730 for train-test-split
4:58:10.770451 INFO: Test AUC: 0.583
4:58:10.770688 INFO: Train AUC: 0.596
4:58:10.770730 INFO: AUC difference: 2.32%
4:58:11.276485 INFO: Resetting torch num_threads to 100
4:58:11.331993 PROGRESS: === Extracted 721121 precursors and 2359495 fragments ===
4:58:11.332725 INFO: === FDR correction performed with classifier version 12 ===
4:58:11.333754 PROGRESS: ============================= Precursor FDR =============================
4:58:11.333870 PROGRESS: Total precursors accumulated: 1,535
4:58:11.333934 PROGRESS: Target precursors: 1,520 (99.02%)
4:58:11.333989 PROGRESS: Decoy precursors: 15 (0.98%)
4:58:11.334038 PROGRESS: 
4:58:11.334084 PROGRESS: Precursor Summary:
4:58:11.335483 PROGRESS: Channel   0:	 0.050 FDR: 1,520; 0.010 FDR: 1,520; 0.001 FDR:     0
4:58:11.335589 PROGRESS: 
4:58:11.335647 PROGRESS: Protein Summary:
4:58:11.337469 PROGRESS: Channel   0:	 0.050 FDR: 1,311; 0.010 FDR: 1,311; 0.001 FDR:     0
4:58:11.337564 PROGRESS: =========================================================================
4:58:11.367953 INFO: Target number of precursors reached.
4:58:11.662273 INFO: fragments_df: keeping 5000 of 2359495 [sum(precursor_idx_mask)=32853 sum(mass_error_mask)=2359495 stop_rank=5000
4:58:12.198660 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:58:12.545027 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:58:13.359370 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:58:13.360173 INFO: Using score_cutoff 10.769527979564666 (fac=0.99, q=1)
4:58:13.360619 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:58:13.360697 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:58:13.360751 INFO: Updating optimization_manager: score_cutoff        : 10.247386479091645 -> 10.769527979564666
4:58:13.360805 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:58:13.537388 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:58:13.814741 INFO: === checking if optimization conditions were reached ===
4:58:13.815336 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
4:58:13.821054 INFO: Updating optimization_manager: rt_error            : 507.1553988309362 -> 524.548554100837
4:58:13.821373 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 524.5486.
4:58:13.821493 INFO: ==============================================
4:58:13.821606 INFO: Starting optimization step 3.
4:58:13.821698 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:58:13.821821 INFO: Using rust extraction backend
4:58:13.821917 PROGRESS: Extracting batch of 250329 precursors
4:58:14.382991 INFO: === Search parameters used ===
4:58:14.383488 INFO: rt_error       : 524.548554100837
4:58:14.383594 INFO: mobility_error : 0.1
4:58:14.383655 INFO: num_candidates : 3
4:58:14.383704 INFO: ms1_error      : 3
4:58:14.383750 INFO: ms2_error      : 10.0
4:58:14.383792 INFO: fwhm_rt        : 3.0
4:58:14.383834 INFO: quant_window   : 3
4:58:14.383875 INFO: ==============================================
4:58:18.232271 INFO: performing precursor FDR with 40 features
4:58:18.232619 INFO: Decoy channel: -1
4:58:18.232652 INFO: competitive: True
4:58:18.754312 INFO: Setting torch num_threads to 2 for FDR classification task
4:58:19.495971 INFO: Estimating optimal hyperparameters - samples: 577,280, batch_size: 2,364, learning_rate: 7.60e-04
4:58:19.498932 INFO: Using random state 759730 for train-test-split
4:58:42.502231 INFO: Test AUC: 0.584
4:58:42.502902 INFO: Train AUC: 0.598
4:58:42.502961 INFO: AUC difference: 2.20%
4:58:43.368649 INFO: Resetting torch num_threads to 100
4:58:43.480330 PROGRESS: === Extracted 721600 precursors and 2366735 fragments ===
4:58:43.481890 INFO: === FDR correction performed with classifier version 12 ===
4:58:43.484557 PROGRESS: ============================= Precursor FDR =============================
4:58:43.484759 PROGRESS: Total precursors accumulated: 1,241
4:58:43.484833 PROGRESS: Target precursors: 1,229 (99.03%)
4:58:43.484913 PROGRESS: Decoy precursors: 12 (0.97%)
4:58:43.484963 PROGRESS: 
4:58:43.485009 PROGRESS: Precursor Summary:
4:58:43.487123 PROGRESS: Channel   0:	 0.050 FDR: 1,229; 0.010 FDR: 1,229; 0.001 FDR:     0
4:58:43.487302 PROGRESS: 
4:58:43.487366 PROGRESS: Protein Summary:
4:58:43.489691 PROGRESS: Channel   0:	 0.050 FDR: 1,085; 0.010 FDR: 1,085; 0.001 FDR:     0
4:58:43.489873 PROGRESS: =========================================================================
4:58:43.563652 INFO: Target number of precursors reached.
4:58:43.867735 INFO: fragments_df: keeping 5000 of 2366735 [sum(precursor_idx_mask)=26820 sum(mass_error_mask)=2366735 stop_rank=5000
4:58:45.067400 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:58:45.420135 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:58:46.524495 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:58:46.526006 INFO: Using score_cutoff 10.184544748306275 (fac=0.99, q=1)
4:58:46.526667 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:58:46.526756 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:58:46.526813 INFO: Updating optimization_manager: score_cutoff        : 10.769527979564666 -> 10.184544748306275
4:58:46.526894 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:58:46.786500 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:58:47.233865 INFO: === checking if optimization conditions were reached ===
4:58:47.235236 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
4:58:47.246102 INFO: Updating optimization_manager: rt_error            : 524.548554100837 -> 505.4359822318623
4:58:47.246885 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 505.4360.
4:58:47.247041 INFO: ==============================================
4:58:47.247244 INFO: Starting optimization step 4.
4:58:47.247460 PROGRESS: === Extracting elution groups 0 to 127000 ===
4:58:47.247609 INFO: Using rust extraction backend
4:58:47.247731 PROGRESS: Extracting batch of 250329 precursors
4:58:48.087095 INFO: === Search parameters used ===
4:58:48.088223 INFO: rt_error       : 505.4359822318623
4:58:48.088287 INFO: mobility_error : 0.1
4:58:48.088341 INFO: num_candidates : 3
4:58:48.088389 INFO: ms1_error      : 3
4:58:48.088434 INFO: ms2_error      : 10.0
4:58:48.088478 INFO: fwhm_rt        : 3.0
4:58:48.088521 INFO: quant_window   : 3
4:58:48.088568 INFO: ==============================================
4:58:55.594291 INFO: performing precursor FDR with 40 features
4:58:55.594671 INFO: Decoy channel: -1
4:58:55.594700 INFO: competitive: True
4:58:56.333499 INFO: Setting torch num_threads to 2 for FDR classification task
4:58:57.490771 INFO: Estimating optimal hyperparameters - samples: 576,847, batch_size: 2,362, learning_rate: 7.59e-04
4:58:57.497890 INFO: Using random state 759730 for train-test-split
4:59:31.589684 INFO: Test AUC: 0.584
4:59:31.590347 INFO: Train AUC: 0.597
4:59:31.590403 INFO: AUC difference: 2.10%
4:59:32.403483 INFO: Resetting torch num_threads to 100
4:59:32.501163 PROGRESS: === Extracted 721059 precursors and 2358650 fragments ===
4:59:32.502787 INFO: === FDR correction performed with classifier version 12 ===
4:59:32.505176 PROGRESS: ============================= Precursor FDR =============================
4:59:32.505383 PROGRESS: Total precursors accumulated: 1,374
4:59:32.505451 PROGRESS: Target precursors: 1,361 (99.05%)
4:59:32.505507 PROGRESS: Decoy precursors: 13 (0.95%)
4:59:32.505556 PROGRESS: 
4:59:32.505604 PROGRESS: Precursor Summary:
4:59:32.508225 PROGRESS: Channel   0:	 0.050 FDR: 1,361; 0.010 FDR: 1,361; 0.001 FDR:     0
4:59:32.508435 PROGRESS: 
4:59:32.508499 PROGRESS: Protein Summary:
4:59:32.510977 PROGRESS: Channel   0:	 0.050 FDR: 1,181; 0.010 FDR: 1,181; 0.001 FDR:     0
4:59:32.511223 PROGRESS: =========================================================================
4:59:32.572939 INFO: Target number of precursors reached.
4:59:32.876207 INFO: fragments_df: keeping 5000 of 2358650 [sum(precursor_idx_mask)=29704 sum(mass_error_mask)=2358650 stop_rank=5000
4:59:34.087447 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
4:59:34.714888 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
4:59:35.707179 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
4:59:35.709145 INFO: Using score_cutoff 10.843713844299316 (fac=0.99, q=1)
4:59:35.710063 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:59:35.710148 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:59:35.710205 INFO: Updating optimization_manager: score_cutoff        : 10.184544748306275 -> 10.843713844299316
4:59:35.710278 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:59:35.961554 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:59:36.365068 INFO: === checking if optimization conditions were reached ===
4:59:36.366241 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
4:59:36.370399 INFO: Updating optimization_manager: rt_error            : 505.4359822318623 -> 507.1553988309362
4:59:36.371388 INFO: Updating optimization_manager: classifier_version  : 12 -> 15
4:59:36.371823 INFO: Updating optimization_manager: score_cutoff        : 10.843713844299316 -> 10.769527979564666
4:59:36.372016 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
4:59:36.372156 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
4:59:36.372314 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 507.1554 found after 5 searches.
4:59:36.372445 INFO: ==============================================
4:59:36.372601 PROGRESS: Optimization finished for rt_error.
4:59:37.509724 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:59:37.740576 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
4:59:38.108424 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
4:59:38.109470 PROGRESS: ==============================================
4:59:38.109673 PROGRESS: ms2_error      : 10.0000
4:59:38.109769 PROGRESS: rt_error       : 507.1554
4:59:38.109841 PROGRESS: ==============================================
4:59:38.114081 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
4:59:48.881309 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:00:06.824251 INFO: Using rust extraction backend
5:00:06.826354 PROGRESS: Extracting batch of 11997144 precursors
5:00:36.704175 INFO: === Search parameters used ===
5:00:36.705387 INFO: rt_error       : 507.1553988309362
5:00:36.705521 INFO: mobility_error : 0.1
5:00:36.705646 INFO: num_candidates : 3
5:00:36.705711 INFO: ms1_error      : 3
5:00:36.705761 INFO: ms2_error      : 10.0
5:00:36.705806 INFO: fwhm_rt        : 3.0
5:00:36.705853 INFO: quant_window   : 3
5:00:36.705896 INFO: ==============================================
5:01:43.549590 INFO: Removed 17331643 precursors with score below cutoff 10.769527979564666
5:02:04.401243 INFO: performing precursor FDR with 40 features
5:02:04.401602 INFO: Decoy channel: -1
5:02:04.401641 INFO: competitive: True
5:02:10.425127 INFO: Setting torch num_threads to 2 for FDR classification task
5:02:34.481165 INFO: Estimating optimal hyperparameters - samples: 14,706,372, batch_size: 4,096, learning_rate: 1.00e-03
5:02:34.656711 INFO: Using random state 678890 for train-test-split
5:15:29.107110 INFO: Test AUC: 0.597
5:15:29.107987 INFO: Train AUC: 0.598
5:15:29.108117 INFO: AUC difference: 0.08%
5:15:35.241117 INFO: Resetting torch num_threads to 100
5:15:40.797411 PROGRESS: ============================= Precursor FDR =============================
5:15:40.798286 PROGRESS: Total precursors accumulated: 101,039
5:15:40.798377 PROGRESS: Target precursors: 100,039 (99.01%)
5:15:40.798438 PROGRESS: Decoy precursors: 1,000 (0.99%)
5:15:40.798491 PROGRESS: 
5:15:40.798555 PROGRESS: Precursor Summary:
5:15:40.918247 PROGRESS: Channel   0:	 0.050 FDR: 100,039; 0.010 FDR: 100,039; 0.001 FDR: 58,336
5:15:40.919249 PROGRESS: 
5:15:40.919329 PROGRESS: Protein Summary:
5:15:41.070695 PROGRESS: Channel   0:	 0.050 FDR: 14,147; 0.010 FDR: 14,147; 0.001 FDR: 9,554
5:15:41.071542 PROGRESS: =========================================================================
5:15:41.300665 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/psm.parquet
5:15:41.859614 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.parquet
5:15:42.491647 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
5:15:44.063172 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 
5:15:44.063665 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant
5:15:44.063866 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/figures
5:15:44.064201 INFO: Initializing TimingManager
5:15:44.066168 INFO: Initializing RawFileManager
5:16:21.028545 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.
5:16:21.052134 INFO: Determining DIA cycle
5:16:21.072766 INFO: Found cycle with start 0.00 min and length 300.
5:16:21.799547 INFO: RT (min)            : 0.0 - 26.9
5:16:21.800093 INFO: RT duration (sec)   : 1611.2
5:16:21.800168 INFO: RT duration (min)   : 26.9
5:16:21.800208 INFO: Cycle len (scans)   : 300
5:16:21.800235 INFO: Cycle len (sec)     : 1.65
5:16:21.800273 INFO: Number of cycles    : 977
5:16:21.800304 INFO: MS2 range (m/z)     : 380.4 - 980.7
5:16:21.800379 INFO: Creating DIA data object took: 37.734010219573975
5:16:23.918339 INFO: Creating DIA data NG object took: 2.1172831058502197
5:16:28.138734 INFO: Initializing CalibrationManager
5:16:28.139686 INFO: Setting up calibration estimators ..
5:16:28.139771 INFO: Found 1 estimator(s) in calibration group 'fragment'
5:16:28.139903 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
5:16:28.140011 INFO: Found 3 estimator(s) in calibration group 'precursor'
5:16:28.140074 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
5:16:28.140175 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
5:16:28.140270 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
5:16:28.140325 INFO: Done setting up calibration estimators.
5:16:28.141181 INFO: Initializing OptimizationManager
5:16:28.141516 INFO: initial parameter: ms1_error = 3
5:16:28.141582 INFO: initial parameter: ms2_error = 10
5:16:28.141642 INFO: initial parameter: rt_error = 805.5982666015625
5:16:28.141688 INFO: initial parameter: mobility_error = 0.1
5:16:28.141732 INFO: initial parameter: num_candidates = 1
5:16:28.141774 INFO: initial parameter: fwhm_rt = 5
5:16:28.141817 INFO: initial parameter: fwhm_mobility = 0.01
5:16:28.141864 INFO: initial parameter: score_cutoff = 0
5:16:28.141907 INFO: initial parameter: classifier_version = -1
5:16:28.142004 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
5:16:28.142923 INFO: FDRManager: loading saved state not requested, will be initialized.
5:16:28.142992 INFO: Initializing FDRManager
5:16:28.143059 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
5:16:32.735281 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
5:16:36.232730 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
5:16:36.234222 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
5:16:36.234486 PROGRESS: Starting initial search for precursors.
5:16:36.234667 INFO: Starting optimization step 0.
5:16:36.234755 PROGRESS: === Extracting elution groups 0 to 1000 ===
5:16:36.234839 INFO: Using rust extraction backend
5:16:36.234946 PROGRESS: Extracting batch of 1967 precursors
5:16:36.254655 INFO: === Search parameters used ===
5:16:36.255669 INFO: rt_error       : 805.5982666015625
5:16:36.255742 INFO: mobility_error : 0.1
5:16:36.255791 INFO: num_candidates : 1
5:16:36.255842 INFO: ms1_error      : 3
5:16:36.255888 INFO: ms2_error      : 10
5:16:36.255933 INFO: fwhm_rt        : 5
5:16:36.255976 INFO: quant_window   : 3
5:16:36.256017 INFO: ==============================================
5:16:36.443218 INFO: performing precursor FDR with 40 features
5:16:36.444732 INFO: Decoy channel: -1
5:16:36.444810 INFO: competitive: True
5:16:36.459238 INFO: Setting torch num_threads to 2 for FDR classification task
5:16:36.479911 INFO: Estimating optimal hyperparameters - samples: 1,524, batch_size: 128, learning_rate: 1.77e-04
5:16:36.487387 INFO: Using random state 498117 for train-test-split
5:16:36.981045 INFO: Test AUC: 0.459
5:16:36.981409 INFO: Train AUC: 0.585
5:16:36.981449 INFO: AUC difference: 21.59%
5:16:36.981483 WARNING: AUC difference > 5%. This may indicate overfitting.
5:16:37.475958 INFO: Resetting torch num_threads to 100
5:16:37.480397 PROGRESS: === Extracted 1905 precursors and 6717 fragments ===
5:16:37.481411 INFO: === FDR correction performed with classifier version -1 ===
5:16:37.482168 PROGRESS: ============================= Precursor FDR =============================
5:16:37.482293 PROGRESS: Total precursors accumulated: 4
5:16:37.482359 PROGRESS: Target precursors: 4 (100.00%)
5:16:37.482413 PROGRESS: Decoy precursors: 0 (0.00%)
5:16:37.482460 PROGRESS: 
5:16:37.482506 PROGRESS: Precursor Summary:
5:16:37.483813 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
5:16:37.483923 PROGRESS: 
5:16:37.484000 PROGRESS: Protein Summary:
5:16:37.485357 PROGRESS: Channel   0:	 0.050 FDR:     4; 0.010 FDR:     4; 0.001 FDR:     4
5:16:37.485464 PROGRESS: =========================================================================
5:16:37.486534 INFO: Target number of precursors not reached yet.
5:16:37.607556 INFO: Starting optimization step 1.
5:16:37.608247 PROGRESS: === Extracting elution groups 1000 to 3000 ===
5:16:37.608425 INFO: Using rust extraction backend
5:16:37.608503 PROGRESS: Extracting batch of 3942 precursors
5:16:37.620557 INFO: === Search parameters used ===
5:16:37.621296 INFO: rt_error       : 805.5982666015625
5:16:37.621353 INFO: mobility_error : 0.1
5:16:37.621402 INFO: num_candidates : 1
5:16:37.621446 INFO: ms1_error      : 3
5:16:37.621488 INFO: ms2_error      : 10
5:16:37.621529 INFO: fwhm_rt        : 5
5:16:37.621569 INFO: quant_window   : 3
5:16:37.621608 INFO: ==============================================
5:16:37.742745 INFO: performing precursor FDR with 40 features
5:16:37.743102 INFO: Decoy channel: -1
5:16:37.743134 INFO: competitive: True
5:16:37.769556 INFO: Setting torch num_threads to 2 for FDR classification task
5:16:37.784764 INFO: Estimating optimal hyperparameters - samples: 4,578, batch_size: 128, learning_rate: 1.77e-04
5:16:37.785259 INFO: Using random state 945094 for train-test-split
5:16:38.562577 INFO: Test AUC: 0.518
5:16:38.562950 INFO: Train AUC: 0.581
5:16:38.562994 INFO: AUC difference: 10.95%
5:16:38.563023 WARNING: AUC difference > 5%. This may indicate overfitting.
5:16:39.038263 INFO: Resetting torch num_threads to 100
5:16:39.051249 PROGRESS: === Extracted 5723 precursors and 19729 fragments ===
5:16:39.053009 INFO: === FDR correction performed with classifier version -1 ===
5:16:39.054455 PROGRESS: ============================= Precursor FDR =============================
5:16:39.054727 PROGRESS: Total precursors accumulated: 31
5:16:39.054804 PROGRESS: Target precursors: 31 (100.00%)
5:16:39.054854 PROGRESS: Decoy precursors: 0 (0.00%)
5:16:39.054901 PROGRESS: 
5:16:39.054963 PROGRESS: Precursor Summary:
5:16:39.056669 PROGRESS: Channel   0:	 0.050 FDR:    31; 0.010 FDR:    31; 0.001 FDR:    31
5:16:39.056893 PROGRESS: 
5:16:39.056954 PROGRESS: Protein Summary:
5:16:39.058459 PROGRESS: Channel   0:	 0.050 FDR:    31; 0.010 FDR:    31; 0.001 FDR:    31
5:16:39.058638 PROGRESS: =========================================================================
5:16:39.060585 INFO: Target number of precursors not reached yet.
5:16:39.206393 INFO: Starting optimization step 2.
5:16:39.207598 PROGRESS: === Extracting elution groups 3000 to 7000 ===
5:16:39.207778 INFO: Using rust extraction backend
5:16:39.207880 PROGRESS: Extracting batch of 7891 precursors
5:16:39.234348 INFO: === Search parameters used ===
5:16:39.235220 INFO: rt_error       : 805.5982666015625
5:16:39.235291 INFO: mobility_error : 0.1
5:16:39.235348 INFO: num_candidates : 1
5:16:39.235397 INFO: ms1_error      : 3
5:16:39.235443 INFO: ms2_error      : 10
5:16:39.235492 INFO: fwhm_rt        : 5
5:16:39.235544 INFO: quant_window   : 3
5:16:39.235594 INFO: ==============================================
5:16:39.463358 INFO: performing precursor FDR with 40 features
5:16:39.463772 INFO: Decoy channel: -1
5:16:39.463810 INFO: competitive: True
5:16:39.497205 INFO: Setting torch num_threads to 2 for FDR classification task
5:16:39.515172 INFO: Estimating optimal hyperparameters - samples: 10,718, batch_size: 128, learning_rate: 1.77e-04
5:16:39.516002 INFO: Using random state 921080 for train-test-split
5:16:41.479874 INFO: Test AUC: 0.533
5:16:41.480259 INFO: Train AUC: 0.581
5:16:41.480301 INFO: AUC difference: 8.32%
5:16:41.480335 WARNING: AUC difference > 5%. This may indicate overfitting.
5:16:41.956487 INFO: Resetting torch num_threads to 100
5:16:41.989369 PROGRESS: === Extracted 13398 precursors and 46466 fragments ===
5:16:41.991674 INFO: === FDR correction performed with classifier version -1 ===
5:16:41.993221 PROGRESS: ============================= Precursor FDR =============================
5:16:41.993383 PROGRESS: Total precursors accumulated: 63
5:16:41.993461 PROGRESS: Target precursors: 63 (100.00%)
5:16:41.993527 PROGRESS: Decoy precursors: 0 (0.00%)
5:16:41.993579 PROGRESS: 
5:16:41.993628 PROGRESS: Precursor Summary:
5:16:41.995055 PROGRESS: Channel   0:	 0.050 FDR:    63; 0.010 FDR:    63; 0.001 FDR:    63
5:16:41.995202 PROGRESS: 
5:16:41.995265 PROGRESS: Protein Summary:
5:16:41.996742 PROGRESS: Channel   0:	 0.050 FDR:    62; 0.010 FDR:    62; 0.001 FDR:    62
5:16:41.996864 PROGRESS: =========================================================================
5:16:42.001660 INFO: Target number of precursors not reached yet.
5:16:42.233287 INFO: Starting optimization step 3.
5:16:42.234916 PROGRESS: === Extracting elution groups 7000 to 15000 ===
5:16:42.235204 INFO: Using rust extraction backend
5:16:42.235347 PROGRESS: Extracting batch of 15751 precursors
5:16:42.300162 INFO: === Search parameters used ===
5:16:42.301211 INFO: rt_error       : 805.5982666015625
5:16:42.301278 INFO: mobility_error : 0.1
5:16:42.301335 INFO: num_candidates : 1
5:16:42.301390 INFO: ms1_error      : 3
5:16:42.301440 INFO: ms2_error      : 10
5:16:42.301521 INFO: fwhm_rt        : 5
5:16:42.301599 INFO: quant_window   : 3
5:16:42.301644 INFO: ==============================================
5:16:42.681733 INFO: performing precursor FDR with 40 features
5:16:42.682196 INFO: Decoy channel: -1
5:16:42.682232 INFO: competitive: True
5:16:42.761610 INFO: Setting torch num_threads to 2 for FDR classification task
5:16:42.809542 INFO: Estimating optimal hyperparameters - samples: 22,998, batch_size: 128, learning_rate: 1.77e-04
5:16:42.810421 INFO: Using random state 917075 for train-test-split
5:16:46.578661 INFO: Test AUC: 0.562
5:16:46.579170 INFO: Train AUC: 0.585
5:16:46.579218 INFO: AUC difference: 3.95%
5:16:47.064162 INFO: Resetting torch num_threads to 100
5:16:47.141063 PROGRESS: === Extracted 28748 precursors and 99746 fragments ===
5:16:47.143117 INFO: === FDR correction performed with classifier version -1 ===
5:16:47.144372 PROGRESS: ============================= Precursor FDR =============================
5:16:47.144540 PROGRESS: Total precursors accumulated: 127
5:16:47.144616 PROGRESS: Target precursors: 126 (99.21%)
5:16:47.144672 PROGRESS: Decoy precursors: 1 (0.79%)
5:16:47.144723 PROGRESS: 
5:16:47.144773 PROGRESS: Precursor Summary:
5:16:47.146284 PROGRESS: Channel   0:	 0.050 FDR:   126; 0.010 FDR:   126; 0.001 FDR:   105
5:16:47.146409 PROGRESS: 
5:16:47.146467 PROGRESS: Protein Summary:
5:16:47.147957 PROGRESS: Channel   0:	 0.050 FDR:   123; 0.010 FDR:   123; 0.001 FDR:   102
5:16:47.148068 PROGRESS: =========================================================================
5:16:47.154628 INFO: Target number of precursors not reached yet.
5:16:47.464205 INFO: Starting optimization step 4.
5:16:47.466112 PROGRESS: === Extracting elution groups 15000 to 31000 ===
5:16:47.466350 INFO: Using rust extraction backend
5:16:47.466508 PROGRESS: Extracting batch of 31575 precursors
5:16:47.598282 INFO: === Search parameters used ===
5:16:47.600278 INFO: rt_error       : 805.5982666015625
5:16:47.600359 INFO: mobility_error : 0.1
5:16:47.600423 INFO: num_candidates : 1
5:16:47.600473 INFO: ms1_error      : 3
5:16:47.600525 INFO: ms2_error      : 10
5:16:47.600584 INFO: fwhm_rt        : 5
5:16:47.600656 INFO: quant_window   : 3
5:16:47.600708 INFO: ==============================================
5:16:48.147496 INFO: performing precursor FDR with 40 features
5:16:48.147922 INFO: Decoy channel: -1
5:16:48.147952 INFO: competitive: True
5:16:48.305451 INFO: Setting torch num_threads to 2 for FDR classification task
5:16:48.395543 INFO: Estimating optimal hyperparameters - samples: 47,584, batch_size: 194, learning_rate: 2.18e-04
5:16:48.396720 INFO: Using random state 947580 for train-test-split
5:16:51.920700 INFO: Test AUC: 0.553
5:16:51.921231 INFO: Train AUC: 0.589
5:16:51.921295 INFO: AUC difference: 6.12%
5:16:51.921327 WARNING: AUC difference > 5%. This may indicate overfitting.
5:16:52.491008 INFO: Resetting torch num_threads to 100
5:16:52.571940 PROGRESS: === Extracted 59481 precursors and 207370 fragments ===
5:16:52.574245 INFO: === FDR correction performed with classifier version -1 ===
5:16:52.576946 PROGRESS: ============================= Precursor FDR =============================
5:16:52.577417 PROGRESS: Total precursors accumulated: 216
5:16:52.577595 PROGRESS: Target precursors: 214 (99.07%)
5:16:52.577679 PROGRESS: Decoy precursors: 2 (0.93%)
5:16:52.577734 PROGRESS: 
5:16:52.577786 PROGRESS: Precursor Summary:
5:16:52.580937 PROGRESS: Channel   0:	 0.050 FDR:   214; 0.010 FDR:   214; 0.001 FDR:     0
5:16:52.581408 PROGRESS: 
5:16:52.581518 PROGRESS: Protein Summary:
5:16:52.584809 PROGRESS: Channel   0:	 0.050 FDR:   206; 0.010 FDR:   206; 0.001 FDR:     0
5:16:52.585116 PROGRESS: =========================================================================
5:16:52.592882 INFO: Target number of precursors not reached yet.
5:16:52.925659 INFO: Starting optimization step 5.
5:16:52.926199 PROGRESS: === Extracting elution groups 31000 to 63000 ===
5:16:52.926312 INFO: Using rust extraction backend
5:16:52.926388 PROGRESS: Extracting batch of 63070 precursors
5:16:53.015098 INFO: === Search parameters used ===
5:16:53.015969 INFO: rt_error       : 805.5982666015625
5:16:53.016083 INFO: mobility_error : 0.1
5:16:53.016141 INFO: num_candidates : 1
5:16:53.016189 INFO: ms1_error      : 3
5:16:53.016232 INFO: ms2_error      : 10
5:16:53.016292 INFO: fwhm_rt        : 5
5:16:53.016337 INFO: quant_window   : 3
5:16:53.016386 INFO: ==============================================
5:16:53.573331 INFO: performing precursor FDR with 40 features
5:16:53.573496 INFO: Decoy channel: -1
5:16:53.573522 INFO: competitive: True
5:16:53.672174 INFO: Setting torch num_threads to 2 for FDR classification task
5:16:53.918357 INFO: Estimating optimal hyperparameters - samples: 96,644, batch_size: 395, learning_rate: 3.11e-04
5:16:53.919843 INFO: Using random state 332315 for train-test-split
5:16:58.706571 INFO: Test AUC: 0.557
5:16:58.707187 INFO: Train AUC: 0.587
5:16:58.707259 INFO: AUC difference: 4.99%
5:16:59.182567 INFO: Resetting torch num_threads to 100
5:16:59.316953 PROGRESS: === Extracted 120805 precursors and 419695 fragments ===
5:16:59.319307 INFO: === FDR correction performed with classifier version -1 ===
5:16:59.321162 PROGRESS: ============================= Precursor FDR =============================
5:16:59.321397 PROGRESS: Total precursors accumulated: 617
5:16:59.321472 PROGRESS: Target precursors: 611 (99.03%)
5:16:59.321528 PROGRESS: Decoy precursors: 6 (0.97%)
5:16:59.321579 PROGRESS: 
5:16:59.321633 PROGRESS: Precursor Summary:
5:16:59.323852 PROGRESS: Channel   0:	 0.050 FDR:   611; 0.010 FDR:   611; 0.001 FDR:   104
5:16:59.323995 PROGRESS: 
5:16:59.324061 PROGRESS: Protein Summary:
5:16:59.325768 PROGRESS: Channel   0:	 0.050 FDR:   567; 0.010 FDR:   567; 0.001 FDR:   102
5:16:59.325907 PROGRESS: =========================================================================
5:16:59.340325 INFO: Target number of precursors not reached yet.
5:16:59.935378 INFO: Starting optimization step 6.
5:16:59.936220 PROGRESS: === Extracting elution groups 63000 to 127000 ===
5:16:59.936464 INFO: Using rust extraction backend
5:16:59.936609 PROGRESS: Extracting batch of 126133 precursors
5:17:00.369028 INFO: === Search parameters used ===
5:17:00.370257 INFO: rt_error       : 805.5982666015625
5:17:00.370409 INFO: mobility_error : 0.1
5:17:00.370497 INFO: num_candidates : 1
5:17:00.370551 INFO: ms1_error      : 3
5:17:00.370596 INFO: ms2_error      : 10
5:17:00.370645 INFO: fwhm_rt        : 5
5:17:00.370687 INFO: quant_window   : 3
5:17:00.370728 INFO: ==============================================
5:17:02.011725 INFO: performing precursor FDR with 40 features
5:17:02.012072 INFO: Decoy channel: -1
5:17:02.012101 INFO: competitive: True
5:17:02.353971 INFO: Setting torch num_threads to 2 for FDR classification task
5:17:02.835350 INFO: Estimating optimal hyperparameters - samples: 194,756, batch_size: 797, learning_rate: 4.41e-04
5:17:02.837674 INFO: Using random state 592011 for train-test-split
5:17:16.850204 INFO: Test AUC: 0.565
5:17:16.850572 INFO: Train AUC: 0.586
5:17:16.850613 INFO: AUC difference: 3.48%
5:17:17.369762 INFO: Resetting torch num_threads to 100
5:17:17.551990 PROGRESS: === Extracted 243446 precursors and 846362 fragments ===
5:17:17.553929 INFO: === FDR correction performed with classifier version -1 ===
5:17:17.556329 PROGRESS: ============================= Precursor FDR =============================
5:17:17.556554 PROGRESS: Total precursors accumulated: 1,319
5:17:17.556626 PROGRESS: Target precursors: 1,306 (99.01%)
5:17:17.556680 PROGRESS: Decoy precursors: 13 (0.99%)
5:17:17.556731 PROGRESS: 
5:17:17.556779 PROGRESS: Precursor Summary:
5:17:17.559450 PROGRESS: Channel   0:	 0.050 FDR: 1,306; 0.010 FDR: 1,306; 0.001 FDR:   799
5:17:17.559658 PROGRESS: 
5:17:17.559717 PROGRESS: Protein Summary:
5:17:17.562099 PROGRESS: Channel   0:	 0.050 FDR: 1,137; 0.010 FDR: 1,137; 0.001 FDR:   724
5:17:17.562288 PROGRESS: =========================================================================
5:17:17.578580 INFO: Target number of precursors reached.
5:17:17.712386 INFO: fragments_df: keeping 5000 of 846362 [sum(precursor_idx_mask)=12535 sum(mass_error_mask)=846362 stop_rank=5000
5:17:18.822839 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:17:19.228204 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:17:20.091683 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
5:17:20.092803 INFO: Using score_cutoff 11.308513054847717 (fac=0.99, q=1)
5:17:20.093382 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
5:17:20.093470 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
5:17:20.093529 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.308513054847717
5:17:20.093603 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:17:20.264326 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:17:20.517348 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
5:17:20.517834 PROGRESS: Required number of precursors found. Starting search parameter optimization.
5:17:20.517991 INFO: Starting optimization step 7.
5:17:20.518075 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:17:20.518177 INFO: Using rust extraction backend
5:17:20.518259 PROGRESS: Extracting batch of 250329 precursors
5:17:21.428566 INFO: === Search parameters used ===
5:17:21.429640 INFO: rt_error       : 805.5982666015625
5:17:21.429791 INFO: mobility_error : 0.1
5:17:21.429872 INFO: num_candidates : 3
5:17:21.429931 INFO: ms1_error      : 3
5:17:21.429988 INFO: ms2_error      : 10
5:17:21.430029 INFO: fwhm_rt        : 3.0
5:17:21.430069 INFO: quant_window   : 3
5:17:21.430110 INFO: ==============================================
5:17:25.419075 INFO: performing precursor FDR with 40 features
5:17:25.420659 INFO: Decoy channel: -1
5:17:25.420721 INFO: competitive: True
5:17:25.887207 INFO: Setting torch num_threads to 2 for FDR classification task
5:17:26.564598 INFO: Estimating optimal hyperparameters - samples: 579,942, batch_size: 2,375, learning_rate: 7.61e-04
5:17:26.567470 INFO: Using random state 542176 for train-test-split
5:17:58.485149 INFO: Test AUC: 0.566
5:17:58.485702 INFO: Train AUC: 0.579
5:17:58.485768 INFO: AUC difference: 2.20%
5:17:59.298864 INFO: Resetting torch num_threads to 100
5:17:59.406976 PROGRESS: === Extracted 724928 precursors and 2414835 fragments ===
5:17:59.408495 INFO: === FDR correction performed with classifier version 6 ===
5:17:59.411279 PROGRESS: ============================= Precursor FDR =============================
5:17:59.411621 PROGRESS: Total precursors accumulated: 1,416
5:17:59.411726 PROGRESS: Target precursors: 1,402 (99.01%)
5:17:59.411783 PROGRESS: Decoy precursors: 14 (0.99%)
5:17:59.411831 PROGRESS: 
5:17:59.411878 PROGRESS: Precursor Summary:
5:17:59.414977 PROGRESS: Channel   0:	 0.050 FDR: 1,402; 0.010 FDR: 1,402; 0.001 FDR:   864
5:17:59.415281 PROGRESS: 
5:17:59.415344 PROGRESS: Protein Summary:
5:17:59.418212 PROGRESS: Channel   0:	 0.050 FDR: 1,223; 0.010 FDR: 1,223; 0.001 FDR:   783
5:17:59.418446 PROGRESS: =========================================================================
5:17:59.493370 INFO: Target number of precursors reached.
5:17:59.800892 INFO: fragments_df: keeping 5000 of 2414835 [sum(precursor_idx_mask)=30879 sum(mass_error_mask)=2414835 stop_rank=5000
5:18:01.014655 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:18:01.491057 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:18:02.574967 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:18:02.576611 INFO: Using score_cutoff 11.628992198467255 (fac=0.99, q=1)
5:18:02.577329 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:18:02.577433 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:18:02.577494 INFO: Updating optimization_manager: score_cutoff        : 11.308513054847717 -> 11.628992198467255
5:18:02.577578 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:18:02.808904 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:18:03.249593 INFO: === checking if optimization conditions were reached ===
5:18:03.258971 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
5:18:03.259799 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
5:18:03.259933 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
5:18:03.260072 INFO: ==============================================
5:18:03.260236 INFO: Starting optimization step 8.
5:18:03.260362 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:18:03.260572 INFO: Using rust extraction backend
5:18:03.260752 PROGRESS: Extracting batch of 250329 precursors
5:18:04.181990 INFO: === Search parameters used ===
5:18:04.182878 INFO: rt_error       : 805.5982666015625
5:18:04.182946 INFO: mobility_error : 0.1
5:18:04.183002 INFO: num_candidates : 3
5:18:04.183050 INFO: ms1_error      : 3
5:18:04.183121 INFO: ms2_error      : 10.0
5:18:04.183237 INFO: fwhm_rt        : 3.0
5:18:04.183281 INFO: quant_window   : 3
5:18:04.183323 INFO: ==============================================
5:18:11.462493 INFO: performing precursor FDR with 40 features
5:18:11.462932 INFO: Decoy channel: -1
5:18:11.462965 INFO: competitive: True
5:18:12.214256 INFO: Setting torch num_threads to 2 for FDR classification task
5:18:13.346373 INFO: Estimating optimal hyperparameters - samples: 579,908, batch_size: 2,375, learning_rate: 7.61e-04
5:18:13.351393 INFO: Using random state 754049 for train-test-split
5:18:53.230948 INFO: Test AUC: 0.571
5:18:53.231427 INFO: Train AUC: 0.588
5:18:53.231477 INFO: AUC difference: 2.96%
5:18:53.956707 INFO: Resetting torch num_threads to 100
5:18:54.040737 PROGRESS: === Extracted 724885 precursors and 2414771 fragments ===
5:18:54.042150 INFO: === FDR correction performed with classifier version 7 ===
5:18:54.044177 PROGRESS: ============================= Precursor FDR =============================
5:18:54.044380 PROGRESS: Total precursors accumulated: 1,552
5:18:54.044542 PROGRESS: Target precursors: 1,537 (99.03%)
5:18:54.044615 PROGRESS: Decoy precursors: 15 (0.97%)
5:18:54.044682 PROGRESS: 
5:18:54.044737 PROGRESS: Precursor Summary:
5:18:54.047109 PROGRESS: Channel   0:	 0.050 FDR: 1,537; 0.010 FDR: 1,537; 0.001 FDR: 1,166
5:18:54.047329 PROGRESS: 
5:18:54.047402 PROGRESS: Protein Summary:
5:18:54.049749 PROGRESS: Channel   0:	 0.050 FDR: 1,329; 0.010 FDR: 1,329; 0.001 FDR: 1,016
5:18:54.049897 PROGRESS: =========================================================================
5:18:54.124692 INFO: Target number of precursors reached.
5:18:54.420487 INFO: fragments_df: keeping 5000 of 2414771 [sum(precursor_idx_mask)=33568 sum(mass_error_mask)=2414771 stop_rank=5000
5:18:55.462691 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:18:55.980456 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:18:56.891056 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:18:56.892318 INFO: Using score_cutoff 11.701516720962523 (fac=0.99, q=1)
5:18:56.892985 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:18:56.893078 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:18:56.893134 INFO: Updating optimization_manager: score_cutoff        : 11.628992198467255 -> 11.701516720962523
5:18:56.893203 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:18:57.084179 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:18:57.594568 INFO: === checking if optimization conditions were reached ===
5:18:57.601181 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
5:18:57.601708 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
5:18:57.601810 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
5:18:57.601898 INFO: ==============================================
5:18:57.602028 INFO: Starting optimization step 9.
5:18:57.602134 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:18:57.602296 INFO: Using rust extraction backend
5:18:57.602448 PROGRESS: Extracting batch of 250329 precursors
5:18:58.435848 INFO: === Search parameters used ===
5:18:58.436976 INFO: rt_error       : 805.5982666015625
5:18:58.437053 INFO: mobility_error : 0.1
5:18:58.437108 INFO: num_candidates : 3
5:18:58.437169 INFO: ms1_error      : 3
5:18:58.437215 INFO: ms2_error      : 10.0
5:18:58.437257 INFO: fwhm_rt        : 3.0
5:18:58.437297 INFO: quant_window   : 3
5:18:58.437338 INFO: ==============================================
5:19:03.588930 INFO: performing precursor FDR with 40 features
5:19:03.589326 INFO: Decoy channel: -1
5:19:03.589362 INFO: competitive: True
5:19:04.288850 INFO: Setting torch num_threads to 2 for FDR classification task
5:19:05.507581 INFO: Estimating optimal hyperparameters - samples: 579,943, batch_size: 2,375, learning_rate: 7.61e-04
5:19:05.516139 INFO: Using random state 121359 for train-test-split
5:19:37.748472 INFO: Test AUC: 0.580
5:19:37.749302 INFO: Train AUC: 0.592
5:19:37.749400 INFO: AUC difference: 2.08%
5:19:38.545204 INFO: Resetting torch num_threads to 100
5:19:38.662542 PROGRESS: === Extracted 724929 precursors and 2414650 fragments ===
5:19:38.665159 INFO: === FDR correction performed with classifier version 8 ===
5:19:38.668020 PROGRESS: ============================= Precursor FDR =============================
5:19:38.668222 PROGRESS: Total precursors accumulated: 1,719
5:19:38.668293 PROGRESS: Target precursors: 1,702 (99.01%)
5:19:38.668346 PROGRESS: Decoy precursors: 17 (0.99%)
5:19:38.668404 PROGRESS: 
5:19:38.668458 PROGRESS: Precursor Summary:
5:19:38.671211 PROGRESS: Channel   0:	 0.050 FDR: 1,702; 0.010 FDR: 1,702; 0.001 FDR: 1,094
5:19:38.671398 PROGRESS: 
5:19:38.671457 PROGRESS: Protein Summary:
5:19:38.674056 PROGRESS: Channel   0:	 0.050 FDR: 1,455; 0.010 FDR: 1,455; 0.001 FDR:   970
5:19:38.674237 PROGRESS: =========================================================================
5:19:38.736596 INFO: Target number of precursors reached.
5:19:39.049727 INFO: fragments_df: keeping 5000 of 2414650 [sum(precursor_idx_mask)=36226 sum(mass_error_mask)=2414650 stop_rank=5000
5:19:40.289623 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:19:41.085253 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:19:42.125634 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:19:42.127754 INFO: Using score_cutoff 11.010213100147247 (fac=0.99, q=1)
5:19:42.128479 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:19:42.128584 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:19:42.128664 INFO: Updating optimization_manager: score_cutoff        : 11.701516720962523 -> 11.010213100147247
5:19:42.128734 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:19:42.363784 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:19:42.834960 INFO: === checking if optimization conditions were reached ===
5:19:42.847320 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
5:19:42.848164 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
5:19:42.848302 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
5:19:42.848438 INFO: ==============================================
5:19:42.848598 INFO: Starting optimization step 10.
5:19:42.848800 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:19:42.848994 INFO: Using rust extraction backend
5:19:42.849174 PROGRESS: Extracting batch of 250329 precursors
5:19:43.666041 INFO: === Search parameters used ===
5:19:43.667158 INFO: rt_error       : 805.5982666015625
5:19:43.667296 INFO: mobility_error : 0.1
5:19:43.667354 INFO: num_candidates : 3
5:19:43.667409 INFO: ms1_error      : 3
5:19:43.667463 INFO: ms2_error      : 10.0
5:19:43.667508 INFO: fwhm_rt        : 3.0
5:19:43.667550 INFO: quant_window   : 3
5:19:43.667593 INFO: ==============================================
5:19:50.655322 INFO: performing precursor FDR with 40 features
5:19:50.655728 INFO: Decoy channel: -1
5:19:50.655780 INFO: competitive: True
5:19:51.470464 INFO: Setting torch num_threads to 2 for FDR classification task
5:19:52.654486 INFO: Estimating optimal hyperparameters - samples: 579,950, batch_size: 2,375, learning_rate: 7.61e-04
5:19:52.661323 INFO: Using random state 925095 for train-test-split
5:20:26.127601 INFO: Test AUC: 0.580
5:20:26.128130 INFO: Train AUC: 0.596
5:20:26.128182 INFO: AUC difference: 2.67%
5:20:27.071679 INFO: Resetting torch num_threads to 100
5:20:27.185234 PROGRESS: === Extracted 724938 precursors and 2414804 fragments ===
5:20:27.187416 INFO: === FDR correction performed with classifier version 9 ===
5:20:27.191311 PROGRESS: ============================= Precursor FDR =============================
5:20:27.191630 PROGRESS: Total precursors accumulated: 1,826
5:20:27.191707 PROGRESS: Target precursors: 1,808 (99.01%)
5:20:27.191764 PROGRESS: Decoy precursors: 18 (0.99%)
5:20:27.191817 PROGRESS: 
5:20:27.191887 PROGRESS: Precursor Summary:
5:20:27.195848 PROGRESS: Channel   0:	 0.050 FDR: 1,808; 0.010 FDR: 1,808; 0.001 FDR: 1,134
5:20:27.196238 PROGRESS: 
5:20:27.196342 PROGRESS: Protein Summary:
5:20:27.200192 PROGRESS: Channel   0:	 0.050 FDR: 1,552; 0.010 FDR: 1,552; 0.001 FDR: 1,003
5:20:27.200563 PROGRESS: =========================================================================
5:20:27.301776 INFO: Target number of precursors reached.
5:20:27.605644 INFO: fragments_df: keeping 5000 of 2414804 [sum(precursor_idx_mask)=37621 sum(mass_error_mask)=2414804 stop_rank=5000
5:20:28.980477 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:20:29.534540 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:20:30.537693 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:20:30.538977 INFO: Using score_cutoff 8.239630260086061 (fac=0.99, q=1)
5:20:30.539612 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:20:30.539720 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:20:30.539780 INFO: Updating optimization_manager: score_cutoff        : 11.010213100147247 -> 8.239630260086061
5:20:30.539865 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:20:30.736601 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:20:31.068153 INFO: === checking if optimization conditions were reached ===
5:20:31.073279 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
5:20:31.073640 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
5:20:31.073781 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
5:20:31.073883 INFO: ==============================================
5:20:31.074019 INFO: Starting optimization step 11.
5:20:31.074131 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:20:31.074258 INFO: Using rust extraction backend
5:20:31.074370 PROGRESS: Extracting batch of 250329 precursors
5:20:31.919394 INFO: === Search parameters used ===
5:20:31.920290 INFO: rt_error       : 805.5982666015625
5:20:31.920355 INFO: mobility_error : 0.1
5:20:31.920412 INFO: num_candidates : 3
5:20:31.920461 INFO: ms1_error      : 3
5:20:31.920504 INFO: ms2_error      : 10.0
5:20:31.920545 INFO: fwhm_rt        : 3.0
5:20:31.920586 INFO: quant_window   : 3
5:20:31.920662 INFO: ==============================================
5:20:38.638825 INFO: performing precursor FDR with 40 features
5:20:38.639317 INFO: Decoy channel: -1
5:20:38.639354 INFO: competitive: True
5:20:39.401118 INFO: Setting torch num_threads to 2 for FDR classification task
5:20:40.504391 INFO: Estimating optimal hyperparameters - samples: 579,931, batch_size: 2,375, learning_rate: 7.61e-04
5:20:40.509774 INFO: Using random state 225040 for train-test-split
5:21:11.336143 INFO: Test AUC: 0.584
5:21:11.336762 INFO: Train AUC: 0.599
5:21:11.336830 INFO: AUC difference: 2.61%
5:21:12.115865 INFO: Resetting torch num_threads to 100
5:21:12.220626 PROGRESS: === Extracted 724914 precursors and 2414844 fragments ===
5:21:12.222313 INFO: === FDR correction performed with classifier version 10 ===
5:21:12.224956 PROGRESS: ============================= Precursor FDR =============================
5:21:12.225154 PROGRESS: Total precursors accumulated: 1,826
5:21:12.225227 PROGRESS: Target precursors: 1,808 (99.01%)
5:21:12.225281 PROGRESS: Decoy precursors: 18 (0.99%)
5:21:12.225332 PROGRESS: 
5:21:12.225379 PROGRESS: Precursor Summary:
5:21:12.227811 PROGRESS: Channel   0:	 0.050 FDR: 1,808; 0.010 FDR: 1,808; 0.001 FDR: 1,230
5:21:12.228006 PROGRESS: 
5:21:12.228070 PROGRESS: Protein Summary:
5:21:12.230792 PROGRESS: Channel   0:	 0.050 FDR: 1,557; 0.010 FDR: 1,557; 0.001 FDR: 1,084
5:21:12.230968 PROGRESS: =========================================================================
5:21:12.310365 INFO: Target number of precursors reached.
5:21:12.630263 INFO: fragments_df: keeping 5000 of 2414844 [sum(precursor_idx_mask)=38172 sum(mass_error_mask)=2414844 stop_rank=5000
5:21:13.814669 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:21:14.332120 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:21:15.313575 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:21:15.315389 INFO: Using score_cutoff 9.558376716041565 (fac=0.99, q=1)
5:21:15.316151 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:21:15.316238 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:21:15.316294 INFO: Updating optimization_manager: score_cutoff        : 8.239630260086061 -> 9.558376716041565
5:21:15.316369 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:21:15.553800 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:21:15.988775 INFO: === checking if optimization conditions were reached ===
5:21:15.996501 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
5:21:15.997067 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
5:21:15.997240 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
5:21:15.997358 INFO: ==============================================
5:21:15.997503 PROGRESS: Optimization finished for ms2_error.
5:21:17.106747 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:21:17.319061 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:21:17.697989 INFO: Starting optimization step 0.
5:21:17.698910 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:21:17.699098 INFO: Using rust extraction backend
5:21:17.699283 PROGRESS: Extracting batch of 250329 precursors
5:21:18.433567 INFO: === Search parameters used ===
5:21:18.434107 INFO: rt_error       : 805.5982666015625
5:21:18.434210 INFO: mobility_error : 0.1
5:21:18.434286 INFO: num_candidates : 3
5:21:18.434337 INFO: ms1_error      : 3
5:21:18.434384 INFO: ms2_error      : 10.0
5:21:18.434428 INFO: fwhm_rt        : 3.0
5:21:18.434471 INFO: quant_window   : 3
5:21:18.434513 INFO: ==============================================
5:21:20.955863 INFO: performing precursor FDR with 40 features
5:21:20.955987 INFO: Decoy channel: -1
5:21:20.956015 INFO: competitive: True
5:21:21.145419 INFO: Setting torch num_threads to 2 for FDR classification task
5:21:21.423283 INFO: Estimating optimal hyperparameters - samples: 579,904, batch_size: 2,375, learning_rate: 7.61e-04
5:21:21.424336 INFO: Using random state 392618 for train-test-split
5:21:33.958498 INFO: Test AUC: 0.585
5:21:33.958659 INFO: Train AUC: 0.601
5:21:33.958692 INFO: AUC difference: 2.73%
5:21:34.426412 INFO: Resetting torch num_threads to 100
5:21:34.453846 PROGRESS: === Extracted 724881 precursors and 2414431 fragments ===
5:21:34.454349 INFO: === FDR correction performed with classifier version 11 ===
5:21:34.455054 PROGRESS: ============================= Precursor FDR =============================
5:21:34.455160 PROGRESS: Total precursors accumulated: 1,651
5:21:34.455226 PROGRESS: Target precursors: 1,635 (99.03%)
5:21:34.455280 PROGRESS: Decoy precursors: 16 (0.97%)
5:21:34.455327 PROGRESS: 
5:21:34.455373 PROGRESS: Precursor Summary:
5:21:34.456758 PROGRESS: Channel   0:	 0.050 FDR: 1,635; 0.010 FDR: 1,635; 0.001 FDR: 1,066
5:21:34.456846 PROGRESS: 
5:21:34.456907 PROGRESS: Protein Summary:
5:21:34.458725 PROGRESS: Channel   0:	 0.050 FDR: 1,407; 0.010 FDR: 1,407; 0.001 FDR:   945
5:21:34.458817 PROGRESS: =========================================================================
5:21:34.472968 INFO: Target number of precursors reached.
5:21:34.739786 INFO: fragments_df: keeping 5000 of 2414431 [sum(precursor_idx_mask)=34578 sum(mass_error_mask)=2414431 stop_rank=5000
5:21:35.119659 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:21:35.386744 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:21:36.104607 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:21:36.105076 INFO: Using score_cutoff 10.029849015426636 (fac=0.99, q=1)
5:21:36.105399 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:21:36.105475 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:21:36.105529 INFO: Updating optimization_manager: score_cutoff        : 9.558376716041565 -> 10.029849015426636
5:21:36.105589 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:21:36.255346 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:21:36.442145 INFO: === checking if optimization conditions were reached ===
5:21:36.442429 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
5:21:36.445154 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 559.4290440949446
5:21:36.445258 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 559.4290.
5:21:36.445319 INFO: ==============================================
5:21:36.445388 INFO: Starting optimization step 1.
5:21:36.445445 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:21:36.445505 INFO: Using rust extraction backend
5:21:36.445559 PROGRESS: Extracting batch of 250329 precursors
5:21:36.698270 INFO: === Search parameters used ===
5:21:36.698557 INFO: rt_error       : 559.4290440949446
5:21:36.698616 INFO: mobility_error : 0.1
5:21:36.698663 INFO: num_candidates : 3
5:21:36.698705 INFO: ms1_error      : 3
5:21:36.698745 INFO: ms2_error      : 10.0
5:21:36.698784 INFO: fwhm_rt        : 3.0
5:21:36.698823 INFO: quant_window   : 3
5:21:36.698860 INFO: ==============================================
5:21:38.860326 INFO: performing precursor FDR with 40 features
5:21:38.860446 INFO: Decoy channel: -1
5:21:38.860473 INFO: competitive: True
5:21:39.043509 INFO: Setting torch num_threads to 2 for FDR classification task
5:21:39.319158 INFO: Estimating optimal hyperparameters - samples: 578,719, batch_size: 2,370, learning_rate: 7.61e-04
5:21:39.320149 INFO: Using random state 392618 for train-test-split
5:21:51.866343 INFO: Test AUC: 0.583
5:21:51.866478 INFO: Train AUC: 0.601
5:21:51.866512 INFO: AUC difference: 3.00%
5:21:52.339783 INFO: Resetting torch num_threads to 100
5:21:52.366631 PROGRESS: === Extracted 723399 precursors and 2393197 fragments ===
5:21:52.367108 INFO: === FDR correction performed with classifier version 11 ===
5:21:52.367933 PROGRESS: ============================= Precursor FDR =============================
5:21:52.368025 PROGRESS: Total precursors accumulated: 1,744
5:21:52.368086 PROGRESS: Target precursors: 1,727 (99.03%)
5:21:52.368137 PROGRESS: Decoy precursors: 17 (0.97%)
5:21:52.368183 PROGRESS: 
5:21:52.368229 PROGRESS: Precursor Summary:
5:21:52.369627 PROGRESS: Channel   0:	 0.050 FDR: 1,727; 0.010 FDR: 1,727; 0.001 FDR: 1,364
5:21:52.369716 PROGRESS: 
5:21:52.369775 PROGRESS: Protein Summary:
5:21:52.371683 PROGRESS: Channel   0:	 0.050 FDR: 1,487; 0.010 FDR: 1,487; 0.001 FDR: 1,190
5:21:52.371781 PROGRESS: =========================================================================
5:21:52.385936 INFO: Target number of precursors reached.
5:21:52.654670 INFO: fragments_df: keeping 5000 of 2393197 [sum(precursor_idx_mask)=36851 sum(mass_error_mask)=2393197 stop_rank=5000
5:21:53.040963 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:21:53.302275 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:21:53.999280 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:21:53.999739 INFO: Using score_cutoff 10.191845159912111 (fac=0.99, q=1)
5:21:54.000044 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:21:54.000123 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:21:54.000179 INFO: Updating optimization_manager: score_cutoff        : 10.029849015426636 -> 10.191845159912111
5:21:54.000233 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:21:54.148399 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:21:54.337777 INFO: === checking if optimization conditions were reached ===
5:21:54.338043 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
5:21:54.340944 INFO: Updating optimization_manager: rt_error            : 559.4290440949446 -> 644.8111296479983
5:21:54.341048 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 644.8111.
5:21:54.341129 INFO: ==============================================
5:21:54.341200 INFO: Starting optimization step 2.
5:21:54.341259 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:21:54.341321 INFO: Using rust extraction backend
5:21:54.341385 PROGRESS: Extracting batch of 250329 precursors
5:21:54.592046 INFO: === Search parameters used ===
5:21:54.592319 INFO: rt_error       : 644.8111296479983
5:21:54.592375 INFO: mobility_error : 0.1
5:21:54.592422 INFO: num_candidates : 3
5:21:54.592467 INFO: ms1_error      : 3
5:21:54.592508 INFO: ms2_error      : 10.0
5:21:54.592548 INFO: fwhm_rt        : 3.0
5:21:54.592590 INFO: quant_window   : 3
5:21:54.592629 INFO: ==============================================
5:21:56.738424 INFO: performing precursor FDR with 40 features
5:21:56.738543 INFO: Decoy channel: -1
5:21:56.738568 INFO: competitive: True
5:21:56.922154 INFO: Setting torch num_threads to 2 for FDR classification task
5:21:57.201356 INFO: Estimating optimal hyperparameters - samples: 579,366, batch_size: 2,373, learning_rate: 7.61e-04
5:21:57.202609 INFO: Using random state 392618 for train-test-split
5:22:09.576511 INFO: Test AUC: 0.583
5:22:09.576635 INFO: Train AUC: 0.600
5:22:09.576669 INFO: AUC difference: 2.72%
5:22:10.045848 INFO: Resetting torch num_threads to 100
5:22:10.072533 PROGRESS: === Extracted 724208 precursors and 2405756 fragments ===
5:22:10.073011 INFO: === FDR correction performed with classifier version 11 ===
5:22:10.073715 PROGRESS: ============================= Precursor FDR =============================
5:22:10.073806 PROGRESS: Total precursors accumulated: 1,822
5:22:10.073866 PROGRESS: Target precursors: 1,804 (99.01%)
5:22:10.073918 PROGRESS: Decoy precursors: 18 (0.99%)
5:22:10.073967 PROGRESS: 
5:22:10.074014 PROGRESS: Precursor Summary:
5:22:10.075474 PROGRESS: Channel   0:	 0.050 FDR: 1,804; 0.010 FDR: 1,804; 0.001 FDR: 1,108
5:22:10.075566 PROGRESS: 
5:22:10.075625 PROGRESS: Protein Summary:
5:22:10.077501 PROGRESS: Channel   0:	 0.050 FDR: 1,561; 0.010 FDR: 1,561; 0.001 FDR:   980
5:22:10.077614 PROGRESS: =========================================================================
5:22:10.091842 INFO: Target number of precursors reached.
5:22:10.354316 INFO: fragments_df: keeping 5000 of 2405756 [sum(precursor_idx_mask)=37246 sum(mass_error_mask)=2405756 stop_rank=5000
5:22:10.716881 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:22:10.991839 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:22:11.709659 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:22:11.710115 INFO: Using score_cutoff 8.249957557868958 (fac=0.99, q=1)
5:22:11.710433 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:22:11.710511 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:22:11.710566 INFO: Updating optimization_manager: score_cutoff        : 10.191845159912111 -> 8.249957557868958
5:22:11.710623 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:22:11.860044 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:22:12.068090 INFO: === checking if optimization conditions were reached ===
5:22:12.068398 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
5:22:12.071978 INFO: Updating optimization_manager: rt_error            : 644.8111296479983 -> 685.1137809520167
5:22:12.072104 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 685.1138.
5:22:12.072181 INFO: ==============================================
5:22:12.072268 INFO: Starting optimization step 3.
5:22:12.072339 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:22:12.072427 INFO: Using rust extraction backend
5:22:12.072498 PROGRESS: Extracting batch of 250329 precursors
5:22:12.325162 INFO: === Search parameters used ===
5:22:12.325435 INFO: rt_error       : 685.1137809520167
5:22:12.325492 INFO: mobility_error : 0.1
5:22:12.325557 INFO: num_candidates : 3
5:22:12.325602 INFO: ms1_error      : 3
5:22:12.325644 INFO: ms2_error      : 10.0
5:22:12.325688 INFO: fwhm_rt        : 3.0
5:22:12.325730 INFO: quant_window   : 3
5:22:12.325770 INFO: ==============================================
5:22:14.472660 INFO: performing precursor FDR with 40 features
5:22:14.472785 INFO: Decoy channel: -1
5:22:14.472811 INFO: competitive: True
5:22:14.640540 INFO: Setting torch num_threads to 2 for FDR classification task
5:22:14.919525 INFO: Estimating optimal hyperparameters - samples: 579,539, batch_size: 2,373, learning_rate: 7.61e-04
5:22:14.920388 INFO: Using random state 392618 for train-test-split
5:22:27.473281 INFO: Test AUC: 0.587
5:22:27.473462 INFO: Train AUC: 0.601
5:22:27.473496 INFO: AUC difference: 2.25%
5:22:27.947399 INFO: Resetting torch num_threads to 100
5:22:27.974220 PROGRESS: === Extracted 724424 precursors and 2409631 fragments ===
5:22:27.974708 INFO: === FDR correction performed with classifier version 11 ===
5:22:27.975447 PROGRESS: ============================= Precursor FDR =============================
5:22:27.975539 PROGRESS: Total precursors accumulated: 1,856
5:22:27.975600 PROGRESS: Target precursors: 1,838 (99.03%)
5:22:27.975652 PROGRESS: Decoy precursors: 18 (0.97%)
5:22:27.975710 PROGRESS: 
5:22:27.975757 PROGRESS: Precursor Summary:
5:22:27.977188 PROGRESS: Channel   0:	 0.050 FDR: 1,838; 0.010 FDR: 1,838; 0.001 FDR: 1,132
5:22:27.977274 PROGRESS: 
5:22:27.977334 PROGRESS: Protein Summary:
5:22:27.979233 PROGRESS: Channel   0:	 0.050 FDR: 1,571; 0.010 FDR: 1,571; 0.001 FDR:   999
5:22:27.979328 PROGRESS: =========================================================================
5:22:27.993176 INFO: Target number of precursors reached.
5:22:28.261144 INFO: fragments_df: keeping 5000 of 2409631 [sum(precursor_idx_mask)=38733 sum(mass_error_mask)=2409631 stop_rank=5000
5:22:28.623448 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:22:28.859388 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:22:29.508029 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:22:29.508495 INFO: Using score_cutoff 10.548073109722138 (fac=0.99, q=1)
5:22:29.508817 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:22:29.508897 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:22:29.508954 INFO: Updating optimization_manager: score_cutoff        : 8.249957557868958 -> 10.548073109722138
5:22:29.509007 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:22:29.653788 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:22:29.856655 INFO: === checking if optimization conditions were reached ===
5:22:29.856960 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
5:22:29.860503 INFO: Updating optimization_manager: rt_error            : 685.1137809520167 -> 364.9762464959661
5:22:29.860632 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 364.9762.
5:22:29.860711 INFO: ==============================================
5:22:29.860810 INFO: Starting optimization step 4.
5:22:29.860886 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:22:29.860960 INFO: Using rust extraction backend
5:22:29.861028 PROGRESS: Extracting batch of 250329 precursors
5:22:30.114709 INFO: === Search parameters used ===
5:22:30.114987 INFO: rt_error       : 364.9762464959661
5:22:30.115044 INFO: mobility_error : 0.1
5:22:30.115093 INFO: num_candidates : 3
5:22:30.115137 INFO: ms1_error      : 3
5:22:30.115197 INFO: ms2_error      : 10.0
5:22:30.115240 INFO: fwhm_rt        : 3.0
5:22:30.115282 INFO: quant_window   : 3
5:22:30.115321 INFO: ==============================================
5:22:32.162709 INFO: performing precursor FDR with 40 features
5:22:32.162836 INFO: Decoy channel: -1
5:22:32.162864 INFO: competitive: True
5:22:32.348007 INFO: Setting torch num_threads to 2 for FDR classification task
5:22:32.629902 INFO: Estimating optimal hyperparameters - samples: 572,237, batch_size: 2,343, learning_rate: 7.56e-04
5:22:32.630867 INFO: Using random state 392618 for train-test-split
5:22:45.973844 INFO: Test AUC: 0.583
5:22:45.974013 INFO: Train AUC: 0.596
5:22:45.974050 INFO: AUC difference: 2.24%
5:22:46.581381 INFO: Resetting torch num_threads to 100
5:22:46.623103 PROGRESS: === Extracted 715297 precursors and 2277318 fragments ===
5:22:46.623693 INFO: === FDR correction performed with classifier version 11 ===
5:22:46.624673 PROGRESS: ============================= Precursor FDR =============================
5:22:46.624771 PROGRESS: Total precursors accumulated: 1,750
5:22:46.624837 PROGRESS: Target precursors: 1,733 (99.03%)
5:22:46.624895 PROGRESS: Decoy precursors: 17 (0.97%)
5:22:46.624948 PROGRESS: 
5:22:46.625014 PROGRESS: Precursor Summary:
5:22:46.626831 PROGRESS: Channel   0:	 0.050 FDR: 1,733; 0.010 FDR: 1,733; 0.001 FDR: 1,252
5:22:46.626930 PROGRESS: 
5:22:46.626990 PROGRESS: Protein Summary:
5:22:46.629311 PROGRESS: Channel   0:	 0.050 FDR: 1,483; 0.010 FDR: 1,483; 0.001 FDR: 1,090
5:22:46.629413 PROGRESS: =========================================================================
5:22:46.649908 INFO: Target number of precursors reached.
5:22:47.012997 INFO: fragments_df: keeping 5000 of 2277318 [sum(precursor_idx_mask)=37179 sum(mass_error_mask)=2277318 stop_rank=5000
5:22:47.503720 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:22:47.963523 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:22:48.948585 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:22:48.949137 INFO: Using score_cutoff 11.068678564453126 (fac=0.99, q=1)
5:22:48.949492 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:22:48.949572 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:22:48.949631 INFO: Updating optimization_manager: score_cutoff        : 10.548073109722138 -> 11.068678564453126
5:22:48.949693 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:22:49.106422 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:22:49.318251 INFO: === checking if optimization conditions were reached ===
5:22:49.318539 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
5:22:49.322118 INFO: Updating optimization_manager: rt_error            : 364.9762464959661 -> 316.90051899135847
5:22:49.322252 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 316.9005.
5:22:49.322325 INFO: ==============================================
5:22:49.322408 INFO: Starting optimization step 5.
5:22:49.322477 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:22:49.322551 INFO: Using rust extraction backend
5:22:49.322623 PROGRESS: Extracting batch of 250329 precursors
5:22:49.582362 INFO: === Search parameters used ===
5:22:49.582674 INFO: rt_error       : 316.90051899135847
5:22:49.582734 INFO: mobility_error : 0.1
5:22:49.582788 INFO: num_candidates : 3
5:22:49.582839 INFO: ms1_error      : 3
5:22:49.582888 INFO: ms2_error      : 10.0
5:22:49.582937 INFO: fwhm_rt        : 3.0
5:22:49.582984 INFO: quant_window   : 3
5:22:49.583032 INFO: ==============================================
5:22:52.388067 INFO: performing precursor FDR with 40 features
5:22:52.388203 INFO: Decoy channel: -1
5:22:52.388233 INFO: competitive: True
5:22:52.602828 INFO: Setting torch num_threads to 2 for FDR classification task
5:22:52.967372 INFO: Estimating optimal hyperparameters - samples: 569,275, batch_size: 2,331, learning_rate: 7.54e-04
5:22:52.968525 INFO: Using random state 392618 for train-test-split
5:23:05.674909 INFO: Test AUC: 0.576
5:23:05.675041 INFO: Train AUC: 0.597
5:23:05.675073 INFO: AUC difference: 3.40%
5:23:06.143999 INFO: Resetting torch num_threads to 100
5:23:06.173360 PROGRESS: === Extracted 711594 precursors and 2227100 fragments ===
5:23:06.173845 INFO: === FDR correction performed with classifier version 11 ===
5:23:06.174717 PROGRESS: ============================= Precursor FDR =============================
5:23:06.174820 PROGRESS: Total precursors accumulated: 2,080
5:23:06.174881 PROGRESS: Target precursors: 2,060 (99.04%)
5:23:06.174932 PROGRESS: Decoy precursors: 20 (0.96%)
5:23:06.174984 PROGRESS: 
5:23:06.175028 PROGRESS: Precursor Summary:
5:23:06.176562 PROGRESS: Channel   0:	 0.050 FDR: 2,060; 0.010 FDR: 2,060; 0.001 FDR: 1,485
5:23:06.176655 PROGRESS: 
5:23:06.176715 PROGRESS: Protein Summary:
5:23:06.178756 PROGRESS: Channel   0:	 0.050 FDR: 1,764; 0.010 FDR: 1,764; 0.001 FDR: 1,276
5:23:06.178850 PROGRESS: =========================================================================
5:23:06.193877 INFO: Target number of precursors reached.
5:23:06.441491 INFO: fragments_df: keeping 5000 of 2227100 [sum(precursor_idx_mask)=41616 sum(mass_error_mask)=2227100 stop_rank=5000
5:23:06.701784 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:23:06.999043 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:23:07.716075 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:23:07.716633 INFO: Using score_cutoff 8.01050886569023 (fac=0.99, q=1)
5:23:07.716978 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:23:07.717053 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:23:07.717105 INFO: Updating optimization_manager: score_cutoff        : 11.068678564453126 -> 8.01050886569023
5:23:07.717162 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:23:07.792055 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:23:07.890703 INFO: === checking if optimization conditions were reached ===
5:23:07.891007 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
5:23:07.894848 INFO: Updating optimization_manager: rt_error            : 316.90051899135847 -> 410.2374380221088
5:23:07.894977 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 410.2374.
5:23:07.895056 INFO: ==============================================
5:23:07.895137 INFO: Starting optimization step 6.
5:23:07.895230 PROGRESS: === Extracting elution groups 0 to 63000 ===
5:23:07.895310 INFO: Using rust extraction backend
5:23:07.895386 PROGRESS: Extracting batch of 124196 precursors
5:23:08.026473 INFO: === Search parameters used ===
5:23:08.026762 INFO: rt_error       : 410.2374380221088
5:23:08.026824 INFO: mobility_error : 0.1
5:23:08.026875 INFO: num_candidates : 3
5:23:08.026921 INFO: ms1_error      : 3
5:23:08.026964 INFO: ms2_error      : 10.0
5:23:08.027012 INFO: fwhm_rt        : 3.0
5:23:08.027058 INFO: quant_window   : 3
5:23:08.027101 INFO: ==============================================
5:23:09.135444 INFO: performing precursor FDR with 40 features
5:23:09.135561 INFO: Decoy channel: -1
5:23:09.135587 INFO: competitive: True
5:23:09.223404 INFO: Setting torch num_threads to 2 for FDR classification task
5:23:09.341472 INFO: Estimating optimal hyperparameters - samples: 285,150, batch_size: 1,167, learning_rate: 5.34e-04
5:23:09.342017 INFO: Using random state 392618 for train-test-split
5:23:17.135580 INFO: Test AUC: 0.575
5:23:17.135750 INFO: Train AUC: 0.606
5:23:17.135781 INFO: AUC difference: 5.02%
5:23:17.135804 WARNING: AUC difference > 5%. This may indicate overfitting.
5:23:17.492175 INFO: Resetting torch num_threads to 100
5:23:17.505452 PROGRESS: === Extracted 356438 precursors and 1150364 fragments ===
5:23:17.505906 INFO: === FDR correction performed with classifier version 11 ===
5:23:17.506508 PROGRESS: ============================= Precursor FDR =============================
5:23:17.506595 PROGRESS: Total precursors accumulated: 967
5:23:17.506660 PROGRESS: Target precursors: 958 (99.07%)
5:23:17.506720 PROGRESS: Decoy precursors: 9 (0.93%)
5:23:17.506767 PROGRESS: 
5:23:17.506810 PROGRESS: Precursor Summary:
5:23:17.508033 PROGRESS: Channel   0:	 0.050 FDR:   958; 0.010 FDR:   958; 0.001 FDR:   598
5:23:17.508126 PROGRESS: 
5:23:17.508184 PROGRESS: Protein Summary:
5:23:17.509679 PROGRESS: Channel   0:	 0.050 FDR:   884; 0.010 FDR:   884; 0.001 FDR:   561
5:23:17.509778 PROGRESS: =========================================================================
5:23:17.515587 INFO: Target number of precursors not reached yet.
5:23:17.757167 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:23:17.832347 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:23:17.935808 INFO: === skipping optimization until target number of precursors are found ===
5:23:17.936123 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
5:23:17.936233 INFO: Starting optimization step 7.
5:23:17.936312 PROGRESS: === Extracting elution groups 63000 to 127000 ===
5:23:17.936395 INFO: Using rust extraction backend
5:23:17.936471 PROGRESS: Extracting batch of 126133 precursors
5:23:18.069595 INFO: === Search parameters used ===
5:23:18.069883 INFO: rt_error       : 410.2374380221088
5:23:18.069940 INFO: mobility_error : 0.1
5:23:18.069999 INFO: num_candidates : 3
5:23:18.070046 INFO: ms1_error      : 3
5:23:18.070088 INFO: ms2_error      : 10.0
5:23:18.070127 INFO: fwhm_rt        : 3.0
5:23:18.070167 INFO: quant_window   : 3
5:23:18.070204 INFO: ==============================================
5:23:19.286898 INFO: performing precursor FDR with 40 features
5:23:19.287024 INFO: Decoy channel: -1
5:23:19.287051 INFO: competitive: True
5:23:19.554447 INFO: Setting torch num_threads to 2 for FDR classification task
5:23:19.834124 INFO: Estimating optimal hyperparameters - samples: 574,664, batch_size: 2,353, learning_rate: 7.58e-04
5:23:19.835057 INFO: Using random state 392618 for train-test-split
5:23:32.340291 INFO: Test AUC: 0.578
5:23:32.340421 INFO: Train AUC: 0.598
5:23:32.340454 INFO: AUC difference: 3.28%
5:23:32.813729 INFO: Resetting torch num_threads to 100
5:23:32.906333 PROGRESS: === Extracted 718331 precursors and 2319823 fragments ===
5:23:32.907080 INFO: === FDR correction performed with classifier version 11 ===
5:23:32.908188 PROGRESS: ============================= Precursor FDR =============================
5:23:32.908282 PROGRESS: Total precursors accumulated: 1,848
5:23:32.908342 PROGRESS: Target precursors: 1,830 (99.03%)
5:23:32.908392 PROGRESS: Decoy precursors: 18 (0.97%)
5:23:32.908437 PROGRESS: 
5:23:32.908482 PROGRESS: Precursor Summary:
5:23:32.909976 PROGRESS: Channel   0:	 0.050 FDR: 1,830; 0.010 FDR: 1,830; 0.001 FDR: 1,270
5:23:32.910066 PROGRESS: 
5:23:32.910121 PROGRESS: Protein Summary:
5:23:32.912068 PROGRESS: Channel   0:	 0.050 FDR: 1,563; 0.010 FDR: 1,563; 0.001 FDR: 1,110
5:23:32.912162 PROGRESS: =========================================================================
5:23:32.925719 INFO: Target number of precursors reached.
5:23:33.198518 INFO: fragments_df: keeping 5000 of 2319823 [sum(precursor_idx_mask)=38819 sum(mass_error_mask)=2319823 stop_rank=5000
5:23:33.584095 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:23:33.820877 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:23:34.469006 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:23:34.469489 INFO: Using score_cutoff 11.209074587917328 (fac=0.99, q=1)
5:23:34.469810 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:23:34.469897 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:23:34.469952 INFO: Updating optimization_manager: score_cutoff        : 8.01050886569023 -> 11.209074587917328
5:23:34.470009 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:23:34.617100 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:23:34.811662 INFO: === checking if optimization conditions were reached ===
5:23:34.811981 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
5:23:34.815557 INFO: Updating optimization_manager: rt_error            : 410.2374380221088 -> 330.60843709360904
5:23:34.815682 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 330.6084.
5:23:34.815763 INFO: ==============================================
5:23:34.815865 INFO: Starting optimization step 8.
5:23:34.815937 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:23:34.816016 INFO: Using rust extraction backend
5:23:34.816091 PROGRESS: Extracting batch of 250329 precursors
5:23:35.072537 INFO: === Search parameters used ===
5:23:35.072859 INFO: rt_error       : 330.60843709360904
5:23:35.072931 INFO: mobility_error : 0.1
5:23:35.072980 INFO: num_candidates : 3
5:23:35.073024 INFO: ms1_error      : 3
5:23:35.073072 INFO: ms2_error      : 10.0
5:23:35.073114 INFO: fwhm_rt        : 3.0
5:23:35.073155 INFO: quant_window   : 3
5:23:35.073195 INFO: ==============================================
5:23:37.123517 INFO: performing precursor FDR with 40 features
5:23:37.123636 INFO: Decoy channel: -1
5:23:37.123663 INFO: competitive: True
5:23:37.299787 INFO: Setting torch num_threads to 2 for FDR classification task
5:23:37.568713 INFO: Estimating optimal hyperparameters - samples: 570,218, batch_size: 2,335, learning_rate: 7.55e-04
5:23:37.569787 INFO: Using random state 392618 for train-test-split
5:23:50.066570 INFO: Test AUC: 0.580
5:23:50.066707 INFO: Train AUC: 0.596
5:23:50.066741 INFO: AUC difference: 2.66%
5:23:50.542967 INFO: Resetting torch num_threads to 100
5:23:50.569184 PROGRESS: === Extracted 712773 precursors and 2242639 fragments ===
5:23:50.569678 INFO: === FDR correction performed with classifier version 11 ===
5:23:50.570391 PROGRESS: ============================= Precursor FDR =============================
5:23:50.570483 PROGRESS: Total precursors accumulated: 1,847
5:23:50.570544 PROGRESS: Target precursors: 1,829 (99.03%)
5:23:50.570596 PROGRESS: Decoy precursors: 18 (0.97%)
5:23:50.570642 PROGRESS: 
5:23:50.570688 PROGRESS: Precursor Summary:
5:23:50.572098 PROGRESS: Channel   0:	 0.050 FDR: 1,829; 0.010 FDR: 1,829; 0.001 FDR:   678
5:23:50.572192 PROGRESS: 
5:23:50.572250 PROGRESS: Protein Summary:
5:23:50.574083 PROGRESS: Channel   0:	 0.050 FDR: 1,567; 0.010 FDR: 1,567; 0.001 FDR:   623
5:23:50.574179 PROGRESS: =========================================================================
5:23:50.587860 INFO: Target number of precursors reached.
5:23:50.831805 INFO: fragments_df: keeping 5000 of 2242639 [sum(precursor_idx_mask)=38233 sum(mass_error_mask)=2242639 stop_rank=5000
5:23:51.214333 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:23:51.463035 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:23:52.110458 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:23:52.110911 INFO: Using score_cutoff 10.213850023269654 (fac=0.99, q=1)
5:23:52.111301 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:23:52.111386 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:23:52.111441 INFO: Updating optimization_manager: score_cutoff        : 11.209074587917328 -> 10.213850023269654
5:23:52.111494 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:23:52.257557 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:23:52.441158 INFO: === checking if optimization conditions were reached ===
5:23:52.441434 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
5:23:52.444453 INFO: Updating optimization_manager: rt_error            : 330.60843709360904 -> 439.9206778091889
5:23:52.444555 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 439.9207.
5:23:52.444620 INFO: ==============================================
5:23:52.444690 INFO: Starting optimization step 9.
5:23:52.444749 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:23:52.444810 INFO: Using rust extraction backend
5:23:52.444867 PROGRESS: Extracting batch of 250329 precursors
5:23:52.695951 INFO: === Search parameters used ===
5:23:52.696219 INFO: rt_error       : 439.9206778091889
5:23:52.696276 INFO: mobility_error : 0.1
5:23:52.696324 INFO: num_candidates : 3
5:23:52.696370 INFO: ms1_error      : 3
5:23:52.696414 INFO: ms2_error      : 10.0
5:23:52.696469 INFO: fwhm_rt        : 3.0
5:23:52.696511 INFO: quant_window   : 3
5:23:52.696550 INFO: ==============================================
5:23:54.775332 INFO: performing precursor FDR with 40 features
5:23:54.775448 INFO: Decoy channel: -1
5:23:54.775474 INFO: competitive: True
5:23:54.957105 INFO: Setting torch num_threads to 2 for FDR classification task
5:23:55.241672 INFO: Estimating optimal hyperparameters - samples: 575,627, batch_size: 2,357, learning_rate: 7.59e-04
5:23:55.242558 INFO: Using random state 392618 for train-test-split
5:24:07.632355 INFO: Test AUC: 0.579
5:24:07.632509 INFO: Train AUC: 0.598
5:24:07.632543 INFO: AUC difference: 3.07%
5:24:08.104360 INFO: Resetting torch num_threads to 100
5:24:08.131287 PROGRESS: === Extracted 719534 precursors and 2336494 fragments ===
5:24:08.131776 INFO: === FDR correction performed with classifier version 11 ===
5:24:08.132534 PROGRESS: ============================= Precursor FDR =============================
5:24:08.132626 PROGRESS: Total precursors accumulated: 1,935
5:24:08.132687 PROGRESS: Target precursors: 1,916 (99.02%)
5:24:08.132740 PROGRESS: Decoy precursors: 19 (0.98%)
5:24:08.132789 PROGRESS: 
5:24:08.132835 PROGRESS: Precursor Summary:
5:24:08.134288 PROGRESS: Channel   0:	 0.050 FDR: 1,916; 0.010 FDR: 1,916; 0.001 FDR: 1,040
5:24:08.134379 PROGRESS: 
5:24:08.134439 PROGRESS: Protein Summary:
5:24:08.136397 PROGRESS: Channel   0:	 0.050 FDR: 1,639; 0.010 FDR: 1,639; 0.001 FDR:   921
5:24:08.136504 PROGRESS: =========================================================================
5:24:08.151422 INFO: Target number of precursors reached.
5:24:08.410143 INFO: fragments_df: keeping 5000 of 2336494 [sum(precursor_idx_mask)=39829 sum(mass_error_mask)=2336494 stop_rank=5000
5:24:08.790902 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:24:09.039046 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:24:09.693574 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:24:09.694076 INFO: Using score_cutoff 9.420012401103973 (fac=0.99, q=1)
5:24:09.694398 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:24:09.694477 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:24:09.694531 INFO: Updating optimization_manager: score_cutoff        : 10.213850023269654 -> 9.420012401103973
5:24:09.694588 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:24:09.844557 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:24:10.028736 INFO: === checking if optimization conditions were reached ===
5:24:10.029017 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
5:24:10.032124 INFO: Updating optimization_manager: rt_error            : 439.9206778091889 -> 465.5365732159779
5:24:10.032229 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 465.5366.
5:24:10.032294 INFO: ==============================================
5:24:10.032363 INFO: Starting optimization step 10.
5:24:10.032422 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:24:10.032500 INFO: Using rust extraction backend
5:24:10.032559 PROGRESS: Extracting batch of 250329 precursors
5:24:10.287591 INFO: === Search parameters used ===
5:24:10.287899 INFO: rt_error       : 465.5365732159779
5:24:10.287958 INFO: mobility_error : 0.1
5:24:10.288007 INFO: num_candidates : 3
5:24:10.288055 INFO: ms1_error      : 3
5:24:10.288099 INFO: ms2_error      : 10.0
5:24:10.288142 INFO: fwhm_rt        : 3.0
5:24:10.288184 INFO: quant_window   : 3
5:24:10.288228 INFO: ==============================================
5:24:12.488783 INFO: performing precursor FDR with 40 features
5:24:12.488907 INFO: Decoy channel: -1
5:24:12.488933 INFO: competitive: True
5:24:12.676068 INFO: Setting torch num_threads to 2 for FDR classification task
5:24:12.964936 INFO: Estimating optimal hyperparameters - samples: 576,524, batch_size: 2,361, learning_rate: 7.59e-04
5:24:12.966019 INFO: Using random state 392618 for train-test-split
5:24:25.474681 INFO: Test AUC: 0.582
5:24:25.474863 INFO: Train AUC: 0.599
5:24:25.474901 INFO: AUC difference: 2.86%
5:24:25.947188 INFO: Resetting torch num_threads to 100
5:24:25.973992 PROGRESS: === Extracted 720656 precursors and 2352410 fragments ===
5:24:25.974517 INFO: === FDR correction performed with classifier version 11 ===
5:24:25.975440 PROGRESS: ============================= Precursor FDR =============================
5:24:25.975542 PROGRESS: Total precursors accumulated: 1,791
5:24:25.975605 PROGRESS: Target precursors: 1,774 (99.05%)
5:24:25.975657 PROGRESS: Decoy precursors: 17 (0.95%)
5:24:25.975707 PROGRESS: 
5:24:25.975751 PROGRESS: Precursor Summary:
5:24:25.977205 PROGRESS: Channel   0:	 0.050 FDR: 1,774; 0.010 FDR: 1,774; 0.001 FDR: 1,173
5:24:25.977296 PROGRESS: 
5:24:25.977353 PROGRESS: Protein Summary:
5:24:25.979292 PROGRESS: Channel   0:	 0.050 FDR: 1,524; 0.010 FDR: 1,524; 0.001 FDR: 1,027
5:24:25.979385 PROGRESS: =========================================================================
5:24:25.994443 INFO: Target number of precursors reached.
5:24:26.258626 INFO: fragments_df: keeping 5000 of 2352410 [sum(precursor_idx_mask)=37684 sum(mass_error_mask)=2352410 stop_rank=5000
5:24:26.680053 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:24:26.946449 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:24:27.658578 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:24:27.659046 INFO: Using score_cutoff 10.9732544383049 (fac=0.99, q=1)
5:24:27.659379 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:24:27.659465 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:24:27.659521 INFO: Updating optimization_manager: score_cutoff        : 9.420012401103973 -> 10.9732544383049
5:24:27.659577 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:24:27.806465 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:24:27.991667 INFO: === checking if optimization conditions were reached ===
5:24:27.991953 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
5:24:27.995123 INFO: Updating optimization_manager: rt_error            : 465.5365732159779 -> 388.2866025845508
5:24:27.995262 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 388.2866.
5:24:27.995329 INFO: ==============================================
5:24:27.995426 INFO: Starting optimization step 11.
5:24:27.995489 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:24:27.995557 INFO: Using rust extraction backend
5:24:27.995617 PROGRESS: Extracting batch of 250329 precursors
5:24:28.246881 INFO: === Search parameters used ===
5:24:28.247168 INFO: rt_error       : 388.2866025845508
5:24:28.247231 INFO: mobility_error : 0.1
5:24:28.247282 INFO: num_candidates : 3
5:24:28.247328 INFO: ms1_error      : 3
5:24:28.247371 INFO: ms2_error      : 10.0
5:24:28.247412 INFO: fwhm_rt        : 3.0
5:24:28.247453 INFO: quant_window   : 3
5:24:28.247494 INFO: ==============================================
5:24:30.331794 INFO: performing precursor FDR with 40 features
5:24:30.331928 INFO: Decoy channel: -1
5:24:30.331954 INFO: competitive: True
5:24:30.520901 INFO: Setting torch num_threads to 2 for FDR classification task
5:24:30.793968 INFO: Estimating optimal hyperparameters - samples: 573,713, batch_size: 2,349, learning_rate: 7.57e-04
5:24:30.795016 INFO: Using random state 392618 for train-test-split
5:24:43.217755 INFO: Test AUC: 0.581
5:24:43.217882 INFO: Train AUC: 0.597
5:24:43.217914 INFO: AUC difference: 2.68%
5:24:43.688658 INFO: Resetting torch num_threads to 100
5:24:43.716451 PROGRESS: === Extracted 717142 precursors and 2302219 fragments ===
5:24:43.716930 INFO: === FDR correction performed with classifier version 11 ===
5:24:43.717656 PROGRESS: ============================= Precursor FDR =============================
5:24:43.717746 PROGRESS: Total precursors accumulated: 1,860
5:24:43.717809 PROGRESS: Target precursors: 1,842 (99.03%)
5:24:43.717874 PROGRESS: Decoy precursors: 18 (0.97%)
5:24:43.717920 PROGRESS: 
5:24:43.717969 PROGRESS: Precursor Summary:
5:24:43.719435 PROGRESS: Channel   0:	 0.050 FDR: 1,842; 0.010 FDR: 1,842; 0.001 FDR: 1,180
5:24:43.719534 PROGRESS: 
5:24:43.719591 PROGRESS: Protein Summary:
5:24:43.721507 PROGRESS: Channel   0:	 0.050 FDR: 1,565; 0.010 FDR: 1,565; 0.001 FDR: 1,032
5:24:43.721603 PROGRESS: =========================================================================
5:24:43.734927 INFO: Target number of precursors reached.
5:24:43.979201 INFO: fragments_df: keeping 5000 of 2302219 [sum(precursor_idx_mask)=39164 sum(mass_error_mask)=2302219 stop_rank=5000
5:24:44.364068 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:24:44.638095 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:24:45.351019 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:24:45.351491 INFO: Using score_cutoff 11.001645674800873 (fac=0.99, q=1)
5:24:45.351803 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:24:45.351878 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:24:45.351933 INFO: Updating optimization_manager: score_cutoff        : 10.9732544383049 -> 11.001645674800873
5:24:45.351987 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:24:45.497822 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:24:45.694477 INFO: === checking if optimization conditions were reached ===
5:24:45.694807 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
5:24:45.698375 INFO: Updating optimization_manager: rt_error            : 388.2866025845508 -> 357.70960601084477
5:24:45.698502 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 357.7096.
5:24:45.698593 INFO: ==============================================
5:24:45.698677 INFO: Starting optimization step 12.
5:24:45.698746 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:24:45.698821 INFO: Using rust extraction backend
5:24:45.698889 PROGRESS: Extracting batch of 250329 precursors
5:24:45.961770 INFO: === Search parameters used ===
5:24:45.962048 INFO: rt_error       : 357.70960601084477
5:24:45.962124 INFO: mobility_error : 0.1
5:24:45.962171 INFO: num_candidates : 3
5:24:45.962212 INFO: ms1_error      : 3
5:24:45.962253 INFO: ms2_error      : 10.0
5:24:45.962292 INFO: fwhm_rt        : 3.0
5:24:45.962330 INFO: quant_window   : 3
5:24:45.962368 INFO: ==============================================
5:24:48.059490 INFO: performing precursor FDR with 40 features
5:24:48.059613 INFO: Decoy channel: -1
5:24:48.059640 INFO: competitive: True
5:24:48.256949 INFO: Setting torch num_threads to 2 for FDR classification task
5:24:48.559282 INFO: Estimating optimal hyperparameters - samples: 571,988, batch_size: 2,342, learning_rate: 7.56e-04
5:24:48.560300 INFO: Using random state 392618 for train-test-split
5:25:00.958706 INFO: Test AUC: 0.582
5:25:00.958862 INFO: Train AUC: 0.595
5:25:00.958896 INFO: AUC difference: 2.24%
5:25:01.425751 INFO: Resetting torch num_threads to 100
5:25:01.453238 PROGRESS: === Extracted 714986 precursors and 2272088 fragments ===
5:25:01.453735 INFO: === FDR correction performed with classifier version 11 ===
5:25:01.454575 PROGRESS: ============================= Precursor FDR =============================
5:25:01.454665 PROGRESS: Total precursors accumulated: 2,002
5:25:01.454726 PROGRESS: Target precursors: 1,983 (99.05%)
5:25:01.454783 PROGRESS: Decoy precursors: 19 (0.95%)
5:25:01.454832 PROGRESS: 
5:25:01.454890 PROGRESS: Precursor Summary:
5:25:01.456381 PROGRESS: Channel   0:	 0.050 FDR: 1,983; 0.010 FDR: 1,983; 0.001 FDR: 1,248
5:25:01.456473 PROGRESS: 
5:25:01.456529 PROGRESS: Protein Summary:
5:25:01.458469 PROGRESS: Channel   0:	 0.050 FDR: 1,694; 0.010 FDR: 1,694; 0.001 FDR: 1,092
5:25:01.458564 PROGRESS: =========================================================================
5:25:01.471947 INFO: Target number of precursors reached.
5:25:01.727642 INFO: fragments_df: keeping 5000 of 2272088 [sum(precursor_idx_mask)=41494 sum(mass_error_mask)=2272088 stop_rank=5000
5:25:02.111954 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:25:02.403111 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:25:03.118245 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:25:03.118715 INFO: Using score_cutoff 10.24179477710724 (fac=0.99, q=1)
5:25:03.119035 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:25:03.119113 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:25:03.119181 INFO: Updating optimization_manager: score_cutoff        : 11.001645674800873 -> 10.24179477710724
5:25:03.119239 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:25:03.265820 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:25:03.459410 INFO: === checking if optimization conditions were reached ===
5:25:03.459727 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 5 ===
5:25:03.463392 INFO: Updating optimization_manager: rt_error            : 357.70960601084477 -> 393.1807268277354
5:25:03.463526 PROGRESS: ❌ rt_error       : optimization incomplete after 12 search(es). Will search with parameter 393.1807.
5:25:03.463604 INFO: ==============================================
5:25:03.463688 INFO: Starting optimization step 13.
5:25:03.463768 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:25:03.463844 INFO: Using rust extraction backend
5:25:03.463915 PROGRESS: Extracting batch of 250329 precursors
5:25:03.727900 INFO: === Search parameters used ===
5:25:03.728178 INFO: rt_error       : 393.1807268277354
5:25:03.728236 INFO: mobility_error : 0.1
5:25:03.728283 INFO: num_candidates : 3
5:25:03.728325 INFO: ms1_error      : 3
5:25:03.728365 INFO: ms2_error      : 10.0
5:25:03.728405 INFO: fwhm_rt        : 3.0
5:25:03.728443 INFO: quant_window   : 3
5:25:03.728482 INFO: ==============================================
5:25:05.818867 INFO: performing precursor FDR with 40 features
5:25:05.818987 INFO: Decoy channel: -1
5:25:05.819013 INFO: competitive: True
5:25:06.004789 INFO: Setting torch num_threads to 2 for FDR classification task
5:25:06.288969 INFO: Estimating optimal hyperparameters - samples: 573,742, batch_size: 2,350, learning_rate: 7.57e-04
5:25:06.289962 INFO: Using random state 392618 for train-test-split
5:25:18.573684 INFO: Test AUC: 0.578
5:25:18.573830 INFO: Train AUC: 0.596
5:25:18.573864 INFO: AUC difference: 3.02%
5:25:19.043854 INFO: Resetting torch num_threads to 100
5:25:19.070137 PROGRESS: === Extracted 717178 precursors and 2303177 fragments ===
5:25:19.070628 INFO: === FDR correction performed with classifier version 11 ===
5:25:19.071353 PROGRESS: ============================= Precursor FDR =============================
5:25:19.071447 PROGRESS: Total precursors accumulated: 1,765
5:25:19.071509 PROGRESS: Target precursors: 1,748 (99.04%)
5:25:19.071573 PROGRESS: Decoy precursors: 17 (0.96%)
5:25:19.071621 PROGRESS: 
5:25:19.071668 PROGRESS: Precursor Summary:
5:25:19.073058 PROGRESS: Channel   0:	 0.050 FDR: 1,748; 0.010 FDR: 1,748; 0.001 FDR:   852
5:25:19.073145 PROGRESS: 
5:25:19.073203 PROGRESS: Protein Summary:
5:25:19.075003 PROGRESS: Channel   0:	 0.050 FDR: 1,493; 0.010 FDR: 1,493; 0.001 FDR:   765
5:25:19.075102 PROGRESS: =========================================================================
5:25:19.088075 INFO: Target number of precursors reached.
5:25:19.346401 INFO: fragments_df: keeping 5000 of 2303177 [sum(precursor_idx_mask)=37438 sum(mass_error_mask)=2303177 stop_rank=5000
5:25:19.724259 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:25:19.981052 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:25:20.696548 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:25:20.697011 INFO: Using score_cutoff 11.079065984916687 (fac=0.99, q=1)
5:25:20.697324 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:25:20.697409 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:25:20.697463 INFO: Updating optimization_manager: score_cutoff        : 10.24179477710724 -> 11.079065984916687
5:25:20.697516 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:25:20.844565 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:25:21.037421 INFO: === checking if optimization conditions were reached ===
5:25:21.037765 PROGRESS: === Optimization of rt_error has been performed 13 time(s); minimum number is 5 ===
5:25:21.041288 INFO: Updating optimization_manager: rt_error            : 393.1807268277354 -> 356.39887653044093
5:25:21.041408 PROGRESS: ❌ rt_error       : optimization incomplete after 13 search(es). Will search with parameter 356.3989.
5:25:21.041481 INFO: ==============================================
5:25:21.041561 INFO: Starting optimization step 14.
5:25:21.041627 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:25:21.041703 INFO: Using rust extraction backend
5:25:21.041772 PROGRESS: Extracting batch of 250329 precursors
5:25:21.294668 INFO: === Search parameters used ===
5:25:21.294938 INFO: rt_error       : 356.39887653044093
5:25:21.294993 INFO: mobility_error : 0.1
5:25:21.295038 INFO: num_candidates : 3
5:25:21.295082 INFO: ms1_error      : 3
5:25:21.295124 INFO: ms2_error      : 10.0
5:25:21.295178 INFO: fwhm_rt        : 3.0
5:25:21.295222 INFO: quant_window   : 3
5:25:21.295260 INFO: ==============================================
5:25:23.348318 INFO: performing precursor FDR with 40 features
5:25:23.348437 INFO: Decoy channel: -1
5:25:23.348461 INFO: competitive: True
5:25:23.538635 INFO: Setting torch num_threads to 2 for FDR classification task
5:25:23.831773 INFO: Estimating optimal hyperparameters - samples: 572,128, batch_size: 2,343, learning_rate: 7.56e-04
5:25:23.832835 INFO: Using random state 392618 for train-test-split
5:25:36.102727 INFO: Test AUC: 0.577
5:25:36.102864 INFO: Train AUC: 0.596
5:25:36.102899 INFO: AUC difference: 3.12%
5:25:36.574692 INFO: Resetting torch num_threads to 100
5:25:36.601627 PROGRESS: === Extracted 715160 precursors and 2274032 fragments ===
5:25:36.602104 INFO: === FDR correction performed with classifier version 11 ===
5:25:36.602824 PROGRESS: ============================= Precursor FDR =============================
5:25:36.602914 PROGRESS: Total precursors accumulated: 1,894
5:25:36.602988 PROGRESS: Target precursors: 1,876 (99.05%)
5:25:36.603042 PROGRESS: Decoy precursors: 18 (0.95%)
5:25:36.603091 PROGRESS: 
5:25:36.603136 PROGRESS: Precursor Summary:
5:25:36.604624 PROGRESS: Channel   0:	 0.050 FDR: 1,876; 0.010 FDR: 1,876; 0.001 FDR: 1,332
5:25:36.604713 PROGRESS: 
5:25:36.604772 PROGRESS: Protein Summary:
5:25:36.606724 PROGRESS: Channel   0:	 0.050 FDR: 1,600; 0.010 FDR: 1,600; 0.001 FDR: 1,160
5:25:36.606817 PROGRESS: =========================================================================
5:25:36.620235 INFO: Target number of precursors reached.
5:25:36.871407 INFO: fragments_df: keeping 5000 of 2274032 [sum(precursor_idx_mask)=38908 sum(mass_error_mask)=2274032 stop_rank=5000
5:25:37.235316 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:25:37.510890 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:25:38.240114 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:25:38.240576 INFO: Using score_cutoff 9.510417916774749 (fac=0.99, q=1)
5:25:38.240883 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:25:38.240960 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:25:38.241014 INFO: Updating optimization_manager: score_cutoff        : 11.079065984916687 -> 9.510417916774749
5:25:38.241067 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:25:38.388393 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:25:38.578808 INFO: === checking if optimization conditions were reached ===
5:25:38.579083 PROGRESS: === Optimization of rt_error has been performed 14 time(s); minimum number is 5 ===
5:25:38.582131 INFO: Updating optimization_manager: rt_error            : 356.39887653044093 -> 420.3032975511967
5:25:38.582235 PROGRESS: ❌ rt_error       : optimization incomplete after 14 search(es). Will search with parameter 420.3033.
5:25:38.582299 INFO: ==============================================
5:25:38.582366 INFO: Starting optimization step 15.
5:25:38.582422 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:25:38.582482 INFO: Using rust extraction backend
5:25:38.582538 PROGRESS: Extracting batch of 250329 precursors
5:25:38.832591 INFO: === Search parameters used ===
5:25:38.832862 INFO: rt_error       : 420.3032975511967
5:25:38.832917 INFO: mobility_error : 0.1
5:25:38.832964 INFO: num_candidates : 3
5:25:38.833005 INFO: ms1_error      : 3
5:25:38.833045 INFO: ms2_error      : 10.0
5:25:38.833085 INFO: fwhm_rt        : 3.0
5:25:38.833124 INFO: quant_window   : 3
5:25:38.833163 INFO: ==============================================
5:25:40.937274 INFO: performing precursor FDR with 40 features
5:25:40.937398 INFO: Decoy channel: -1
5:25:40.937424 INFO: competitive: True
5:25:41.114529 INFO: Setting torch num_threads to 2 for FDR classification task
5:25:41.392581 INFO: Estimating optimal hyperparameters - samples: 575,110, batch_size: 2,355, learning_rate: 7.58e-04
5:25:41.393648 INFO: Using random state 392618 for train-test-split
5:25:53.804751 INFO: Test AUC: 0.579
5:25:53.804878 INFO: Train AUC: 0.600
5:25:53.804911 INFO: AUC difference: 3.37%
5:25:54.274568 INFO: Resetting torch num_threads to 100
5:25:54.301768 PROGRESS: === Extracted 718888 precursors and 2326782 fragments ===
5:25:54.302244 INFO: === FDR correction performed with classifier version 11 ===
5:25:54.302952 PROGRESS: ============================= Precursor FDR =============================
5:25:54.303042 PROGRESS: Total precursors accumulated: 1,753
5:25:54.303102 PROGRESS: Target precursors: 1,736 (99.03%)
5:25:54.303167 PROGRESS: Decoy precursors: 17 (0.97%)
5:25:54.303217 PROGRESS: 
5:25:54.303261 PROGRESS: Precursor Summary:
5:25:54.304657 PROGRESS: Channel   0:	 0.050 FDR: 1,736; 0.010 FDR: 1,736; 0.001 FDR: 1,046
5:25:54.304743 PROGRESS: 
5:25:54.304797 PROGRESS: Protein Summary:
5:25:54.306636 PROGRESS: Channel   0:	 0.050 FDR: 1,494; 0.010 FDR: 1,494; 0.001 FDR:   928
5:25:54.306727 PROGRESS: =========================================================================
5:25:54.321010 INFO: Target number of precursors reached.
5:25:54.572430 INFO: fragments_df: keeping 5000 of 2326782 [sum(precursor_idx_mask)=36031 sum(mass_error_mask)=2326782 stop_rank=5000
5:25:54.938220 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:25:57.420050 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:25:58.078297 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:25:58.078757 INFO: Using score_cutoff 9.844039361000062 (fac=0.99, q=1)
5:25:58.079082 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:25:58.079171 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:25:58.079228 INFO: Updating optimization_manager: score_cutoff        : 9.510417916774749 -> 9.844039361000062
5:25:58.079289 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:25:58.226678 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:25:58.430386 INFO: === checking if optimization conditions were reached ===
5:25:58.430702 PROGRESS: === Optimization of rt_error has been performed 15 time(s); minimum number is 5 ===
5:25:58.434386 INFO: Updating optimization_manager: rt_error            : 420.3032975511967 -> 374.2898850267468
5:25:58.434517 PROGRESS: ❌ rt_error       : optimization incomplete after 15 search(es). Will search with parameter 374.2899.
5:25:58.434594 INFO: ==============================================
5:25:58.434681 INFO: Starting optimization step 16.
5:25:58.434756 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:25:58.434830 INFO: Using rust extraction backend
5:25:58.434899 PROGRESS: Extracting batch of 250329 precursors
5:25:58.689141 INFO: === Search parameters used ===
5:25:58.689434 INFO: rt_error       : 374.2898850267468
5:25:58.689493 INFO: mobility_error : 0.1
5:25:58.689538 INFO: num_candidates : 3
5:25:58.689580 INFO: ms1_error      : 3
5:25:58.689620 INFO: ms2_error      : 10.0
5:25:58.689657 INFO: fwhm_rt        : 3.0
5:25:58.689694 INFO: quant_window   : 3
5:25:58.689730 INFO: ==============================================
5:26:00.741478 INFO: performing precursor FDR with 40 features
5:26:00.741623 INFO: Decoy channel: -1
5:26:00.741650 INFO: competitive: True
5:26:00.927079 INFO: Setting torch num_threads to 2 for FDR classification task
5:26:01.213560 INFO: Estimating optimal hyperparameters - samples: 572,905, batch_size: 2,346, learning_rate: 7.57e-04
5:26:01.214624 INFO: Using random state 392618 for train-test-split
5:26:14.416359 INFO: Test AUC: 0.581
5:26:14.416507 INFO: Train AUC: 0.596
5:26:14.416540 INFO: AUC difference: 2.43%
5:26:14.898576 INFO: Resetting torch num_threads to 100
5:26:14.925019 PROGRESS: === Extracted 716132 precursors and 2288475 fragments ===
5:26:14.925532 INFO: === FDR correction performed with classifier version 11 ===
5:26:14.926409 PROGRESS: ============================= Precursor FDR =============================
5:26:14.926499 PROGRESS: Total precursors accumulated: 1,642
5:26:14.926560 PROGRESS: Target precursors: 1,626 (99.03%)
5:26:14.926610 PROGRESS: Decoy precursors: 16 (0.97%)
5:26:14.926657 PROGRESS: 
5:26:14.926702 PROGRESS: Precursor Summary:
5:26:14.928156 PROGRESS: Channel   0:	 0.050 FDR: 1,626; 0.010 FDR: 1,626; 0.001 FDR:   550
5:26:14.928254 PROGRESS: 
5:26:14.928311 PROGRESS: Protein Summary:
5:26:14.930112 PROGRESS: Channel   0:	 0.050 FDR: 1,399; 0.010 FDR: 1,399; 0.001 FDR:   510
5:26:14.930204 PROGRESS: =========================================================================
5:26:14.943703 INFO: Target number of precursors reached.
5:26:15.192824 INFO: fragments_df: keeping 5000 of 2288475 [sum(precursor_idx_mask)=34303 sum(mass_error_mask)=2288475 stop_rank=5000
5:26:15.601321 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:26:15.823263 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:26:16.478229 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:26:16.478682 INFO: Using score_cutoff 10.191679029464721 (fac=0.99, q=1)
5:26:16.479009 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:26:16.479086 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:26:16.479157 INFO: Updating optimization_manager: score_cutoff        : 9.844039361000062 -> 10.191679029464721
5:26:16.479222 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:26:16.626189 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:26:16.822489 INFO: === checking if optimization conditions were reached ===
5:26:16.822805 PROGRESS: === Optimization of rt_error has been performed 16 time(s); minimum number is 5 ===
5:26:16.826379 INFO: Updating optimization_manager: rt_error            : 374.2898850267468 -> 417.31771853934754
5:26:16.826502 PROGRESS: ❌ rt_error       : optimization incomplete after 16 search(es). Will search with parameter 417.3177.
5:26:16.826578 INFO: ==============================================
5:26:16.826661 INFO: Starting optimization step 17.
5:26:16.826729 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:26:16.826805 INFO: Using rust extraction backend
5:26:16.826873 PROGRESS: Extracting batch of 250329 precursors
5:26:17.082352 INFO: === Search parameters used ===
5:26:17.082630 INFO: rt_error       : 417.31771853934754
5:26:17.082690 INFO: mobility_error : 0.1
5:26:17.082740 INFO: num_candidates : 3
5:26:17.082787 INFO: ms1_error      : 3
5:26:17.082833 INFO: ms2_error      : 10.0
5:26:17.082878 INFO: fwhm_rt        : 3.0
5:26:17.082921 INFO: quant_window   : 3
5:26:17.082975 INFO: ==============================================
5:26:19.171473 INFO: performing precursor FDR with 40 features
5:26:19.171594 INFO: Decoy channel: -1
5:26:19.171635 INFO: competitive: True
5:26:19.353657 INFO: Setting torch num_threads to 2 for FDR classification task
5:26:19.631800 INFO: Estimating optimal hyperparameters - samples: 574,952, batch_size: 2,355, learning_rate: 7.58e-04
5:26:19.632850 INFO: Using random state 392618 for train-test-split
5:26:32.243579 INFO: Test AUC: 0.582
5:26:32.243707 INFO: Train AUC: 0.599
5:26:32.243742 INFO: AUC difference: 2.79%
5:26:32.718919 INFO: Resetting torch num_threads to 100
5:26:32.745387 PROGRESS: === Extracted 718690 precursors and 2324925 fragments ===
5:26:32.745870 INFO: === FDR correction performed with classifier version 11 ===
5:26:32.746751 PROGRESS: ============================= Precursor FDR =============================
5:26:32.746844 PROGRESS: Total precursors accumulated: 1,788
5:26:32.746907 PROGRESS: Target precursors: 1,771 (99.05%)
5:26:32.746960 PROGRESS: Decoy precursors: 17 (0.95%)
5:26:32.747007 PROGRESS: 
5:26:32.747053 PROGRESS: Precursor Summary:
5:26:32.748488 PROGRESS: Channel   0:	 0.050 FDR: 1,771; 0.010 FDR: 1,771; 0.001 FDR:   439
5:26:32.748583 PROGRESS: 
5:26:32.748644 PROGRESS: Protein Summary:
5:26:32.750479 PROGRESS: Channel   0:	 0.050 FDR: 1,511; 0.010 FDR: 1,511; 0.001 FDR:   414
5:26:32.750584 PROGRESS: =========================================================================
5:26:32.764436 INFO: Target number of precursors reached.
5:26:33.017612 INFO: fragments_df: keeping 5000 of 2324925 [sum(precursor_idx_mask)=37470 sum(mass_error_mask)=2324925 stop_rank=5000
5:26:33.417096 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:26:33.685964 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:26:34.406275 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:26:34.406744 INFO: Using score_cutoff 10.465539916992187 (fac=0.99, q=1)
5:26:34.407066 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:26:34.407155 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:26:34.407218 INFO: Updating optimization_manager: score_cutoff        : 10.191679029464721 -> 10.465539916992187
5:26:34.407272 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:26:34.553408 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:26:34.750185 INFO: === checking if optimization conditions were reached ===
5:26:34.750485 PROGRESS: === Optimization of rt_error has been performed 17 time(s); minimum number is 5 ===
5:26:34.754112 INFO: Updating optimization_manager: rt_error            : 417.31771853934754 -> 384.35576233755
5:26:34.754236 PROGRESS: ❌ rt_error       : optimization incomplete after 17 search(es). Will search with parameter 384.3558.
5:26:34.754311 INFO: ==============================================
5:26:34.754393 INFO: Starting optimization step 18.
5:26:34.754461 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:26:34.754534 INFO: Using rust extraction backend
5:26:34.754601 PROGRESS: Extracting batch of 250329 precursors
5:26:35.012993 INFO: === Search parameters used ===
5:26:35.013264 INFO: rt_error       : 384.35576233755
5:26:35.013318 INFO: mobility_error : 0.1
5:26:35.013365 INFO: num_candidates : 3
5:26:35.013408 INFO: ms1_error      : 3
5:26:35.013450 INFO: ms2_error      : 10.0
5:26:35.013505 INFO: fwhm_rt        : 3.0
5:26:35.013548 INFO: quant_window   : 3
5:26:35.013588 INFO: ==============================================
5:26:37.095653 INFO: performing precursor FDR with 40 features
5:26:37.095773 INFO: Decoy channel: -1
5:26:37.095799 INFO: competitive: True
5:26:37.271968 INFO: Setting torch num_threads to 2 for FDR classification task
5:26:37.541876 INFO: Estimating optimal hyperparameters - samples: 573,386, batch_size: 2,348, learning_rate: 7.57e-04
5:26:37.542940 INFO: Using random state 392618 for train-test-split
5:26:49.161722 INFO: Test AUC: 0.579
5:26:49.161870 INFO: Train AUC: 0.594
5:26:49.161904 INFO: AUC difference: 2.65%
5:26:49.637639 INFO: Resetting torch num_threads to 100
5:26:49.663467 PROGRESS: === Extracted 716733 precursors and 2297054 fragments ===
5:26:49.663971 INFO: === FDR correction performed with classifier version 11 ===
5:26:49.664702 PROGRESS: ============================= Precursor FDR =============================
5:26:49.664793 PROGRESS: Total precursors accumulated: 1,697
5:26:49.664853 PROGRESS: Target precursors: 1,681 (99.06%)
5:26:49.664904 PROGRESS: Decoy precursors: 16 (0.94%)
5:26:49.664959 PROGRESS: 
5:26:49.665007 PROGRESS: Precursor Summary:
5:26:49.666492 PROGRESS: Channel   0:	 0.050 FDR: 1,681; 0.010 FDR: 1,681; 0.001 FDR: 1,211
5:26:49.666594 PROGRESS: 
5:26:49.666650 PROGRESS: Protein Summary:
5:26:49.668627 PROGRESS: Channel   0:	 0.050 FDR: 1,444; 0.010 FDR: 1,444; 0.001 FDR: 1,062
5:26:49.668734 PROGRESS: =========================================================================
5:26:49.682250 INFO: Target number of precursors reached.
5:26:49.934042 INFO: fragments_df: keeping 5000 of 2297054 [sum(precursor_idx_mask)=35567 sum(mass_error_mask)=2297054 stop_rank=5000
5:26:50.297876 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:26:50.559091 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:26:51.281329 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:26:51.281799 INFO: Using score_cutoff 10.805339183807373 (fac=0.99, q=1)
5:26:51.282112 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:26:51.282188 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:26:51.282241 INFO: Updating optimization_manager: score_cutoff        : 10.465539916992187 -> 10.805339183807373
5:26:51.282292 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:26:51.430132 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:26:51.624833 INFO: === checking if optimization conditions were reached ===
5:26:51.625147 PROGRESS: === Optimization of rt_error has been performed 18 time(s); minimum number is 5 ===
5:26:51.628728 INFO: Updating optimization_manager: rt_error            : 384.35576233755 -> 294.1778480338211
5:26:51.628853 PROGRESS: ❌ rt_error       : optimization incomplete after 18 search(es). Will search with parameter 294.1778.
5:26:51.628931 INFO: ==============================================
5:26:51.629014 INFO: Starting optimization step 19.
5:26:51.629082 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:26:51.629154 INFO: Using rust extraction backend
5:26:51.629221 PROGRESS: Extracting batch of 250329 precursors
5:26:51.883488 INFO: === Search parameters used ===
5:26:51.883766 INFO: rt_error       : 294.1778480338211
5:26:51.883822 INFO: mobility_error : 0.1
5:26:51.883870 INFO: num_candidates : 3
5:26:51.883942 INFO: ms1_error      : 3
5:26:51.883987 INFO: ms2_error      : 10.0
5:26:51.884028 INFO: fwhm_rt        : 3.0
5:26:51.884067 INFO: quant_window   : 3
5:26:51.884104 INFO: ==============================================
5:26:53.917399 INFO: performing precursor FDR with 40 features
5:26:53.917527 INFO: Decoy channel: -1
5:26:53.917552 INFO: competitive: True
5:26:54.104441 INFO: Setting torch num_threads to 2 for FDR classification task
5:26:54.393014 INFO: Estimating optimal hyperparameters - samples: 567,530, batch_size: 2,324, learning_rate: 7.53e-04
5:26:54.394044 INFO: Using random state 392618 for train-test-split
5:27:06.024629 INFO: Test AUC: 0.579
5:27:06.024758 INFO: Train AUC: 0.595
5:27:06.024795 INFO: AUC difference: 2.77%
5:27:06.492783 INFO: Resetting torch num_threads to 100
5:27:06.519881 PROGRESS: === Extracted 709413 precursors and 2197889 fragments ===
5:27:06.520362 INFO: === FDR correction performed with classifier version 11 ===
5:27:06.521206 PROGRESS: ============================= Precursor FDR =============================
5:27:06.521295 PROGRESS: Total precursors accumulated: 1,900
5:27:06.521356 PROGRESS: Target precursors: 1,882 (99.05%)
5:27:06.521406 PROGRESS: Decoy precursors: 18 (0.95%)
5:27:06.521452 PROGRESS: 
5:27:06.521496 PROGRESS: Precursor Summary:
5:27:06.522989 PROGRESS: Channel   0:	 0.050 FDR: 1,882; 0.010 FDR: 1,882; 0.001 FDR: 1,156
5:27:06.523094 PROGRESS: 
5:27:06.523159 PROGRESS: Protein Summary:
5:27:06.525129 PROGRESS: Channel   0:	 0.050 FDR: 1,604; 0.010 FDR: 1,604; 0.001 FDR: 1,016
5:27:06.525226 PROGRESS: =========================================================================
5:27:06.539111 INFO: Target number of precursors reached.
5:27:06.788336 INFO: fragments_df: keeping 5000 of 2197889 [sum(precursor_idx_mask)=39423 sum(mass_error_mask)=2197889 stop_rank=5000
5:27:07.152408 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:27:07.437254 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:27:08.159889 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:27:08.160351 INFO: Using score_cutoff 10.551693981170654 (fac=0.99, q=1)
5:27:08.160662 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:27:08.160735 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:27:08.160786 INFO: Updating optimization_manager: score_cutoff        : 10.805339183807373 -> 10.551693981170654
5:27:08.160839 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:27:08.307034 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:27:08.511386 INFO: === checking if optimization conditions were reached ===
5:27:08.511680 PROGRESS: === Optimization of rt_error has been performed 19 time(s); minimum number is 5 ===
5:27:08.515351 INFO: Updating optimization_manager: rt_error            : 294.1778480338211 -> 266.6777422373423
5:27:08.515474 PROGRESS: ❌ rt_error       : optimization incomplete after 19 search(es). Will search with parameter 266.6777.
5:27:08.515549 INFO: ==============================================
5:27:08.515615 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
5:27:08.515678 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
5:27:08.515733 PROGRESS: ==============================================
5:27:08.515791 PROGRESS: ms2_error      : 10.0000
5:27:08.515849 PROGRESS: rt_error       : 266.6777
5:27:08.515901 PROGRESS: ==============================================
5:27:08.516726 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:27:15.964244 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:27:25.307174 INFO: Using rust extraction backend
5:27:25.307467 PROGRESS: Extracting batch of 11997144 precursors
5:27:35.523091 INFO: === Search parameters used ===
5:27:35.523402 INFO: rt_error       : 266.6777422373423
5:27:35.523467 INFO: mobility_error : 0.1
5:27:35.523519 INFO: num_candidates : 3
5:27:35.523565 INFO: ms1_error      : 3
5:27:35.523609 INFO: ms2_error      : 10.0
5:27:35.523653 INFO: fwhm_rt        : 3.0
5:27:35.523699 INFO: quant_window   : 3
5:27:35.523746 INFO: ==============================================
5:27:54.434604 INFO: Removed 19000235 precursors with score below cutoff 10.551693981170654
5:28:13.171030 INFO: performing precursor FDR with 40 features
5:28:13.171164 INFO: Decoy channel: -1
5:28:13.171192 INFO: competitive: True
5:28:14.929581 INFO: Setting torch num_threads to 2 for FDR classification task
5:28:21.721513 INFO: Estimating optimal hyperparameters - samples: 13,029,837, batch_size: 4,096, learning_rate: 1.00e-03
5:28:21.761621 INFO: Using random state 392618 for train-test-split
5:32:33.594883 INFO: Test AUC: 0.593
5:32:33.595163 INFO: Train AUC: 0.595
5:32:33.595206 INFO: AUC difference: 0.22%
5:32:37.700264 INFO: Resetting torch num_threads to 100
5:32:39.479801 PROGRESS: ============================= Precursor FDR =============================
5:32:39.480112 PROGRESS: Total precursors accumulated: 107,906
5:32:39.480180 PROGRESS: Target precursors: 106,838 (99.01%)
5:32:39.480234 PROGRESS: Decoy precursors: 1,068 (0.99%)
5:32:39.480283 PROGRESS: 
5:32:39.480328 PROGRESS: Precursor Summary:
5:32:39.512303 PROGRESS: Channel   0:	 0.050 FDR: 106,838; 0.010 FDR: 106,838; 0.001 FDR: 72,087
5:32:39.512596 PROGRESS: 
5:32:39.512662 PROGRESS: Protein Summary:
5:32:39.556335 PROGRESS: Channel   0:	 0.050 FDR: 14,921; 0.010 FDR: 14,921; 0.001 FDR: 10,443
5:32:39.556592 PROGRESS: =========================================================================
5:32:39.657800 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/psm.parquet
5:32:39.856287 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.parquet
5:32:40.099140 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
5:32:40.594569 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 
5:32:40.594714 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant
5:32:40.594797 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/figures
5:32:40.594956 INFO: Initializing TimingManager
5:32:40.595459 INFO: Initializing RawFileManager
5:32:50.788109 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.
5:32:50.795765 INFO: Determining DIA cycle
5:32:50.813471 INFO: Found cycle with start 0.00 min and length 300.
5:32:50.993809 INFO: RT (min)            : 0.0 - 26.9
5:32:50.993925 INFO: RT duration (sec)   : 1611.2
5:32:50.993954 INFO: RT duration (min)   : 26.9
5:32:50.993976 INFO: Cycle len (scans)   : 300
5:32:50.993996 INFO: Cycle len (sec)     : 1.65
5:32:50.994017 INFO: Number of cycles    : 977
5:32:50.994040 INFO: MS2 range (m/z)     : 380.4 - 980.7
5:32:50.994073 INFO: Creating DIA data object took: 10.398519277572632
5:32:51.709911 INFO: Creating DIA data NG object took: 0.7156987190246582
5:32:52.909756 INFO: Initializing CalibrationManager
5:32:52.910035 INFO: Setting up calibration estimators ..
5:32:52.910101 INFO: Found 1 estimator(s) in calibration group 'fragment'
5:32:52.910176 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
5:32:52.910246 INFO: Found 3 estimator(s) in calibration group 'precursor'
5:32:52.910301 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
5:32:52.910355 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
5:32:52.910405 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
5:32:52.910455 INFO: Done setting up calibration estimators.
5:32:52.910652 INFO: Initializing OptimizationManager
5:32:52.910802 INFO: initial parameter: ms1_error = 3
5:32:52.910857 INFO: initial parameter: ms2_error = 10
5:32:52.910906 INFO: initial parameter: rt_error = 805.6002197265625
5:32:52.910951 INFO: initial parameter: mobility_error = 0.1
5:32:52.910995 INFO: initial parameter: num_candidates = 1
5:32:52.911038 INFO: initial parameter: fwhm_rt = 5
5:32:52.911080 INFO: initial parameter: fwhm_mobility = 0.01
5:32:52.911122 INFO: initial parameter: score_cutoff = 0
5:32:52.911177 INFO: initial parameter: classifier_version = -1
5:32:52.911255 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
5:32:52.911513 INFO: FDRManager: loading saved state not requested, will be initialized.
5:32:52.911546 INFO: Initializing FDRManager
5:32:52.911578 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
5:32:54.227979 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
5:32:55.137573 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
5:32:55.137975 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
5:32:55.138069 PROGRESS: Starting initial search for precursors.
5:32:55.138147 INFO: Starting optimization step 0.
5:32:55.138206 PROGRESS: === Extracting elution groups 0 to 1000 ===
5:32:55.138261 INFO: Using rust extraction backend
5:32:55.138314 PROGRESS: Extracting batch of 1967 precursors
5:32:55.142060 INFO: === Search parameters used ===
5:32:55.142159 INFO: rt_error       : 805.6002197265625
5:32:55.142209 INFO: mobility_error : 0.1
5:32:55.142252 INFO: num_candidates : 1
5:32:55.142292 INFO: ms1_error      : 3
5:32:55.142333 INFO: ms2_error      : 10
5:32:55.142372 INFO: fwhm_rt        : 5
5:32:55.142411 INFO: quant_window   : 3
5:32:55.142451 INFO: ==============================================
5:32:55.172224 INFO: performing precursor FDR with 40 features
5:32:55.172296 INFO: Decoy channel: -1
5:32:55.172319 INFO: competitive: True
5:32:55.173773 INFO: Setting torch num_threads to 2 for FDR classification task
5:32:55.175643 INFO: Estimating optimal hyperparameters - samples: 1,518, batch_size: 128, learning_rate: 1.77e-04
5:32:55.176458 INFO: Using random state 748804 for train-test-split
5:32:55.315898 INFO: Test AUC: 0.440
5:32:55.315976 INFO: Train AUC: 0.537
5:32:55.316004 INFO: AUC difference: 18.08%
5:32:55.316024 WARNING: AUC difference > 5%. This may indicate overfitting.
5:32:55.562417 INFO: Resetting torch num_threads to 100
5:32:55.564050 PROGRESS: === Extracted 1898 precursors and 6698 fragments ===
5:32:55.564411 INFO: === FDR correction performed with classifier version -1 ===
5:32:55.564907 PROGRESS: ============================= Precursor FDR =============================
5:32:55.564990 PROGRESS: Total precursors accumulated: 1
5:32:55.565047 PROGRESS: Target precursors: 1 (100.00%)
5:32:55.565095 PROGRESS: Decoy precursors: 0 (0.00%)
5:32:55.565139 PROGRESS: 
5:32:55.565181 PROGRESS: Precursor Summary:
5:32:55.566251 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
5:32:55.566331 PROGRESS: 
5:32:55.566383 PROGRESS: Protein Summary:
5:32:55.567559 PROGRESS: Channel   0:	 0.050 FDR:     1; 0.010 FDR:     1; 0.001 FDR:     1
5:32:55.567647 PROGRESS: =========================================================================
5:32:55.567884 INFO: Target number of precursors not reached yet.
5:32:55.651489 INFO: Starting optimization step 1.
5:32:55.651714 PROGRESS: === Extracting elution groups 1000 to 3000 ===
5:32:55.651793 INFO: Using rust extraction backend
5:32:55.651850 PROGRESS: Extracting batch of 3942 precursors
5:32:55.657696 INFO: === Search parameters used ===
5:32:55.657823 INFO: rt_error       : 805.6002197265625
5:32:55.657872 INFO: mobility_error : 0.1
5:32:55.657916 INFO: num_candidates : 1
5:32:55.657958 INFO: ms1_error      : 3
5:32:55.657998 INFO: ms2_error      : 10
5:32:55.658038 INFO: fwhm_rt        : 5
5:32:55.658084 INFO: quant_window   : 3
5:32:55.658129 INFO: ==============================================
5:32:55.698946 INFO: performing precursor FDR with 40 features
5:32:55.699037 INFO: Decoy channel: -1
5:32:55.699071 INFO: competitive: True
5:32:55.703600 INFO: Setting torch num_threads to 2 for FDR classification task
5:32:55.706111 INFO: Estimating optimal hyperparameters - samples: 4,574, batch_size: 128, learning_rate: 1.77e-04
5:32:55.706194 INFO: Using random state 836643 for train-test-split
5:32:56.153099 INFO: Test AUC: 0.516
5:32:56.153184 INFO: Train AUC: 0.562
5:32:56.153214 INFO: AUC difference: 8.16%
5:32:56.153237 WARNING: AUC difference > 5%. This may indicate overfitting.
5:32:56.392276 INFO: Resetting torch num_threads to 100
5:32:56.395343 PROGRESS: === Extracted 5718 precursors and 19812 fragments ===
5:32:56.395721 INFO: === FDR correction performed with classifier version -1 ===
5:32:56.396197 PROGRESS: ============================= Precursor FDR =============================
5:32:56.396282 PROGRESS: Total precursors accumulated: 0
5:32:56.396353 PROGRESS: Target precursors: 0 (0.00%)
5:32:56.396406 PROGRESS: Decoy precursors: 0 (0.00%)
5:32:56.396455 PROGRESS: 
5:32:56.396501 PROGRESS: Precursor Summary:
5:32:56.396618 PROGRESS: 
5:32:56.396681 PROGRESS: Protein Summary:
5:32:56.396756 PROGRESS: =========================================================================
5:32:56.397019 INFO: Target number of precursors not reached yet.
5:32:56.485126 INFO: Starting optimization step 2.
5:32:56.485357 PROGRESS: === Extracting elution groups 3000 to 7000 ===
5:32:56.485438 INFO: Using rust extraction backend
5:32:56.485498 PROGRESS: Extracting batch of 7891 precursors
5:32:56.495321 INFO: === Search parameters used ===
5:32:56.495460 INFO: rt_error       : 805.6002197265625
5:32:56.495511 INFO: mobility_error : 0.1
5:32:56.495557 INFO: num_candidates : 1
5:32:56.495601 INFO: ms1_error      : 3
5:32:56.495642 INFO: ms2_error      : 10
5:32:56.495682 INFO: fwhm_rt        : 5
5:32:56.495723 INFO: quant_window   : 3
5:32:56.495761 INFO: ==============================================
5:32:56.560319 INFO: performing precursor FDR with 40 features
5:32:56.560426 INFO: Decoy channel: -1
5:32:56.560451 INFO: competitive: True
5:32:56.567338 INFO: Setting torch num_threads to 2 for FDR classification task
5:32:56.571086 INFO: Estimating optimal hyperparameters - samples: 10,714, batch_size: 128, learning_rate: 1.77e-04
5:32:56.571242 INFO: Using random state 409910 for train-test-split
5:32:57.644878 INFO: Test AUC: 0.537
5:32:57.644965 INFO: Train AUC: 0.575
5:32:57.645012 INFO: AUC difference: 6.63%
5:32:57.645033 WARNING: AUC difference > 5%. This may indicate overfitting.
5:32:57.894806 INFO: Resetting torch num_threads to 100
5:32:57.898982 PROGRESS: === Extracted 13393 precursors and 46385 fragments ===
5:32:57.899391 INFO: === FDR correction performed with classifier version -1 ===
5:32:57.899876 PROGRESS: ============================= Precursor FDR =============================
5:32:57.899957 PROGRESS: Total precursors accumulated: 0
5:32:57.900020 PROGRESS: Target precursors: 0 (0.00%)
5:32:57.900070 PROGRESS: Decoy precursors: 0 (0.00%)
5:32:57.900115 PROGRESS: 
5:32:57.900160 PROGRESS: Precursor Summary:
5:32:57.900271 PROGRESS: 
5:32:57.900331 PROGRESS: Protein Summary:
5:32:57.900404 PROGRESS: =========================================================================
5:32:57.900728 INFO: Target number of precursors not reached yet.
5:32:57.997156 INFO: Starting optimization step 3.
5:32:57.997402 PROGRESS: === Extracting elution groups 7000 to 15000 ===
5:32:57.997484 INFO: Using rust extraction backend
5:32:57.997544 PROGRESS: Extracting batch of 15751 precursors
5:32:58.015164 INFO: === Search parameters used ===
5:32:58.015345 INFO: rt_error       : 805.6002197265625
5:32:58.015398 INFO: mobility_error : 0.1
5:32:58.015444 INFO: num_candidates : 1
5:32:58.015489 INFO: ms1_error      : 3
5:32:58.015536 INFO: ms2_error      : 10
5:32:58.015578 INFO: fwhm_rt        : 5
5:32:58.015618 INFO: quant_window   : 3
5:32:58.015658 INFO: ==============================================
5:32:58.124316 INFO: performing precursor FDR with 40 features
5:32:58.124434 INFO: Decoy channel: -1
5:32:58.124459 INFO: competitive: True
5:32:58.136025 INFO: Setting torch num_threads to 2 for FDR classification task
5:32:58.143053 INFO: Estimating optimal hyperparameters - samples: 22,988, batch_size: 128, learning_rate: 1.77e-04
5:32:58.143238 INFO: Using random state 402220 for train-test-split
5:33:00.441945 INFO: Test AUC: 0.557
5:33:00.442037 INFO: Train AUC: 0.589
5:33:00.442065 INFO: AUC difference: 5.41%
5:33:00.442087 WARNING: AUC difference > 5%. This may indicate overfitting.
5:33:00.703072 INFO: Resetting torch num_threads to 100
5:33:00.709552 PROGRESS: === Extracted 28735 precursors and 99437 fragments ===
5:33:00.710051 INFO: === FDR correction performed with classifier version -1 ===
5:33:00.710554 PROGRESS: ============================= Precursor FDR =============================
5:33:00.710636 PROGRESS: Total precursors accumulated: 0
5:33:00.710703 PROGRESS: Target precursors: 0 (0.00%)
5:33:00.710753 PROGRESS: Decoy precursors: 0 (0.00%)
5:33:00.710795 PROGRESS: 
5:33:00.710838 PROGRESS: Precursor Summary:
5:33:00.710953 PROGRESS: 
5:33:00.711011 PROGRESS: Protein Summary:
5:33:00.711083 PROGRESS: =========================================================================
5:33:00.711568 INFO: Target number of precursors not reached yet.
5:33:00.828874 INFO: Starting optimization step 4.
5:33:00.829127 PROGRESS: === Extracting elution groups 15000 to 31000 ===
5:33:00.829208 INFO: Using rust extraction backend
5:33:00.829270 PROGRESS: Extracting batch of 31575 precursors
5:33:00.863448 INFO: === Search parameters used ===
5:33:00.863652 INFO: rt_error       : 805.6002197265625
5:33:00.863702 INFO: mobility_error : 0.1
5:33:00.863746 INFO: num_candidates : 1
5:33:00.863787 INFO: ms1_error      : 3
5:33:00.863827 INFO: ms2_error      : 10
5:33:00.863867 INFO: fwhm_rt        : 5
5:33:00.863918 INFO: quant_window   : 3
5:33:00.863961 INFO: ==============================================
5:33:01.069186 INFO: performing precursor FDR with 40 features
5:33:01.069304 INFO: Decoy channel: -1
5:33:01.069327 INFO: competitive: True
5:33:01.094880 INFO: Setting torch num_threads to 2 for FDR classification task
5:33:01.109096 INFO: Estimating optimal hyperparameters - samples: 47,556, batch_size: 194, learning_rate: 2.18e-04
5:33:01.109319 INFO: Using random state 538353 for train-test-split
5:33:04.663647 INFO: Test AUC: 0.562
5:33:04.663743 INFO: Train AUC: 0.586
5:33:04.663774 INFO: AUC difference: 4.18%
5:33:04.930672 INFO: Resetting torch num_threads to 100
5:33:04.941769 PROGRESS: === Extracted 59446 precursors and 206784 fragments ===
5:33:04.942401 INFO: === FDR correction performed with classifier version -1 ===
5:33:04.942972 PROGRESS: ============================= Precursor FDR =============================
5:33:04.943062 PROGRESS: Total precursors accumulated: 119
5:33:04.943123 PROGRESS: Target precursors: 118 (99.16%)
5:33:04.943189 PROGRESS: Decoy precursors: 1 (0.84%)
5:33:04.943239 PROGRESS: 
5:33:04.943287 PROGRESS: Precursor Summary:
5:33:04.944284 PROGRESS: Channel   0:	 0.050 FDR:   118; 0.010 FDR:   118; 0.001 FDR:     0
5:33:04.944370 PROGRESS: 
5:33:04.944427 PROGRESS: Protein Summary:
5:33:04.945534 PROGRESS: Channel   0:	 0.050 FDR:   115; 0.010 FDR:   115; 0.001 FDR:     0
5:33:04.945622 PROGRESS: =========================================================================
5:33:04.946525 INFO: Target number of precursors not reached yet.
5:33:05.094676 INFO: Starting optimization step 5.
5:33:05.094959 PROGRESS: === Extracting elution groups 31000 to 63000 ===
5:33:05.095046 INFO: Using rust extraction backend
5:33:05.095113 PROGRESS: Extracting batch of 63070 precursors
5:33:05.160451 INFO: === Search parameters used ===
5:33:05.160737 INFO: rt_error       : 805.6002197265625
5:33:05.160795 INFO: mobility_error : 0.1
5:33:05.160844 INFO: num_candidates : 1
5:33:05.160890 INFO: ms1_error      : 3
5:33:05.160934 INFO: ms2_error      : 10
5:33:05.160978 INFO: fwhm_rt        : 5
5:33:05.161021 INFO: quant_window   : 3
5:33:05.161064 INFO: ==============================================
5:33:05.510445 INFO: performing precursor FDR with 40 features
5:33:05.510580 INFO: Decoy channel: -1
5:33:05.510605 INFO: competitive: True
5:33:05.558377 INFO: Setting torch num_threads to 2 for FDR classification task
5:33:05.591505 INFO: Estimating optimal hyperparameters - samples: 96,593, batch_size: 395, learning_rate: 3.11e-04
5:33:05.591819 INFO: Using random state 494458 for train-test-split
5:33:10.241047 INFO: Test AUC: 0.567
5:33:10.241155 INFO: Train AUC: 0.590
5:33:10.241188 INFO: AUC difference: 3.83%
5:33:10.530740 INFO: Resetting torch num_threads to 100
5:33:10.561640 PROGRESS: === Extracted 120742 precursors and 418886 fragments ===
5:33:10.562294 INFO: === FDR correction performed with classifier version -1 ===
5:33:10.562873 PROGRESS: ============================= Precursor FDR =============================
5:33:10.562961 PROGRESS: Total precursors accumulated: 0
5:33:10.563035 PROGRESS: Target precursors: 0 (0.00%)
5:33:10.563089 PROGRESS: Decoy precursors: 0 (0.00%)
5:33:10.563136 PROGRESS: 
5:33:10.563195 PROGRESS: Precursor Summary:
5:33:10.563321 PROGRESS: 
5:33:10.563383 PROGRESS: Protein Summary:
5:33:10.563458 PROGRESS: =========================================================================
5:33:10.566406 INFO: Target number of precursors not reached yet.
5:33:10.867857 INFO: Starting optimization step 6.
5:33:10.868125 PROGRESS: === Extracting elution groups 63000 to 127000 ===
5:33:10.868222 INFO: Using rust extraction backend
5:33:10.868291 PROGRESS: Extracting batch of 126133 precursors
5:33:11.001183 INFO: === Search parameters used ===
5:33:11.001476 INFO: rt_error       : 805.6002197265625
5:33:11.001530 INFO: mobility_error : 0.1
5:33:11.001576 INFO: num_candidates : 1
5:33:11.001621 INFO: ms1_error      : 3
5:33:11.001663 INFO: ms2_error      : 10
5:33:11.001704 INFO: fwhm_rt        : 5
5:33:11.001745 INFO: quant_window   : 3
5:33:11.001786 INFO: ==============================================
5:33:11.628009 INFO: performing precursor FDR with 40 features
5:33:11.628131 INFO: Decoy channel: -1
5:33:11.628159 INFO: competitive: True
5:33:11.731070 INFO: Setting torch num_threads to 2 for FDR classification task
5:33:11.808301 INFO: Estimating optimal hyperparameters - samples: 194,736, batch_size: 797, learning_rate: 4.41e-04
5:33:11.808767 INFO: Using random state 118486 for train-test-split
5:33:18.140074 INFO: Test AUC: 0.566
5:33:18.140291 INFO: Train AUC: 0.585
5:33:18.140325 INFO: AUC difference: 3.29%
5:33:18.470540 INFO: Resetting torch num_threads to 100
5:33:18.513116 PROGRESS: === Extracted 243420 precursors and 844095 fragments ===
5:33:18.513813 INFO: === FDR correction performed with classifier version -1 ===
5:33:18.514603 PROGRESS: ============================= Precursor FDR =============================
5:33:18.514692 PROGRESS: Total precursors accumulated: 1,168
5:33:18.514753 PROGRESS: Target precursors: 1,157 (99.06%)
5:33:18.514805 PROGRESS: Decoy precursors: 11 (0.94%)
5:33:18.514851 PROGRESS: 
5:33:18.514896 PROGRESS: Precursor Summary:
5:33:18.516186 PROGRESS: Channel   0:	 0.050 FDR: 1,157; 0.010 FDR: 1,157; 0.001 FDR:    70
5:33:18.516279 PROGRESS: 
5:33:18.516335 PROGRESS: Protein Summary:
5:33:18.517904 PROGRESS: Channel   0:	 0.050 FDR: 1,020; 0.010 FDR: 1,020; 0.001 FDR:    68
5:33:18.517994 PROGRESS: =========================================================================
5:33:18.521825 INFO: Target number of precursors reached.
5:33:18.620450 INFO: fragments_df: keeping 5000 of 844095 [sum(precursor_idx_mask)=11350 sum(mass_error_mask)=844095 stop_rank=5000
5:33:18.981934 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:33:19.188974 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:33:19.875171 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
5:33:19.875632 INFO: Using score_cutoff 11.710188737869263 (fac=0.99, q=1)
5:33:19.875965 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
5:33:19.876042 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
5:33:19.876096 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.710188737869263
5:33:19.876148 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:33:20.022826 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:33:20.225581 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
5:33:20.225876 PROGRESS: Required number of precursors found. Starting search parameter optimization.
5:33:20.225998 INFO: Starting optimization step 7.
5:33:20.226077 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:33:20.226170 INFO: Using rust extraction backend
5:33:20.226248 PROGRESS: Extracting batch of 250329 precursors
5:33:20.482648 INFO: === Search parameters used ===
5:33:20.482916 INFO: rt_error       : 805.6002197265625
5:33:20.482973 INFO: mobility_error : 0.1
5:33:20.483020 INFO: num_candidates : 3
5:33:20.483078 INFO: ms1_error      : 3
5:33:20.483120 INFO: ms2_error      : 10
5:33:20.483170 INFO: fwhm_rt        : 3.0
5:33:20.483213 INFO: quant_window   : 3
5:33:20.483252 INFO: ==============================================
5:33:22.709331 INFO: performing precursor FDR with 40 features
5:33:22.709452 INFO: Decoy channel: -1
5:33:22.709478 INFO: competitive: True
5:33:22.900492 INFO: Setting torch num_threads to 2 for FDR classification task
5:33:23.198007 INFO: Estimating optimal hyperparameters - samples: 579,704, batch_size: 2,374, learning_rate: 7.61e-04
5:33:23.198882 INFO: Using random state 640646 for train-test-split
5:33:35.560959 INFO: Test AUC: 0.567
5:33:35.561087 INFO: Train AUC: 0.579
5:33:35.561119 INFO: AUC difference: 2.07%
5:33:36.038491 INFO: Resetting torch num_threads to 100
5:33:36.071056 PROGRESS: === Extracted 724630 precursors and 2405896 fragments ===
5:33:36.071544 INFO: === FDR correction performed with classifier version 6 ===
5:33:36.072303 PROGRESS: ============================= Precursor FDR =============================
5:33:36.072392 PROGRESS: Total precursors accumulated: 1,504
5:33:36.072452 PROGRESS: Target precursors: 1,490 (99.07%)
5:33:36.072508 PROGRESS: Decoy precursors: 14 (0.93%)
5:33:36.072556 PROGRESS: 
5:33:36.072601 PROGRESS: Precursor Summary:
5:33:36.073995 PROGRESS: Channel   0:	 0.050 FDR: 1,490; 0.010 FDR: 1,490; 0.001 FDR: 1,086
5:33:36.074086 PROGRESS: 
5:33:36.074142 PROGRESS: Protein Summary:
5:33:36.075958 PROGRESS: Channel   0:	 0.050 FDR: 1,290; 0.010 FDR: 1,290; 0.001 FDR:   956
5:33:36.076053 PROGRESS: =========================================================================
5:33:36.090279 INFO: Target number of precursors reached.
5:33:36.361552 INFO: fragments_df: keeping 5000 of 2405896 [sum(precursor_idx_mask)=32357 sum(mass_error_mask)=2405896 stop_rank=5000
5:33:36.870723 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:33:37.107188 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:33:37.825035 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:33:37.825483 INFO: Using score_cutoff 11.673654824638366 (fac=0.99, q=1)
5:33:37.825792 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:33:37.825867 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:33:37.825921 INFO: Updating optimization_manager: score_cutoff        : 11.710188737869263 -> 11.673654824638366
5:33:37.825974 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:33:37.973251 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:33:38.176008 INFO: === checking if optimization conditions were reached ===
5:33:38.178760 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
5:33:38.178885 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
5:33:38.178968 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
5:33:38.179041 INFO: ==============================================
5:33:38.179124 INFO: Starting optimization step 8.
5:33:38.179218 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:33:38.179296 INFO: Using rust extraction backend
5:33:38.179384 PROGRESS: Extracting batch of 250329 precursors
5:33:38.435357 INFO: === Search parameters used ===
5:33:38.435634 INFO: rt_error       : 805.6002197265625
5:33:38.435694 INFO: mobility_error : 0.1
5:33:38.435742 INFO: num_candidates : 3
5:33:38.435786 INFO: ms1_error      : 3
5:33:38.435827 INFO: ms2_error      : 10.0
5:33:38.435869 INFO: fwhm_rt        : 3.0
5:33:38.435910 INFO: quant_window   : 3
5:33:38.435950 INFO: ==============================================
5:33:40.684643 INFO: performing precursor FDR with 40 features
5:33:40.684763 INFO: Decoy channel: -1
5:33:40.684789 INFO: competitive: True
5:33:40.871403 INFO: Setting torch num_threads to 2 for FDR classification task
5:33:41.161890 INFO: Estimating optimal hyperparameters - samples: 579,744, batch_size: 2,374, learning_rate: 7.61e-04
5:33:41.162939 INFO: Using random state 277901 for train-test-split
5:33:52.884868 INFO: Test AUC: 0.571
5:33:52.885001 INFO: Train AUC: 0.584
5:33:52.885035 INFO: AUC difference: 2.16%
5:33:53.354635 INFO: Resetting torch num_threads to 100
5:33:53.380569 PROGRESS: === Extracted 724681 precursors and 2406011 fragments ===
5:33:53.381053 INFO: === FDR correction performed with classifier version 7 ===
5:33:53.381747 PROGRESS: ============================= Precursor FDR =============================
5:33:53.381838 PROGRESS: Total precursors accumulated: 1,601
5:33:53.381898 PROGRESS: Target precursors: 1,586 (99.06%)
5:33:53.381949 PROGRESS: Decoy precursors: 15 (0.94%)
5:33:53.381997 PROGRESS: 
5:33:53.382044 PROGRESS: Precursor Summary:
5:33:53.383554 PROGRESS: Channel   0:	 0.050 FDR: 1,586; 0.010 FDR: 1,586; 0.001 FDR: 1,129
5:33:53.383648 PROGRESS: 
5:33:53.383709 PROGRESS: Protein Summary:
5:33:53.385525 PROGRESS: Channel   0:	 0.050 FDR: 1,359; 0.010 FDR: 1,359; 0.001 FDR:   995
5:33:53.385626 PROGRESS: =========================================================================
5:33:53.399462 INFO: Target number of precursors reached.
5:33:53.664121 INFO: fragments_df: keeping 5000 of 2406011 [sum(precursor_idx_mask)=34359 sum(mass_error_mask)=2406011 stop_rank=5000
5:33:54.035547 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:33:54.245779 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:33:54.901155 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:33:54.901614 INFO: Using score_cutoff 11.290815620899199 (fac=0.99, q=1)
5:33:54.901923 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:33:54.901999 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:33:54.902053 INFO: Updating optimization_manager: score_cutoff        : 11.673654824638366 -> 11.290815620899199
5:33:54.902107 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:33:55.046614 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:33:55.235622 INFO: === checking if optimization conditions were reached ===
5:33:55.238256 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
5:33:55.238374 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
5:33:55.238451 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
5:33:55.238523 INFO: ==============================================
5:33:55.238603 INFO: Starting optimization step 9.
5:33:55.238674 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:33:55.238764 INFO: Using rust extraction backend
5:33:55.238837 PROGRESS: Extracting batch of 250329 precursors
5:33:55.495854 INFO: === Search parameters used ===
5:33:55.496144 INFO: rt_error       : 805.6002197265625
5:33:55.496203 INFO: mobility_error : 0.1
5:33:55.496249 INFO: num_candidates : 3
5:33:55.496292 INFO: ms1_error      : 3
5:33:55.496332 INFO: ms2_error      : 10.0
5:33:55.496372 INFO: fwhm_rt        : 3.0
5:33:55.496412 INFO: quant_window   : 3
5:33:55.496452 INFO: ==============================================
5:33:57.708142 INFO: performing precursor FDR with 40 features
5:33:57.708266 INFO: Decoy channel: -1
5:33:57.708292 INFO: competitive: True
5:33:57.900833 INFO: Setting torch num_threads to 2 for FDR classification task
5:33:58.197117 INFO: Estimating optimal hyperparameters - samples: 579,718, batch_size: 2,374, learning_rate: 7.61e-04
5:33:58.198197 INFO: Using random state 963991 for train-test-split
5:34:10.573232 INFO: Test AUC: 0.576
5:34:10.573360 INFO: Train AUC: 0.588
5:34:10.573395 INFO: AUC difference: 2.05%
5:34:11.043132 INFO: Resetting torch num_threads to 100
5:34:11.069359 PROGRESS: === Extracted 724648 precursors and 2406422 fragments ===
5:34:11.069825 INFO: === FDR correction performed with classifier version 8 ===
5:34:11.070555 PROGRESS: ============================= Precursor FDR =============================
5:34:11.070647 PROGRESS: Total precursors accumulated: 1,619
5:34:11.070710 PROGRESS: Target precursors: 1,603 (99.01%)
5:34:11.070764 PROGRESS: Decoy precursors: 16 (0.99%)
5:34:11.070813 PROGRESS: 
5:34:11.070874 PROGRESS: Precursor Summary:
5:34:11.072282 PROGRESS: Channel   0:	 0.050 FDR: 1,603; 0.010 FDR: 1,603; 0.001 FDR: 1,013
5:34:11.072378 PROGRESS: 
5:34:11.072434 PROGRESS: Protein Summary:
5:34:11.074268 PROGRESS: Channel   0:	 0.050 FDR: 1,384; 0.010 FDR: 1,384; 0.001 FDR:   899
5:34:11.074361 PROGRESS: =========================================================================
5:34:11.088614 INFO: Target number of precursors reached.
5:34:11.350024 INFO: fragments_df: keeping 5000 of 2406422 [sum(precursor_idx_mask)=34250 sum(mass_error_mask)=2406422 stop_rank=5000
5:34:11.715568 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:34:11.962697 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:34:12.677256 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:34:12.677709 INFO: Using score_cutoff 10.70748784046173 (fac=0.99, q=1)
5:34:12.678010 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:34:12.678084 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:34:12.678137 INFO: Updating optimization_manager: score_cutoff        : 11.290815620899199 -> 10.70748784046173
5:34:12.678189 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:34:12.824646 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:34:13.005800 INFO: === checking if optimization conditions were reached ===
5:34:13.007999 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
5:34:13.008109 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
5:34:13.008173 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
5:34:13.008232 INFO: ==============================================
5:34:13.008312 INFO: Starting optimization step 10.
5:34:13.008370 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:34:13.008429 INFO: Using rust extraction backend
5:34:13.008487 PROGRESS: Extracting batch of 250329 precursors
5:34:13.258272 INFO: === Search parameters used ===
5:34:13.258547 INFO: rt_error       : 805.6002197265625
5:34:13.258604 INFO: mobility_error : 0.1
5:34:13.258651 INFO: num_candidates : 3
5:34:13.258695 INFO: ms1_error      : 3
5:34:13.258736 INFO: ms2_error      : 10.0
5:34:13.258778 INFO: fwhm_rt        : 3.0
5:34:13.258818 INFO: quant_window   : 3
5:34:13.258857 INFO: ==============================================
5:34:15.483038 INFO: performing precursor FDR with 40 features
5:34:15.483196 INFO: Decoy channel: -1
5:34:15.483224 INFO: competitive: True
5:34:15.674990 INFO: Setting torch num_threads to 2 for FDR classification task
5:34:15.959539 INFO: Estimating optimal hyperparameters - samples: 579,676, batch_size: 2,374, learning_rate: 7.61e-04
5:34:15.960601 INFO: Using random state 727695 for train-test-split
5:34:28.734740 INFO: Test AUC: 0.581
5:34:28.734872 INFO: Train AUC: 0.592
5:34:28.734943 INFO: AUC difference: 1.72%
5:34:29.202778 INFO: Resetting torch num_threads to 100
5:34:29.229379 PROGRESS: === Extracted 724596 precursors and 2405759 fragments ===
5:34:29.229859 INFO: === FDR correction performed with classifier version 9 ===
5:34:29.230656 PROGRESS: ============================= Precursor FDR =============================
5:34:29.230748 PROGRESS: Total precursors accumulated: 1,773
5:34:29.230810 PROGRESS: Target precursors: 1,756 (99.04%)
5:34:29.230862 PROGRESS: Decoy precursors: 17 (0.96%)
5:34:29.230911 PROGRESS: 
5:34:29.230958 PROGRESS: Precursor Summary:
5:34:29.232430 PROGRESS: Channel   0:	 0.050 FDR: 1,756; 0.010 FDR: 1,756; 0.001 FDR: 1,166
5:34:29.232533 PROGRESS: 
5:34:29.232592 PROGRESS: Protein Summary:
5:34:29.234470 PROGRESS: Channel   0:	 0.050 FDR: 1,496; 0.010 FDR: 1,496; 0.001 FDR: 1,020
5:34:29.234562 PROGRESS: =========================================================================
5:34:29.248755 INFO: Target number of precursors reached.
5:34:29.508269 INFO: fragments_df: keeping 5000 of 2405759 [sum(precursor_idx_mask)=37151 sum(mass_error_mask)=2405759 stop_rank=5000
5:34:29.876321 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:34:30.110607 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:34:30.761642 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:34:30.762099 INFO: Using score_cutoff 10.40990628004074 (fac=0.99, q=1)
5:34:30.762414 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:34:30.762492 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:34:30.762548 INFO: Updating optimization_manager: score_cutoff        : 10.70748784046173 -> 10.40990628004074
5:34:30.762603 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:34:30.909607 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:34:31.101648 INFO: === checking if optimization conditions were reached ===
5:34:31.104300 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
5:34:31.104424 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
5:34:31.104506 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
5:34:31.104596 INFO: ==============================================
5:34:31.104680 INFO: Starting optimization step 11.
5:34:31.104751 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:34:31.104829 INFO: Using rust extraction backend
5:34:31.104902 PROGRESS: Extracting batch of 250329 precursors
5:34:31.356918 INFO: === Search parameters used ===
5:34:31.357186 INFO: rt_error       : 805.6002197265625
5:34:31.357240 INFO: mobility_error : 0.1
5:34:31.357287 INFO: num_candidates : 3
5:34:31.357330 INFO: ms1_error      : 3
5:34:31.357380 INFO: ms2_error      : 10.0
5:34:31.357421 INFO: fwhm_rt        : 3.0
5:34:31.357462 INFO: quant_window   : 3
5:34:31.357504 INFO: ==============================================
5:34:33.586872 INFO: performing precursor FDR with 40 features
5:34:33.586988 INFO: Decoy channel: -1
5:34:33.587014 INFO: competitive: True
5:34:33.775402 INFO: Setting torch num_threads to 2 for FDR classification task
5:34:34.051124 INFO: Estimating optimal hyperparameters - samples: 579,684, batch_size: 2,374, learning_rate: 7.61e-04
5:34:34.052082 INFO: Using random state 194759 for train-test-split
5:34:46.554666 INFO: Test AUC: 0.583
5:34:46.554793 INFO: Train AUC: 0.595
5:34:46.554825 INFO: AUC difference: 2.05%
5:34:47.027431 INFO: Resetting torch num_threads to 100
5:34:47.054410 PROGRESS: === Extracted 724606 precursors and 2405849 fragments ===
5:34:47.054887 INFO: === FDR correction performed with classifier version 10 ===
5:34:47.055701 PROGRESS: ============================= Precursor FDR =============================
5:34:47.055797 PROGRESS: Total precursors accumulated: 1,891
5:34:47.055858 PROGRESS: Target precursors: 1,873 (99.05%)
5:34:47.055910 PROGRESS: Decoy precursors: 18 (0.95%)
5:34:47.055958 PROGRESS: 
5:34:47.056004 PROGRESS: Precursor Summary:
5:34:47.057499 PROGRESS: Channel   0:	 0.050 FDR: 1,873; 0.010 FDR: 1,873; 0.001 FDR: 1,141
5:34:47.057590 PROGRESS: 
5:34:47.057647 PROGRESS: Protein Summary:
5:34:47.059594 PROGRESS: Channel   0:	 0.050 FDR: 1,610; 0.010 FDR: 1,610; 0.001 FDR: 1,005
5:34:47.059688 PROGRESS: =========================================================================
5:34:47.073493 INFO: Target number of precursors reached.
5:34:47.339252 INFO: fragments_df: keeping 5000 of 2405849 [sum(precursor_idx_mask)=38534 sum(mass_error_mask)=2405849 stop_rank=5000
5:34:47.706010 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:34:47.949688 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:34:48.597982 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:34:48.598442 INFO: Using score_cutoff 9.966498932647704 (fac=0.99, q=1)
5:34:48.598753 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:34:48.598832 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:34:48.598886 INFO: Updating optimization_manager: score_cutoff        : 10.40990628004074 -> 9.966498932647704
5:34:48.598939 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:34:48.745993 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:34:48.931669 INFO: === checking if optimization conditions were reached ===
5:34:48.933863 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
5:34:48.933966 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
5:34:48.934043 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
5:34:48.934104 INFO: ==============================================
5:34:48.934170 PROGRESS: Optimization finished for ms2_error.
5:34:49.280655 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:34:49.427754 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:34:49.613640 INFO: Starting optimization step 0.
5:34:49.613911 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:34:49.613990 INFO: Using rust extraction backend
5:34:49.614053 PROGRESS: Extracting batch of 250329 precursors
5:34:49.863239 INFO: === Search parameters used ===
5:34:49.863498 INFO: rt_error       : 805.6002197265625
5:34:49.863566 INFO: mobility_error : 0.1
5:34:49.863612 INFO: num_candidates : 3
5:34:49.863654 INFO: ms1_error      : 3
5:34:49.863695 INFO: ms2_error      : 10.0
5:34:49.863734 INFO: fwhm_rt        : 3.0
5:34:49.863773 INFO: quant_window   : 3
5:34:49.863812 INFO: ==============================================
5:34:52.093707 INFO: performing precursor FDR with 40 features
5:34:52.093835 INFO: Decoy channel: -1
5:34:52.093863 INFO: competitive: True
5:34:52.290688 INFO: Setting torch num_threads to 2 for FDR classification task
5:34:52.568573 INFO: Estimating optimal hyperparameters - samples: 579,692, batch_size: 2,374, learning_rate: 7.61e-04
5:34:52.569628 INFO: Using random state 958353 for train-test-split
5:35:05.301761 INFO: Test AUC: 0.582
5:35:05.301954 INFO: Train AUC: 0.597
5:35:05.301991 INFO: AUC difference: 2.48%
5:35:05.774498 INFO: Resetting torch num_threads to 100
5:35:05.804173 PROGRESS: === Extracted 724616 precursors and 2406290 fragments ===
5:35:05.804680 INFO: === FDR correction performed with classifier version 11 ===
5:35:05.805371 PROGRESS: ============================= Precursor FDR =============================
5:35:05.805475 PROGRESS: Total precursors accumulated: 1,476
5:35:05.805537 PROGRESS: Target precursors: 1,462 (99.05%)
5:35:05.805589 PROGRESS: Decoy precursors: 14 (0.95%)
5:35:05.805637 PROGRESS: 
5:35:05.805683 PROGRESS: Precursor Summary:
5:35:05.807029 PROGRESS: Channel   0:	 0.050 FDR: 1,462; 0.010 FDR: 1,462; 0.001 FDR:   736
5:35:05.807123 PROGRESS: 
5:35:05.807199 PROGRESS: Protein Summary:
5:35:05.808941 PROGRESS: Channel   0:	 0.050 FDR: 1,258; 0.010 FDR: 1,258; 0.001 FDR:   678
5:35:05.809031 PROGRESS: =========================================================================
5:35:05.823054 INFO: Target number of precursors reached.
5:35:06.098606 INFO: fragments_df: keeping 5000 of 2406290 [sum(precursor_idx_mask)=31483 sum(mass_error_mask)=2406290 stop_rank=5000
5:35:06.465476 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:35:06.668378 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:35:07.317769 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:35:07.318227 INFO: Using score_cutoff 11.072008650970458 (fac=0.99, q=1)
5:35:07.318547 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:35:07.318624 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:35:07.318681 INFO: Updating optimization_manager: score_cutoff        : 9.966498932647704 -> 11.072008650970458
5:35:07.318737 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:35:07.465383 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:35:07.658437 INFO: === checking if optimization conditions were reached ===
5:35:07.658752 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
5:35:07.661849 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 385.08555972926086
5:35:07.661971 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 385.0856.
5:35:07.662109 INFO: ==============================================
5:35:07.662193 INFO: Starting optimization step 1.
5:35:07.662278 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:35:07.662349 INFO: Using rust extraction backend
5:35:07.662416 PROGRESS: Extracting batch of 250329 precursors
5:35:07.916510 INFO: === Search parameters used ===
5:35:07.916798 INFO: rt_error       : 385.08555972926086
5:35:07.916856 INFO: mobility_error : 0.1
5:35:07.916900 INFO: num_candidates : 3
5:35:07.916941 INFO: ms1_error      : 3
5:35:07.916979 INFO: ms2_error      : 10.0
5:35:07.917017 INFO: fwhm_rt        : 3.0
5:35:07.917054 INFO: quant_window   : 3
5:35:07.917090 INFO: ==============================================
5:35:10.019113 INFO: performing precursor FDR with 40 features
5:35:10.019273 INFO: Decoy channel: -1
5:35:10.019300 INFO: competitive: True
5:35:10.206923 INFO: Setting torch num_threads to 2 for FDR classification task
5:35:10.480026 INFO: Estimating optimal hyperparameters - samples: 573,525, batch_size: 2,349, learning_rate: 7.57e-04
5:35:10.481065 INFO: Using random state 958353 for train-test-split
5:35:22.875878 INFO: Test AUC: 0.577
5:35:22.876031 INFO: Train AUC: 0.593
5:35:22.876065 INFO: AUC difference: 2.73%
5:35:23.345152 INFO: Resetting torch num_threads to 100
5:35:23.373478 PROGRESS: === Extracted 716907 precursors and 2296019 fragments ===
5:35:23.373962 INFO: === FDR correction performed with classifier version 11 ===
5:35:23.374820 PROGRESS: ============================= Precursor FDR =============================
5:35:23.374916 PROGRESS: Total precursors accumulated: 1,985
5:35:23.374978 PROGRESS: Target precursors: 1,966 (99.04%)
5:35:23.375031 PROGRESS: Decoy precursors: 19 (0.96%)
5:35:23.375077 PROGRESS: 
5:35:23.375123 PROGRESS: Precursor Summary:
5:35:23.376658 PROGRESS: Channel   0:	 0.050 FDR: 1,966; 0.010 FDR: 1,966; 0.001 FDR: 1,274
5:35:23.376752 PROGRESS: 
5:35:23.376807 PROGRESS: Protein Summary:
5:35:23.378778 PROGRESS: Channel   0:	 0.050 FDR: 1,675; 0.010 FDR: 1,675; 0.001 FDR: 1,107
5:35:23.378872 PROGRESS: =========================================================================
5:35:23.393189 INFO: Target number of precursors reached.
5:35:23.648380 INFO: fragments_df: keeping 5000 of 2296019 [sum(precursor_idx_mask)=40639 sum(mass_error_mask)=2296019 stop_rank=5000
5:35:24.076194 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:35:24.366357 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:35:25.085574 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:35:25.086078 INFO: Using score_cutoff 10.079145714282989 (fac=0.99, q=1)
5:35:25.086414 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:35:25.086493 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:35:25.086554 INFO: Updating optimization_manager: score_cutoff        : 11.072008650970458 -> 10.079145714282989
5:35:25.086615 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:35:25.235354 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:35:25.427676 INFO: === checking if optimization conditions were reached ===
5:35:25.427958 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
5:35:25.431013 INFO: Updating optimization_manager: rt_error            : 385.08555972926086 -> 480.7662229579934
5:35:25.431127 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 480.7662.
5:35:25.431213 INFO: ==============================================
5:35:25.431285 INFO: Starting optimization step 2.
5:35:25.431345 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:35:25.431414 INFO: Using rust extraction backend
5:35:25.431472 PROGRESS: Extracting batch of 250329 precursors
5:35:25.682594 INFO: === Search parameters used ===
5:35:25.682865 INFO: rt_error       : 480.7662229579934
5:35:25.682922 INFO: mobility_error : 0.1
5:35:25.682983 INFO: num_candidates : 3
5:35:25.683027 INFO: ms1_error      : 3
5:35:25.683070 INFO: ms2_error      : 10.0
5:35:25.683117 INFO: fwhm_rt        : 3.0
5:35:25.683169 INFO: quant_window   : 3
5:35:25.683213 INFO: ==============================================
5:35:27.881535 INFO: performing precursor FDR with 40 features
5:35:27.881653 INFO: Decoy channel: -1
5:35:27.881677 INFO: competitive: True
5:35:28.075826 INFO: Setting torch num_threads to 2 for FDR classification task
5:35:28.369284 INFO: Estimating optimal hyperparameters - samples: 576,595, batch_size: 2,361, learning_rate: 7.59e-04
5:35:28.370415 INFO: Using random state 958353 for train-test-split
5:35:40.709120 INFO: Test AUC: 0.582
5:35:40.709295 INFO: Train AUC: 0.595
5:35:40.709328 INFO: AUC difference: 2.24%
5:35:41.178629 INFO: Resetting torch num_threads to 100
5:35:41.205598 PROGRESS: === Extracted 720744 precursors and 2351791 fragments ===
5:35:41.206106 INFO: === FDR correction performed with classifier version 11 ===
5:35:41.206901 PROGRESS: ============================= Precursor FDR =============================
5:35:41.206992 PROGRESS: Total precursors accumulated: 1,906
5:35:41.207053 PROGRESS: Target precursors: 1,888 (99.06%)
5:35:41.207105 PROGRESS: Decoy precursors: 18 (0.94%)
5:35:41.207167 PROGRESS: 
5:35:41.207218 PROGRESS: Precursor Summary:
5:35:41.208716 PROGRESS: Channel   0:	 0.050 FDR: 1,888; 0.010 FDR: 1,888; 0.001 FDR: 1,309
5:35:41.208806 PROGRESS: 
5:35:41.208867 PROGRESS: Protein Summary:
5:35:41.210819 PROGRESS: Channel   0:	 0.050 FDR: 1,620; 0.010 FDR: 1,620; 0.001 FDR: 1,140
5:35:41.210913 PROGRESS: =========================================================================
5:35:41.226174 INFO: Target number of precursors reached.
5:35:41.486936 INFO: fragments_df: keeping 5000 of 2351791 [sum(precursor_idx_mask)=39214 sum(mass_error_mask)=2351791 stop_rank=5000
5:35:41.899405 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:35:42.178334 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:35:42.896522 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:35:42.896990 INFO: Using score_cutoff 9.819295280742645 (fac=0.99, q=1)
5:35:42.897319 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:35:42.897404 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:35:42.897465 INFO: Updating optimization_manager: score_cutoff        : 10.079145714282989 -> 9.819295280742645
5:35:42.897519 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:35:43.043990 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:35:43.237403 INFO: === checking if optimization conditions were reached ===
5:35:43.237732 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
5:35:43.241372 INFO: Updating optimization_manager: rt_error            : 480.7662229579934 -> 593.45702320494
5:35:43.241491 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 593.4570.
5:35:43.241567 INFO: ==============================================
5:35:43.241650 INFO: Starting optimization step 3.
5:35:43.241719 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:35:43.241801 INFO: Using rust extraction backend
5:35:43.241873 PROGRESS: Extracting batch of 250329 precursors
5:35:43.494746 INFO: === Search parameters used ===
5:35:43.495013 INFO: rt_error       : 593.45702320494
5:35:43.495072 INFO: mobility_error : 0.1
5:35:43.495121 INFO: num_candidates : 3
5:35:43.495183 INFO: ms1_error      : 3
5:35:43.495231 INFO: ms2_error      : 10.0
5:35:43.495274 INFO: fwhm_rt        : 3.0
5:35:43.495334 INFO: quant_window   : 3
5:35:43.495377 INFO: ==============================================
5:35:45.697929 INFO: performing precursor FDR with 40 features
5:35:45.698053 INFO: Decoy channel: -1
5:35:45.698079 INFO: competitive: True
5:35:45.886897 INFO: Setting torch num_threads to 2 for FDR classification task
5:35:46.165339 INFO: Estimating optimal hyperparameters - samples: 578,736, batch_size: 2,370, learning_rate: 7.61e-04
5:35:46.166375 INFO: Using random state 958353 for train-test-split
5:35:58.543349 INFO: Test AUC: 0.578
5:35:58.543474 INFO: Train AUC: 0.596
5:35:58.543507 INFO: AUC difference: 3.00%
5:35:59.009158 INFO: Resetting torch num_threads to 100
5:35:59.037095 PROGRESS: === Extracted 723421 precursors and 2389261 fragments ===
5:35:59.037583 INFO: === FDR correction performed with classifier version 11 ===
5:35:59.038455 PROGRESS: ============================= Precursor FDR =============================
5:35:59.038546 PROGRESS: Total precursors accumulated: 1,905
5:35:59.038607 PROGRESS: Target precursors: 1,887 (99.06%)
5:35:59.038661 PROGRESS: Decoy precursors: 18 (0.94%)
5:35:59.038708 PROGRESS: 
5:35:59.038754 PROGRESS: Precursor Summary:
5:35:59.040327 PROGRESS: Channel   0:	 0.050 FDR: 1,887; 0.010 FDR: 1,887; 0.001 FDR: 1,201
5:35:59.040422 PROGRESS: 
5:35:59.040483 PROGRESS: Protein Summary:
5:35:59.042423 PROGRESS: Channel   0:	 0.050 FDR: 1,626; 0.010 FDR: 1,626; 0.001 FDR: 1,058
5:35:59.042518 PROGRESS: =========================================================================
5:35:59.070777 INFO: Target number of precursors reached.
5:35:59.337251 INFO: fragments_df: keeping 5000 of 2389261 [sum(precursor_idx_mask)=38752 sum(mass_error_mask)=2389261 stop_rank=5000
5:35:59.799116 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:36:00.077506 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:36:00.794951 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:36:00.795431 INFO: Using score_cutoff 9.977449153518677 (fac=0.99, q=1)
5:36:00.795749 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:36:00.795825 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:36:00.795880 INFO: Updating optimization_manager: score_cutoff        : 9.819295280742645 -> 9.977449153518677
5:36:00.795932 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:36:00.943741 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:36:01.145285 INFO: === checking if optimization conditions were reached ===
5:36:01.145615 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
5:36:01.149297 INFO: Updating optimization_manager: rt_error            : 593.45702320494 -> 746.1865216087267
5:36:01.149424 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 746.1865.
5:36:01.149503 INFO: ==============================================
5:36:01.149592 INFO: Starting optimization step 4.
5:36:01.149665 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:36:01.149743 INFO: Using rust extraction backend
5:36:01.149812 PROGRESS: Extracting batch of 250329 precursors
5:36:01.402214 INFO: === Search parameters used ===
5:36:01.402485 INFO: rt_error       : 746.1865216087267
5:36:01.402541 INFO: mobility_error : 0.1
5:36:01.402589 INFO: num_candidates : 3
5:36:01.402633 INFO: ms1_error      : 3
5:36:01.402688 INFO: ms2_error      : 10.0
5:36:01.402732 INFO: fwhm_rt        : 3.0
5:36:01.402773 INFO: quant_window   : 3
5:36:01.402813 INFO: ==============================================
5:36:03.647295 INFO: performing precursor FDR with 40 features
5:36:03.647416 INFO: Decoy channel: -1
5:36:03.647442 INFO: competitive: True
5:36:03.836642 INFO: Setting torch num_threads to 2 for FDR classification task
5:36:04.116098 INFO: Estimating optimal hyperparameters - samples: 579,656, batch_size: 2,374, learning_rate: 7.61e-04
5:36:04.117252 INFO: Using random state 958353 for train-test-split
5:36:16.508474 INFO: Test AUC: 0.586
5:36:16.508603 INFO: Train AUC: 0.596
5:36:16.508637 INFO: AUC difference: 1.72%
5:36:16.982859 INFO: Resetting torch num_threads to 100
5:36:17.010911 PROGRESS: === Extracted 724571 precursors and 2405013 fragments ===
5:36:17.011414 INFO: === FDR correction performed with classifier version 11 ===
5:36:17.012182 PROGRESS: ============================= Precursor FDR =============================
5:36:17.012288 PROGRESS: Total precursors accumulated: 2,020
5:36:17.012350 PROGRESS: Target precursors: 2,000 (99.01%)
5:36:17.012402 PROGRESS: Decoy precursors: 20 (0.99%)
5:36:17.012450 PROGRESS: 
5:36:17.012495 PROGRESS: Precursor Summary:
5:36:17.013976 PROGRESS: Channel   0:	 0.050 FDR: 2,000; 0.010 FDR: 1,978; 0.001 FDR: 1,192
5:36:17.014066 PROGRESS: 
5:36:17.014122 PROGRESS: Protein Summary:
5:36:17.016093 PROGRESS: Channel   0:	 0.050 FDR: 1,716; 0.010 FDR: 1,698; 0.001 FDR: 1,048
5:36:17.016188 PROGRESS: =========================================================================
5:36:17.030771 INFO: Target number of precursors reached.
5:36:17.301054 INFO: fragments_df: keeping 5000 of 2405013 [sum(precursor_idx_mask)=40145 sum(mass_error_mask)=2405013 stop_rank=5000
5:36:17.679875 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:36:17.973329 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:36:18.688188 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:36:18.688658 INFO: Using score_cutoff 8.715514750385283 (fac=0.99, q=1)
5:36:18.688963 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:36:18.689038 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:36:18.689089 INFO: Updating optimization_manager: score_cutoff        : 9.977449153518677 -> 8.715514750385283
5:36:18.689141 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:36:18.833513 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:36:19.025715 INFO: === checking if optimization conditions were reached ===
5:36:19.026031 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
5:36:19.029635 INFO: Updating optimization_manager: rt_error            : 746.1865216087267 -> 905.6219073879233
5:36:19.029758 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 905.6219.
5:36:19.029833 INFO: ==============================================
5:36:19.029913 INFO: Starting optimization step 5.
5:36:19.029979 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:36:19.030052 INFO: Using rust extraction backend
5:36:19.030120 PROGRESS: Extracting batch of 250329 precursors
5:36:19.282140 INFO: === Search parameters used ===
5:36:19.282412 INFO: rt_error       : 905.6219073879233
5:36:19.282467 INFO: mobility_error : 0.1
5:36:19.282528 INFO: num_candidates : 3
5:36:19.282573 INFO: ms1_error      : 3
5:36:19.282615 INFO: ms2_error      : 10.0
5:36:19.282654 INFO: fwhm_rt        : 3.0
5:36:19.282692 INFO: quant_window   : 3
5:36:19.282730 INFO: ==============================================
5:36:21.521029 INFO: performing precursor FDR with 40 features
5:36:21.521157 INFO: Decoy channel: -1
5:36:21.521185 INFO: competitive: True
5:36:21.714597 INFO: Setting torch num_threads to 2 for FDR classification task
5:36:22.009010 INFO: Estimating optimal hyperparameters - samples: 579,829, batch_size: 2,374, learning_rate: 7.61e-04
5:36:22.010016 INFO: Using random state 958353 for train-test-split
5:36:34.529944 INFO: Test AUC: 0.582
5:36:34.530076 INFO: Train AUC: 0.597
5:36:34.530108 INFO: AUC difference: 2.56%
5:36:35.003118 INFO: Resetting torch num_threads to 100
5:36:35.029620 PROGRESS: === Extracted 724787 precursors and 2407579 fragments ===
5:36:35.030105 INFO: === FDR correction performed with classifier version 11 ===
5:36:35.030836 PROGRESS: ============================= Precursor FDR =============================
5:36:35.030932 PROGRESS: Total precursors accumulated: 1,798
5:36:35.030995 PROGRESS: Target precursors: 1,781 (99.05%)
5:36:35.031049 PROGRESS: Decoy precursors: 17 (0.95%)
5:36:35.031100 PROGRESS: 
5:36:35.031166 PROGRESS: Precursor Summary:
5:36:35.032673 PROGRESS: Channel   0:	 0.050 FDR: 1,781; 0.010 FDR: 1,781; 0.001 FDR: 1,116
5:36:35.032775 PROGRESS: 
5:36:35.032837 PROGRESS: Protein Summary:
5:36:35.034724 PROGRESS: Channel   0:	 0.050 FDR: 1,521; 0.010 FDR: 1,521; 0.001 FDR:   980
5:36:35.034830 PROGRESS: =========================================================================
5:36:35.048816 INFO: Target number of precursors reached.
5:36:35.313421 INFO: fragments_df: keeping 5000 of 2407579 [sum(precursor_idx_mask)=37621 sum(mass_error_mask)=2407579 stop_rank=5000
5:36:35.684053 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:36:35.918099 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:36:36.564269 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:36:36.564738 INFO: Using score_cutoff 10.783441423416138 (fac=0.99, q=1)
5:36:36.565048 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:36:36.565129 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:36:36.565186 INFO: Updating optimization_manager: score_cutoff        : 8.715514750385283 -> 10.783441423416138
5:36:36.565242 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:36:36.712402 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:36:36.902680 INFO: === checking if optimization conditions were reached ===
5:36:36.902984 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
5:36:36.906010 INFO: Updating optimization_manager: rt_error            : 905.6219073879233 -> 440.49986544314226
5:36:36.906118 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 440.4999.
5:36:36.906184 INFO: ==============================================
5:36:36.906255 INFO: Starting optimization step 6.
5:36:36.906316 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:36:36.906382 INFO: Using rust extraction backend
5:36:36.906441 PROGRESS: Extracting batch of 250329 precursors
5:36:37.158584 INFO: === Search parameters used ===
5:36:37.158899 INFO: rt_error       : 440.49986544314226
5:36:37.158959 INFO: mobility_error : 0.1
5:36:37.159008 INFO: num_candidates : 3
5:36:37.159050 INFO: ms1_error      : 3
5:36:37.159092 INFO: ms2_error      : 10.0
5:36:37.159133 INFO: fwhm_rt        : 3.0
5:36:37.159185 INFO: quant_window   : 3
5:36:37.159226 INFO: ==============================================
5:36:39.291258 INFO: performing precursor FDR with 40 features
5:36:39.291374 INFO: Decoy channel: -1
5:36:39.291400 INFO: competitive: True
5:36:39.480205 INFO: Setting torch num_threads to 2 for FDR classification task
5:36:39.772434 INFO: Estimating optimal hyperparameters - samples: 575,357, batch_size: 2,356, learning_rate: 7.58e-04
5:36:39.773515 INFO: Using random state 958353 for train-test-split
5:36:51.837116 INFO: Test AUC: 0.582
5:36:51.837317 INFO: Train AUC: 0.595
5:36:51.837353 INFO: AUC difference: 2.17%
5:36:52.315125 INFO: Resetting torch num_threads to 100
5:36:52.346808 PROGRESS: === Extracted 719197 precursors and 2329734 fragments ===
5:36:52.347361 INFO: === FDR correction performed with classifier version 11 ===
5:36:52.348284 PROGRESS: ============================= Precursor FDR =============================
5:36:52.348401 PROGRESS: Total precursors accumulated: 1,970
5:36:52.348488 PROGRESS: Target precursors: 1,951 (99.04%)
5:36:52.348563 PROGRESS: Decoy precursors: 19 (0.96%)
5:36:52.348650 PROGRESS: 
5:36:52.348722 PROGRESS: Precursor Summary:
5:36:52.350633 PROGRESS: Channel   0:	 0.050 FDR: 1,951; 0.010 FDR: 1,951; 0.001 FDR: 1,120
5:36:52.350730 PROGRESS: 
5:36:52.350788 PROGRESS: Protein Summary:
5:36:52.353029 PROGRESS: Channel   0:	 0.050 FDR: 1,664; 0.010 FDR: 1,664; 0.001 FDR:   990
5:36:52.353129 PROGRESS: =========================================================================
5:36:52.370075 INFO: Target number of precursors reached.
5:36:52.628505 INFO: fragments_df: keeping 5000 of 2329734 [sum(precursor_idx_mask)=40711 sum(mass_error_mask)=2329734 stop_rank=5000
5:36:53.046482 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:36:53.342327 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:36:54.058390 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:36:54.058844 INFO: Using score_cutoff 9.79645218372345 (fac=0.99, q=1)
5:36:54.059189 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:36:54.059276 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:36:54.059328 INFO: Updating optimization_manager: score_cutoff        : 10.783441423416138 -> 9.79645218372345
5:36:54.059380 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:36:54.205567 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:36:54.396392 INFO: === checking if optimization conditions were reached ===
5:36:54.396680 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
5:36:54.399834 INFO: Updating optimization_manager: rt_error            : 440.49986544314226 -> 528.5327382357493
5:36:54.399938 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 528.5327.
5:36:54.400002 INFO: ==============================================
5:36:54.400072 INFO: Starting optimization step 7.
5:36:54.400130 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:36:54.400195 INFO: Using rust extraction backend
5:36:54.400263 PROGRESS: Extracting batch of 250329 precursors
5:36:54.651741 INFO: === Search parameters used ===
5:36:54.652007 INFO: rt_error       : 528.5327382357493
5:36:54.652063 INFO: mobility_error : 0.1
5:36:54.652110 INFO: num_candidates : 3
5:36:54.652152 INFO: ms1_error      : 3
5:36:54.652191 INFO: ms2_error      : 10.0
5:36:54.652230 INFO: fwhm_rt        : 3.0
5:36:54.652269 INFO: quant_window   : 3
5:36:54.652307 INFO: ==============================================
5:36:56.847388 INFO: performing precursor FDR with 40 features
5:36:56.847506 INFO: Decoy channel: -1
5:36:56.847530 INFO: competitive: True
5:36:57.039676 INFO: Setting torch num_threads to 2 for FDR classification task
5:36:57.335500 INFO: Estimating optimal hyperparameters - samples: 577,800, batch_size: 2,366, learning_rate: 7.60e-04
5:36:57.336387 INFO: Using random state 958353 for train-test-split
5:37:09.696473 INFO: Test AUC: 0.580
5:37:09.696597 INFO: Train AUC: 0.595
5:37:09.696631 INFO: AUC difference: 2.38%
5:37:10.164567 INFO: Resetting torch num_threads to 100
5:37:10.212025 PROGRESS: === Extracted 722250 precursors and 2373096 fragments ===
5:37:10.212510 INFO: === FDR correction performed with classifier version 11 ===
5:37:10.213248 PROGRESS: ============================= Precursor FDR =============================
5:37:10.213337 PROGRESS: Total precursors accumulated: 1,871
5:37:10.213400 PROGRESS: Target precursors: 1,853 (99.04%)
5:37:10.213451 PROGRESS: Decoy precursors: 18 (0.96%)
5:37:10.213497 PROGRESS: 
5:37:10.213543 PROGRESS: Precursor Summary:
5:37:10.214990 PROGRESS: Channel   0:	 0.050 FDR: 1,853; 0.010 FDR: 1,853; 0.001 FDR: 1,138
5:37:10.215082 PROGRESS: 
5:37:10.215140 PROGRESS: Protein Summary:
5:37:10.217052 PROGRESS: Channel   0:	 0.050 FDR: 1,598; 0.010 FDR: 1,598; 0.001 FDR: 1,002
5:37:10.217149 PROGRESS: =========================================================================
5:37:10.233019 INFO: Target number of precursors reached.
5:37:10.496453 INFO: fragments_df: keeping 5000 of 2373096 [sum(precursor_idx_mask)=38157 sum(mass_error_mask)=2373096 stop_rank=5000
5:37:10.945866 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:37:11.219790 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:37:11.937672 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:37:11.938153 INFO: Using score_cutoff 9.214188890075683 (fac=0.99, q=1)
5:37:11.938459 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:37:11.938536 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:37:11.938590 INFO: Updating optimization_manager: score_cutoff        : 9.79645218372345 -> 9.214188890075683
5:37:11.938643 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:37:12.085076 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:37:12.272917 INFO: === checking if optimization conditions were reached ===
5:37:12.273219 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
5:37:12.276266 INFO: Updating optimization_manager: rt_error            : 528.5327382357493 -> 691.9576988052884
5:37:12.276376 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 691.9577.
5:37:12.276441 INFO: ==============================================
5:37:12.276514 INFO: Starting optimization step 8.
5:37:12.276581 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:37:12.276647 INFO: Using rust extraction backend
5:37:12.276702 PROGRESS: Extracting batch of 250329 precursors
5:37:12.527947 INFO: === Search parameters used ===
5:37:12.528217 INFO: rt_error       : 691.9576988052884
5:37:12.528280 INFO: mobility_error : 0.1
5:37:12.528331 INFO: num_candidates : 3
5:37:12.528378 INFO: ms1_error      : 3
5:37:12.528423 INFO: ms2_error      : 10.0
5:37:12.528470 INFO: fwhm_rt        : 3.0
5:37:12.528517 INFO: quant_window   : 3
5:37:12.528562 INFO: ==============================================
5:37:14.781196 INFO: performing precursor FDR with 40 features
5:37:14.781318 INFO: Decoy channel: -1
5:37:14.781345 INFO: competitive: True
5:37:14.977851 INFO: Setting torch num_threads to 2 for FDR classification task
5:37:15.271569 INFO: Estimating optimal hyperparameters - samples: 579,500, batch_size: 2,373, learning_rate: 7.61e-04
5:37:15.272650 INFO: Using random state 958353 for train-test-split
5:37:27.521533 INFO: Test AUC: 0.583
5:37:27.521673 INFO: Train AUC: 0.596
5:37:27.521705 INFO: AUC difference: 2.23%
5:37:27.990384 INFO: Resetting torch num_threads to 100
5:37:28.020824 PROGRESS: === Extracted 724376 precursors and 2402591 fragments ===
5:37:28.021302 INFO: === FDR correction performed with classifier version 11 ===
5:37:28.022068 PROGRESS: ============================= Precursor FDR =============================
5:37:28.022158 PROGRESS: Total precursors accumulated: 2,038
5:37:28.022218 PROGRESS: Target precursors: 2,018 (99.02%)
5:37:28.022268 PROGRESS: Decoy precursors: 20 (0.98%)
5:37:28.022314 PROGRESS: 
5:37:28.022359 PROGRESS: Precursor Summary:
5:37:28.023845 PROGRESS: Channel   0:	 0.050 FDR: 2,018; 0.010 FDR: 2,018; 0.001 FDR: 1,100
5:37:28.023937 PROGRESS: 
5:37:28.024007 PROGRESS: Protein Summary:
5:37:28.026024 PROGRESS: Channel   0:	 0.050 FDR: 1,742; 0.010 FDR: 1,742; 0.001 FDR:   971
5:37:28.026114 PROGRESS: =========================================================================
5:37:28.040679 INFO: Target number of precursors reached.
5:37:28.312348 INFO: fragments_df: keeping 5000 of 2402591 [sum(precursor_idx_mask)=40092 sum(mass_error_mask)=2402591 stop_rank=5000
5:37:28.553684 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:37:28.853058 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:37:29.568938 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:37:29.569405 INFO: Using score_cutoff 5.997023020362854 (fac=0.99, q=1)
5:37:29.569721 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:37:29.569799 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:37:29.569854 INFO: Updating optimization_manager: score_cutoff        : 9.214188890075683 -> 5.997023020362854
5:37:29.569909 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:37:29.643104 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:37:29.742243 INFO: === checking if optimization conditions were reached ===
5:37:29.742533 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
5:37:29.746179 INFO: Updating optimization_manager: rt_error            : 691.9576988052884 -> 786.516929832844
5:37:29.746302 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 786.5169.
5:37:29.746398 INFO: ==============================================
5:37:29.746485 INFO: Starting optimization step 9.
5:37:29.746556 PROGRESS: === Extracting elution groups 0 to 63000 ===
5:37:29.746640 INFO: Using rust extraction backend
5:37:29.746709 PROGRESS: Extracting batch of 124196 precursors
5:37:29.875431 INFO: === Search parameters used ===
5:37:29.875717 INFO: rt_error       : 786.516929832844
5:37:29.875775 INFO: mobility_error : 0.1
5:37:29.875823 INFO: num_candidates : 3
5:37:29.875866 INFO: ms1_error      : 3
5:37:29.875909 INFO: ms2_error      : 10.0
5:37:29.875964 INFO: fwhm_rt        : 3.0
5:37:29.876014 INFO: quant_window   : 3
5:37:29.876064 INFO: ==============================================
5:37:31.049157 INFO: performing precursor FDR with 40 features
5:37:31.049284 INFO: Decoy channel: -1
5:37:31.049309 INFO: competitive: True
5:37:31.140429 INFO: Setting torch num_threads to 2 for FDR classification task
5:37:31.265956 INFO: Estimating optimal hyperparameters - samples: 287,646, batch_size: 1,178, learning_rate: 5.36e-04
5:37:31.266586 INFO: Using random state 958353 for train-test-split
5:37:39.060919 INFO: Test AUC: 0.577
5:37:39.061045 INFO: Train AUC: 0.604
5:37:39.061077 INFO: AUC difference: 4.58%
5:37:39.417265 INFO: Resetting torch num_threads to 100
5:37:39.431210 PROGRESS: === Extracted 359558 precursors and 1193695 fragments ===
5:37:39.431646 INFO: === FDR correction performed with classifier version 11 ===
5:37:39.432240 PROGRESS: ============================= Precursor FDR =============================
5:37:39.432329 PROGRESS: Total precursors accumulated: 965
5:37:39.432390 PROGRESS: Target precursors: 956 (99.07%)
5:37:39.432442 PROGRESS: Decoy precursors: 9 (0.93%)
5:37:39.432489 PROGRESS: 
5:37:39.432535 PROGRESS: Precursor Summary:
5:37:39.433732 PROGRESS: Channel   0:	 0.050 FDR:   956; 0.010 FDR:   956; 0.001 FDR:   595
5:37:39.433820 PROGRESS: 
5:37:39.433876 PROGRESS: Protein Summary:
5:37:39.435384 PROGRESS: Channel   0:	 0.050 FDR:   885; 0.010 FDR:   885; 0.001 FDR:   558
5:37:39.435477 PROGRESS: =========================================================================
5:37:39.441829 INFO: Target number of precursors not reached yet.
5:37:39.665429 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:37:39.740606 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:37:39.842775 INFO: === skipping optimization until target number of precursors are found ===
5:37:39.843078 PROGRESS: === Optimization of rt_error has been skipped 1 time(s); maximum number is 1 ===
5:37:39.843204 INFO: Starting optimization step 10.
5:37:39.843286 PROGRESS: === Extracting elution groups 63000 to 127000 ===
5:37:39.843367 INFO: Using rust extraction backend
5:37:39.843442 PROGRESS: Extracting batch of 126133 precursors
5:37:39.975356 INFO: === Search parameters used ===
5:37:39.975648 INFO: rt_error       : 786.516929832844
5:37:39.975723 INFO: mobility_error : 0.1
5:37:39.975773 INFO: num_candidates : 3
5:37:39.975818 INFO: ms1_error      : 3
5:37:39.975862 INFO: ms2_error      : 10.0
5:37:39.975904 INFO: fwhm_rt        : 3.0
5:37:39.975957 INFO: quant_window   : 3
5:37:39.975999 INFO: ==============================================
5:37:41.281180 INFO: performing precursor FDR with 40 features
5:37:41.281304 INFO: Decoy channel: -1
5:37:41.281330 INFO: competitive: True
5:37:41.599128 INFO: Setting torch num_threads to 2 for FDR classification task
5:37:41.883425 INFO: Estimating optimal hyperparameters - samples: 579,749, batch_size: 2,374, learning_rate: 7.61e-04
5:37:41.884301 INFO: Using random state 958353 for train-test-split
5:37:54.443703 INFO: Test AUC: 0.584
5:37:54.443830 INFO: Train AUC: 0.596
5:37:54.443862 INFO: AUC difference: 1.97%
5:37:54.914684 INFO: Resetting torch num_threads to 100
5:37:55.005092 PROGRESS: === Extracted 724687 precursors and 2406589 fragments ===
5:37:55.005810 INFO: === FDR correction performed with classifier version 11 ===
5:37:55.006858 PROGRESS: ============================= Precursor FDR =============================
5:37:55.006962 PROGRESS: Total precursors accumulated: 1,652
5:37:55.007021 PROGRESS: Target precursors: 1,636 (99.03%)
5:37:55.007073 PROGRESS: Decoy precursors: 16 (0.97%)
5:37:55.007120 PROGRESS: 
5:37:55.007185 PROGRESS: Precursor Summary:
5:37:55.008594 PROGRESS: Channel   0:	 0.050 FDR: 1,636; 0.010 FDR: 1,636; 0.001 FDR:   691
5:37:55.008685 PROGRESS: 
5:37:55.008740 PROGRESS: Protein Summary:
5:37:55.010524 PROGRESS: Channel   0:	 0.050 FDR: 1,408; 0.010 FDR: 1,408; 0.001 FDR:   644
5:37:55.010613 PROGRESS: =========================================================================
5:37:55.019957 INFO: Target number of precursors reached.
5:37:55.297504 INFO: fragments_df: keeping 5000 of 2406589 [sum(precursor_idx_mask)=35092 sum(mass_error_mask)=2406589 stop_rank=5000
5:37:55.658400 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:37:55.914276 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:37:56.628458 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:37:56.628933 INFO: Using score_cutoff 10.864153242588042 (fac=0.99, q=1)
5:37:56.629243 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:37:56.629321 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:37:56.629376 INFO: Updating optimization_manager: score_cutoff        : 5.997023020362854 -> 10.864153242588042
5:37:56.629428 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:37:56.773746 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:37:56.961189 INFO: === checking if optimization conditions were reached ===
5:37:56.961466 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
5:37:56.962343 INFO: Updating optimization_manager: rt_error            : 786.516929832844 -> 691.9576988052884
5:37:56.962467 INFO: Updating optimization_manager: classifier_version  : 11 -> 20
5:37:56.962565 INFO: Updating optimization_manager: score_cutoff        : 10.864153242588042 -> 5.997023020362854
5:37:56.962655 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:37:56.962741 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:37:56.962829 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 691.9577 found after 10 searches.
5:37:56.962892 INFO: ==============================================
5:37:56.962963 PROGRESS: Optimization finished for rt_error.
5:37:57.182979 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:37:57.255064 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:37:57.337031 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
5:37:57.337294 PROGRESS: ==============================================
5:37:57.337376 PROGRESS: ms2_error      : 10.0000
5:37:57.337433 PROGRESS: rt_error       : 691.9577
5:37:57.337481 PROGRESS: ==============================================
5:37:57.349570 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:38:04.666945 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:38:13.522635 INFO: Using rust extraction backend
5:38:13.522947 PROGRESS: Extracting batch of 11997144 precursors
5:38:23.806247 INFO: === Search parameters used ===
5:38:23.806817 INFO: rt_error       : 691.9576988052884
5:38:23.806885 INFO: mobility_error : 0.1
5:38:23.806937 INFO: num_candidates : 3
5:38:23.806982 INFO: ms1_error      : 3
5:38:23.807024 INFO: ms2_error      : 10.0
5:38:23.807066 INFO: fwhm_rt        : 3.0
5:38:23.807107 INFO: quant_window   : 3
5:38:23.807161 INFO: ==============================================
5:38:45.992028 INFO: Removed 2808334 precursors with score below cutoff 5.997023020362854
5:39:11.845011 INFO: performing precursor FDR with 40 features
5:39:11.845236 INFO: Decoy channel: -1
5:39:11.845269 INFO: competitive: True
5:39:15.324734 INFO: Setting torch num_threads to 2 for FDR classification task
5:39:29.114535 INFO: Estimating optimal hyperparameters - samples: 26,392,207, batch_size: 4,096, learning_rate: 1.00e-03
5:39:29.194088 INFO: Using random state 431099 for train-test-split
5:47:55.614598 INFO: Test AUC: 0.592
5:47:55.614926 INFO: Train AUC: 0.593
5:47:55.614970 INFO: AUC difference: 0.06%
5:48:01.988306 INFO: Resetting torch num_threads to 100
5:48:04.130521 PROGRESS: ============================= Precursor FDR =============================
5:48:04.130859 PROGRESS: Total precursors accumulated: 101,654
5:48:04.130931 PROGRESS: Target precursors: 100,649 (99.01%)
5:48:04.130997 PROGRESS: Decoy precursors: 1,005 (0.99%)
5:48:04.131046 PROGRESS: 
5:48:04.131096 PROGRESS: Precursor Summary:
5:48:04.159968 PROGRESS: Channel   0:	 0.050 FDR: 100,649; 0.010 FDR: 100,649; 0.001 FDR: 66,007
5:48:04.160218 PROGRESS: 
5:48:04.160278 PROGRESS: Protein Summary:
5:48:04.202116 PROGRESS: Channel   0:	 0.050 FDR: 14,116; 0.010 FDR: 14,116; 0.001 FDR: 9,927
5:48:04.202339 PROGRESS: =========================================================================
5:48:04.393405 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/psm.parquet
5:48:04.577373 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.parquet
5:48:04.808269 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
5:48:05.299075 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 
5:48:05.299253 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant
5:48:05.299345 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/figures
5:48:05.299525 INFO: Initializing TimingManager
5:48:05.299995 INFO: Initializing RawFileManager
5:48:17.237297 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.
5:48:17.245050 INFO: Determining DIA cycle
5:48:17.261357 INFO: Found cycle with start 0.00 min and length 300.
5:48:17.432566 INFO: RT (min)            : 0.0 - 26.9
5:48:17.432690 INFO: RT duration (sec)   : 1611.2
5:48:17.432720 INFO: RT duration (min)   : 26.9
5:48:17.432743 INFO: Cycle len (scans)   : 300
5:48:17.432764 INFO: Cycle len (sec)     : 1.65
5:48:17.432783 INFO: Number of cycles    : 978
5:48:17.432802 INFO: MS2 range (m/z)     : 380.4 - 980.7
5:48:17.432834 INFO: Creating DIA data object took: 12.13274097442627
5:48:18.140048 INFO: Creating DIA data NG object took: 0.7070658206939697
5:48:19.349737 INFO: Initializing CalibrationManager
5:48:19.350018 INFO: Setting up calibration estimators ..
5:48:19.350085 INFO: Found 1 estimator(s) in calibration group 'fragment'
5:48:19.350176 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
5:48:19.350267 INFO: Found 3 estimator(s) in calibration group 'precursor'
5:48:19.350326 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
5:48:19.350384 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
5:48:19.350438 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
5:48:19.350497 INFO: Done setting up calibration estimators.
5:48:19.350695 INFO: Initializing OptimizationManager
5:48:19.350845 INFO: initial parameter: ms1_error = 3
5:48:19.350899 INFO: initial parameter: ms2_error = 10
5:48:19.350947 INFO: initial parameter: rt_error = 805.611083984375
5:48:19.350991 INFO: initial parameter: mobility_error = 0.1
5:48:19.351032 INFO: initial parameter: num_candidates = 1
5:48:19.351072 INFO: initial parameter: fwhm_rt = 5
5:48:19.351120 INFO: initial parameter: fwhm_mobility = 0.01
5:48:19.351170 INFO: initial parameter: score_cutoff = 0
5:48:19.351214 INFO: initial parameter: classifier_version = -1
5:48:19.351284 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
5:48:19.351554 INFO: FDRManager: loading saved state not requested, will be initialized.
5:48:19.351585 INFO: Initializing FDRManager
5:48:19.351619 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
5:48:20.673030 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
5:48:21.582691 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
5:48:21.583109 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
5:48:21.583225 PROGRESS: Starting initial search for precursors.
5:48:21.583314 INFO: Starting optimization step 0.
5:48:21.583378 PROGRESS: === Extracting elution groups 0 to 1000 ===
5:48:21.583436 INFO: Using rust extraction backend
5:48:21.583498 PROGRESS: Extracting batch of 1967 precursors
5:48:21.586909 INFO: === Search parameters used ===
5:48:21.587010 INFO: rt_error       : 805.611083984375
5:48:21.587059 INFO: mobility_error : 0.1
5:48:21.587102 INFO: num_candidates : 1
5:48:21.587160 INFO: ms1_error      : 3
5:48:21.587213 INFO: ms2_error      : 10
5:48:21.587254 INFO: fwhm_rt        : 5
5:48:21.587293 INFO: quant_window   : 3
5:48:21.587332 INFO: ==============================================
5:48:21.613650 INFO: performing precursor FDR with 40 features
5:48:21.613720 INFO: Decoy channel: -1
5:48:21.613744 INFO: competitive: True
5:48:21.615085 INFO: Setting torch num_threads to 2 for FDR classification task
5:48:21.617249 INFO: Estimating optimal hyperparameters - samples: 1,519, batch_size: 128, learning_rate: 1.77e-04
5:48:21.618056 INFO: Using random state 483925 for train-test-split
5:48:21.727783 INFO: Test AUC: 0.504
5:48:21.727861 INFO: Train AUC: 0.513
5:48:21.727889 INFO: AUC difference: 1.77%
5:48:21.968282 INFO: Resetting torch num_threads to 100
5:48:21.969883 PROGRESS: === Extracted 1899 precursors and 6705 fragments ===
5:48:21.970247 INFO: === FDR correction performed with classifier version -1 ===
5:48:21.970717 PROGRESS: ============================= Precursor FDR =============================
5:48:21.970803 PROGRESS: Total precursors accumulated: 0
5:48:21.970860 PROGRESS: Target precursors: 0 (0.00%)
5:48:21.970908 PROGRESS: Decoy precursors: 0 (0.00%)
5:48:21.970954 PROGRESS: 
5:48:21.971003 PROGRESS: Precursor Summary:
5:48:21.971114 PROGRESS: 
5:48:21.971187 PROGRESS: Protein Summary:
5:48:21.971267 PROGRESS: =========================================================================
5:48:21.971481 INFO: Target number of precursors not reached yet.
5:48:22.056513 INFO: Starting optimization step 1.
5:48:22.056758 PROGRESS: === Extracting elution groups 1000 to 3000 ===
5:48:22.056839 INFO: Using rust extraction backend
5:48:22.056901 PROGRESS: Extracting batch of 3942 precursors
5:48:22.062426 INFO: === Search parameters used ===
5:48:22.062574 INFO: rt_error       : 805.611083984375
5:48:22.062630 INFO: mobility_error : 0.1
5:48:22.062676 INFO: num_candidates : 1
5:48:22.062741 INFO: ms1_error      : 3
5:48:22.062798 INFO: ms2_error      : 10
5:48:22.062843 INFO: fwhm_rt        : 5
5:48:22.062885 INFO: quant_window   : 3
5:48:22.062925 INFO: ==============================================
5:48:22.102860 INFO: performing precursor FDR with 40 features
5:48:22.102942 INFO: Decoy channel: -1
5:48:22.102966 INFO: competitive: True
5:48:22.107390 INFO: Setting torch num_threads to 2 for FDR classification task
5:48:22.109874 INFO: Estimating optimal hyperparameters - samples: 4,588, batch_size: 128, learning_rate: 1.77e-04
5:48:22.109956 INFO: Using random state 299248 for train-test-split
5:48:22.520841 INFO: Test AUC: 0.515
5:48:22.520926 INFO: Train AUC: 0.555
5:48:22.520954 INFO: AUC difference: 7.30%
5:48:22.520974 WARNING: AUC difference > 5%. This may indicate overfitting.
5:48:22.764805 INFO: Resetting torch num_threads to 100
5:48:22.767901 PROGRESS: === Extracted 5735 precursors and 19739 fragments ===
5:48:22.768281 INFO: === FDR correction performed with classifier version -1 ===
5:48:22.768788 PROGRESS: ============================= Precursor FDR =============================
5:48:22.768878 PROGRESS: Total precursors accumulated: 19
5:48:22.768938 PROGRESS: Target precursors: 19 (100.00%)
5:48:22.768991 PROGRESS: Decoy precursors: 0 (0.00%)
5:48:22.769038 PROGRESS: 
5:48:22.769083 PROGRESS: Precursor Summary:
5:48:22.770165 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
5:48:22.770253 PROGRESS: 
5:48:22.770317 PROGRESS: Protein Summary:
5:48:22.771528 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
5:48:22.771623 PROGRESS: =========================================================================
5:48:22.771902 INFO: Target number of precursors not reached yet.
5:48:22.859751 INFO: Starting optimization step 2.
5:48:22.859981 PROGRESS: === Extracting elution groups 3000 to 7000 ===
5:48:22.860061 INFO: Using rust extraction backend
5:48:22.860123 PROGRESS: Extracting batch of 7891 precursors
5:48:22.869677 INFO: === Search parameters used ===
5:48:22.869823 INFO: rt_error       : 805.611083984375
5:48:22.869875 INFO: mobility_error : 0.1
5:48:22.869923 INFO: num_candidates : 1
5:48:22.869968 INFO: ms1_error      : 3
5:48:22.870024 INFO: ms2_error      : 10
5:48:22.870069 INFO: fwhm_rt        : 5
5:48:22.870110 INFO: quant_window   : 3
5:48:22.870151 INFO: ==============================================
5:48:22.937340 INFO: performing precursor FDR with 40 features
5:48:22.937444 INFO: Decoy channel: -1
5:48:22.937469 INFO: competitive: True
5:48:22.944151 INFO: Setting torch num_threads to 2 for FDR classification task
5:48:22.947853 INFO: Estimating optimal hyperparameters - samples: 10,728, batch_size: 128, learning_rate: 1.77e-04
5:48:22.947968 INFO: Using random state 673298 for train-test-split
5:48:24.053907 INFO: Test AUC: 0.533
5:48:24.054013 INFO: Train AUC: 0.567
5:48:24.054042 INFO: AUC difference: 5.89%
5:48:24.054064 WARNING: AUC difference > 5%. This may indicate overfitting.
5:48:24.296707 INFO: Resetting torch num_threads to 100
5:48:24.301103 PROGRESS: === Extracted 13411 precursors and 46412 fragments ===
5:48:24.301503 INFO: === FDR correction performed with classifier version -1 ===
5:48:24.302010 PROGRESS: ============================= Precursor FDR =============================
5:48:24.302095 PROGRESS: Total precursors accumulated: 82
5:48:24.302162 PROGRESS: Target precursors: 82 (100.00%)
5:48:24.302215 PROGRESS: Decoy precursors: 0 (0.00%)
5:48:24.302263 PROGRESS: 
5:48:24.302309 PROGRESS: Precursor Summary:
5:48:24.303404 PROGRESS: Channel   0:	 0.050 FDR:    82; 0.010 FDR:    82; 0.001 FDR:    82
5:48:24.303493 PROGRESS: 
5:48:24.303547 PROGRESS: Protein Summary:
5:48:24.304751 PROGRESS: Channel   0:	 0.050 FDR:    81; 0.010 FDR:    81; 0.001 FDR:    81
5:48:24.304840 PROGRESS: =========================================================================
5:48:24.305195 INFO: Target number of precursors not reached yet.
5:48:24.401472 INFO: Starting optimization step 3.
5:48:24.401703 PROGRESS: === Extracting elution groups 7000 to 15000 ===
5:48:24.401786 INFO: Using rust extraction backend
5:48:24.401849 PROGRESS: Extracting batch of 15751 precursors
5:48:24.419060 INFO: === Search parameters used ===
5:48:24.419244 INFO: rt_error       : 805.611083984375
5:48:24.419303 INFO: mobility_error : 0.1
5:48:24.419352 INFO: num_candidates : 1
5:48:24.419401 INFO: ms1_error      : 3
5:48:24.419447 INFO: ms2_error      : 10
5:48:24.419489 INFO: fwhm_rt        : 5
5:48:24.419530 INFO: quant_window   : 3
5:48:24.419582 INFO: ==============================================
5:48:24.533606 INFO: performing precursor FDR with 40 features
5:48:24.533720 INFO: Decoy channel: -1
5:48:24.533746 INFO: competitive: True
5:48:24.545266 INFO: Setting torch num_threads to 2 for FDR classification task
5:48:24.552302 INFO: Estimating optimal hyperparameters - samples: 22,970, batch_size: 128, learning_rate: 1.77e-04
5:48:24.552476 INFO: Using random state 383017 for train-test-split
5:48:26.881679 INFO: Test AUC: 0.537
5:48:26.881789 INFO: Train AUC: 0.578
5:48:26.881819 INFO: AUC difference: 7.11%
5:48:26.881841 WARNING: AUC difference > 5%. This may indicate overfitting.
5:48:27.141708 INFO: Resetting torch num_threads to 100
5:48:27.148297 PROGRESS: === Extracted 28713 precursors and 99347 fragments ===
5:48:27.148777 INFO: === FDR correction performed with classifier version -1 ===
5:48:27.149288 PROGRESS: ============================= Precursor FDR =============================
5:48:27.149373 PROGRESS: Total precursors accumulated: 125
5:48:27.149432 PROGRESS: Target precursors: 124 (99.20%)
5:48:27.149482 PROGRESS: Decoy precursors: 1 (0.80%)
5:48:27.149525 PROGRESS: 
5:48:27.149567 PROGRESS: Precursor Summary:
5:48:27.150596 PROGRESS: Channel   0:	 0.050 FDR:   124; 0.010 FDR:   124; 0.001 FDR:   116
5:48:27.150679 PROGRESS: 
5:48:27.150731 PROGRESS: Protein Summary:
5:48:27.151840 PROGRESS: Channel   0:	 0.050 FDR:   121; 0.010 FDR:   121; 0.001 FDR:   114
5:48:27.151929 PROGRESS: =========================================================================
5:48:27.152427 INFO: Target number of precursors not reached yet.
5:48:27.265441 INFO: Starting optimization step 4.
5:48:27.265702 PROGRESS: === Extracting elution groups 15000 to 31000 ===
5:48:27.265780 INFO: Using rust extraction backend
5:48:27.265839 PROGRESS: Extracting batch of 31575 precursors
5:48:27.299305 INFO: === Search parameters used ===
5:48:27.299535 INFO: rt_error       : 805.611083984375
5:48:27.299602 INFO: mobility_error : 0.1
5:48:27.299649 INFO: num_candidates : 1
5:48:27.299691 INFO: ms1_error      : 3
5:48:27.299731 INFO: ms2_error      : 10
5:48:27.299771 INFO: fwhm_rt        : 5
5:48:27.299811 INFO: quant_window   : 3
5:48:27.299857 INFO: ==============================================
5:48:27.501791 INFO: performing precursor FDR with 40 features
5:48:27.501910 INFO: Decoy channel: -1
5:48:27.501934 INFO: competitive: True
5:48:27.525358 INFO: Setting torch num_threads to 2 for FDR classification task
5:48:27.538778 INFO: Estimating optimal hyperparameters - samples: 47,527, batch_size: 194, learning_rate: 2.18e-04
5:48:27.539000 INFO: Using random state 672179 for train-test-split
5:48:31.148086 INFO: Test AUC: 0.559
5:48:31.148183 INFO: Train AUC: 0.582
5:48:31.148215 INFO: AUC difference: 3.81%
5:48:31.414552 INFO: Resetting torch num_threads to 100
5:48:31.425856 PROGRESS: === Extracted 59409 precursors and 206806 fragments ===
5:48:31.426485 INFO: === FDR correction performed with classifier version -1 ===
5:48:31.427039 PROGRESS: ============================= Precursor FDR =============================
5:48:31.427134 PROGRESS: Total precursors accumulated: 0
5:48:31.427226 PROGRESS: Target precursors: 0 (0.00%)
5:48:31.427280 PROGRESS: Decoy precursors: 0 (0.00%)
5:48:31.427329 PROGRESS: 
5:48:31.427376 PROGRESS: Precursor Summary:
5:48:31.427501 PROGRESS: 
5:48:31.427565 PROGRESS: Protein Summary:
5:48:31.427643 PROGRESS: =========================================================================
5:48:31.428520 INFO: Target number of precursors not reached yet.
5:48:31.576626 INFO: Starting optimization step 5.
5:48:31.576914 PROGRESS: === Extracting elution groups 31000 to 63000 ===
5:48:31.577001 INFO: Using rust extraction backend
5:48:31.577081 PROGRESS: Extracting batch of 63070 precursors
5:48:31.641614 INFO: === Search parameters used ===
5:48:31.641905 INFO: rt_error       : 805.611083984375
5:48:31.641961 INFO: mobility_error : 0.1
5:48:31.642008 INFO: num_candidates : 1
5:48:31.642054 INFO: ms1_error      : 3
5:48:31.642096 INFO: ms2_error      : 10
5:48:31.642139 INFO: fwhm_rt        : 5
5:48:31.642422 INFO: quant_window   : 3
5:48:31.642493 INFO: ==============================================
5:48:31.988033 INFO: performing precursor FDR with 40 features
5:48:31.988145 INFO: Decoy channel: -1
5:48:31.988171 INFO: competitive: True
5:48:32.036674 INFO: Setting torch num_threads to 2 for FDR classification task
5:48:32.069184 INFO: Estimating optimal hyperparameters - samples: 96,571, batch_size: 395, learning_rate: 3.11e-04
5:48:32.069503 INFO: Using random state 605749 for train-test-split
5:48:36.692418 INFO: Test AUC: 0.561
5:48:36.692532 INFO: Train AUC: 0.586
5:48:36.692568 INFO: AUC difference: 4.17%
5:48:36.979506 INFO: Resetting torch num_threads to 100
5:48:37.002944 PROGRESS: === Extracted 120714 precursors and 418482 fragments ===
5:48:37.003636 INFO: === FDR correction performed with classifier version -1 ===
5:48:37.004283 PROGRESS: ============================= Precursor FDR =============================
5:48:37.004372 PROGRESS: Total precursors accumulated: 516
5:48:37.004432 PROGRESS: Target precursors: 511 (99.03%)
5:48:37.004484 PROGRESS: Decoy precursors: 5 (0.97%)
5:48:37.004532 PROGRESS: 
5:48:37.004578 PROGRESS: Precursor Summary:
5:48:37.005722 PROGRESS: Channel   0:	 0.050 FDR:   511; 0.010 FDR:   511; 0.001 FDR:   472
5:48:37.005811 PROGRESS: 
5:48:37.005869 PROGRESS: Protein Summary:
5:48:37.007230 PROGRESS: Channel   0:	 0.050 FDR:   482; 0.010 FDR:   482; 0.001 FDR:   445
5:48:37.007335 PROGRESS: =========================================================================
5:48:37.009414 INFO: Target number of precursors not reached yet.
5:48:37.230927 INFO: Starting optimization step 6.
5:48:37.231225 PROGRESS: === Extracting elution groups 63000 to 127000 ===
5:48:37.231312 INFO: Using rust extraction backend
5:48:37.231377 PROGRESS: Extracting batch of 126133 precursors
5:48:37.360063 INFO: === Search parameters used ===
5:48:37.360334 INFO: rt_error       : 805.611083984375
5:48:37.360390 INFO: mobility_error : 0.1
5:48:37.360439 INFO: num_candidates : 1
5:48:37.360485 INFO: ms1_error      : 3
5:48:37.360528 INFO: ms2_error      : 10
5:48:37.360569 INFO: fwhm_rt        : 5
5:48:37.360611 INFO: quant_window   : 3
5:48:37.360652 INFO: ==============================================
5:48:37.981221 INFO: performing precursor FDR with 40 features
5:48:37.981350 INFO: Decoy channel: -1
5:48:37.981376 INFO: competitive: True
5:48:38.080305 INFO: Setting torch num_threads to 2 for FDR classification task
5:48:38.155165 INFO: Estimating optimal hyperparameters - samples: 194,676, batch_size: 797, learning_rate: 4.41e-04
5:48:38.155604 INFO: Using random state 176311 for train-test-split
5:48:44.563230 INFO: Test AUC: 0.564
5:48:44.563355 INFO: Train AUC: 0.586
5:48:44.563387 INFO: AUC difference: 3.65%
5:48:44.890478 INFO: Resetting torch num_threads to 100
5:48:44.931419 PROGRESS: === Extracted 243346 precursors and 843320 fragments ===
5:48:44.932106 INFO: === FDR correction performed with classifier version -1 ===
5:48:44.932906 PROGRESS: ============================= Precursor FDR =============================
5:48:44.932999 PROGRESS: Total precursors accumulated: 1,221
5:48:44.933063 PROGRESS: Target precursors: 1,209 (99.02%)
5:48:44.933115 PROGRESS: Decoy precursors: 12 (0.98%)
5:48:44.933176 PROGRESS: 
5:48:44.933226 PROGRESS: Precursor Summary:
5:48:44.934547 PROGRESS: Channel   0:	 0.050 FDR: 1,209; 0.010 FDR: 1,209; 0.001 FDR:   838
5:48:44.934642 PROGRESS: 
5:48:44.934697 PROGRESS: Protein Summary:
5:48:44.936355 PROGRESS: Channel   0:	 0.050 FDR: 1,069; 0.010 FDR: 1,069; 0.001 FDR:   751
5:48:44.936449 PROGRESS: =========================================================================
5:48:44.940512 INFO: Target number of precursors reached.
5:48:45.040157 INFO: fragments_df: keeping 5000 of 843320 [sum(precursor_idx_mask)=11731 sum(mass_error_mask)=843320 stop_rank=5000
5:48:45.391793 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:48:45.595698 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:48:46.314588 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
5:48:46.315050 INFO: Using score_cutoff 11.643050812911987 (fac=0.99, q=1)
5:48:46.315377 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
5:48:46.315458 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
5:48:46.315521 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.643050812911987
5:48:46.315581 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:48:46.463923 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:48:46.645401 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
5:48:46.645675 PROGRESS: Required number of precursors found. Starting search parameter optimization.
5:48:46.645784 INFO: Starting optimization step 7.
5:48:46.645849 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:48:46.645918 INFO: Using rust extraction backend
5:48:46.645976 PROGRESS: Extracting batch of 250329 precursors
5:48:46.900759 INFO: === Search parameters used ===
5:48:46.901054 INFO: rt_error       : 805.611083984375
5:48:46.901114 INFO: mobility_error : 0.1
5:48:46.901161 INFO: num_candidates : 3
5:48:46.901204 INFO: ms1_error      : 3
5:48:46.901244 INFO: ms2_error      : 10
5:48:46.901286 INFO: fwhm_rt        : 3.0
5:48:46.901325 INFO: quant_window   : 3
5:48:46.901374 INFO: ==============================================
5:48:49.288025 INFO: performing precursor FDR with 40 features
5:48:49.288251 INFO: Decoy channel: -1
5:48:49.288282 INFO: competitive: True
5:48:49.475898 INFO: Setting torch num_threads to 2 for FDR classification task
5:48:49.769019 INFO: Estimating optimal hyperparameters - samples: 579,680, batch_size: 2,374, learning_rate: 7.61e-04
5:48:49.770041 INFO: Using random state 239382 for train-test-split
5:49:02.569488 INFO: Test AUC: 0.567
5:49:02.569751 INFO: Train AUC: 0.580
5:49:02.569786 INFO: AUC difference: 2.11%
5:49:03.046284 INFO: Resetting torch num_threads to 100
5:49:03.078865 PROGRESS: === Extracted 724601 precursors and 2406623 fragments ===
5:49:03.079471 INFO: === FDR correction performed with classifier version 6 ===
5:49:03.080194 PROGRESS: ============================= Precursor FDR =============================
5:49:03.080285 PROGRESS: Total precursors accumulated: 1,519
5:49:03.080347 PROGRESS: Target precursors: 1,504 (99.01%)
5:49:03.080399 PROGRESS: Decoy precursors: 15 (0.99%)
5:49:03.080445 PROGRESS: 
5:49:03.080490 PROGRESS: Precursor Summary:
5:49:03.081914 PROGRESS: Channel   0:	 0.050 FDR: 1,504; 0.010 FDR: 1,504; 0.001 FDR: 1,094
5:49:03.082006 PROGRESS: 
5:49:03.082062 PROGRESS: Protein Summary:
5:49:03.083891 PROGRESS: Channel   0:	 0.050 FDR: 1,298; 0.010 FDR: 1,298; 0.001 FDR:   956
5:49:03.083990 PROGRESS: =========================================================================
5:49:03.098485 INFO: Target number of precursors reached.
5:49:03.370317 INFO: fragments_df: keeping 5000 of 2406623 [sum(precursor_idx_mask)=32621 sum(mass_error_mask)=2406623 stop_rank=5000
5:49:03.828100 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:49:04.064397 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:49:04.780784 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:49:04.781249 INFO: Using score_cutoff 11.980475413227081 (fac=0.99, q=1)
5:49:04.781594 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:49:04.781673 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:49:04.781729 INFO: Updating optimization_manager: score_cutoff        : 11.643050812911987 -> 11.980475413227081
5:49:04.781788 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:49:04.927444 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:49:05.106237 INFO: === checking if optimization conditions were reached ===
5:49:05.108510 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
5:49:05.108625 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
5:49:05.108695 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
5:49:05.108768 INFO: ==============================================
5:49:05.108843 INFO: Starting optimization step 8.
5:49:05.108900 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:49:05.108975 INFO: Using rust extraction backend
5:49:05.109054 PROGRESS: Extracting batch of 250329 precursors
5:49:05.362833 INFO: === Search parameters used ===
5:49:05.363109 INFO: rt_error       : 805.611083984375
5:49:05.363177 INFO: mobility_error : 0.1
5:49:05.363228 INFO: num_candidates : 3
5:49:05.363272 INFO: ms1_error      : 3
5:49:05.363316 INFO: ms2_error      : 10.0
5:49:05.363362 INFO: fwhm_rt        : 3.0
5:49:05.363411 INFO: quant_window   : 3
5:49:05.363455 INFO: ==============================================
5:49:07.639465 INFO: performing precursor FDR with 40 features
5:49:07.639589 INFO: Decoy channel: -1
5:49:07.639615 INFO: competitive: True
5:49:07.827762 INFO: Setting torch num_threads to 2 for FDR classification task
5:49:08.109154 INFO: Estimating optimal hyperparameters - samples: 579,743, batch_size: 2,374, learning_rate: 7.61e-04
5:49:08.110117 INFO: Using random state 216524 for train-test-split
5:49:20.548920 INFO: Test AUC: 0.573
5:49:20.549073 INFO: Train AUC: 0.586
5:49:20.549108 INFO: AUC difference: 2.23%
5:49:21.017983 INFO: Resetting torch num_threads to 100
5:49:21.047110 PROGRESS: === Extracted 724679 precursors and 2406405 fragments ===
5:49:21.047626 INFO: === FDR correction performed with classifier version 7 ===
5:49:21.048377 PROGRESS: ============================= Precursor FDR =============================
5:49:21.048473 PROGRESS: Total precursors accumulated: 1,664
5:49:21.048534 PROGRESS: Target precursors: 1,648 (99.04%)
5:49:21.048584 PROGRESS: Decoy precursors: 16 (0.96%)
5:49:21.048634 PROGRESS: 
5:49:21.048691 PROGRESS: Precursor Summary:
5:49:21.050081 PROGRESS: Channel   0:	 0.050 FDR: 1,648; 0.010 FDR: 1,648; 0.001 FDR:   907
5:49:21.050174 PROGRESS: 
5:49:21.050229 PROGRESS: Protein Summary:
5:49:21.052046 PROGRESS: Channel   0:	 0.050 FDR: 1,411; 0.010 FDR: 1,411; 0.001 FDR:   802
5:49:21.052142 PROGRESS: =========================================================================
5:49:21.067178 INFO: Target number of precursors reached.
5:49:21.328540 INFO: fragments_df: keeping 5000 of 2406405 [sum(precursor_idx_mask)=35257 sum(mass_error_mask)=2406405 stop_rank=5000
5:49:21.716175 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:49:21.965615 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:49:22.681672 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:49:22.682413 INFO: Using score_cutoff 11.367413218975067 (fac=0.99, q=1)
5:49:22.682726 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:49:22.682804 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:49:22.682859 INFO: Updating optimization_manager: score_cutoff        : 11.980475413227081 -> 11.367413218975067
5:49:22.682913 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:49:22.833744 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:49:23.037409 INFO: === checking if optimization conditions were reached ===
5:49:23.040040 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
5:49:23.040180 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
5:49:23.040276 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
5:49:23.040350 INFO: ==============================================
5:49:23.040431 INFO: Starting optimization step 9.
5:49:23.040500 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:49:23.040575 INFO: Using rust extraction backend
5:49:23.040642 PROGRESS: Extracting batch of 250329 precursors
5:49:23.293945 INFO: === Search parameters used ===
5:49:23.294200 INFO: rt_error       : 805.611083984375
5:49:23.294257 INFO: mobility_error : 0.1
5:49:23.294305 INFO: num_candidates : 3
5:49:23.294350 INFO: ms1_error      : 3
5:49:23.294393 INFO: ms2_error      : 10.0
5:49:23.294434 INFO: fwhm_rt        : 3.0
5:49:23.294475 INFO: quant_window   : 3
5:49:23.294516 INFO: ==============================================
5:49:25.514512 INFO: performing precursor FDR with 40 features
5:49:25.514636 INFO: Decoy channel: -1
5:49:25.514663 INFO: competitive: True
5:49:25.707799 INFO: Setting torch num_threads to 2 for FDR classification task
5:49:25.999658 INFO: Estimating optimal hyperparameters - samples: 579,749, batch_size: 2,374, learning_rate: 7.61e-04
5:49:26.000633 INFO: Using random state 221081 for train-test-split
5:49:38.371137 INFO: Test AUC: 0.576
5:49:38.371283 INFO: Train AUC: 0.589
5:49:38.371315 INFO: AUC difference: 2.25%
5:49:38.832391 INFO: Resetting torch num_threads to 100
5:49:38.862753 PROGRESS: === Extracted 724687 precursors and 2406651 fragments ===
5:49:38.863240 INFO: === FDR correction performed with classifier version 8 ===
5:49:38.863923 PROGRESS: ============================= Precursor FDR =============================
5:49:38.864021 PROGRESS: Total precursors accumulated: 1,540
5:49:38.864081 PROGRESS: Target precursors: 1,525 (99.03%)
5:49:38.864133 PROGRESS: Decoy precursors: 15 (0.97%)
5:49:38.864192 PROGRESS: 
5:49:38.864239 PROGRESS: Precursor Summary:
5:49:38.865617 PROGRESS: Channel   0:	 0.050 FDR: 1,525; 0.010 FDR: 1,525; 0.001 FDR:   806
5:49:38.865707 PROGRESS: 
5:49:38.865763 PROGRESS: Protein Summary:
5:49:38.867539 PROGRESS: Channel   0:	 0.050 FDR: 1,323; 0.010 FDR: 1,323; 0.001 FDR:   720
5:49:38.867635 PROGRESS: =========================================================================
5:49:38.881383 INFO: Target number of precursors reached.
5:49:39.151368 INFO: fragments_df: keeping 5000 of 2406651 [sum(precursor_idx_mask)=31769 sum(mass_error_mask)=2406651 stop_rank=5000
5:49:39.513638 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:49:39.765378 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:49:40.480729 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:49:40.481198 INFO: Using score_cutoff 8.552965690612794 (fac=0.99, q=1)
5:49:40.481501 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:49:40.481578 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:49:40.481632 INFO: Updating optimization_manager: score_cutoff        : 11.367413218975067 -> 8.552965690612794
5:49:40.481686 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:49:40.627979 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:49:40.825293 INFO: === checking if optimization conditions were reached ===
5:49:40.827920 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
5:49:40.828042 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
5:49:40.828119 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
5:49:40.828188 INFO: ==============================================
5:49:40.828267 INFO: Starting optimization step 10.
5:49:40.828336 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:49:40.828407 INFO: Using rust extraction backend
5:49:40.828476 PROGRESS: Extracting batch of 250329 precursors
5:49:41.083136 INFO: === Search parameters used ===
5:49:41.083442 INFO: rt_error       : 805.611083984375
5:49:41.083500 INFO: mobility_error : 0.1
5:49:41.083549 INFO: num_candidates : 3
5:49:41.083593 INFO: ms1_error      : 3
5:49:41.083636 INFO: ms2_error      : 10.0
5:49:41.083678 INFO: fwhm_rt        : 3.0
5:49:41.083720 INFO: quant_window   : 3
5:49:41.083762 INFO: ==============================================
5:49:43.270806 INFO: performing precursor FDR with 40 features
5:49:43.270929 INFO: Decoy channel: -1
5:49:43.270959 INFO: competitive: True
5:49:43.449064 INFO: Setting torch num_threads to 2 for FDR classification task
5:49:43.729561 INFO: Estimating optimal hyperparameters - samples: 579,736, batch_size: 2,374, learning_rate: 7.61e-04
5:49:43.730672 INFO: Using random state 356372 for train-test-split
5:49:56.285402 INFO: Test AUC: 0.579
5:49:56.285533 INFO: Train AUC: 0.593
5:49:56.285566 INFO: AUC difference: 2.52%
5:49:56.759090 INFO: Resetting torch num_threads to 100
5:49:56.790735 PROGRESS: === Extracted 724670 precursors and 2407401 fragments ===
5:49:56.791253 INFO: === FDR correction performed with classifier version 9 ===
5:49:56.791989 PROGRESS: ============================= Precursor FDR =============================
5:49:56.792091 PROGRESS: Total precursors accumulated: 1,662
5:49:56.792156 PROGRESS: Target precursors: 1,646 (99.04%)
5:49:56.792208 PROGRESS: Decoy precursors: 16 (0.96%)
5:49:56.792256 PROGRESS: 
5:49:56.792301 PROGRESS: Precursor Summary:
5:49:56.793710 PROGRESS: Channel   0:	 0.050 FDR: 1,646; 0.010 FDR: 1,646; 0.001 FDR: 1,021
5:49:56.793795 PROGRESS: 
5:49:56.793857 PROGRESS: Protein Summary:
5:49:56.795716 PROGRESS: Channel   0:	 0.050 FDR: 1,406; 0.010 FDR: 1,406; 0.001 FDR:   892
5:49:56.795810 PROGRESS: =========================================================================
5:49:56.810130 INFO: Target number of precursors reached.
5:49:57.072002 INFO: fragments_df: keeping 5000 of 2407401 [sum(precursor_idx_mask)=35115 sum(mass_error_mask)=2407401 stop_rank=5000
5:49:57.449988 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:49:57.699706 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:49:58.416299 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:49:58.416762 INFO: Using score_cutoff 11.386034019470214 (fac=0.99, q=1)
5:49:58.417067 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:49:58.417145 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:49:58.417200 INFO: Updating optimization_manager: score_cutoff        : 8.552965690612794 -> 11.386034019470214
5:49:58.417255 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:49:58.565029 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:49:58.765649 INFO: === checking if optimization conditions were reached ===
5:49:58.768302 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
5:49:58.768425 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
5:49:58.768507 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
5:49:58.768579 INFO: ==============================================
5:49:58.768659 INFO: Starting optimization step 11.
5:49:58.768728 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:49:58.768802 INFO: Using rust extraction backend
5:49:58.768872 PROGRESS: Extracting batch of 250329 precursors
5:49:59.022755 INFO: === Search parameters used ===
5:49:59.023040 INFO: rt_error       : 805.611083984375
5:49:59.023098 INFO: mobility_error : 0.1
5:49:59.023155 INFO: num_candidates : 3
5:49:59.023206 INFO: ms1_error      : 3
5:49:59.023249 INFO: ms2_error      : 10.0
5:49:59.023290 INFO: fwhm_rt        : 3.0
5:49:59.023331 INFO: quant_window   : 3
5:49:59.023371 INFO: ==============================================
5:50:01.289906 INFO: performing precursor FDR with 40 features
5:50:01.290043 INFO: Decoy channel: -1
5:50:01.290068 INFO: competitive: True
5:50:01.486745 INFO: Setting torch num_threads to 2 for FDR classification task
5:50:01.782899 INFO: Estimating optimal hyperparameters - samples: 579,736, batch_size: 2,374, learning_rate: 7.61e-04
5:50:01.784009 INFO: Using random state 856039 for train-test-split
5:50:14.260973 INFO: Test AUC: 0.582
5:50:14.261101 INFO: Train AUC: 0.598
5:50:14.261133 INFO: AUC difference: 2.70%
5:50:14.731457 INFO: Resetting torch num_threads to 100
5:50:14.758313 PROGRESS: === Extracted 724671 precursors and 2406545 fragments ===
5:50:14.758766 INFO: === FDR correction performed with classifier version 10 ===
5:50:14.759499 PROGRESS: ============================= Precursor FDR =============================
5:50:14.759606 PROGRESS: Total precursors accumulated: 1,786
5:50:14.759667 PROGRESS: Target precursors: 1,769 (99.05%)
5:50:14.759719 PROGRESS: Decoy precursors: 17 (0.95%)
5:50:14.759767 PROGRESS: 
5:50:14.759815 PROGRESS: Precursor Summary:
5:50:14.761252 PROGRESS: Channel   0:	 0.050 FDR: 1,769; 0.010 FDR: 1,769; 0.001 FDR: 1,127
5:50:14.761342 PROGRESS: 
5:50:14.761401 PROGRESS: Protein Summary:
5:50:14.763314 PROGRESS: Channel   0:	 0.050 FDR: 1,515; 0.010 FDR: 1,515; 0.001 FDR:   987
5:50:14.763411 PROGRESS: =========================================================================
5:50:14.778307 INFO: Target number of precursors reached.
5:50:15.050921 INFO: fragments_df: keeping 5000 of 2406545 [sum(precursor_idx_mask)=37482 sum(mass_error_mask)=2406545 stop_rank=5000
5:50:15.419780 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:50:15.689786 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:50:16.406262 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:50:16.406733 INFO: Using score_cutoff 10.994416819381714 (fac=0.99, q=1)
5:50:16.407050 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:50:16.407126 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:50:16.407197 INFO: Updating optimization_manager: score_cutoff        : 11.386034019470214 -> 10.994416819381714
5:50:16.407258 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:50:16.554899 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:50:16.751406 INFO: === checking if optimization conditions were reached ===
5:50:16.754005 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
5:50:16.754122 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
5:50:16.754200 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
5:50:16.754268 INFO: ==============================================
5:50:16.754361 PROGRESS: Optimization finished for ms2_error.
5:50:17.114795 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:50:17.262662 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:50:17.452403 INFO: Starting optimization step 0.
5:50:17.452661 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:50:17.452740 INFO: Using rust extraction backend
5:50:17.452803 PROGRESS: Extracting batch of 250329 precursors
5:50:17.702794 INFO: === Search parameters used ===
5:50:17.703051 INFO: rt_error       : 805.611083984375
5:50:17.703108 INFO: mobility_error : 0.1
5:50:17.703165 INFO: num_candidates : 3
5:50:17.703214 INFO: ms1_error      : 3
5:50:17.703256 INFO: ms2_error      : 10.0
5:50:17.703296 INFO: fwhm_rt        : 3.0
5:50:17.703338 INFO: quant_window   : 3
5:50:17.703389 INFO: ==============================================
5:50:19.920184 INFO: performing precursor FDR with 40 features
5:50:19.920306 INFO: Decoy channel: -1
5:50:19.920333 INFO: competitive: True
5:50:20.106240 INFO: Setting torch num_threads to 2 for FDR classification task
5:50:20.388942 INFO: Estimating optimal hyperparameters - samples: 579,758, batch_size: 2,374, learning_rate: 7.61e-04
5:50:20.389862 INFO: Using random state 4206 for train-test-split
5:50:33.014923 INFO: Test AUC: 0.587
5:50:33.015195 INFO: Train AUC: 0.599
5:50:33.015233 INFO: AUC difference: 2.05%
5:50:33.489915 INFO: Resetting torch num_threads to 100
5:50:33.519074 PROGRESS: === Extracted 724698 precursors and 2406922 fragments ===
5:50:33.519639 INFO: === FDR correction performed with classifier version 11 ===
5:50:33.520471 PROGRESS: ============================= Precursor FDR =============================
5:50:33.520562 PROGRESS: Total precursors accumulated: 1,821
5:50:33.520624 PROGRESS: Target precursors: 1,803 (99.01%)
5:50:33.520675 PROGRESS: Decoy precursors: 18 (0.99%)
5:50:33.520723 PROGRESS: 
5:50:33.520770 PROGRESS: Precursor Summary:
5:50:33.522208 PROGRESS: Channel   0:	 0.050 FDR: 1,803; 0.010 FDR: 1,803; 0.001 FDR: 1,061
5:50:33.522299 PROGRESS: 
5:50:33.522356 PROGRESS: Protein Summary:
5:50:33.524256 PROGRESS: Channel   0:	 0.050 FDR: 1,556; 0.010 FDR: 1,556; 0.001 FDR:   936
5:50:33.524354 PROGRESS: =========================================================================
5:50:33.538561 INFO: Target number of precursors reached.
5:50:33.807211 INFO: fragments_df: keeping 5000 of 2406922 [sum(precursor_idx_mask)=37745 sum(mass_error_mask)=2406922 stop_rank=5000
5:50:34.215132 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:50:34.455999 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:50:35.176020 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:50:35.176526 INFO: Using score_cutoff 10.141251282119752 (fac=0.99, q=1)
5:50:35.176862 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:50:35.176939 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:50:35.176993 INFO: Updating optimization_manager: score_cutoff        : 10.994416819381714 -> 10.141251282119752
5:50:35.177056 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:50:35.326489 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:50:35.526708 INFO: === checking if optimization conditions were reached ===
5:50:35.527019 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
5:50:35.530402 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 972.8751693307279
5:50:35.530522 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 972.8752.
5:50:35.530618 INFO: ==============================================
5:50:35.530712 INFO: Starting optimization step 1.
5:50:35.530781 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:50:35.530873 INFO: Using rust extraction backend
5:50:35.530958 PROGRESS: Extracting batch of 250329 precursors
5:50:35.786648 INFO: === Search parameters used ===
5:50:35.786915 INFO: rt_error       : 972.8751693307279
5:50:35.786973 INFO: mobility_error : 0.1
5:50:35.787020 INFO: num_candidates : 3
5:50:35.787063 INFO: ms1_error      : 3
5:50:35.787104 INFO: ms2_error      : 10.0
5:50:35.787170 INFO: fwhm_rt        : 3.0
5:50:35.787219 INFO: quant_window   : 3
5:50:35.787259 INFO: ==============================================
5:50:38.098369 INFO: performing precursor FDR with 40 features
5:50:38.098484 INFO: Decoy channel: -1
5:50:38.098508 INFO: competitive: True
5:50:38.286820 INFO: Setting torch num_threads to 2 for FDR classification task
5:50:38.565428 INFO: Estimating optimal hyperparameters - samples: 579,848, batch_size: 2,375, learning_rate: 7.61e-04
5:50:38.566501 INFO: Using random state 4206 for train-test-split
5:50:51.092214 INFO: Test AUC: 0.587
5:50:51.092384 INFO: Train AUC: 0.599
5:50:51.092419 INFO: AUC difference: 2.08%
5:50:51.569438 INFO: Resetting torch num_threads to 100
5:50:51.595468 PROGRESS: === Extracted 724811 precursors and 2408153 fragments ===
5:50:51.595985 INFO: === FDR correction performed with classifier version 11 ===
5:50:51.596704 PROGRESS: ============================= Precursor FDR =============================
5:50:51.596796 PROGRESS: Total precursors accumulated: 1,630
5:50:51.596857 PROGRESS: Target precursors: 1,614 (99.02%)
5:50:51.596910 PROGRESS: Decoy precursors: 16 (0.98%)
5:50:51.596960 PROGRESS: 
5:50:51.597008 PROGRESS: Precursor Summary:
5:50:51.598457 PROGRESS: Channel   0:	 0.050 FDR: 1,614; 0.010 FDR: 1,614; 0.001 FDR: 1,306
5:50:51.598547 PROGRESS: 
5:50:51.598604 PROGRESS: Protein Summary:
5:50:51.600482 PROGRESS: Channel   0:	 0.050 FDR: 1,407; 0.010 FDR: 1,407; 0.001 FDR: 1,139
5:50:51.600588 PROGRESS: =========================================================================
5:50:51.614635 INFO: Target number of precursors reached.
5:50:51.883807 INFO: fragments_df: keeping 5000 of 2408153 [sum(precursor_idx_mask)=33196 sum(mass_error_mask)=2408153 stop_rank=5000
5:50:52.265033 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:50:52.482446 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:50:53.132304 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:50:53.132766 INFO: Using score_cutoff 7.094776875114441 (fac=0.99, q=1)
5:50:53.133083 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:50:53.133160 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:50:53.133214 INFO: Updating optimization_manager: score_cutoff        : 10.141251282119752 -> 7.094776875114441
5:50:53.133272 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:50:53.278100 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:50:53.458729 INFO: === checking if optimization conditions were reached ===
5:50:53.458986 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
5:50:53.461809 INFO: Updating optimization_manager: rt_error            : 972.8751693307279 -> 964.2100285346364
5:50:53.461910 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 964.2100.
5:50:53.461971 INFO: ==============================================
5:50:53.462050 INFO: Starting optimization step 2.
5:50:53.462106 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:50:53.462176 INFO: Using rust extraction backend
5:50:53.462240 PROGRESS: Extracting batch of 250329 precursors
5:50:53.712699 INFO: === Search parameters used ===
5:50:53.712965 INFO: rt_error       : 964.2100285346364
5:50:53.713022 INFO: mobility_error : 0.1
5:50:53.713071 INFO: num_candidates : 3
5:50:53.713128 INFO: ms1_error      : 3
5:50:53.713184 INFO: ms2_error      : 10.0
5:50:53.713227 INFO: fwhm_rt        : 3.0
5:50:53.713266 INFO: quant_window   : 3
5:50:53.713306 INFO: ==============================================
5:50:55.888624 INFO: performing precursor FDR with 40 features
5:50:55.888745 INFO: Decoy channel: -1
5:50:55.888771 INFO: competitive: True
5:50:56.065352 INFO: Setting torch num_threads to 2 for FDR classification task
5:50:56.338334 INFO: Estimating optimal hyperparameters - samples: 579,839, batch_size: 2,375, learning_rate: 7.61e-04
5:50:56.339387 INFO: Using random state 4206 for train-test-split
5:51:09.065701 INFO: Test AUC: 0.585
5:51:09.065847 INFO: Train AUC: 0.600
5:51:09.065882 INFO: AUC difference: 2.50%
5:51:12.190451 INFO: Resetting torch num_threads to 100
5:51:12.275742 PROGRESS: === Extracted 724799 precursors and 2408059 fragments ===
5:51:12.276237 INFO: === FDR correction performed with classifier version 11 ===
5:51:12.277211 PROGRESS: ============================= Precursor FDR =============================
5:51:12.277305 PROGRESS: Total precursors accumulated: 1,756
5:51:12.277366 PROGRESS: Target precursors: 1,739 (99.03%)
5:51:12.277418 PROGRESS: Decoy precursors: 17 (0.97%)
5:51:12.277465 PROGRESS: 
5:51:12.277510 PROGRESS: Precursor Summary:
5:51:12.279033 PROGRESS: Channel   0:	 0.050 FDR: 1,739; 0.010 FDR: 1,739; 0.001 FDR: 1,185
5:51:12.279128 PROGRESS: 
5:51:12.279194 PROGRESS: Protein Summary:
5:51:12.281143 PROGRESS: Channel   0:	 0.050 FDR: 1,497; 0.010 FDR: 1,497; 0.001 FDR: 1,036
5:51:12.281238 PROGRESS: =========================================================================
5:51:12.310707 INFO: Target number of precursors reached.
5:51:12.574572 INFO: fragments_df: keeping 5000 of 2408059 [sum(precursor_idx_mask)=36276 sum(mass_error_mask)=2408059 stop_rank=5000
5:51:12.999077 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:51:13.263944 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:51:13.984416 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:51:13.984884 INFO: Using score_cutoff 8.249824170112609 (fac=0.99, q=1)
5:51:13.985202 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:51:13.985279 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:51:13.985335 INFO: Updating optimization_manager: score_cutoff        : 7.094776875114441 -> 8.249824170112609
5:51:13.985398 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:51:14.133435 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:51:14.330058 INFO: === checking if optimization conditions were reached ===
5:51:14.330361 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
5:51:14.334118 INFO: Updating optimization_manager: rt_error            : 964.2100285346364 -> 975.9964042374856
5:51:14.334247 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 975.9964.
5:51:14.334322 INFO: ==============================================
5:51:14.334409 INFO: Starting optimization step 3.
5:51:14.334503 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:51:14.334586 INFO: Using rust extraction backend
5:51:14.334660 PROGRESS: Extracting batch of 250329 precursors
5:51:14.587453 INFO: === Search parameters used ===
5:51:14.587734 INFO: rt_error       : 975.9964042374856
5:51:14.587802 INFO: mobility_error : 0.1
5:51:14.587850 INFO: num_candidates : 3
5:51:14.587894 INFO: ms1_error      : 3
5:51:14.587936 INFO: ms2_error      : 10.0
5:51:14.587974 INFO: fwhm_rt        : 3.0
5:51:14.588014 INFO: quant_window   : 3
5:51:14.588053 INFO: ==============================================
5:51:16.817018 INFO: performing precursor FDR with 40 features
5:51:16.817141 INFO: Decoy channel: -1
5:51:16.817168 INFO: competitive: True
5:51:17.010043 INFO: Setting torch num_threads to 2 for FDR classification task
5:51:17.302141 INFO: Estimating optimal hyperparameters - samples: 579,837, batch_size: 2,375, learning_rate: 7.61e-04
5:51:17.303229 INFO: Using random state 4206 for train-test-split
5:51:29.713118 INFO: Test AUC: 0.587
5:51:29.713247 INFO: Train AUC: 0.601
5:51:29.713280 INFO: AUC difference: 2.28%
5:51:30.200651 INFO: Resetting torch num_threads to 100
5:51:30.276078 PROGRESS: === Extracted 724797 precursors and 2408096 fragments ===
5:51:30.276571 INFO: === FDR correction performed with classifier version 11 ===
5:51:30.277332 PROGRESS: ============================= Precursor FDR =============================
5:51:30.277431 PROGRESS: Total precursors accumulated: 1,776
5:51:30.277495 PROGRESS: Target precursors: 1,759 (99.04%)
5:51:30.277548 PROGRESS: Decoy precursors: 17 (0.96%)
5:51:30.277596 PROGRESS: 
5:51:30.277643 PROGRESS: Precursor Summary:
5:51:30.279113 PROGRESS: Channel   0:	 0.050 FDR: 1,759; 0.010 FDR: 1,759; 0.001 FDR: 1,150
5:51:30.279220 PROGRESS: 
5:51:30.279279 PROGRESS: Protein Summary:
5:51:30.281211 PROGRESS: Channel   0:	 0.050 FDR: 1,509; 0.010 FDR: 1,509; 0.001 FDR: 1,005
5:51:30.281304 PROGRESS: =========================================================================
5:51:30.294757 INFO: Target number of precursors reached.
5:51:30.565440 INFO: fragments_df: keeping 5000 of 2408096 [sum(precursor_idx_mask)=36903 sum(mass_error_mask)=2408096 stop_rank=5000
5:51:31.024672 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:51:31.262441 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:51:31.918016 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:51:31.918491 INFO: Using score_cutoff 10.336103584098817 (fac=0.99, q=1)
5:51:31.918807 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:51:31.918883 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:51:31.918938 INFO: Updating optimization_manager: score_cutoff        : 8.249824170112609 -> 10.336103584098817
5:51:31.918990 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:51:32.065815 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:51:32.260710 INFO: === checking if optimization conditions were reached ===
5:51:32.261027 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
5:51:32.264617 INFO: Updating optimization_manager: rt_error            : 975.9964042374856 -> 718.4538668474374
5:51:32.264741 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 718.4539.
5:51:32.264817 INFO: ==============================================
5:51:32.264902 INFO: Starting optimization step 4.
5:51:32.264972 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:51:32.265052 INFO: Using rust extraction backend
5:51:32.265121 PROGRESS: Extracting batch of 250329 precursors
5:51:32.519538 INFO: === Search parameters used ===
5:51:32.519822 INFO: rt_error       : 718.4538668474374
5:51:32.519881 INFO: mobility_error : 0.1
5:51:32.519928 INFO: num_candidates : 3
5:51:32.519971 INFO: ms1_error      : 3
5:51:32.520011 INFO: ms2_error      : 10.0
5:51:32.520053 INFO: fwhm_rt        : 3.0
5:51:32.520094 INFO: quant_window   : 3
5:51:32.520147 INFO: ==============================================
5:51:34.761512 INFO: performing precursor FDR with 40 features
5:51:34.761634 INFO: Decoy channel: -1
5:51:34.761661 INFO: competitive: True
5:51:34.947720 INFO: Setting torch num_threads to 2 for FDR classification task
5:51:35.234638 INFO: Estimating optimal hyperparameters - samples: 579,565, batch_size: 2,373, learning_rate: 7.61e-04
5:51:35.235638 INFO: Using random state 4206 for train-test-split
5:51:47.567760 INFO: Test AUC: 0.584
5:51:47.567893 INFO: Train AUC: 0.599
5:51:47.567926 INFO: AUC difference: 2.52%
5:51:48.040392 INFO: Resetting torch num_threads to 100
5:51:48.068181 PROGRESS: === Extracted 724457 precursors and 2404243 fragments ===
5:51:48.068684 INFO: === FDR correction performed with classifier version 11 ===
5:51:48.069414 PROGRESS: ============================= Precursor FDR =============================
5:51:48.069509 PROGRESS: Total precursors accumulated: 1,803
5:51:48.069570 PROGRESS: Target precursors: 1,786 (99.06%)
5:51:48.069623 PROGRESS: Decoy precursors: 17 (0.94%)
5:51:48.069670 PROGRESS: 
5:51:48.069716 PROGRESS: Precursor Summary:
5:51:48.071212 PROGRESS: Channel   0:	 0.050 FDR: 1,786; 0.010 FDR: 1,786; 0.001 FDR: 1,026
5:51:48.071304 PROGRESS: 
5:51:48.071368 PROGRESS: Protein Summary:
5:51:48.073247 PROGRESS: Channel   0:	 0.050 FDR: 1,536; 0.010 FDR: 1,536; 0.001 FDR:   894
5:51:48.073344 PROGRESS: =========================================================================
5:51:48.087848 INFO: Target number of precursors reached.
5:51:48.346420 INFO: fragments_df: keeping 5000 of 2404243 [sum(precursor_idx_mask)=37160 sum(mass_error_mask)=2404243 stop_rank=5000
5:51:48.715266 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:51:48.960540 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:51:49.656783 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:51:49.657251 INFO: Using score_cutoff 10.020816753387452 (fac=0.99, q=1)
5:51:49.657577 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:51:49.657655 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:51:49.657711 INFO: Updating optimization_manager: score_cutoff        : 10.336103584098817 -> 10.020816753387452
5:51:49.657768 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:51:49.804654 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:51:49.999676 INFO: === checking if optimization conditions were reached ===
5:51:49.999970 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
5:51:50.003580 INFO: Updating optimization_manager: rt_error            : 718.4538668474374 -> 907.5658914469814
5:51:50.003706 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 907.5659.
5:51:50.003786 INFO: ==============================================
5:51:50.003882 INFO: Starting optimization step 5.
5:51:50.003954 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:51:50.004060 INFO: Using rust extraction backend
5:51:50.004144 PROGRESS: Extracting batch of 250329 precursors
5:51:50.256415 INFO: === Search parameters used ===
5:51:50.256683 INFO: rt_error       : 907.5658914469814
5:51:50.256742 INFO: mobility_error : 0.1
5:51:50.256789 INFO: num_candidates : 3
5:51:50.256833 INFO: ms1_error      : 3
5:51:50.256876 INFO: ms2_error      : 10.0
5:51:50.256917 INFO: fwhm_rt        : 3.0
5:51:50.256957 INFO: quant_window   : 3
5:51:50.256997 INFO: ==============================================
5:51:52.491004 INFO: performing precursor FDR with 40 features
5:51:52.491125 INFO: Decoy channel: -1
5:51:52.491171 INFO: competitive: True
5:51:52.681892 INFO: Setting torch num_threads to 2 for FDR classification task
5:51:52.975386 INFO: Estimating optimal hyperparameters - samples: 579,822, batch_size: 2,374, learning_rate: 7.61e-04
5:51:52.976462 INFO: Using random state 4206 for train-test-split
5:52:05.267500 INFO: Test AUC: 0.585
5:52:05.267640 INFO: Train AUC: 0.600
5:52:05.267685 INFO: AUC difference: 2.60%
5:52:05.751174 INFO: Resetting torch num_threads to 100
5:52:05.777505 PROGRESS: === Extracted 724778 precursors and 2407992 fragments ===
5:52:05.777985 INFO: === FDR correction performed with classifier version 11 ===
5:52:05.778738 PROGRESS: ============================= Precursor FDR =============================
5:52:05.778831 PROGRESS: Total precursors accumulated: 1,755
5:52:05.778892 PROGRESS: Target precursors: 1,738 (99.03%)
5:52:05.778941 PROGRESS: Decoy precursors: 17 (0.97%)
5:52:05.778988 PROGRESS: 
5:52:05.779033 PROGRESS: Precursor Summary:
5:52:05.780532 PROGRESS: Channel   0:	 0.050 FDR: 1,738; 0.010 FDR: 1,738; 0.001 FDR: 1,018
5:52:05.780627 PROGRESS: 
5:52:05.780686 PROGRESS: Protein Summary:
5:52:05.782631 PROGRESS: Channel   0:	 0.050 FDR: 1,490; 0.010 FDR: 1,490; 0.001 FDR:   890
5:52:05.782728 PROGRESS: =========================================================================
5:52:05.802754 INFO: Target number of precursors reached.
5:52:06.066255 INFO: fragments_df: keeping 5000 of 2407992 [sum(precursor_idx_mask)=36538 sum(mass_error_mask)=2407992 stop_rank=5000
5:52:06.433508 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:52:06.708299 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:52:07.428681 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:52:07.429145 INFO: Using score_cutoff 10.4652245844841 (fac=0.99, q=1)
5:52:07.429454 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:52:07.429529 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:52:07.429581 INFO: Updating optimization_manager: score_cutoff        : 10.020816753387452 -> 10.4652245844841
5:52:07.429632 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:52:07.576294 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:52:07.769514 INFO: === checking if optimization conditions were reached ===
5:52:07.769813 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
5:52:07.773345 INFO: Updating optimization_manager: rt_error            : 907.5658914469814 -> 934.7812627519497
5:52:07.773480 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 934.7813.
5:52:07.773557 INFO: ==============================================
5:52:07.773651 INFO: Starting optimization step 6.
5:52:07.773722 PROGRESS: === Extracting elution groups 0 to 127000 ===
5:52:07.773794 INFO: Using rust extraction backend
5:52:07.773860 PROGRESS: Extracting batch of 250329 precursors
5:52:08.028316 INFO: === Search parameters used ===
5:52:08.028609 INFO: rt_error       : 934.7812627519497
5:52:08.028666 INFO: mobility_error : 0.1
5:52:08.028716 INFO: num_candidates : 3
5:52:08.028759 INFO: ms1_error      : 3
5:52:08.028801 INFO: ms2_error      : 10.0
5:52:08.028841 INFO: fwhm_rt        : 3.0
5:52:08.028880 INFO: quant_window   : 3
5:52:08.028918 INFO: ==============================================
5:52:10.255013 INFO: performing precursor FDR with 40 features
5:52:10.255142 INFO: Decoy channel: -1
5:52:10.255188 INFO: competitive: True
5:52:10.452036 INFO: Setting torch num_threads to 2 for FDR classification task
5:52:10.749060 INFO: Estimating optimal hyperparameters - samples: 579,829, batch_size: 2,374, learning_rate: 7.61e-04
5:52:10.749931 INFO: Using random state 4206 for train-test-split
5:52:23.523410 INFO: Test AUC: 0.585
5:52:23.523536 INFO: Train AUC: 0.600
5:52:23.523571 INFO: AUC difference: 2.53%
5:52:24.004271 INFO: Resetting torch num_threads to 100
5:52:24.031286 PROGRESS: === Extracted 724787 precursors and 2407803 fragments ===
5:52:24.031770 INFO: === FDR correction performed with classifier version 11 ===
5:52:24.032507 PROGRESS: ============================= Precursor FDR =============================
5:52:24.032598 PROGRESS: Total precursors accumulated: 1,826
5:52:24.032659 PROGRESS: Target precursors: 1,808 (99.01%)
5:52:24.032723 PROGRESS: Decoy precursors: 18 (0.99%)
5:52:24.032776 PROGRESS: 
5:52:24.032821 PROGRESS: Precursor Summary:
5:52:24.034343 PROGRESS: Channel   0:	 0.050 FDR: 1,808; 0.010 FDR: 1,808; 0.001 FDR: 1,303
5:52:24.034445 PROGRESS: 
5:52:24.034501 PROGRESS: Protein Summary:
5:52:24.036489 PROGRESS: Channel   0:	 0.050 FDR: 1,554; 0.010 FDR: 1,554; 0.001 FDR: 1,134
5:52:24.036586 PROGRESS: =========================================================================
5:52:24.050857 INFO: Target number of precursors reached.
5:52:24.318398 INFO: fragments_df: keeping 5000 of 2407803 [sum(precursor_idx_mask)=37964 sum(mass_error_mask)=2407803 stop_rank=5000
5:52:24.687313 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
5:52:24.931303 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
5:52:25.589842 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
5:52:25.590314 INFO: Using score_cutoff 10.300288405036925 (fac=0.99, q=1)
5:52:25.590629 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:52:25.590709 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:52:25.590766 INFO: Updating optimization_manager: score_cutoff        : 10.4652245844841 -> 10.300288405036925
5:52:25.590822 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:52:25.738478 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:52:25.930056 INFO: === checking if optimization conditions were reached ===
5:52:25.930319 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
5:52:25.931242 INFO: Updating optimization_manager: rt_error            : 934.7812627519497 -> 934.7812627519497
5:52:25.931370 INFO: Updating optimization_manager: classifier_version  : 11 -> 18
5:52:25.931484 INFO: Updating optimization_manager: score_cutoff        : 10.300288405036925 -> 10.300288405036925
5:52:25.931576 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
5:52:25.931664 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
5:52:25.931754 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 934.7813 found after 7 searches.
5:52:25.931818 INFO: ==============================================
5:52:25.931898 PROGRESS: Optimization finished for rt_error.
5:52:26.283935 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:52:26.431740 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:52:26.619360 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
5:52:26.619611 PROGRESS: ==============================================
5:52:26.619687 PROGRESS: ms2_error      : 10.0000
5:52:26.619745 PROGRESS: rt_error       : 934.7813
5:52:26.619792 PROGRESS: ==============================================
5:52:26.620597 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
5:52:34.067290 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
5:52:43.453122 INFO: Using rust extraction backend
5:52:43.453412 PROGRESS: Extracting batch of 11997144 precursors
5:52:53.686732 INFO: === Search parameters used ===
5:52:53.687022 INFO: rt_error       : 934.7812627519497
5:52:53.687095 INFO: mobility_error : 0.1
5:52:53.687157 INFO: num_candidates : 3
5:52:53.687207 INFO: ms1_error      : 3
5:52:53.687251 INFO: ms2_error      : 10.0
5:52:53.687296 INFO: fwhm_rt        : 3.0
5:52:53.687351 INFO: quant_window   : 3
5:52:53.687394 INFO: ==============================================
5:53:23.985824 INFO: Removed 15767083 precursors with score below cutoff 10.300288405036925
5:53:43.020762 INFO: performing precursor FDR with 40 features
5:53:43.020971 INFO: Decoy channel: -1
5:53:43.020999 INFO: competitive: True
5:53:47.772052 INFO: Setting torch num_threads to 2 for FDR classification task
5:54:13.658267 INFO: Estimating optimal hyperparameters - samples: 16,045,151, batch_size: 4,096, learning_rate: 1.00e-03
5:54:13.848392 INFO: Using random state 948568 for train-test-split
6:07:01.762842 INFO: Test AUC: 0.597
6:07:01.763628 INFO: Train AUC: 0.598
6:07:01.763917 INFO: AUC difference: 0.12%
6:07:08.585565 INFO: Resetting torch num_threads to 100
6:07:13.908574 PROGRESS: ============================= Precursor FDR =============================
6:07:13.909513 PROGRESS: Total precursors accumulated: 102,425
6:07:13.909600 PROGRESS: Target precursors: 101,411 (99.01%)
6:07:13.909668 PROGRESS: Decoy precursors: 1,014 (0.99%)
6:07:13.909725 PROGRESS: 
6:07:13.909781 PROGRESS: Precursor Summary:
6:07:14.028518 PROGRESS: Channel   0:	 0.050 FDR: 101,411; 0.010 FDR: 101,411; 0.001 FDR: 70,298
6:07:14.029710 PROGRESS: 
6:07:14.029787 PROGRESS: Protein Summary:
6:07:14.212147 PROGRESS: Channel   0:	 0.050 FDR: 14,173; 0.010 FDR: 14,173; 0.001 FDR: 10,323
6:07:14.213156 PROGRESS: =========================================================================
6:07:14.591333 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/psm.parquet
6:07:15.127077 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.parquet
6:07:15.778058 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
6:07:59.830911 PROGRESS: Processing search outputs
6:07:59.831598 PROGRESS: === Performing protein grouping and FDR ===
6:07:59.831704 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
6:07:59.978357 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
6:08:00.144929 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
6:08:00.296300 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
6:08:00.465090 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
6:08:00.648672 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
6:08:00.861644 INFO: Performing protein inference
6:08:01.916931 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
6:14:59.673454 INFO: Performing protein FDR
6:15:13.565657 INFO: Normalizing q-values using 20,746 targets and 4,183 decoys
6:15:13.573770 INFO: Test AUC: 0.850
6:15:13.574155 INFO: Train AUC: 0.863
6:15:13.574205 INFO: AUC difference: 1.44%
6:15:15.380778 INFO: ================ Protein FDR =================
6:15:15.381413 INFO: Unique protein groups in output
6:15:15.381485 INFO:   1% protein FDR: 10,661
6:15:15.381517 INFO: 
6:15:15.381545 INFO: Unique precursor in output
6:15:15.381567 INFO:   1% protein FDR: 146,300
6:15:15.381587 INFO: ================================================
6:15:15.550862 PROGRESS: Building search statistics
6:15:15.865268 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
6:15:15.865916 INFO: Initializing OptimizationManager
6:15:15.866527 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
6:15:15.866617 INFO: Initializing CalibrationManager
6:15:15.867074 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
6:15:15.867182 INFO: Initializing RawFileManager
6:15:15.946476 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
6:15:15.947059 INFO: Initializing OptimizationManager
6:15:15.947635 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
6:15:15.947849 INFO: Initializing CalibrationManager
6:15:15.948312 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
6:15:15.948499 INFO: Initializing RawFileManager
6:15:16.030590 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
6:15:16.031117 INFO: Initializing OptimizationManager
6:15:16.031518 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
6:15:16.031627 INFO: Initializing CalibrationManager
6:15:16.031983 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
6:15:16.032059 INFO: Initializing RawFileManager
6:15:16.117311 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
6:15:16.117901 INFO: Initializing OptimizationManager
6:15:16.118263 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
6:15:16.118347 INFO: Initializing CalibrationManager
6:15:16.118704 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
6:15:16.118788 INFO: Initializing RawFileManager
6:15:16.203596 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
6:15:16.204198 INFO: Initializing OptimizationManager
6:15:16.204564 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
6:15:16.204662 INFO: Initializing CalibrationManager
6:15:16.205052 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
6:15:16.205165 INFO: Initializing RawFileManager
6:15:16.297736 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
6:15:16.298336 INFO: Initializing OptimizationManager
6:15:16.298913 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
6:15:16.299195 INFO: Initializing CalibrationManager
6:15:16.299721 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
6:15:16.299892 INFO: Initializing RawFileManager
6:15:16.314151 INFO: Writing stat output to disk
6:15:16.314689 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/stat.tsv to disk
6:15:16.350755 PROGRESS: Building internal statistics
6:15:16.352141 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
6:15:16.352210 INFO: Initializing TimingManager
6:15:16.353366 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
6:15:16.353469 INFO: Initializing TimingManager
6:15:16.353754 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
6:15:16.353789 INFO: Initializing TimingManager
6:15:16.354055 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
6:15:16.354094 INFO: Initializing TimingManager
6:15:16.354334 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
6:15:16.354375 INFO: Initializing TimingManager
6:15:16.354636 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
6:15:16.354675 INFO: Initializing TimingManager
6:15:16.355681 INFO: Writing internal output to disk
6:15:16.355765 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/internal.tsv to disk
6:15:16.625395 INFO: Performing label free quantification
6:15:16.625868 INFO: Accumulating fragment data
6:15:16.626025 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
6:15:16.890472 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
6:15:20.804010 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
6:15:24.499625 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
6:15:28.984650 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
6:15:33.660448 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
6:15:39.618766 INFO: Performing label free quantification on the precursor level
6:15:39.619406 INFO: Filtering fragments by quality
6:15:40.660881 INFO: Performing label-free quantification with directlfq normalization
6:15:42.215697 INFO: Applying directLFQ normalization
6:15:42.984427 INFO: 146300 lfq-groups total
6:17:39.544831 INFO: using 100 processes
6:17:39.808087 INFO: lfq-object 0
6:17:39.907326 INFO: lfq-object 100
6:17:39.948696 INFO: lfq-object 400
6:17:40.021202 INFO: lfq-object 200
6:17:40.054190 INFO: lfq-object 500
6:17:40.109794 INFO: lfq-object 800
6:17:40.132565 INFO: lfq-object 300
6:17:40.153110 INFO: lfq-object 600
6:17:40.154768 INFO: lfq-object 1100
6:17:40.218100 INFO: lfq-object 900
6:17:40.253581 INFO: lfq-object 700
6:17:40.264242 INFO: lfq-object 1200
6:17:40.285105 INFO: lfq-object 1500
6:17:40.324924 INFO: lfq-object 1000
6:17:40.362448 INFO: lfq-object 1300
6:17:40.385724 INFO: lfq-object 1600
6:17:40.425053 INFO: lfq-object 1900
6:17:40.464543 INFO: lfq-object 1400
6:17:40.486944 INFO: lfq-object 1700
6:17:40.493000 INFO: lfq-object 2200
6:17:40.523955 INFO: lfq-object 2000
6:17:40.592629 INFO: lfq-object 1800
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6:17:40.619869 INFO: lfq-object 2100
6:17:40.692759 INFO: lfq-object 2600
6:17:40.698074 INFO: lfq-object 2400
6:17:40.802848 INFO: lfq-object 2500
6:17:40.815436 INFO: lfq-object 2700
6:17:40.891580 INFO: lfq-object 3000
6:17:40.968897 INFO: lfq-object 2800
6:17:40.995115 INFO: lfq-object 3100
6:17:41.005995 INFO: lfq-object 3300
6:17:41.093585 INFO: lfq-object 3200
6:17:41.102997 INFO: lfq-object 3400
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6:17:41.507226 INFO: lfq-object 4200
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6:17:41.622010 INFO: lfq-object 4000
6:17:41.630657 INFO: lfq-object 4300
6:17:41.685267 INFO: lfq-object 4600
6:17:41.724950 INFO: lfq-object 4800
6:17:41.806354 INFO: lfq-object 4700
6:17:41.872357 INFO: lfq-object 4900
6:17:42.000519 INFO: lfq-object 5000
6:17:42.134792 INFO: lfq-object 5100
6:17:47.933234 INFO: lfq-object 5200
6:17:48.040127 INFO: lfq-object 5500
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6:17:50.413573 INFO: lfq-object 10000
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6:23:01.089130 INFO: lfq-object 131000
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6:23:13.072978 INFO: Performing label free quantification on the pg level
6:23:13.073503 INFO: Filtering fragments by quality
6:23:13.467034 INFO: Performing label-free quantification with directlfq normalization
6:23:13.668508 INFO: Applying directLFQ normalization
6:23:13.872935 INFO: 10661 lfq-groups total
6:26:38.924903 INFO: using 100 processes
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6:26:48.252423 INFO: lfq-object 8000
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6:26:48.839660 INFO: lfq-object 8600
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6:26:49.102167 INFO: lfq-object 8700
6:26:49.344115 INFO: lfq-object 8900
6:26:49.395117 INFO: lfq-object 9000
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6:26:49.474858 INFO: lfq-object 8800
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6:26:50.194914 INFO: lfq-object 9500
6:26:50.501271 INFO: lfq-object 9700
6:26:50.571630 INFO: lfq-object 9600
6:26:50.572503 INFO: lfq-object 9800
6:26:50.663682 INFO: lfq-object 9900
6:26:50.784714 INFO: lfq-object 10000
6:26:50.916867 INFO: lfq-object 10100
6:26:51.077139 INFO: lfq-object 10200
6:26:51.173209 INFO: lfq-object 10300
6:26:51.355897 INFO: lfq-object 10400
6:26:51.875290 INFO: lfq-object 10500
6:26:52.183256 INFO: lfq-object 10600
6:26:58.179996 INFO: Writing psm output to disk
6:26:58.410774 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/precursors.parquet to disk
6:26:59.486703 INFO: Writing precursor output to disk
6:26:59.497211 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/precursor.matrix.parquet to disk
6:26:59.648794 INFO: Writing peptide output to disk
6:26:59.659858 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/peptide.matrix.parquet to disk
6:26:59.778617 INFO: Writing pg output to disk
6:26:59.783816 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/pg.matrix.parquet to disk
6:26:59.943522 PROGRESS: Building MBR spectral library
6:26:59.943956 INFO: Running MbrLibraryBuilder
6:27:05.435977 INFO: MBR spectral library contains 146,300 precursors, 10,661 proteins
6:27:05.437077 INFO: Writing MBR spectral library to disk
6:27:09.821754 PROGRESS: =================== Search step 'library' finished ===================
6:27:12.676667 INFO: =================== Running step 'mbr' ===================
6:27:12.678910 INFO: loading default config from /home/robbe/bin/alphadia/alphadia/constants/default.yaml
6:27:12.706458 INFO: loading additional config provided via CLI
6:27:12.707352 INFO: loading additional config provided via CLI parameters
6:27:12.708633 INFO: Updating config with 'user defined'
6:27:12.708881 INFO: Updating config with 'user defined (cli)'
6:27:12.709494 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/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1', 'general': {'thread_count': 100, 'mbr_step_enabled': True, 'transfer_step_enabled': True}, 'library_prediction': {'enabled': True, 'enzyme': 'trypsin/p', 'missed_cleavages': 1, 'fixed_modifications': 'Carbamidomethyl@C', 'variable_modifications': 'Oxidation@M', 'max_var_mod_num': 1, 'precursor_len': [6, 30], 'precursor_charge': [1, 5], 'precursor_mz': [380.0, 980.0], 'fragment_mz': [150.0, 2000.0]}, 'search': {'target_ms1_tolerance': 3, 'target_ms2_tolerance': 10, 'extraction_backend': 'rust'}, 'fdr': {'fdr': 0.01, 'group_level': 'proteins'}, 'search_output': {'normalize_directlfq': True}, 'search_initial': {'ms1_tolerance': 3, 'ms2_tolerance': 10}}, {'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': [], 'fdr': {'inference_strategy': 'library'}, 'search': {'target_ms1_tolerance': 3.0, 'target_ms2_tolerance': 10.0}, 'quant_directory': None, 'library_prediction': {'enabled': False}, 'transfer_library': {'enabled': False}, 'transfer_learning': {'enabled': False}, 'library_path': '/home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf', 'output_directory': '/home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1'}]
6:27:12.709851 INFO: Updating config with 'user defined'
6:27:12.709911 INFO: Updating config with 'user defined (cli)'
6:27:12.709931 INFO: Updating config with 'multistep search'
6:27:12.710085 INFO: ├──version: None
6:27:12.710129 INFO: ├──workflow_name: None
6:27:12.710168 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1 [multistep search, default: None][0m
6:27:12.710240 INFO: [32;20m├──library_path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf [multistep search, default: None][0m
6:27:12.710281 INFO: ├──raw_paths:
6:27:12.710308 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
6:27:12.710335 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
6:27:12.710381 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
6:27:12.710398 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
6:27:12.710418 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
6:27:12.710436 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
6:27:12.710453 INFO: ├──fasta_paths:
6:27:12.710470 INFO: ├──quant_directory: None
6:27:12.710490 INFO: ├──general
6:27:12.710510 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
6:27:12.710546 INFO: │   [32;20m├──transfer_step_enabled: True [user defined, default: False][0m
6:27:12.710576 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
6:27:12.710593 INFO: │   ├──reuse_calibration: False
6:27:12.710615 INFO: │   ├──reuse_quant: False
6:27:12.710633 INFO: │   ├──log_level: INFO
6:27:12.710650 INFO: │   ├──use_gpu: True
6:27:12.710673 INFO: │   ├──save_figures: True
6:27:12.710690 INFO: │   ├──save_library: True
6:27:12.710710 INFO: │   ├──save_flat_library: False
6:27:12.710730 INFO: │   ├──input_library_type: base
6:27:12.710748 INFO: │   ├──save_mbr_library: True
6:27:12.710767 INFO: │   ├──random_state: None
6:27:12.710791 INFO: │   └──fail_fast: False
6:27:12.710808 INFO: ├──library_loading
6:27:12.710827 INFO: │   └──drop_decoys: False
6:27:12.710844 INFO: ├──library_prediction
6:27:12.710862 INFO: │   ├──enabled: False
6:27:12.710879 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
6:27:12.710902 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
6:27:12.710927 INFO: │   [32;20m├──variable_modifications: Oxidation@M [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
6:27:12.710950 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
6:27:12.710968 INFO: │   ├──missed_cleavages: 1
6:27:12.710985 INFO: │   ├──precursor_len:
6:27:12.711004 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
6:27:12.711021 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
6:27:12.711040 INFO: │   ├──precursor_charge:
6:27:12.711061 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
6:27:12.711080 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
6:27:12.711098 INFO: │   ├──precursor_mz:
6:27:12.711122 INFO: │   │   [32;20m- 380.0 [user defined, default: 400][0m
6:27:12.711169 INFO: │   │   [32;20m- 980.0 [user defined, default: 1200][0m
6:27:12.711196 INFO: │   ├──fragment_mz:
6:27:12.711220 INFO: │   │   [32;20m- 150.0 [user defined, default: 200][0m
6:27:12.711240 INFO: │   │   - 2000.0
6:27:12.711258 INFO: │   ├──nce: 25.0
6:27:12.711276 INFO: │   ├──fragment_types:
6:27:12.711293 INFO: │   │   - b
6:27:12.711309 INFO: │   │   - y
6:27:12.711332 INFO: │   ├──max_fragment_charge: 2
6:27:12.711352 INFO: │   ├──instrument: Lumos
6:27:12.711371 INFO: │   ├──peptdeep_model_path: None
6:27:12.711389 INFO: │   ├──peptdeep_model_type: generic
6:27:12.711409 INFO: │   ├──predict_charge: False
6:27:12.711429 INFO: │   └──min_charge_probability: 0.1
6:27:12.711448 INFO: ├──custom_modifications:
6:27:12.711467 INFO: │   ├──name: Dimethyl:d12@K
6:27:12.711486 INFO: │   └──composition: H(-2)2H(8)13C(2)
6:27:12.711504 INFO: │   ├──name: Dimethyl:d12@Any_N-term
6:27:12.711522 INFO: │   └──composition: H(-2)2H(8)13C(2)
6:27:12.711540 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
6:27:12.711567 INFO: │   └──composition: H(-2)2H(8)13C(2)
6:27:12.711585 INFO: │   ├──name: mTRAQ:d12@K
6:27:12.711602 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
6:27:12.711620 INFO: │   ├──name: mTRAQ:d12@Any_N-term
6:27:12.711639 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
6:27:12.711657 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
6:27:12.711674 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
6:27:12.711692 INFO: │   ├──name: Label:13C(12)@K
6:27:12.711709 INFO: │   └──composition: C(12)
6:27:12.711725 INFO: ├──search
6:27:12.711743 INFO: │   ├──extraction_backend: rust
6:27:12.711775 INFO: │   [32;20m├──target_ms1_tolerance: 3.0 [multistep search, default: 5][0m
6:27:12.711794 INFO: │   ├──target_ms2_tolerance: 10.0
6:27:12.711812 INFO: │   ├──target_rt_tolerance: 0.0
6:27:12.711829 INFO: │   ├──target_mobility_tolerance: 0.0
6:27:12.711847 INFO: │   ├──quant_window: 3
6:27:12.711865 INFO: │   ├──target_num_candidates: 3
6:27:12.711883 INFO: │   ├──channel_filter: 
6:27:12.711900 INFO: │   ├──compete_for_fragments: True
6:27:12.711918 INFO: │   ├──top_k_fragments_selection: 12
6:27:12.711936 INFO: │   ├──top_k_fragments_scoring: 12
6:27:12.711953 INFO: │   ├──min_fragment_intensity: 0.01
6:27:12.711972 INFO: │   ├──optimized_peak_group_score: False
6:27:12.711989 INFO: │   ├──exclude_shared_ions: True
6:27:12.712006 INFO: │   ├──quant_all: True
6:27:12.712023 INFO: │   └──experimental_xic: True
6:27:12.712040 INFO: ├──calibration
6:27:12.712058 INFO: │   ├──batch_size: 1000
6:27:12.712076 INFO: │   ├──optimization_lock_target: 1000
6:27:12.712094 INFO: │   ├──max_steps: 20
6:27:12.712112 INFO: │   ├──min_steps: 5
6:27:12.712129 INFO: │   ├──max_skips: 1
6:27:12.712146 INFO: │   ├──max_fragments: 5000
6:27:12.712164 INFO: │   └──min_correlation: 0.7
6:27:12.712180 INFO: ├──search_initial
6:27:12.712198 INFO: │   ├──num_candidates: 1
6:27:12.712216 INFO: │   [32;20m├──ms1_tolerance: 3 [user defined, default: 30][0m
6:27:12.712233 INFO: │   [32;20m├──ms2_tolerance: 10 [user defined, default: 30][0m
6:27:12.712250 INFO: │   ├──mobility_tolerance: 0.1
6:27:12.712268 INFO: │   └──rt_tolerance: 0.5
6:27:12.712285 INFO: ├──library_multiplexing
6:27:12.712302 INFO: │   ├──enabled: False
6:27:12.712319 INFO: │   ├──input_channel: 0
6:27:12.712339 INFO: │   └──multiplex_mapping:
6:27:12.712356 INFO: ├──multiplexing
6:27:12.712374 INFO: │   ├──enabled: False
6:27:12.712393 INFO: │   ├──target_channels: 4,8
6:27:12.712415 INFO: │   ├──decoy_channel: 12
6:27:12.712436 INFO: │   ├──reference_channel: 0
6:27:12.712457 INFO: │   └──competitive_scoring: True
6:27:12.712473 INFO: ├──fdr
6:27:12.712494 INFO: │   ├──fdr: 0.01
6:27:12.712511 INFO: │   ├──group_level: proteins
6:27:12.712528 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
6:27:12.712547 INFO: │   ├──competitive_scoring: True
6:27:12.712565 INFO: │   ├──keep_decoys: False
6:27:12.712582 INFO: │   ├──keep_decoys_in_mbr_library: False
6:27:12.712601 INFO: │   ├──channel_wise_fdr: False
6:27:12.712620 INFO: │   └──enable_nn_hyperparameter_tuning: True
6:27:12.712637 INFO: ├──search_output
6:27:12.712656 INFO: │   ├──file_format: parquet
6:27:12.712675 INFO: │   ├──precursor_level_lfq: True
6:27:12.712694 INFO: │   ├──peptide_level_lfq: True
6:27:12.712712 INFO: │   ├──save_fragment_quant_matrix: False
6:27:12.712730 INFO: │   ├──min_k_fragments: 12
6:27:12.712749 INFO: │   ├──min_correlation: 0.9
6:27:12.712767 INFO: │   ├──num_samples_quadratic: 50
6:27:12.712785 INFO: │   ├──min_nonnan: 3
6:27:12.712807 INFO: │   ├──normalization_method: directlfq
6:27:12.712827 INFO: │   └──normalize_directlfq: True
6:27:12.712845 INFO: ├──optimization
6:27:12.712864 INFO: │   ├──order_of_optimization: None
6:27:12.712881 INFO: │   ├──ms2_error
6:27:12.712901 INFO: │   │   ├──targeted_update_percentile_range: 0.95
6:27:12.712920 INFO: │   │   ├──targeted_update_factor: 1.0
6:27:12.712939 INFO: │   │   ├──automatic_update_percentile_range: 0.99
6:27:12.712956 INFO: │   │   ├──automatic_update_factor: 1.1
6:27:12.712974 INFO: │   │   ├──try_narrower_values: True
6:27:12.712992 INFO: │   │   ├──maximal_decrease: 0.5
6:27:12.713010 INFO: │   │   ├──favour_narrower_optimum: False
6:27:12.713028 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
6:27:12.713044 INFO: │   ├──ms1_error
6:27:12.713063 INFO: │   │   ├──targeted_update_percentile_range: 0.95
6:27:12.713081 INFO: │   │   ├──targeted_update_factor: 1.0
6:27:12.713099 INFO: │   │   ├──automatic_update_percentile_range: 0.99
6:27:12.713116 INFO: │   │   ├──automatic_update_factor: 1.1
6:27:12.713133 INFO: │   │   ├──try_narrower_values: False
6:27:12.713151 INFO: │   │   ├──maximal_decrease: 0.2
6:27:12.713168 INFO: │   │   ├──favour_narrower_optimum: False
6:27:12.713185 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
6:27:12.713204 INFO: │   ├──mobility_error
6:27:12.713222 INFO: │   │   ├──targeted_update_percentile_range: 0.95
6:27:12.713239 INFO: │   │   ├──targeted_update_factor: 1.0
6:27:12.713256 INFO: │   │   ├──automatic_update_percentile_range: 0.99
6:27:12.713280 INFO: │   │   ├──automatic_update_factor: 1.1
6:27:12.713300 INFO: │   │   ├──try_narrower_values: False
6:27:12.713317 INFO: │   │   ├──maximal_decrease: 0.2
6:27:12.713335 INFO: │   │   ├──favour_narrower_optimum: False
6:27:12.713352 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
6:27:12.713370 INFO: │   └──rt_error
6:27:12.713389 INFO: │       ├──targeted_update_percentile_range: 0.95
6:27:12.713406 INFO: │       ├──targeted_update_factor: 1.0
6:27:12.713424 INFO: │       ├──automatic_update_percentile_range: 0.999
6:27:12.713442 INFO: │       ├──automatic_update_factor: 1.5
6:27:12.713459 INFO: │       ├──try_narrower_values: True
6:27:12.713478 INFO: │       ├──maximal_decrease: 0.1
6:27:12.713495 INFO: │       ├──favour_narrower_optimum: False
6:27:12.713512 INFO: │       └──maximum_decrease_from_maximum: 0.5
6:27:12.713531 INFO: ├──optimization_manager
6:27:12.713548 INFO: │   ├──fwhm_rt: 5
6:27:12.713566 INFO: │   ├──fwhm_mobility: 0.01
6:27:12.713583 INFO: │   └──score_cutoff: 0
6:27:12.713605 INFO: ├──transfer_library
6:27:12.713623 INFO: │   ├──enabled: False
6:27:12.713640 INFO: │   ├──fragment_types:
6:27:12.713659 INFO: │   │   - b
6:27:12.713677 INFO: │   │   - y
6:27:12.713696 INFO: │   ├──max_charge: 2
6:27:12.713713 INFO: │   ├──top_k_samples: 3
6:27:12.713731 INFO: │   ├──norm_delta_max: True
6:27:12.713751 INFO: │   ├──precursor_correlation_cutoff: 0.5
6:27:12.713769 INFO: │   └──fragment_correlation_ratio: 0.75
6:27:12.713785 INFO: └──transfer_learning
6:27:12.713803 INFO:     ├──enabled: False
6:27:12.713820 INFO:     ├──batch_size: 2000
6:27:12.713839 INFO:     ├──max_lr: 0.0001
6:27:12.713857 INFO:     ├──train_fraction: 0.7
6:27:12.713876 INFO:     ├──validation_fraction: 0.2
6:27:12.713895 INFO:     ├──test_fraction: 0.1
6:27:12.713913 INFO:     ├──test_interval: 1
6:27:12.713931 INFO:     ├──lr_patience: 3
6:27:12.713950 INFO:     ├──epochs: 51
6:27:12.713968 INFO:     ├──warmup_epochs: 5
6:27:12.713986 INFO:     ├──nce: 25
6:27:12.714007 INFO:     └──instrument: Lumos
6:27:12.726108 INFO: Registering 7 custom modifications
6:27:12.794642 INFO: Searching 6 files:
6:27:12.795535 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
6:27:12.795569 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
6:27:12.795593 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
6:27:12.795614 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
6:27:12.795634 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
6:27:12.795655 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
6:27:12.795674 INFO: Using 0 fasta files:
6:27:12.795694 INFO: Using library: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf
6:27:12.795719 INFO: Saving output to: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1
6:27:12.795811 PROGRESS: Loading spectral library
6:27:12.795920 PROGRESS: Loading library (type: base) from disk..
6:27:12.795994 INFO: Running DynamicLoader
6:27:12.796279 INFO: Loading .hdf library from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf
6:27:15.574503 INFO: Running PrecursorInitializer
6:27:15.576167 INFO: Channel column already present, skipping initialization
6:27:15.576213 INFO: Elution group indices already present, skipping initialization
6:27:15.576241 INFO: Precursor indices already present, skipping initialization
6:27:15.576276 INFO: Running AnnotateFasta
6:27:15.646111 INFO: Running IsotopeGenerator
6:27:15.647292 INFO: Isotope information already present, skipping isotope generation
6:27:15.647344 INFO: Running RTNormalization
6:27:15.659774 INFO: Saving library to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/speclib.hdf
6:27:18.331336 INFO: Running DecoyGenerator
6:27:38.255938 INFO: Running FlattenLibrary
6:27:41.107520 INFO: Running InitFlatColumns
6:27:41.128356 INFO: Running LogFlatLibraryStats
6:27:41.128731 INFO: ============ Library Stats ============
6:27:41.128793 INFO: Number of precursors: 292,556
6:27:41.301599 INFO: 	thereof targets:146,300
6:27:41.302150 INFO: 	thereof decoys: 146,256
6:27:41.317346 INFO: Number of elution groups: 146,300
6:27:41.317806 INFO: 	average size: 2.00
6:27:41.401246 INFO: Number of proteins: 10,661
6:27:41.403916 INFO: Number of channels: 1 ([0])
6:27:41.404229 INFO: Isotopes Distribution for 4 isotopes
6:27:41.404260 INFO: =======================================
6:27:41.404605 PROGRESS: =================== Starting Search Workflows for step mbr ===================
6:27:41.404756 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 
6:27:41.404933 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant
6:27:41.405144 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/figures
6:27:41.405563 INFO: Initializing TimingManager
6:27:41.406721 INFO: Initializing RawFileManager
6:28:03.780186 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.
6:28:03.794807 INFO: Determining DIA cycle
6:28:03.815032 INFO: Found cycle with start 0.00 min and length 300.
6:28:04.563745 INFO: RT (min)            : 0.0 - 26.9
6:28:04.564035 INFO: RT duration (sec)   : 1611.2
6:28:04.564070 INFO: RT duration (min)   : 26.9
6:28:04.564100 INFO: Cycle len (scans)   : 300
6:28:04.564123 INFO: Cycle len (sec)     : 1.65
6:28:04.564143 INFO: Number of cycles    : 977
6:28:04.564163 INFO: MS2 range (m/z)     : 380.4 - 980.7
6:28:04.564230 INFO: Creating DIA data object took: 23.1573646068573
6:28:06.418521 INFO: Creating DIA data NG object took: 1.8538129329681396
6:28:06.546900 INFO: Initializing CalibrationManager
6:28:06.548010 INFO: Setting up calibration estimators ..
6:28:06.548197 INFO: Found 1 estimator(s) in calibration group 'fragment'
6:28:06.548489 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'}' ..
6:28:06.548700 INFO: Found 3 estimator(s) in calibration group 'precursor'
6:28:06.548778 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
6:28:06.548882 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}}' ..
6:28:06.548956 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
6:28:06.549006 INFO: Done setting up calibration estimators.
6:28:06.549924 INFO: Initializing OptimizationManager
6:28:06.550290 INFO: initial parameter: ms1_error = 3
6:28:06.550349 INFO: initial parameter: ms2_error = 10
6:28:06.550418 INFO: initial parameter: rt_error = 805.5992431640625
6:28:06.550477 INFO: initial parameter: mobility_error = 0.1
6:28:06.550521 INFO: initial parameter: num_candidates = 1
6:28:06.550563 INFO: initial parameter: fwhm_rt = 5
6:28:06.550606 INFO: initial parameter: fwhm_mobility = 0.01
6:28:06.550656 INFO: initial parameter: score_cutoff = 0
6:28:06.550700 INFO: initial parameter: classifier_version = -1
6:28:06.550828 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
6:28:06.552708 INFO: FDRManager: loading saved state not requested, will be initialized.
6:28:06.552824 INFO: Initializing FDRManager
6:28:06.552915 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
6:28:06.723301 PROGRESS: Initializing spectral library: 146,300 target precursors potentially observable (0 removed)
6:28:06.852048 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
6:28:06.854720 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
6:28:06.855031 PROGRESS: Starting initial search for precursors.
6:28:06.855372 INFO: Starting optimization step 0.
6:28:06.855491 PROGRESS: === Extracting elution groups 0 to 1000 ===
6:28:06.855641 INFO: Using rust extraction backend
6:28:06.855827 PROGRESS: Extracting batch of 1979 precursors
6:28:06.870131 INFO: === Search parameters used ===
6:28:06.871732 INFO: rt_error       : 805.5992431640625
6:28:06.871795 INFO: mobility_error : 0.1
6:28:06.871843 INFO: num_candidates : 1
6:28:06.871888 INFO: ms1_error      : 3
6:28:06.871936 INFO: ms2_error      : 10
6:28:06.872008 INFO: fwhm_rt        : 5
6:28:06.872058 INFO: quant_window   : 3
6:28:06.872099 INFO: ==============================================
6:28:06.973534 INFO: performing precursor FDR with 40 features
6:28:06.973844 INFO: Decoy channel: -1
6:28:06.973873 INFO: competitive: True
6:28:06.977950 INFO: Setting torch num_threads to 2 for FDR classification task
6:28:06.986632 INFO: Estimating optimal hyperparameters - samples: 1,580, batch_size: 128, learning_rate: 1.77e-04
6:28:06.990099 INFO: Using random state 293049 for train-test-split
6:28:07.343417 INFO: Test AUC: 0.819
6:28:07.344168 INFO: Train AUC: 0.853
6:28:07.344215 INFO: AUC difference: 4.00%
6:28:07.844296 INFO: Resetting torch num_threads to 100
6:28:07.849535 PROGRESS: === Extracted 1976 precursors and 13112 fragments ===
6:28:07.850679 INFO: === FDR correction performed with classifier version -1 ===
6:28:07.851897 PROGRESS: ============================= Precursor FDR =============================
6:28:07.852078 PROGRESS: Total precursors accumulated: 381
6:28:07.852150 PROGRESS: Target precursors: 378 (99.21%)
6:28:07.852231 PROGRESS: Decoy precursors: 3 (0.79%)
6:28:07.852279 PROGRESS: 
6:28:07.852327 PROGRESS: Precursor Summary:
6:28:07.853933 PROGRESS: Channel   0:	 0.050 FDR:   378; 0.010 FDR:   378; 0.001 FDR:   184
6:28:07.854069 PROGRESS: 
6:28:07.854130 PROGRESS: Protein Summary:
6:28:07.856536 PROGRESS: Channel   0:	 0.050 FDR:   355; 0.010 FDR:   355; 0.001 FDR:   178
6:28:07.856703 PROGRESS: =========================================================================
6:28:07.857586 INFO: Target number of precursors not reached yet.
6:28:07.879510 INFO: Starting optimization step 1.
6:28:07.880197 PROGRESS: === Extracting elution groups 1000 to 3000 ===
6:28:07.880318 INFO: Using rust extraction backend
6:28:07.880399 PROGRESS: Extracting batch of 3964 precursors
6:28:07.898491 INFO: === Search parameters used ===
6:28:07.899285 INFO: rt_error       : 805.5992431640625
6:28:07.899347 INFO: mobility_error : 0.1
6:28:07.899400 INFO: num_candidates : 1
6:28:07.899460 INFO: ms1_error      : 3
6:28:07.899505 INFO: ms2_error      : 10
6:28:07.899545 INFO: fwhm_rt        : 5
6:28:07.899587 INFO: quant_window   : 3
6:28:07.899629 INFO: ==============================================
6:28:08.010949 INFO: performing precursor FDR with 40 features
6:28:08.011368 INFO: Decoy channel: -1
6:28:08.011406 INFO: competitive: True
6:28:08.034610 INFO: Setting torch num_threads to 2 for FDR classification task
6:28:08.050741 INFO: Estimating optimal hyperparameters - samples: 4,748, batch_size: 128, learning_rate: 1.77e-04
6:28:08.051268 INFO: Using random state 487743 for train-test-split
6:28:08.761452 INFO: Test AUC: 0.870
6:28:08.761776 INFO: Train AUC: 0.874
6:28:08.761823 INFO: AUC difference: 0.48%
6:28:09.204963 INFO: Resetting torch num_threads to 100
6:28:09.220947 PROGRESS: === Extracted 5935 precursors and 39734 fragments ===
6:28:09.223336 INFO: === FDR correction performed with classifier version -1 ===
6:28:09.226639 PROGRESS: ============================= Precursor FDR =============================
6:28:09.227014 PROGRESS: Total precursors accumulated: 1,428
6:28:09.227077 PROGRESS: Target precursors: 1,414 (99.02%)
6:28:09.227133 PROGRESS: Decoy precursors: 14 (0.98%)
6:28:09.227213 PROGRESS: 
6:28:09.227275 PROGRESS: Precursor Summary:
6:28:09.230619 PROGRESS: Channel   0:	 0.050 FDR: 1,414; 0.010 FDR: 1,414; 0.001 FDR:   874
6:28:09.230844 PROGRESS: 
6:28:09.230900 PROGRESS: Protein Summary:
6:28:09.234161 PROGRESS: Channel   0:	 0.050 FDR: 1,186; 0.010 FDR: 1,186; 0.001 FDR:   767
6:28:09.234635 PROGRESS: =========================================================================
6:28:09.236130 INFO: Target number of precursors reached.
6:28:09.258301 INFO: fragments_df: keeping 5000 of 39734 [sum(precursor_idx_mask)=13352 sum(mass_error_mask)=39734 stop_rank=5000
6:28:09.305876 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:28:09.739701 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:28:10.723646 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
6:28:10.725077 INFO: Using score_cutoff 12.03522961435318 (fac=0.99, q=1)
6:28:10.725814 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
6:28:10.725934 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
6:28:10.725991 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.03522961435318
6:28:10.726119 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:28:10.735422 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:28:10.749506 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
6:28:10.750603 PROGRESS: Required number of precursors found. Starting search parameter optimization.
6:28:10.750785 INFO: Starting optimization step 2.
6:28:10.750893 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:28:10.751038 INFO: Using rust extraction backend
6:28:10.751173 PROGRESS: Extracting batch of 5943 precursors
6:28:10.790522 INFO: === Search parameters used ===
6:28:10.791523 INFO: rt_error       : 805.5992431640625
6:28:10.791586 INFO: mobility_error : 0.1
6:28:10.791632 INFO: num_candidates : 3
6:28:10.791675 INFO: ms1_error      : 3
6:28:10.791715 INFO: ms2_error      : 10
6:28:10.791754 INFO: fwhm_rt        : 3.0
6:28:10.791793 INFO: quant_window   : 3
6:28:10.791857 INFO: ==============================================
6:28:11.178352 INFO: performing precursor FDR with 40 features
6:28:11.178857 INFO: Decoy channel: -1
6:28:11.178891 INFO: competitive: True
6:28:11.213126 INFO: Setting torch num_threads to 2 for FDR classification task
6:28:11.236187 INFO: Estimating optimal hyperparameters - samples: 14,237, batch_size: 128, learning_rate: 1.77e-04
6:28:11.237022 INFO: Using random state 483772 for train-test-split
6:28:13.684202 INFO: Test AUC: 0.708
6:28:13.684423 INFO: Train AUC: 0.719
6:28:13.684461 INFO: AUC difference: 1.52%
6:28:13.993095 INFO: Resetting torch num_threads to 100
6:28:13.998515 PROGRESS: === Extracted 17797 precursors and 104480 fragments ===
6:28:13.999131 INFO: === FDR correction performed with classifier version 1 ===
6:28:14.000140 PROGRESS: ============================= Precursor FDR =============================
6:28:14.000247 PROGRESS: Total precursors accumulated: 1,945
6:28:14.000314 PROGRESS: Target precursors: 1,926 (99.02%)
6:28:14.000367 PROGRESS: Decoy precursors: 19 (0.98%)
6:28:14.000416 PROGRESS: 
6:28:14.000464 PROGRESS: Precursor Summary:
6:28:14.002155 PROGRESS: Channel   0:	 0.050 FDR: 1,926; 0.010 FDR: 1,926; 0.001 FDR: 1,233
6:28:14.002254 PROGRESS: 
6:28:14.002330 PROGRESS: Protein Summary:
6:28:14.004525 PROGRESS: Channel   0:	 0.050 FDR: 1,575; 0.010 FDR: 1,575; 0.001 FDR: 1,056
6:28:14.004633 PROGRESS: =========================================================================
6:28:14.005733 INFO: Target number of precursors reached.
6:28:14.028531 INFO: fragments_df: keeping 5000 of 104480 [sum(precursor_idx_mask)=39958 sum(mass_error_mask)=104480 stop_rank=5000
6:28:14.052069 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:28:14.606653 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:28:15.559707 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:28:15.561600 INFO: Using score_cutoff 10.457755644321441 (fac=0.99, q=1)
6:28:15.562624 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:28:15.562737 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:28:15.562805 INFO: Updating optimization_manager: score_cutoff        : 12.03522961435318 -> 10.457755644321441
6:28:15.562916 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:28:15.570779 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:28:15.582664 INFO: === checking if optimization conditions were reached ===
6:28:15.587599 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
6:28:15.588197 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
6:28:15.588303 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:28:15.588406 INFO: ==============================================
6:28:15.588537 INFO: Starting optimization step 3.
6:28:15.588657 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:28:15.588787 INFO: Using rust extraction backend
6:28:15.588907 PROGRESS: Extracting batch of 5943 precursors
6:28:15.610925 INFO: === Search parameters used ===
6:28:15.611657 INFO: rt_error       : 805.5992431640625
6:28:15.611719 INFO: mobility_error : 0.1
6:28:15.611769 INFO: num_candidates : 3
6:28:15.611813 INFO: ms1_error      : 3
6:28:15.611854 INFO: ms2_error      : 10.0
6:28:15.611895 INFO: fwhm_rt        : 3.0
6:28:15.611943 INFO: quant_window   : 3
6:28:15.611983 INFO: ==============================================
6:28:15.943768 INFO: performing precursor FDR with 40 features
6:28:15.944093 INFO: Decoy channel: -1
6:28:15.944123 INFO: competitive: True
6:28:15.974400 INFO: Setting torch num_threads to 2 for FDR classification task
6:28:15.992047 INFO: Estimating optimal hyperparameters - samples: 14,237, batch_size: 128, learning_rate: 1.77e-04
6:28:15.992649 INFO: Using random state 404659 for train-test-split
6:28:18.153083 INFO: Test AUC: 0.723
6:28:18.153466 INFO: Train AUC: 0.732
6:28:18.153510 INFO: AUC difference: 1.28%
6:28:18.542001 INFO: Resetting torch num_threads to 100
6:28:18.551135 PROGRESS: === Extracted 17797 precursors and 104463 fragments ===
6:28:18.552573 INFO: === FDR correction performed with classifier version 2 ===
6:28:18.555455 PROGRESS: ============================= Precursor FDR =============================
6:28:18.555755 PROGRESS: Total precursors accumulated: 1,986
6:28:18.555830 PROGRESS: Target precursors: 1,967 (99.04%)
6:28:18.555891 PROGRESS: Decoy precursors: 19 (0.96%)
6:28:18.555941 PROGRESS: 
6:28:18.555987 PROGRESS: Precursor Summary:
6:28:18.558895 PROGRESS: Channel   0:	 0.050 FDR: 1,967; 0.010 FDR: 1,967; 0.001 FDR: 1,249
6:28:18.559598 PROGRESS: 
6:28:18.559671 PROGRESS: Protein Summary:
6:28:18.563836 PROGRESS: Channel   0:	 0.050 FDR: 1,605; 0.010 FDR: 1,605; 0.001 FDR: 1,059
6:28:18.564451 PROGRESS: =========================================================================
6:28:18.566358 INFO: Target number of precursors reached.
6:28:18.595286 INFO: fragments_df: keeping 5000 of 104463 [sum(precursor_idx_mask)=40721 sum(mass_error_mask)=104463 stop_rank=5000
6:28:18.637807 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:28:19.047635 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:28:19.985578 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:28:19.986370 INFO: Using score_cutoff 10.615805397605895 (fac=0.99, q=1)
6:28:19.986857 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:28:19.986955 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:28:19.987011 INFO: Updating optimization_manager: score_cutoff        : 10.457755644321441 -> 10.615805397605895
6:28:19.987072 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:28:19.992259 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:28:20.002006 INFO: === checking if optimization conditions were reached ===
6:28:20.006243 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:28:20.006772 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
6:28:20.006853 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:28:20.006956 INFO: ==============================================
6:28:20.007045 INFO: Starting optimization step 4.
6:28:20.007110 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:28:20.007264 INFO: Using rust extraction backend
6:28:20.007375 PROGRESS: Extracting batch of 5943 precursors
6:28:20.026699 INFO: === Search parameters used ===
6:28:20.027498 INFO: rt_error       : 805.5992431640625
6:28:20.027565 INFO: mobility_error : 0.1
6:28:20.027615 INFO: num_candidates : 3
6:28:20.027660 INFO: ms1_error      : 3
6:28:20.027702 INFO: ms2_error      : 10.0
6:28:20.027743 INFO: fwhm_rt        : 3.0
6:28:20.027782 INFO: quant_window   : 3
6:28:20.027822 INFO: ==============================================
6:28:20.232458 INFO: performing precursor FDR with 40 features
6:28:20.232753 INFO: Decoy channel: -1
6:28:20.232779 INFO: competitive: True
6:28:20.257236 INFO: Setting torch num_threads to 2 for FDR classification task
6:28:20.276141 INFO: Estimating optimal hyperparameters - samples: 14,236, batch_size: 128, learning_rate: 1.77e-04
6:28:20.276434 INFO: Using random state 502627 for train-test-split
6:28:22.852574 INFO: Test AUC: 0.734
6:28:22.853176 INFO: Train AUC: 0.747
6:28:22.853224 INFO: AUC difference: 1.73%
6:28:23.313311 INFO: Resetting torch num_threads to 100
6:28:23.321695 PROGRESS: === Extracted 17796 precursors and 104528 fragments ===
6:28:23.322951 INFO: === FDR correction performed with classifier version 3 ===
6:28:23.325307 PROGRESS: ============================= Precursor FDR =============================
6:28:23.325530 PROGRESS: Total precursors accumulated: 2,105
6:28:23.325600 PROGRESS: Target precursors: 2,085 (99.05%)
6:28:23.325657 PROGRESS: Decoy precursors: 20 (0.95%)
6:28:23.325708 PROGRESS: 
6:28:23.325786 PROGRESS: Precursor Summary:
6:28:23.328705 PROGRESS: Channel   0:	 0.050 FDR: 2,085; 0.010 FDR: 2,085; 0.001 FDR: 1,349
6:28:23.328934 PROGRESS: 
6:28:23.329032 PROGRESS: Protein Summary:
6:28:23.332094 PROGRESS: Channel   0:	 0.050 FDR: 1,695; 0.010 FDR: 1,695; 0.001 FDR: 1,146
6:28:23.332360 PROGRESS: =========================================================================
6:28:23.334162 INFO: Target number of precursors reached.
6:28:23.367205 INFO: fragments_df: keeping 5000 of 104528 [sum(precursor_idx_mask)=42730 sum(mass_error_mask)=104528 stop_rank=5000
6:28:23.408658 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:28:23.948987 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:28:24.835256 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:28:24.837330 INFO: Using score_cutoff 10.259189775466918 (fac=0.99, q=1)
6:28:24.837877 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:28:24.837956 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:28:24.838031 INFO: Updating optimization_manager: score_cutoff        : 10.615805397605895 -> 10.259189775466918
6:28:24.838092 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:28:24.844407 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:28:24.855795 INFO: === checking if optimization conditions were reached ===
6:28:24.862981 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:28:24.863890 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
6:28:24.864063 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:28:24.864175 INFO: ==============================================
6:28:24.864309 INFO: Starting optimization step 5.
6:28:24.864416 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:28:24.864501 INFO: Using rust extraction backend
6:28:24.864635 PROGRESS: Extracting batch of 5943 precursors
6:28:24.892355 INFO: === Search parameters used ===
6:28:24.894235 INFO: rt_error       : 805.5992431640625
6:28:24.894367 INFO: mobility_error : 0.1
6:28:24.894431 INFO: num_candidates : 3
6:28:24.894510 INFO: ms1_error      : 3
6:28:24.894557 INFO: ms2_error      : 10.0
6:28:24.894598 INFO: fwhm_rt        : 3.0
6:28:24.894640 INFO: quant_window   : 3
6:28:24.894682 INFO: ==============================================
6:28:25.221491 INFO: performing precursor FDR with 40 features
6:28:25.221870 INFO: Decoy channel: -1
6:28:25.221905 INFO: competitive: True
6:28:25.250005 INFO: Setting torch num_threads to 2 for FDR classification task
6:28:25.267510 INFO: Estimating optimal hyperparameters - samples: 14,236, batch_size: 128, learning_rate: 1.77e-04
6:28:25.268122 INFO: Using random state 198190 for train-test-split
6:28:27.937454 INFO: Test AUC: 0.740
6:28:27.938182 INFO: Train AUC: 0.758
6:28:27.938235 INFO: AUC difference: 2.39%
6:28:28.377231 INFO: Resetting torch num_threads to 100
6:28:28.385132 PROGRESS: === Extracted 17796 precursors and 104517 fragments ===
6:28:28.386267 INFO: === FDR correction performed with classifier version 4 ===
6:28:28.387838 PROGRESS: ============================= Precursor FDR =============================
6:28:28.387991 PROGRESS: Total precursors accumulated: 2,150
6:28:28.388066 PROGRESS: Target precursors: 2,129 (99.02%)
6:28:28.388120 PROGRESS: Decoy precursors: 21 (0.98%)
6:28:28.388198 PROGRESS: 
6:28:28.388247 PROGRESS: Precursor Summary:
6:28:28.390301 PROGRESS: Channel   0:	 0.050 FDR: 2,129; 0.010 FDR: 2,129; 0.001 FDR: 1,368
6:28:28.390414 PROGRESS: 
6:28:28.390479 PROGRESS: Protein Summary:
6:28:28.393325 PROGRESS: Channel   0:	 0.050 FDR: 1,728; 0.010 FDR: 1,728; 0.001 FDR: 1,160
6:28:28.393463 PROGRESS: =========================================================================
6:28:28.395285 INFO: Target number of precursors reached.
6:28:28.426336 INFO: fragments_df: keeping 5000 of 104517 [sum(precursor_idx_mask)=43499 sum(mass_error_mask)=104517 stop_rank=5000
6:28:28.458558 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:28:28.979208 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:28:29.912092 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:28:29.913473 INFO: Using score_cutoff 10.180808682632447 (fac=0.99, q=1)
6:28:29.914277 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:28:29.914363 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:28:29.914416 INFO: Updating optimization_manager: score_cutoff        : 10.259189775466918 -> 10.180808682632447
6:28:29.914478 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:28:29.923784 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:28:29.935123 INFO: === checking if optimization conditions were reached ===
6:28:29.940920 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:28:29.941746 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
6:28:29.941830 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:28:29.941906 INFO: ==============================================
6:28:29.941991 INFO: Starting optimization step 6.
6:28:29.942061 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:28:29.942162 INFO: Using rust extraction backend
6:28:29.942253 PROGRESS: Extracting batch of 5943 precursors
6:28:29.974063 INFO: === Search parameters used ===
6:28:29.974909 INFO: rt_error       : 805.5992431640625
6:28:29.974969 INFO: mobility_error : 0.1
6:28:29.975030 INFO: num_candidates : 3
6:28:29.975091 INFO: ms1_error      : 3
6:28:29.975137 INFO: ms2_error      : 10.0
6:28:29.975206 INFO: fwhm_rt        : 3.0
6:28:29.975262 INFO: quant_window   : 3
6:28:29.975304 INFO: ==============================================
6:28:30.305303 INFO: performing precursor FDR with 40 features
6:28:30.305616 INFO: Decoy channel: -1
6:28:30.305644 INFO: competitive: True
6:28:30.325834 INFO: Setting torch num_threads to 2 for FDR classification task
6:28:30.340213 INFO: Estimating optimal hyperparameters - samples: 14,236, batch_size: 128, learning_rate: 1.77e-04
6:28:30.340702 INFO: Using random state 889331 for train-test-split
6:28:32.548308 INFO: Test AUC: 0.749
6:28:32.548627 INFO: Train AUC: 0.765
6:28:32.548660 INFO: AUC difference: 2.09%
6:28:32.985369 INFO: Resetting torch num_threads to 100
6:28:32.994813 PROGRESS: === Extracted 17796 precursors and 104521 fragments ===
6:28:32.996152 INFO: === FDR correction performed with classifier version 5 ===
6:28:32.997902 PROGRESS: ============================= Precursor FDR =============================
6:28:32.998043 PROGRESS: Total precursors accumulated: 2,134
6:28:32.998115 PROGRESS: Target precursors: 2,113 (99.02%)
6:28:32.998192 PROGRESS: Decoy precursors: 21 (0.98%)
6:28:32.998244 PROGRESS: 
6:28:32.998291 PROGRESS: Precursor Summary:
6:28:33.000492 PROGRESS: Channel   0:	 0.050 FDR: 2,113; 0.010 FDR: 2,113; 0.001 FDR: 1,358
6:28:33.000615 PROGRESS: 
6:28:33.000680 PROGRESS: Protein Summary:
6:28:33.003803 PROGRESS: Channel   0:	 0.050 FDR: 1,714; 0.010 FDR: 1,714; 0.001 FDR: 1,155
6:28:33.003964 PROGRESS: =========================================================================
6:28:33.006424 INFO: Target number of precursors reached.
6:28:33.037943 INFO: fragments_df: keeping 5000 of 104521 [sum(precursor_idx_mask)=43069 sum(mass_error_mask)=104521 stop_rank=5000
6:28:33.073327 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:28:33.624716 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:28:34.603873 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:28:34.605251 INFO: Using score_cutoff 10.09616063117981 (fac=0.99, q=1)
6:28:34.605848 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:28:34.605939 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:28:34.605995 INFO: Updating optimization_manager: score_cutoff        : 10.180808682632447 -> 10.09616063117981
6:28:34.606067 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:28:34.612717 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:28:34.623719 INFO: === checking if optimization conditions were reached ===
6:28:34.628988 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:28:34.629415 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
6:28:34.629527 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
6:28:34.629618 INFO: ==============================================
6:28:34.629734 PROGRESS: Optimization finished for ms2_error.
6:28:34.659560 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:28:34.667353 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:28:34.677826 INFO: Starting optimization step 0.
6:28:34.678553 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:28:34.678679 INFO: Using rust extraction backend
6:28:34.678764 PROGRESS: Extracting batch of 5943 precursors
6:28:34.701560 INFO: === Search parameters used ===
6:28:34.702572 INFO: rt_error       : 805.5992431640625
6:28:34.702638 INFO: mobility_error : 0.1
6:28:34.702690 INFO: num_candidates : 3
6:28:34.702734 INFO: ms1_error      : 3
6:28:34.702775 INFO: ms2_error      : 10.0
6:28:34.702817 INFO: fwhm_rt        : 3.0
6:28:34.702859 INFO: quant_window   : 3
6:28:34.702903 INFO: ==============================================
6:28:35.058990 INFO: performing precursor FDR with 40 features
6:28:35.059363 INFO: Decoy channel: -1
6:28:35.059392 INFO: competitive: True
6:28:35.083643 INFO: Setting torch num_threads to 2 for FDR classification task
6:28:35.097568 INFO: Estimating optimal hyperparameters - samples: 14,236, batch_size: 128, learning_rate: 1.77e-04
6:28:35.098165 INFO: Using random state 383919 for train-test-split
6:28:37.325740 INFO: Test AUC: 0.758
6:28:37.326060 INFO: Train AUC: 0.773
6:28:37.326095 INFO: AUC difference: 1.91%
6:28:37.729916 INFO: Resetting torch num_threads to 100
6:28:37.735704 PROGRESS: === Extracted 17796 precursors and 104521 fragments ===
6:28:37.736496 INFO: === FDR correction performed with classifier version 6 ===
6:28:37.738274 PROGRESS: ============================= Precursor FDR =============================
6:28:37.738465 PROGRESS: Total precursors accumulated: 2,158
6:28:37.738529 PROGRESS: Target precursors: 2,137 (99.03%)
6:28:37.738580 PROGRESS: Decoy precursors: 21 (0.97%)
6:28:37.738640 PROGRESS: 
6:28:37.738685 PROGRESS: Precursor Summary:
6:28:37.741109 PROGRESS: Channel   0:	 0.050 FDR: 2,137; 0.010 FDR: 2,137; 0.001 FDR: 1,449
6:28:37.741330 PROGRESS: 
6:28:37.741387 PROGRESS: Protein Summary:
6:28:37.744228 PROGRESS: Channel   0:	 0.050 FDR: 1,735; 0.010 FDR: 1,735; 0.001 FDR: 1,222
6:28:37.744477 PROGRESS: =========================================================================
6:28:37.745956 INFO: Target number of precursors reached.
6:28:37.775097 INFO: fragments_df: keeping 5000 of 104521 [sum(precursor_idx_mask)=43485 sum(mass_error_mask)=104521 stop_rank=5000
6:28:37.808917 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:28:38.299355 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:28:39.182677 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:28:39.183729 INFO: Using score_cutoff 9.898824813079834 (fac=0.99, q=1)
6:28:39.184225 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:28:39.184313 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:28:39.184407 INFO: Updating optimization_manager: score_cutoff        : 10.09616063117981 -> 9.898824813079834
6:28:39.184470 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:28:39.189728 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:28:39.198914 INFO: === checking if optimization conditions were reached ===
6:28:39.199501 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
6:28:39.203863 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 400.7039374304501
6:28:39.204142 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 400.7039.
6:28:39.204218 INFO: ==============================================
6:28:39.204304 INFO: Starting optimization step 1.
6:28:39.204392 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:28:39.204492 INFO: Using rust extraction backend
6:28:39.204565 PROGRESS: Extracting batch of 5943 precursors
6:28:39.218616 INFO: === Search parameters used ===
6:28:39.219090 INFO: rt_error       : 400.7039374304501
6:28:39.219155 INFO: mobility_error : 0.1
6:28:39.219211 INFO: num_candidates : 3
6:28:39.219257 INFO: ms1_error      : 3
6:28:39.219299 INFO: ms2_error      : 10.0
6:28:39.219339 INFO: fwhm_rt        : 3.0
6:28:39.219381 INFO: quant_window   : 3
6:28:39.219435 INFO: ==============================================
6:28:39.467709 INFO: performing precursor FDR with 40 features
6:28:39.467940 INFO: Decoy channel: -1
6:28:39.467968 INFO: competitive: True
6:28:39.479374 INFO: Setting torch num_threads to 2 for FDR classification task
6:28:39.487817 INFO: Estimating optimal hyperparameters - samples: 14,240, batch_size: 128, learning_rate: 1.77e-04
6:28:39.488234 INFO: Using random state 383919 for train-test-split
6:28:41.813683 INFO: Test AUC: 0.757
6:28:41.814001 INFO: Train AUC: 0.769
6:28:41.814043 INFO: AUC difference: 1.52%
6:28:42.202358 INFO: Resetting torch num_threads to 100
6:28:42.210660 PROGRESS: === Extracted 17801 precursors and 104114 fragments ===
6:28:42.211977 INFO: === FDR correction performed with classifier version 6 ===
6:28:42.214297 PROGRESS: ============================= Precursor FDR =============================
6:28:42.214486 PROGRESS: Total precursors accumulated: 2,244
6:28:42.214563 PROGRESS: Target precursors: 2,222 (99.02%)
6:28:42.214617 PROGRESS: Decoy precursors: 22 (0.98%)
6:28:42.214662 PROGRESS: 
6:28:42.214707 PROGRESS: Precursor Summary:
6:28:42.217371 PROGRESS: Channel   0:	 0.050 FDR: 2,222; 0.010 FDR: 2,222; 0.001 FDR: 1,407
6:28:42.217602 PROGRESS: 
6:28:42.217661 PROGRESS: Protein Summary:
6:28:42.220580 PROGRESS: Channel   0:	 0.050 FDR: 1,798; 0.010 FDR: 1,798; 0.001 FDR: 1,184
6:28:42.220783 PROGRESS: =========================================================================
6:28:42.222427 INFO: Target number of precursors reached.
6:28:42.255586 INFO: fragments_df: keeping 5000 of 104114 [sum(precursor_idx_mask)=44981 sum(mass_error_mask)=104114 stop_rank=5000
6:28:42.286054 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:28:42.835163 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:28:43.913171 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:28:43.916792 INFO: Using score_cutoff 9.835705335903167 (fac=0.99, q=1)
6:28:43.918010 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:28:43.918138 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:28:43.918198 INFO: Updating optimization_manager: score_cutoff        : 9.898824813079834 -> 9.835705335903167
6:28:43.918280 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:28:43.926315 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:28:43.939610 INFO: === checking if optimization conditions were reached ===
6:28:43.941020 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
6:28:43.950207 INFO: Updating optimization_manager: rt_error            : 400.7039374304501 -> 396.5554878873744
6:28:43.951118 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 396.5555.
6:28:43.951289 INFO: ==============================================
6:28:43.951454 INFO: Starting optimization step 2.
6:28:43.951556 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:28:43.951752 INFO: Using rust extraction backend
6:28:43.951921 PROGRESS: Extracting batch of 5943 precursors
6:28:43.983222 INFO: === Search parameters used ===
6:28:43.985026 INFO: rt_error       : 396.5554878873744
6:28:43.985102 INFO: mobility_error : 0.1
6:28:43.985171 INFO: num_candidates : 3
6:28:43.985224 INFO: ms1_error      : 3
6:28:43.985271 INFO: ms2_error      : 10.0
6:28:43.985397 INFO: fwhm_rt        : 3.0
6:28:43.985449 INFO: quant_window   : 3
6:28:43.985501 INFO: ==============================================
6:28:44.322601 INFO: performing precursor FDR with 40 features
6:28:44.322979 INFO: Decoy channel: -1
6:28:44.323013 INFO: competitive: True
6:28:44.362107 INFO: Setting torch num_threads to 2 for FDR classification task
6:28:44.384597 INFO: Estimating optimal hyperparameters - samples: 14,240, batch_size: 128, learning_rate: 1.77e-04
6:28:44.385187 INFO: Using random state 383919 for train-test-split
6:28:47.210767 INFO: Test AUC: 0.745
6:28:47.211332 INFO: Train AUC: 0.770
6:28:47.211396 INFO: AUC difference: 3.24%
6:28:47.682985 INFO: Resetting torch num_threads to 100
6:28:47.691392 PROGRESS: === Extracted 17801 precursors and 104063 fragments ===
6:28:47.692760 INFO: === FDR correction performed with classifier version 6 ===
6:28:47.695361 PROGRESS: ============================= Precursor FDR =============================
6:28:47.695583 PROGRESS: Total precursors accumulated: 2,253
6:28:47.695651 PROGRESS: Target precursors: 2,231 (99.02%)
6:28:47.695699 PROGRESS: Decoy precursors: 22 (0.98%)
6:28:47.695745 PROGRESS: 
6:28:47.695789 PROGRESS: Precursor Summary:
6:28:47.698668 PROGRESS: Channel   0:	 0.050 FDR: 2,231; 0.010 FDR: 2,231; 0.001 FDR: 1,297
6:28:47.698876 PROGRESS: 
6:28:47.698931 PROGRESS: Protein Summary:
6:28:47.701998 PROGRESS: Channel   0:	 0.050 FDR: 1,797; 0.010 FDR: 1,797; 0.001 FDR: 1,113
6:28:47.702287 PROGRESS: =========================================================================
6:28:47.703923 INFO: Target number of precursors reached.
6:28:47.737657 INFO: fragments_df: keeping 5000 of 104063 [sum(precursor_idx_mask)=44851 sum(mass_error_mask)=104063 stop_rank=5000
6:28:47.772769 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:28:48.408393 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:28:49.350694 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:28:49.353148 INFO: Using score_cutoff 9.668177876472473 (fac=0.99, q=1)
6:28:49.354419 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:28:49.354532 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:28:49.354594 INFO: Updating optimization_manager: score_cutoff        : 9.835705335903167 -> 9.668177876472473
6:28:49.354708 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:28:49.362332 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:28:49.372234 INFO: === checking if optimization conditions were reached ===
6:28:49.372907 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
6:28:49.381887 INFO: Updating optimization_manager: rt_error            : 396.5554878873744 -> 351.9408528944713
6:28:49.382818 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 351.9409.
6:28:49.382950 INFO: ==============================================
6:28:49.383106 INFO: Starting optimization step 3.
6:28:49.383243 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:28:49.383455 INFO: Using rust extraction backend
6:28:49.383605 PROGRESS: Extracting batch of 5943 precursors
6:28:49.415565 INFO: === Search parameters used ===
6:28:49.417348 INFO: rt_error       : 351.9408528944713
6:28:49.417414 INFO: mobility_error : 0.1
6:28:49.417470 INFO: num_candidates : 3
6:28:49.417570 INFO: ms1_error      : 3
6:28:49.417625 INFO: ms2_error      : 10.0
6:28:49.417681 INFO: fwhm_rt        : 3.0
6:28:49.417733 INFO: quant_window   : 3
6:28:49.417780 INFO: ==============================================
6:28:49.810608 INFO: performing precursor FDR with 40 features
6:28:49.811072 INFO: Decoy channel: -1
6:28:49.811105 INFO: competitive: True
6:28:49.851761 INFO: Setting torch num_threads to 2 for FDR classification task
6:28:49.872832 INFO: Estimating optimal hyperparameters - samples: 14,242, batch_size: 128, learning_rate: 1.77e-04
6:28:49.873589 INFO: Using random state 383919 for train-test-split
6:28:52.484780 INFO: Test AUC: 0.755
6:28:52.485069 INFO: Train AUC: 0.766
6:28:52.485105 INFO: AUC difference: 1.34%
6:28:52.956497 INFO: Resetting torch num_threads to 100
6:28:52.967142 PROGRESS: === Extracted 17803 precursors and 103770 fragments ===
6:28:52.968579 INFO: === FDR correction performed with classifier version 6 ===
6:28:52.971100 PROGRESS: ============================= Precursor FDR =============================
6:28:52.971339 PROGRESS: Total precursors accumulated: 2,196
6:28:52.971416 PROGRESS: Target precursors: 2,175 (99.04%)
6:28:52.971469 PROGRESS: Decoy precursors: 21 (0.96%)
6:28:52.971522 PROGRESS: 
6:28:52.971566 PROGRESS: Precursor Summary:
6:28:52.974346 PROGRESS: Channel   0:	 0.050 FDR: 2,175; 0.010 FDR: 2,175; 0.001 FDR: 1,403
6:28:52.974599 PROGRESS: 
6:28:52.974659 PROGRESS: Protein Summary:
6:28:52.977836 PROGRESS: Channel   0:	 0.050 FDR: 1,765; 0.010 FDR: 1,765; 0.001 FDR: 1,177
6:28:52.978274 PROGRESS: =========================================================================
6:28:52.980121 INFO: Target number of precursors reached.
6:28:53.017564 INFO: fragments_df: keeping 5000 of 103770 [sum(precursor_idx_mask)=44016 sum(mass_error_mask)=103770 stop_rank=5000
6:28:53.059970 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:28:53.637025 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:28:54.530383 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:28:54.531699 INFO: Using score_cutoff 9.873200145149232 (fac=0.99, q=1)
6:28:54.532332 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:28:54.532435 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:28:54.532499 INFO: Updating optimization_manager: score_cutoff        : 9.668177876472473 -> 9.873200145149232
6:28:54.532586 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:28:54.539428 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:28:54.550910 INFO: === checking if optimization conditions were reached ===
6:28:54.551669 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
6:28:54.557529 INFO: Updating optimization_manager: rt_error            : 351.9408528944713 -> 274.24624279480025
6:28:54.558119 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 274.2462.
6:28:54.558210 INFO: ==============================================
6:28:54.558316 INFO: Starting optimization step 4.
6:28:54.558388 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:28:54.558512 INFO: Using rust extraction backend
6:28:54.558603 PROGRESS: Extracting batch of 5943 precursors
6:28:54.578497 INFO: === Search parameters used ===
6:28:54.579341 INFO: rt_error       : 274.24624279480025
6:28:54.579452 INFO: mobility_error : 0.1
6:28:54.579510 INFO: num_candidates : 3
6:28:54.579559 INFO: ms1_error      : 3
6:28:54.579602 INFO: ms2_error      : 10.0
6:28:54.579654 INFO: fwhm_rt        : 3.0
6:28:54.579700 INFO: quant_window   : 3
6:28:54.579743 INFO: ==============================================
6:28:54.848475 INFO: performing precursor FDR with 40 features
6:28:54.848828 INFO: Decoy channel: -1
6:28:54.848860 INFO: competitive: True
6:28:54.877469 INFO: Setting torch num_threads to 2 for FDR classification task
6:28:54.892879 INFO: Estimating optimal hyperparameters - samples: 14,232, batch_size: 128, learning_rate: 1.77e-04
6:28:54.893419 INFO: Using random state 383919 for train-test-split
6:28:57.484065 INFO: Test AUC: 0.749
6:28:57.484637 INFO: Train AUC: 0.770
6:28:57.484678 INFO: AUC difference: 2.70%
6:28:58.038650 INFO: Resetting torch num_threads to 100
6:28:58.050359 PROGRESS: === Extracted 17790 precursors and 102675 fragments ===
6:28:58.052115 INFO: === FDR correction performed with classifier version 6 ===
6:28:58.054999 PROGRESS: ============================= Precursor FDR =============================
6:28:58.055274 PROGRESS: Total precursors accumulated: 2,275
6:28:58.055346 PROGRESS: Target precursors: 2,253 (99.03%)
6:28:58.055405 PROGRESS: Decoy precursors: 22 (0.97%)
6:28:58.055467 PROGRESS: 
6:28:58.055517 PROGRESS: Precursor Summary:
6:28:58.059249 PROGRESS: Channel   0:	 0.050 FDR: 2,253; 0.010 FDR: 2,253; 0.001 FDR: 1,436
6:28:58.059495 PROGRESS: 
6:28:58.059550 PROGRESS: Protein Summary:
6:28:58.064360 PROGRESS: Channel   0:	 0.050 FDR: 1,821; 0.010 FDR: 1,821; 0.001 FDR: 1,210
6:28:58.064760 PROGRESS: =========================================================================
6:28:58.067690 INFO: Target number of precursors reached.
6:28:58.104677 INFO: fragments_df: keeping 5000 of 102675 [sum(precursor_idx_mask)=45151 sum(mass_error_mask)=102675 stop_rank=5000
6:28:58.161223 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:28:58.650025 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:28:59.510271 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:28:59.511539 INFO: Using score_cutoff 9.721733834838867 (fac=0.99, q=1)
6:28:59.512233 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:28:59.512344 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:28:59.512401 INFO: Updating optimization_manager: score_cutoff        : 9.873200145149232 -> 9.721733834838867
6:28:59.512490 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:28:59.519040 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:28:59.531438 INFO: === checking if optimization conditions were reached ===
6:28:59.532344 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
6:28:59.538279 INFO: Updating optimization_manager: rt_error            : 274.24624279480025 -> 222.99543349355392
6:28:59.538798 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 222.9954.
6:28:59.538881 INFO: ==============================================
6:28:59.538994 INFO: Starting optimization step 5.
6:28:59.539069 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:28:59.539216 INFO: Using rust extraction backend
6:28:59.539310 PROGRESS: Extracting batch of 5943 precursors
6:28:59.555860 INFO: === Search parameters used ===
6:28:59.556603 INFO: rt_error       : 222.99543349355392
6:28:59.556675 INFO: mobility_error : 0.1
6:28:59.556742 INFO: num_candidates : 3
6:28:59.556797 INFO: ms1_error      : 3
6:28:59.556841 INFO: ms2_error      : 10.0
6:28:59.556883 INFO: fwhm_rt        : 3.0
6:28:59.556925 INFO: quant_window   : 3
6:28:59.556972 INFO: ==============================================
6:28:59.792600 INFO: performing precursor FDR with 40 features
6:28:59.792839 INFO: Decoy channel: -1
6:28:59.792866 INFO: competitive: True
6:28:59.805000 INFO: Setting torch num_threads to 2 for FDR classification task
6:28:59.812949 INFO: Estimating optimal hyperparameters - samples: 14,228, batch_size: 128, learning_rate: 1.77e-04
6:28:59.813308 INFO: Using random state 383919 for train-test-split
6:29:01.470508 INFO: Test AUC: 0.763
6:29:01.470881 INFO: Train AUC: 0.767
6:29:01.470919 INFO: AUC difference: 0.57%
6:29:01.797759 INFO: Resetting torch num_threads to 100
6:29:01.802900 PROGRESS: === Extracted 17786 precursors and 101512 fragments ===
6:29:01.803817 INFO: === FDR correction performed with classifier version 6 ===
6:29:01.804819 PROGRESS: ============================= Precursor FDR =============================
6:29:01.804923 PROGRESS: Total precursors accumulated: 2,280
6:29:01.804986 PROGRESS: Target precursors: 2,258 (99.04%)
6:29:01.805037 PROGRESS: Decoy precursors: 22 (0.96%)
6:29:01.805086 PROGRESS: 
6:29:01.805131 PROGRESS: Precursor Summary:
6:29:01.806870 PROGRESS: Channel   0:	 0.050 FDR: 2,258; 0.010 FDR: 2,258; 0.001 FDR: 1,541
6:29:01.806973 PROGRESS: 
6:29:01.807029 PROGRESS: Protein Summary:
6:29:01.809516 PROGRESS: Channel   0:	 0.050 FDR: 1,822; 0.010 FDR: 1,822; 0.001 FDR: 1,289
6:29:01.809658 PROGRESS: =========================================================================
6:29:01.811023 INFO: Target number of precursors reached.
6:29:01.835782 INFO: fragments_df: keeping 5000 of 101512 [sum(precursor_idx_mask)=44806 sum(mass_error_mask)=101512 stop_rank=5000
6:29:01.864002 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:29:02.460311 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:29:03.500607 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:29:03.502104 INFO: Using score_cutoff 9.647051636981963 (fac=0.99, q=1)
6:29:03.502788 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:29:03.502888 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:29:03.502942 INFO: Updating optimization_manager: score_cutoff        : 9.721733834838867 -> 9.647051636981963
6:29:03.503031 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:29:03.510456 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:29:03.522358 INFO: === checking if optimization conditions were reached ===
6:29:03.523108 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
6:29:03.529207 INFO: Updating optimization_manager: rt_error            : 222.99543349355392 -> 194.8105046578089
6:29:03.529819 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 194.8105.
6:29:03.529906 INFO: ==============================================
6:29:03.530020 INFO: Starting optimization step 6.
6:29:03.530088 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:29:03.530229 INFO: Using rust extraction backend
6:29:03.530346 PROGRESS: Extracting batch of 5943 precursors
6:29:03.553610 INFO: === Search parameters used ===
6:29:03.554426 INFO: rt_error       : 194.8105046578089
6:29:03.554486 INFO: mobility_error : 0.1
6:29:03.554532 INFO: num_candidates : 3
6:29:03.554574 INFO: ms1_error      : 3
6:29:03.554649 INFO: ms2_error      : 10.0
6:29:03.554690 INFO: fwhm_rt        : 3.0
6:29:03.554731 INFO: quant_window   : 3
6:29:03.554770 INFO: ==============================================
6:29:03.815776 INFO: performing precursor FDR with 40 features
6:29:03.816147 INFO: Decoy channel: -1
6:29:03.816181 INFO: competitive: True
6:29:03.844002 INFO: Setting torch num_threads to 2 for FDR classification task
6:29:03.867654 INFO: Estimating optimal hyperparameters - samples: 14,226, batch_size: 128, learning_rate: 1.77e-04
6:29:03.868304 INFO: Using random state 383919 for train-test-split
6:29:06.150501 INFO: Test AUC: 0.745
6:29:06.151047 INFO: Train AUC: 0.769
6:29:06.151084 INFO: AUC difference: 3.10%
6:29:06.625040 INFO: Resetting torch num_threads to 100
6:29:06.633553 PROGRESS: === Extracted 17783 precursors and 100546 fragments ===
6:29:06.634905 INFO: === FDR correction performed with classifier version 6 ===
6:29:06.637495 PROGRESS: ============================= Precursor FDR =============================
6:29:06.637717 PROGRESS: Total precursors accumulated: 2,283
6:29:06.637792 PROGRESS: Target precursors: 2,261 (99.04%)
6:29:06.637849 PROGRESS: Decoy precursors: 22 (0.96%)
6:29:06.637902 PROGRESS: 
6:29:06.637952 PROGRESS: Precursor Summary:
6:29:06.640584 PROGRESS: Channel   0:	 0.050 FDR: 2,261; 0.010 FDR: 2,261; 0.001 FDR: 1,367
6:29:06.640796 PROGRESS: 
6:29:06.640856 PROGRESS: Protein Summary:
6:29:06.643703 PROGRESS: Channel   0:	 0.050 FDR: 1,827; 0.010 FDR: 1,827; 0.001 FDR: 1,160
6:29:06.644037 PROGRESS: =========================================================================
6:29:06.645675 INFO: Target number of precursors reached.
6:29:06.675175 INFO: fragments_df: keeping 5000 of 100546 [sum(precursor_idx_mask)=44735 sum(mass_error_mask)=100546 stop_rank=5000
6:29:06.711600 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:29:07.231490 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:29:08.133694 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:29:08.135092 INFO: Using score_cutoff 9.648017801284789 (fac=0.99, q=1)
6:29:08.135860 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:29:08.135967 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:29:08.136027 INFO: Updating optimization_manager: score_cutoff        : 9.647051636981963 -> 9.648017801284789
6:29:08.136135 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:29:08.143364 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:29:08.156812 INFO: === checking if optimization conditions were reached ===
6:29:08.157611 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
6:29:08.163993 INFO: Updating optimization_manager: rt_error            : 194.8105046578089 -> 184.93955732018412
6:29:08.164665 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 184.9396.
6:29:08.164757 INFO: ==============================================
6:29:08.164841 INFO: Starting optimization step 7.
6:29:08.164929 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:29:08.165094 INFO: Using rust extraction backend
6:29:08.165188 PROGRESS: Extracting batch of 5943 precursors
6:29:08.190278 INFO: === Search parameters used ===
6:29:08.191185 INFO: rt_error       : 184.93955732018412
6:29:08.191267 INFO: mobility_error : 0.1
6:29:08.191324 INFO: num_candidates : 3
6:29:08.191377 INFO: ms1_error      : 3
6:29:08.191431 INFO: ms2_error      : 10.0
6:29:08.191483 INFO: fwhm_rt        : 3.0
6:29:08.191536 INFO: quant_window   : 3
6:29:08.191594 INFO: ==============================================
6:29:08.460357 INFO: performing precursor FDR with 40 features
6:29:08.460746 INFO: Decoy channel: -1
6:29:08.460773 INFO: competitive: True
6:29:08.493142 INFO: Setting torch num_threads to 2 for FDR classification task
6:29:08.509262 INFO: Estimating optimal hyperparameters - samples: 14,223, batch_size: 128, learning_rate: 1.77e-04
6:29:08.509825 INFO: Using random state 383919 for train-test-split
6:29:09.735315 INFO: Test AUC: 0.759
6:29:09.735528 INFO: Train AUC: 0.769
6:29:09.735562 INFO: AUC difference: 1.31%
6:29:10.056247 INFO: Resetting torch num_threads to 100
6:29:10.061410 PROGRESS: === Extracted 17779 precursors and 100255 fragments ===
6:29:10.062324 INFO: === FDR correction performed with classifier version 6 ===
6:29:10.063460 PROGRESS: ============================= Precursor FDR =============================
6:29:10.063581 PROGRESS: Total precursors accumulated: 2,295
6:29:10.063651 PROGRESS: Target precursors: 2,273 (99.04%)
6:29:10.063709 PROGRESS: Decoy precursors: 22 (0.96%)
6:29:10.063758 PROGRESS: 
6:29:10.063805 PROGRESS: Precursor Summary:
6:29:10.065668 PROGRESS: Channel   0:	 0.050 FDR: 2,273; 0.010 FDR: 2,273; 0.001 FDR: 1,488
6:29:10.065793 PROGRESS: 
6:29:10.065876 PROGRESS: Protein Summary:
6:29:10.068318 PROGRESS: Channel   0:	 0.050 FDR: 1,842; 0.010 FDR: 1,842; 0.001 FDR: 1,252
6:29:10.068437 PROGRESS: =========================================================================
6:29:10.069767 INFO: Target number of precursors reached.
6:29:10.093602 INFO: fragments_df: keeping 5000 of 100255 [sum(precursor_idx_mask)=44955 sum(mass_error_mask)=100255 stop_rank=5000
6:29:10.117308 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:29:10.612664 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:29:11.475374 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:29:11.476412 INFO: Using score_cutoff 9.718225004196167 (fac=0.99, q=1)
6:29:11.476873 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:29:11.476952 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:29:11.477008 INFO: Updating optimization_manager: score_cutoff        : 9.648017801284789 -> 9.718225004196167
6:29:11.477070 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:29:11.482415 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:29:11.490713 INFO: === checking if optimization conditions were reached ===
6:29:11.491164 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
6:29:11.495812 INFO: Updating optimization_manager: rt_error            : 184.93955732018412 -> 151.93811009433773
6:29:11.496056 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 151.9381.
6:29:11.496180 INFO: ==============================================
6:29:11.496268 INFO: Starting optimization step 8.
6:29:11.496334 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:29:11.496422 INFO: Using rust extraction backend
6:29:11.496489 PROGRESS: Extracting batch of 5943 precursors
6:29:11.511093 INFO: === Search parameters used ===
6:29:11.511762 INFO: rt_error       : 151.93811009433773
6:29:11.511818 INFO: mobility_error : 0.1
6:29:11.511864 INFO: num_candidates : 3
6:29:11.511906 INFO: ms1_error      : 3
6:29:11.511947 INFO: ms2_error      : 10.0
6:29:11.511988 INFO: fwhm_rt        : 3.0
6:29:11.512032 INFO: quant_window   : 3
6:29:11.512071 INFO: ==============================================
6:29:11.718819 INFO: performing precursor FDR with 40 features
6:29:11.719079 INFO: Decoy channel: -1
6:29:11.719105 INFO: competitive: True
6:29:11.741731 INFO: Setting torch num_threads to 2 for FDR classification task
6:29:11.750508 INFO: Estimating optimal hyperparameters - samples: 14,212, batch_size: 128, learning_rate: 1.77e-04
6:29:11.750726 INFO: Using random state 383919 for train-test-split
6:29:14.110087 INFO: Test AUC: 0.752
6:29:14.110522 INFO: Train AUC: 0.774
6:29:14.110568 INFO: AUC difference: 2.83%
6:29:14.540037 INFO: Resetting torch num_threads to 100
6:29:14.549543 PROGRESS: === Extracted 17765 precursors and 98765 fragments ===
6:29:14.551208 INFO: === FDR correction performed with classifier version 6 ===
6:29:14.553446 PROGRESS: ============================= Precursor FDR =============================
6:29:14.553722 PROGRESS: Total precursors accumulated: 2,266
6:29:14.553800 PROGRESS: Target precursors: 2,244 (99.03%)
6:29:14.553864 PROGRESS: Decoy precursors: 22 (0.97%)
6:29:14.553924 PROGRESS: 
6:29:14.553976 PROGRESS: Precursor Summary:
6:29:14.556776 PROGRESS: Channel   0:	 0.050 FDR: 2,244; 0.010 FDR: 2,244; 0.001 FDR: 1,500
6:29:14.557027 PROGRESS: 
6:29:14.557126 PROGRESS: Protein Summary:
6:29:14.560257 PROGRESS: Channel   0:	 0.050 FDR: 1,819; 0.010 FDR: 1,819; 0.001 FDR: 1,258
6:29:14.560722 PROGRESS: =========================================================================
6:29:14.562806 INFO: Target number of precursors reached.
6:29:14.595074 INFO: fragments_df: keeping 5000 of 98765 [sum(precursor_idx_mask)=44129 sum(mass_error_mask)=98765 stop_rank=5000
6:29:14.632924 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:29:15.145449 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:29:16.137426 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:29:16.140036 INFO: Using score_cutoff 9.705091134738922 (fac=0.99, q=1)
6:29:16.141474 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:29:16.141647 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:29:16.141730 INFO: Updating optimization_manager: score_cutoff        : 9.718225004196167 -> 9.705091134738922
6:29:16.141816 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:29:16.150891 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:29:16.164286 INFO: === checking if optimization conditions were reached ===
6:29:16.165208 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
6:29:16.174090 INFO: Updating optimization_manager: rt_error            : 151.93811009433773 -> 132.78676969931558
6:29:16.174705 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 132.7868.
6:29:16.174835 INFO: ==============================================
6:29:16.174964 INFO: Starting optimization step 9.
6:29:16.175043 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:29:16.175237 INFO: Using rust extraction backend
6:29:16.175443 PROGRESS: Extracting batch of 5943 precursors
6:29:16.207314 INFO: === Search parameters used ===
6:29:16.208565 INFO: rt_error       : 132.78676969931558
6:29:16.208639 INFO: mobility_error : 0.1
6:29:16.208701 INFO: num_candidates : 3
6:29:16.208835 INFO: ms1_error      : 3
6:29:16.208879 INFO: ms2_error      : 10.0
6:29:16.208919 INFO: fwhm_rt        : 3.0
6:29:16.208960 INFO: quant_window   : 3
6:29:16.208999 INFO: ==============================================
6:29:16.568410 INFO: performing precursor FDR with 40 features
6:29:16.568845 INFO: Decoy channel: -1
6:29:16.568882 INFO: competitive: True
6:29:16.602173 INFO: Setting torch num_threads to 2 for FDR classification task
6:29:16.622331 INFO: Estimating optimal hyperparameters - samples: 14,200, batch_size: 128, learning_rate: 1.77e-04
6:29:16.623220 INFO: Using random state 383919 for train-test-split
6:29:18.879886 INFO: Test AUC: 0.744
6:29:18.880266 INFO: Train AUC: 0.777
6:29:18.880312 INFO: AUC difference: 4.25%
6:29:34.869281 INFO: Resetting torch num_threads to 100
6:29:34.890204 PROGRESS: === Extracted 17751 precursors and 97644 fragments ===
6:29:34.892420 INFO: === FDR correction performed with classifier version 6 ===
6:29:34.898664 PROGRESS: ============================= Precursor FDR =============================
6:29:34.899539 PROGRESS: Total precursors accumulated: 2,298
6:29:34.899741 PROGRESS: Target precursors: 2,276 (99.04%)
6:29:34.899815 PROGRESS: Decoy precursors: 22 (0.96%)
6:29:34.899895 PROGRESS: 
6:29:34.899986 PROGRESS: Precursor Summary:
6:29:34.910814 PROGRESS: Channel   0:	 0.050 FDR: 2,276; 0.010 FDR: 2,276; 0.001 FDR: 1,425
6:29:34.911763 PROGRESS: 
6:29:34.911911 PROGRESS: Protein Summary:
6:29:34.924762 PROGRESS: Channel   0:	 0.050 FDR: 1,846; 0.010 FDR: 1,846; 0.001 FDR: 1,202
6:29:34.925623 PROGRESS: =========================================================================
6:29:34.929426 INFO: Target number of precursors reached.
6:29:34.971332 INFO: fragments_df: keeping 5000 of 97644 [sum(precursor_idx_mask)=44287 sum(mass_error_mask)=97644 stop_rank=5000
6:29:35.051064 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:29:35.730322 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:29:36.795200 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:29:36.797323 INFO: Using score_cutoff 9.569993233680725 (fac=0.99, q=1)
6:29:36.798274 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:29:36.798387 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:29:36.798483 INFO: Updating optimization_manager: score_cutoff        : 9.705091134738922 -> 9.569993233680725
6:29:36.798595 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:29:36.808125 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:29:36.823256 INFO: === checking if optimization conditions were reached ===
6:29:36.825264 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
6:29:36.834804 INFO: Updating optimization_manager: rt_error            : 132.78676969931558 -> 129.37246266940286
6:29:36.835766 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 129.3725.
6:29:36.835881 INFO: ==============================================
6:29:36.836023 INFO: Starting optimization step 10.
6:29:36.836107 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:29:36.836284 INFO: Using rust extraction backend
6:29:36.836638 PROGRESS: Extracting batch of 5943 precursors
6:29:36.869999 INFO: === Search parameters used ===
6:29:36.872097 INFO: rt_error       : 129.37246266940286
6:29:36.872210 INFO: mobility_error : 0.1
6:29:36.872279 INFO: num_candidates : 3
6:29:36.872336 INFO: ms1_error      : 3
6:29:36.872390 INFO: ms2_error      : 10.0
6:29:36.872437 INFO: fwhm_rt        : 3.0
6:29:36.872487 INFO: quant_window   : 3
6:29:36.872544 INFO: ==============================================
6:29:37.287895 INFO: performing precursor FDR with 40 features
6:29:37.288274 INFO: Decoy channel: -1
6:29:37.288312 INFO: competitive: True
6:29:37.323586 INFO: Setting torch num_threads to 2 for FDR classification task
6:29:37.342979 INFO: Estimating optimal hyperparameters - samples: 14,202, batch_size: 128, learning_rate: 1.77e-04
6:29:37.343920 INFO: Using random state 383919 for train-test-split
6:29:38.811309 INFO: Test AUC: 0.756
6:29:38.811990 INFO: Train AUC: 0.777
6:29:38.812027 INFO: AUC difference: 2.66%
6:29:39.388259 INFO: Resetting torch num_threads to 100
6:29:39.399875 PROGRESS: === Extracted 17753 precursors and 97450 fragments ===
6:29:39.401435 INFO: === FDR correction performed with classifier version 6 ===
6:29:39.404217 PROGRESS: ============================= Precursor FDR =============================
6:29:39.404473 PROGRESS: Total precursors accumulated: 2,287
6:29:39.404545 PROGRESS: Target precursors: 2,265 (99.04%)
6:29:39.404630 PROGRESS: Decoy precursors: 22 (0.96%)
6:29:39.404678 PROGRESS: 
6:29:39.404724 PROGRESS: Precursor Summary:
6:29:39.408007 PROGRESS: Channel   0:	 0.050 FDR: 2,265; 0.010 FDR: 2,265; 0.001 FDR: 1,463
6:29:39.408467 PROGRESS: 
6:29:39.408533 PROGRESS: Protein Summary:
6:29:39.412799 PROGRESS: Channel   0:	 0.050 FDR: 1,836; 0.010 FDR: 1,836; 0.001 FDR: 1,235
6:29:39.413017 PROGRESS: =========================================================================
6:29:39.415486 INFO: Target number of precursors reached.
6:29:39.448790 INFO: fragments_df: keeping 5000 of 97450 [sum(precursor_idx_mask)=44083 sum(mass_error_mask)=97450 stop_rank=5000
6:29:39.506442 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:29:40.245244 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:29:41.339217 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:29:41.341256 INFO: Using score_cutoff 9.6231454788208 (fac=0.99, q=1)
6:29:41.342067 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:29:41.342163 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:29:41.342221 INFO: Updating optimization_manager: score_cutoff        : 9.569993233680725 -> 9.6231454788208
6:29:41.342319 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:29:41.350628 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:29:41.364915 INFO: === checking if optimization conditions were reached ===
6:29:41.365810 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
6:29:41.368370 INFO: Updating optimization_manager: rt_error            : 129.37246266940286 -> 132.78676969931558
6:29:41.368757 INFO: Updating optimization_manager: classifier_version  : 6 -> 16
6:29:41.368865 INFO: Updating optimization_manager: score_cutoff        : 9.6231454788208 -> 9.569993233680725
6:29:41.368963 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:29:41.369054 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:29:41.369180 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 132.7868 found after 11 searches.
6:29:41.369282 INFO: ==============================================
6:29:41.369435 PROGRESS: Optimization finished for rt_error.
6:29:41.410697 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:29:41.419778 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:29:41.431558 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
6:29:41.432359 PROGRESS: ==============================================
6:29:41.432494 PROGRESS: ms2_error      : 10.0000
6:29:41.432564 PROGRESS: rt_error       : 132.7868
6:29:41.432619 PROGRESS: ==============================================
6:29:41.435623 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:29:41.656247 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:29:42.310809 INFO: Using rust extraction backend
6:29:42.312958 PROGRESS: Extracting batch of 289499 precursors
6:29:43.224771 INFO: === Search parameters used ===
6:29:43.225786 INFO: rt_error       : 132.78676969931558
6:29:43.225861 INFO: mobility_error : 0.1
6:29:43.225920 INFO: num_candidates : 3
6:29:43.225974 INFO: ms1_error      : 3
6:29:43.226025 INFO: ms2_error      : 10.0
6:29:43.226072 INFO: fwhm_rt        : 3.0
6:29:43.226122 INFO: quant_window   : 3
6:29:43.226184 INFO: ==============================================
6:29:44.737749 INFO: Removed 199689 precursors with score below cutoff 9.569993233680725
6:29:45.640361 INFO: performing precursor FDR with 40 features
6:29:45.640566 INFO: Decoy channel: -1
6:29:45.640593 INFO: competitive: True
6:29:45.734265 INFO: Setting torch num_threads to 2 for FDR classification task
6:29:45.788399 WARNING: FDR calculation for 368474 target and 300056 decoy PSMs
6:29:45.788654 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
6:29:46.187568 INFO: Estimating optimal hyperparameters - samples: 534,824, batch_size: 2,190, learning_rate: 7.31e-04
6:29:46.190158 INFO: Using random state 52028 for train-test-split
6:30:16.630798 INFO: Test AUC: 0.794
6:30:16.631350 INFO: Train AUC: 0.797
6:30:16.631410 INFO: AUC difference: 0.28%
6:30:17.487238 INFO: Resetting torch num_threads to 100
6:30:18.902689 PROGRESS: ============================= Precursor FDR =============================
6:30:18.903876 PROGRESS: Total precursors accumulated: 128,872
6:30:18.904113 PROGRESS: Target precursors: 127,598 (99.01%)
6:30:18.904200 PROGRESS: Decoy precursors: 1,274 (0.99%)
6:30:18.904263 PROGRESS: 
6:30:18.904315 PROGRESS: Precursor Summary:
6:30:19.064043 PROGRESS: Channel   0:	 0.050 FDR: 127,598; 0.010 FDR: 127,598; 0.001 FDR: 106,263
6:30:19.065181 PROGRESS: 
6:30:19.065251 PROGRESS: Protein Summary:
6:30:19.390386 PROGRESS: Channel   0:	 0.050 FDR: 10,628; 0.010 FDR: 10,628; 0.001 FDR: 10,439
6:30:19.391617 PROGRESS: =========================================================================
6:30:19.411553 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/psm.parquet
6:30:20.044353 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.parquet
6:30:20.768068 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
6:30:21.119297 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 
6:30:21.119811 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant
6:30:21.120010 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/figures
6:30:21.120399 INFO: Initializing TimingManager
6:30:21.122456 INFO: Initializing RawFileManager
6:30:50.461147 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.
6:30:50.477892 INFO: Determining DIA cycle
6:30:50.497328 INFO: Found cycle with start 0.00 min and length 300.
6:30:51.218607 INFO: RT (min)            : 0.0 - 26.9
6:30:51.218873 INFO: RT duration (sec)   : 1611.2
6:30:51.218911 INFO: RT duration (min)   : 26.9
6:30:51.218938 INFO: Cycle len (scans)   : 300
6:30:51.218960 INFO: Cycle len (sec)     : 1.65
6:30:51.218981 INFO: Number of cycles    : 978
6:30:51.219003 INFO: MS2 range (m/z)     : 380.4 - 980.7
6:30:51.219061 INFO: Creating DIA data object took: 30.096388339996338
6:30:53.223726 INFO: Creating DIA data NG object took: 2.0042035579681396
6:30:53.358559 INFO: Initializing CalibrationManager
6:30:53.359377 INFO: Setting up calibration estimators ..
6:30:53.359455 INFO: Found 1 estimator(s) in calibration group 'fragment'
6:30:53.359615 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'}' ..
6:30:53.359734 INFO: Found 3 estimator(s) in calibration group 'precursor'
6:30:53.359803 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
6:30:53.359913 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}}' ..
6:30:53.359977 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
6:30:53.360029 INFO: Done setting up calibration estimators.
6:30:53.360705 INFO: Initializing OptimizationManager
6:30:53.360939 INFO: initial parameter: ms1_error = 3
6:30:53.361000 INFO: initial parameter: ms2_error = 10
6:30:53.361053 INFO: initial parameter: rt_error = 805.6019897460938
6:30:53.361098 INFO: initial parameter: mobility_error = 0.1
6:30:53.361153 INFO: initial parameter: num_candidates = 1
6:30:53.361206 INFO: initial parameter: fwhm_rt = 5
6:30:53.361251 INFO: initial parameter: fwhm_mobility = 0.01
6:30:53.361293 INFO: initial parameter: score_cutoff = 0
6:30:53.361337 INFO: initial parameter: classifier_version = -1
6:30:53.361437 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
6:30:53.362285 INFO: FDRManager: loading saved state not requested, will be initialized.
6:30:53.362343 INFO: Initializing FDRManager
6:30:53.362406 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
6:30:53.497220 PROGRESS: Initializing spectral library: 146,300 target precursors potentially observable (0 removed)
6:30:53.596546 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
6:30:53.598092 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
6:30:53.598340 PROGRESS: Starting initial search for precursors.
6:30:53.598520 INFO: Starting optimization step 0.
6:30:53.598601 PROGRESS: === Extracting elution groups 0 to 1000 ===
6:30:53.598687 INFO: Using rust extraction backend
6:30:53.598985 PROGRESS: Extracting batch of 1979 precursors
6:30:53.610585 INFO: === Search parameters used ===
6:30:53.611606 INFO: rt_error       : 805.6019897460938
6:30:53.611682 INFO: mobility_error : 0.1
6:30:53.611735 INFO: num_candidates : 1
6:30:53.611787 INFO: ms1_error      : 3
6:30:53.611832 INFO: ms2_error      : 10
6:30:53.611874 INFO: fwhm_rt        : 5
6:30:53.611917 INFO: quant_window   : 3
6:30:53.611956 INFO: ==============================================
6:30:53.689317 INFO: performing precursor FDR with 40 features
6:30:53.689597 INFO: Decoy channel: -1
6:30:53.689625 INFO: competitive: True
6:30:53.694908 INFO: Setting torch num_threads to 2 for FDR classification task
6:30:53.701974 INFO: Estimating optimal hyperparameters - samples: 1,580, batch_size: 128, learning_rate: 1.77e-04
6:30:53.709948 INFO: Using random state 418662 for train-test-split
6:30:54.123671 INFO: Test AUC: 0.839
6:30:54.124006 INFO: Train AUC: 0.844
6:30:54.124042 INFO: AUC difference: 0.60%
6:30:54.579575 INFO: Resetting torch num_threads to 100
6:30:54.585392 PROGRESS: === Extracted 1976 precursors and 13008 fragments ===
6:30:54.586471 INFO: === FDR correction performed with classifier version -1 ===
6:30:54.587950 PROGRESS: ============================= Precursor FDR =============================
6:30:54.588176 PROGRESS: Total precursors accumulated: 345
6:30:54.588246 PROGRESS: Target precursors: 342 (99.13%)
6:30:54.588302 PROGRESS: Decoy precursors: 3 (0.87%)
6:30:54.588346 PROGRESS: 
6:30:54.588391 PROGRESS: Precursor Summary:
6:30:54.589982 PROGRESS: Channel   0:	 0.050 FDR:   342; 0.010 FDR:   342; 0.001 FDR:   299
6:30:54.590099 PROGRESS: 
6:30:54.590155 PROGRESS: Protein Summary:
6:30:54.591796 PROGRESS: Channel   0:	 0.050 FDR:   329; 0.010 FDR:   329; 0.001 FDR:   288
6:30:54.591912 PROGRESS: =========================================================================
6:30:54.593017 INFO: Target number of precursors not reached yet.
6:30:54.616437 INFO: Starting optimization step 1.
6:30:54.617406 PROGRESS: === Extracting elution groups 1000 to 3000 ===
6:30:54.617600 INFO: Using rust extraction backend
6:30:54.617753 PROGRESS: Extracting batch of 3964 precursors
6:30:54.635746 INFO: === Search parameters used ===
6:30:54.636654 INFO: rt_error       : 805.6019897460938
6:30:54.636726 INFO: mobility_error : 0.1
6:30:54.636773 INFO: num_candidates : 1
6:30:54.636818 INFO: ms1_error      : 3
6:30:54.636865 INFO: ms2_error      : 10
6:30:54.636916 INFO: fwhm_rt        : 5
6:30:54.636966 INFO: quant_window   : 3
6:30:54.637028 INFO: ==============================================
6:30:54.790494 INFO: performing precursor FDR with 40 features
6:30:54.790812 INFO: Decoy channel: -1
6:30:54.790839 INFO: competitive: True
6:30:54.808394 INFO: Setting torch num_threads to 2 for FDR classification task
6:30:54.817925 INFO: Estimating optimal hyperparameters - samples: 4,749, batch_size: 128, learning_rate: 1.77e-04
6:30:54.818367 INFO: Using random state 660716 for train-test-split
6:30:55.659277 INFO: Test AUC: 0.874
6:30:55.659596 INFO: Train AUC: 0.877
6:30:55.659634 INFO: AUC difference: 0.32%
6:30:56.055340 INFO: Resetting torch num_threads to 100
6:30:56.067268 PROGRESS: === Extracted 5937 precursors and 39571 fragments ===
6:30:56.068858 INFO: === FDR correction performed with classifier version -1 ===
6:30:56.071130 PROGRESS: ============================= Precursor FDR =============================
6:30:56.071361 PROGRESS: Total precursors accumulated: 1,732
6:30:56.071434 PROGRESS: Target precursors: 1,715 (99.02%)
6:30:56.071491 PROGRESS: Decoy precursors: 17 (0.98%)
6:30:56.071544 PROGRESS: 
6:30:56.071597 PROGRESS: Precursor Summary:
6:30:56.074671 PROGRESS: Channel   0:	 0.050 FDR: 1,715; 0.010 FDR: 1,715; 0.001 FDR:   923
6:30:56.074885 PROGRESS: 
6:30:56.074960 PROGRESS: Protein Summary:
6:30:56.077957 PROGRESS: Channel   0:	 0.050 FDR: 1,418; 0.010 FDR: 1,418; 0.001 FDR:   805
6:30:56.078249 PROGRESS: =========================================================================
6:30:56.079451 INFO: Target number of precursors reached.
6:30:56.096988 INFO: fragments_df: keeping 5000 of 39571 [sum(precursor_idx_mask)=15528 sum(mass_error_mask)=39571 stop_rank=5000
6:30:56.140036 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:30:56.507089 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:30:57.515180 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
6:30:57.517489 INFO: Using score_cutoff 10.657996790885925 (fac=0.99, q=1)
6:30:57.518491 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
6:30:57.518581 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
6:30:57.518636 INFO: Updating optimization_manager: score_cutoff        : 0 -> 10.657996790885925
6:30:57.518725 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:30:57.525731 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:30:57.540586 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
6:30:57.541292 PROGRESS: Required number of precursors found. Starting search parameter optimization.
6:30:57.541439 INFO: Starting optimization step 2.
6:30:57.541556 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:30:57.541672 INFO: Using rust extraction backend
6:30:57.541759 PROGRESS: Extracting batch of 5943 precursors
6:30:57.572827 INFO: === Search parameters used ===
6:30:57.573549 INFO: rt_error       : 805.6019897460938
6:30:57.573626 INFO: mobility_error : 0.1
6:30:57.573716 INFO: num_candidates : 3
6:30:57.573773 INFO: ms1_error      : 3
6:30:57.573841 INFO: ms2_error      : 10
6:30:57.573898 INFO: fwhm_rt        : 3.0
6:30:57.573949 INFO: quant_window   : 3
6:30:57.574013 INFO: ==============================================
6:30:57.964048 INFO: performing precursor FDR with 40 features
6:30:57.964391 INFO: Decoy channel: -1
6:30:57.964421 INFO: competitive: True
6:30:57.992522 INFO: Setting torch num_threads to 2 for FDR classification task
6:30:58.009827 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
6:30:58.010624 INFO: Using random state 326332 for train-test-split
6:30:59.252152 INFO: Test AUC: 0.703
6:30:59.252425 INFO: Train AUC: 0.716
6:30:59.252458 INFO: AUC difference: 1.80%
6:30:59.563879 INFO: Resetting torch num_threads to 100
6:30:59.569423 PROGRESS: === Extracted 17806 precursors and 104079 fragments ===
6:30:59.570235 INFO: === FDR correction performed with classifier version 1 ===
6:30:59.571217 PROGRESS: ============================= Precursor FDR =============================
6:30:59.571322 PROGRESS: Total precursors accumulated: 1,963
6:30:59.571384 PROGRESS: Target precursors: 1,944 (99.03%)
6:30:59.571432 PROGRESS: Decoy precursors: 19 (0.97%)
6:30:59.571474 PROGRESS: 
6:30:59.571516 PROGRESS: Precursor Summary:
6:30:59.573169 PROGRESS: Channel   0:	 0.050 FDR: 1,944; 0.010 FDR: 1,944; 0.001 FDR: 1,165
6:30:59.573268 PROGRESS: 
6:30:59.573344 PROGRESS: Protein Summary:
6:30:59.575569 PROGRESS: Channel   0:	 0.050 FDR: 1,595; 0.010 FDR: 1,595; 0.001 FDR: 1,003
6:30:59.575676 PROGRESS: =========================================================================
6:30:59.577104 INFO: Target number of precursors reached.
6:30:59.601530 INFO: fragments_df: keeping 5000 of 104079 [sum(precursor_idx_mask)=40201 sum(mass_error_mask)=104079 stop_rank=5000
6:30:59.624377 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:31:00.136414 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:31:01.149174 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:31:01.151223 INFO: Using score_cutoff 10.194741641807557 (fac=0.99, q=1)
6:31:01.152042 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:31:01.152168 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:31:01.152240 INFO: Updating optimization_manager: score_cutoff        : 10.657996790885925 -> 10.194741641807557
6:31:01.152356 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:31:01.163099 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:31:01.178184 INFO: === checking if optimization conditions were reached ===
6:31:01.186808 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
6:31:01.188208 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
6:31:01.188375 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:31:01.188533 INFO: ==============================================
6:31:01.188817 INFO: Starting optimization step 3.
6:31:01.188965 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:31:01.189073 INFO: Using rust extraction backend
6:31:01.189194 PROGRESS: Extracting batch of 5943 precursors
6:31:01.221608 INFO: === Search parameters used ===
6:31:01.222670 INFO: rt_error       : 805.6019897460938
6:31:01.222747 INFO: mobility_error : 0.1
6:31:01.222801 INFO: num_candidates : 3
6:31:01.222860 INFO: ms1_error      : 3
6:31:01.222907 INFO: ms2_error      : 10.0
6:31:01.222955 INFO: fwhm_rt        : 3.0
6:31:01.223003 INFO: quant_window   : 3
6:31:01.223054 INFO: ==============================================
6:31:01.606986 INFO: performing precursor FDR with 40 features
6:31:01.607897 INFO: Decoy channel: -1
6:31:01.607967 INFO: competitive: True
6:31:01.637741 INFO: Setting torch num_threads to 2 for FDR classification task
6:31:01.656368 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
6:31:01.658854 INFO: Using random state 680479 for train-test-split
6:31:04.073877 INFO: Test AUC: 0.710
6:31:04.074152 INFO: Train AUC: 0.733
6:31:04.074186 INFO: AUC difference: 3.11%
6:31:04.458895 INFO: Resetting torch num_threads to 100
6:31:04.467188 PROGRESS: === Extracted 17806 precursors and 104070 fragments ===
6:31:04.468551 INFO: === FDR correction performed with classifier version 2 ===
6:31:04.470880 PROGRESS: ============================= Precursor FDR =============================
6:31:04.471097 PROGRESS: Total precursors accumulated: 1,984
6:31:04.471183 PROGRESS: Target precursors: 1,965 (99.04%)
6:31:04.471243 PROGRESS: Decoy precursors: 19 (0.96%)
6:31:04.471293 PROGRESS: 
6:31:04.471341 PROGRESS: Precursor Summary:
6:31:04.473900 PROGRESS: Channel   0:	 0.050 FDR: 1,965; 0.010 FDR: 1,965; 0.001 FDR: 1,092
6:31:04.474133 PROGRESS: 
6:31:04.474194 PROGRESS: Protein Summary:
6:31:04.476993 PROGRESS: Channel   0:	 0.050 FDR: 1,610; 0.010 FDR: 1,610; 0.001 FDR:   942
6:31:04.477260 PROGRESS: =========================================================================
6:31:04.478933 INFO: Target number of precursors reached.
6:31:04.514018 INFO: fragments_df: keeping 5000 of 104070 [sum(precursor_idx_mask)=40292 sum(mass_error_mask)=104070 stop_rank=5000
6:31:04.564095 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:31:05.083262 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:31:05.936770 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:31:05.937795 INFO: Using score_cutoff 9.892607176208497 (fac=0.99, q=1)
6:31:05.938268 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:31:05.938357 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:31:05.938413 INFO: Updating optimization_manager: score_cutoff        : 10.194741641807557 -> 9.892607176208497
6:31:05.938475 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:31:05.943979 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:31:05.952429 INFO: === checking if optimization conditions were reached ===
6:31:05.955672 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:31:05.955894 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
6:31:05.955966 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:31:05.956058 INFO: ==============================================
6:31:05.956142 INFO: Starting optimization step 4.
6:31:05.956210 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:31:05.956303 INFO: Using rust extraction backend
6:31:05.956384 PROGRESS: Extracting batch of 5943 precursors
6:31:05.971527 INFO: === Search parameters used ===
6:31:05.972264 INFO: rt_error       : 805.6019897460938
6:31:05.972324 INFO: mobility_error : 0.1
6:31:05.972376 INFO: num_candidates : 3
6:31:05.972422 INFO: ms1_error      : 3
6:31:05.972468 INFO: ms2_error      : 10.0
6:31:05.972511 INFO: fwhm_rt        : 3.0
6:31:05.972553 INFO: quant_window   : 3
6:31:05.972595 INFO: ==============================================
6:31:06.192577 INFO: performing precursor FDR with 40 features
6:31:06.192851 INFO: Decoy channel: -1
6:31:06.192879 INFO: competitive: True
6:31:06.203778 INFO: Setting torch num_threads to 2 for FDR classification task
6:31:06.212616 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
6:31:06.213053 INFO: Using random state 807151 for train-test-split
6:31:08.044086 INFO: Test AUC: 0.726
6:31:08.044255 INFO: Train AUC: 0.744
6:31:08.044286 INFO: AUC difference: 2.42%
6:31:08.345940 INFO: Resetting torch num_threads to 100
6:31:08.351048 PROGRESS: === Extracted 17805 precursors and 104063 fragments ===
6:31:08.351767 INFO: === FDR correction performed with classifier version 3 ===
6:31:08.352707 PROGRESS: ============================= Precursor FDR =============================
6:31:08.352808 PROGRESS: Total precursors accumulated: 2,132
6:31:08.352873 PROGRESS: Target precursors: 2,111 (99.02%)
6:31:08.352924 PROGRESS: Decoy precursors: 21 (0.98%)
6:31:08.352970 PROGRESS: 
6:31:08.353013 PROGRESS: Precursor Summary:
6:31:08.354690 PROGRESS: Channel   0:	 0.050 FDR: 2,111; 0.010 FDR: 2,111; 0.001 FDR: 1,198
6:31:08.354789 PROGRESS: 
6:31:08.354849 PROGRESS: Protein Summary:
6:31:08.357084 PROGRESS: Channel   0:	 0.050 FDR: 1,717; 0.010 FDR: 1,717; 0.001 FDR: 1,025
6:31:08.357194 PROGRESS: =========================================================================
6:31:08.358305 INFO: Target number of precursors reached.
6:31:08.382309 INFO: fragments_df: keeping 5000 of 104063 [sum(precursor_idx_mask)=42799 sum(mass_error_mask)=104063 stop_rank=5000
6:31:08.404847 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:31:08.910569 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:31:09.934947 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:31:09.937066 INFO: Using score_cutoff 9.766512731552124 (fac=0.99, q=1)
6:31:09.937642 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:31:09.937760 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:31:09.937821 INFO: Updating optimization_manager: score_cutoff        : 9.892607176208497 -> 9.766512731552124
6:31:09.937902 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:31:09.948229 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:31:09.963953 INFO: === checking if optimization conditions were reached ===
6:31:09.972417 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:31:09.973632 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
6:31:09.973815 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:31:09.973899 INFO: ==============================================
6:31:09.974000 INFO: Starting optimization step 5.
6:31:09.974118 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:31:09.974309 INFO: Using rust extraction backend
6:31:09.974419 PROGRESS: Extracting batch of 5943 precursors
6:31:10.006625 INFO: === Search parameters used ===
6:31:10.008131 INFO: rt_error       : 805.6019897460938
6:31:10.008199 INFO: mobility_error : 0.1
6:31:10.008253 INFO: num_candidates : 3
6:31:10.008320 INFO: ms1_error      : 3
6:31:10.008375 INFO: ms2_error      : 10.0
6:31:10.008424 INFO: fwhm_rt        : 3.0
6:31:10.008472 INFO: quant_window   : 3
6:31:10.008532 INFO: ==============================================
6:31:10.376661 INFO: performing precursor FDR with 40 features
6:31:10.377525 INFO: Decoy channel: -1
6:31:10.377565 INFO: competitive: True
6:31:10.413375 INFO: Setting torch num_threads to 2 for FDR classification task
6:31:10.436738 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
6:31:10.437426 INFO: Using random state 804765 for train-test-split
6:31:13.148383 INFO: Test AUC: 0.737
6:31:13.148690 INFO: Train AUC: 0.753
6:31:13.148728 INFO: AUC difference: 2.15%
6:31:13.626623 INFO: Resetting torch num_threads to 100
6:31:13.637091 PROGRESS: === Extracted 17805 precursors and 104073 fragments ===
6:31:13.639293 INFO: === FDR correction performed with classifier version 4 ===
6:31:13.642177 PROGRESS: ============================= Precursor FDR =============================
6:31:13.642604 PROGRESS: Total precursors accumulated: 2,165
6:31:13.642718 PROGRESS: Target precursors: 2,144 (99.03%)
6:31:13.642797 PROGRESS: Decoy precursors: 21 (0.97%)
6:31:13.642923 PROGRESS: 
6:31:13.642981 PROGRESS: Precursor Summary:
6:31:13.646378 PROGRESS: Channel   0:	 0.050 FDR: 2,144; 0.010 FDR: 2,144; 0.001 FDR: 1,208
6:31:13.646594 PROGRESS: 
6:31:13.646656 PROGRESS: Protein Summary:
6:31:13.650640 PROGRESS: Channel   0:	 0.050 FDR: 1,747; 0.010 FDR: 1,747; 0.001 FDR: 1,032
6:31:13.651018 PROGRESS: =========================================================================
6:31:13.653870 INFO: Target number of precursors reached.
6:31:13.686796 INFO: fragments_df: keeping 5000 of 104073 [sum(precursor_idx_mask)=43312 sum(mass_error_mask)=104073 stop_rank=5000
6:31:13.731122 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:31:14.260993 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:31:15.192924 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:31:15.195781 INFO: Using score_cutoff 9.547427108860015 (fac=0.99, q=1)
6:31:15.196913 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:31:15.197042 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:31:15.197110 INFO: Updating optimization_manager: score_cutoff        : 9.766512731552124 -> 9.547427108860015
6:31:15.197195 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:31:15.206371 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:31:15.221858 INFO: === checking if optimization conditions were reached ===
6:31:15.228896 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:31:15.229512 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
6:31:15.229605 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:31:15.229690 INFO: ==============================================
6:31:15.229794 INFO: Starting optimization step 6.
6:31:15.229869 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:31:15.229979 INFO: Using rust extraction backend
6:31:15.230087 PROGRESS: Extracting batch of 5943 precursors
6:31:15.259867 INFO: === Search parameters used ===
6:31:15.261541 INFO: rt_error       : 805.6019897460938
6:31:15.261634 INFO: mobility_error : 0.1
6:31:15.261693 INFO: num_candidates : 3
6:31:15.261742 INFO: ms1_error      : 3
6:31:15.261790 INFO: ms2_error      : 10.0
6:31:15.261842 INFO: fwhm_rt        : 3.0
6:31:15.261885 INFO: quant_window   : 3
6:31:15.262019 INFO: ==============================================
6:31:15.583185 INFO: performing precursor FDR with 40 features
6:31:15.583611 INFO: Decoy channel: -1
6:31:15.583648 INFO: competitive: True
6:31:15.615844 INFO: Setting torch num_threads to 2 for FDR classification task
6:31:15.633080 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
6:31:15.634136 INFO: Using random state 286088 for train-test-split
6:31:18.513756 INFO: Test AUC: 0.735
6:31:18.514129 INFO: Train AUC: 0.762
6:31:18.514183 INFO: AUC difference: 3.56%
6:31:18.934406 INFO: Resetting torch num_threads to 100
6:31:18.941506 PROGRESS: === Extracted 17806 precursors and 104092 fragments ===
6:31:18.943068 INFO: === FDR correction performed with classifier version 5 ===
6:31:18.947671 PROGRESS: ============================= Precursor FDR =============================
6:31:18.947950 PROGRESS: Total precursors accumulated: 2,176
6:31:18.948017 PROGRESS: Target precursors: 2,155 (99.03%)
6:31:18.948105 PROGRESS: Decoy precursors: 21 (0.97%)
6:31:18.948157 PROGRESS: 
6:31:18.948208 PROGRESS: Precursor Summary:
6:31:18.950734 PROGRESS: Channel   0:	 0.050 FDR: 2,155; 0.010 FDR: 2,155; 0.001 FDR: 1,206
6:31:18.950927 PROGRESS: 
6:31:18.950986 PROGRESS: Protein Summary:
6:31:18.953723 PROGRESS: Channel   0:	 0.050 FDR: 1,755; 0.010 FDR: 1,755; 0.001 FDR: 1,031
6:31:18.953914 PROGRESS: =========================================================================
6:31:18.956248 INFO: Target number of precursors reached.
6:31:18.988330 INFO: fragments_df: keeping 5000 of 104092 [sum(precursor_idx_mask)=43516 sum(mass_error_mask)=104092 stop_rank=5000
6:31:19.022038 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:31:19.598969 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:31:20.597218 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:31:20.599060 INFO: Using score_cutoff 9.511794762039186 (fac=0.99, q=1)
6:31:20.599776 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:31:20.599873 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:31:20.599931 INFO: Updating optimization_manager: score_cutoff        : 9.547427108860015 -> 9.511794762039186
6:31:20.600007 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:31:20.606893 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:31:20.618826 INFO: === checking if optimization conditions were reached ===
6:31:20.623881 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:31:20.624416 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
6:31:20.624498 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
6:31:20.624592 INFO: ==============================================
6:31:20.624716 PROGRESS: Optimization finished for ms2_error.
6:31:20.656573 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:31:20.664737 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:31:20.676600 INFO: Starting optimization step 0.
6:31:20.677283 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:31:20.677438 INFO: Using rust extraction backend
6:31:20.677523 PROGRESS: Extracting batch of 5943 precursors
6:31:20.701763 INFO: === Search parameters used ===
6:31:20.702563 INFO: rt_error       : 805.6019897460938
6:31:20.702624 INFO: mobility_error : 0.1
6:31:20.702677 INFO: num_candidates : 3
6:31:20.702723 INFO: ms1_error      : 3
6:31:20.702765 INFO: ms2_error      : 10.0
6:31:20.702806 INFO: fwhm_rt        : 3.0
6:31:20.702846 INFO: quant_window   : 3
6:31:20.702892 INFO: ==============================================
6:31:20.865515 INFO: performing precursor FDR with 40 features
6:31:20.865649 INFO: Decoy channel: -1
6:31:20.865674 INFO: competitive: True
6:31:20.872252 INFO: Setting torch num_threads to 2 for FDR classification task
6:31:20.877701 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
6:31:20.877876 INFO: Using random state 303099 for train-test-split
6:31:22.862869 INFO: Test AUC: 0.764
6:31:22.863306 INFO: Train AUC: 0.766
6:31:22.863344 INFO: AUC difference: 0.29%
6:31:23.384316 INFO: Resetting torch num_threads to 100
6:31:23.396339 PROGRESS: === Extracted 17806 precursors and 104084 fragments ===
6:31:23.397746 INFO: === FDR correction performed with classifier version 6 ===
6:31:23.399510 PROGRESS: ============================= Precursor FDR =============================
6:31:23.399695 PROGRESS: Total precursors accumulated: 2,249
6:31:23.399771 PROGRESS: Target precursors: 2,227 (99.02%)
6:31:23.399825 PROGRESS: Decoy precursors: 22 (0.98%)
6:31:23.399874 PROGRESS: 
6:31:23.399923 PROGRESS: Precursor Summary:
6:31:23.403261 PROGRESS: Channel   0:	 0.050 FDR: 2,227; 0.010 FDR: 2,227; 0.001 FDR: 1,341
6:31:23.403440 PROGRESS: 
6:31:23.403504 PROGRESS: Protein Summary:
6:31:23.406483 PROGRESS: Channel   0:	 0.050 FDR: 1,804; 0.010 FDR: 1,804; 0.001 FDR: 1,127
6:31:23.406806 PROGRESS: =========================================================================
6:31:23.410395 INFO: Target number of precursors reached.
6:31:23.443527 INFO: fragments_df: keeping 5000 of 104084 [sum(precursor_idx_mask)=44576 sum(mass_error_mask)=104084 stop_rank=5000
6:31:23.487606 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:31:24.093539 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:31:24.940367 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:31:24.941844 INFO: Using score_cutoff 9.319431735420226 (fac=0.99, q=1)
6:31:24.942441 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:31:24.942580 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:31:24.942662 INFO: Updating optimization_manager: score_cutoff        : 9.511794762039186 -> 9.319431735420226
6:31:24.942757 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:31:24.949523 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:31:24.961299 INFO: === checking if optimization conditions were reached ===
6:31:24.962135 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
6:31:24.967996 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 368.69663863538005
6:31:24.968588 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 368.6966.
6:31:24.968671 INFO: ==============================================
6:31:24.968777 INFO: Starting optimization step 1.
6:31:24.968852 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:31:24.968987 INFO: Using rust extraction backend
6:31:24.969075 PROGRESS: Extracting batch of 5943 precursors
6:31:24.989088 INFO: === Search parameters used ===
6:31:24.989893 INFO: rt_error       : 368.69663863538005
6:31:24.989956 INFO: mobility_error : 0.1
6:31:24.990005 INFO: num_candidates : 3
6:31:24.990049 INFO: ms1_error      : 3
6:31:24.990094 INFO: ms2_error      : 10.0
6:31:24.990137 INFO: fwhm_rt        : 3.0
6:31:24.990210 INFO: quant_window   : 3
6:31:24.990256 INFO: ==============================================
6:31:25.216718 INFO: performing precursor FDR with 40 features
6:31:25.217008 INFO: Decoy channel: -1
6:31:25.217039 INFO: competitive: True
6:31:25.250048 INFO: Setting torch num_threads to 2 for FDR classification task
6:31:25.264884 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
6:31:25.265499 INFO: Using random state 303099 for train-test-split
6:31:26.933347 INFO: Test AUC: 0.748
6:31:26.933615 INFO: Train AUC: 0.768
6:31:26.933650 INFO: AUC difference: 2.55%
6:31:27.244980 INFO: Resetting torch num_threads to 100
6:31:27.250187 PROGRESS: === Extracted 17806 precursors and 103386 fragments ===
6:31:27.250882 INFO: === FDR correction performed with classifier version 6 ===
6:31:27.252216 PROGRESS: ============================= Precursor FDR =============================
6:31:27.252342 PROGRESS: Total precursors accumulated: 2,339
6:31:27.252406 PROGRESS: Target precursors: 2,316 (99.02%)
6:31:27.252460 PROGRESS: Decoy precursors: 23 (0.98%)
6:31:27.252508 PROGRESS: 
6:31:27.252553 PROGRESS: Precursor Summary:
6:31:27.254310 PROGRESS: Channel   0:	 0.050 FDR: 2,316; 0.010 FDR: 2,316; 0.001 FDR: 1,450
6:31:27.254417 PROGRESS: 
6:31:27.254475 PROGRESS: Protein Summary:
6:31:27.256833 PROGRESS: Channel   0:	 0.050 FDR: 1,868; 0.010 FDR: 1,868; 0.001 FDR: 1,214
6:31:27.256940 PROGRESS: =========================================================================
6:31:27.258107 INFO: Target number of precursors reached.
6:31:27.285085 INFO: fragments_df: keeping 5000 of 103386 [sum(precursor_idx_mask)=46176 sum(mass_error_mask)=103386 stop_rank=5000
6:31:27.305276 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:31:27.818591 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:31:28.771418 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:31:28.772514 INFO: Using score_cutoff 9.307310698986054 (fac=0.99, q=1)
6:31:28.773038 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:31:28.773119 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:31:28.773174 INFO: Updating optimization_manager: score_cutoff        : 9.319431735420226 -> 9.307310698986054
6:31:28.773238 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:31:28.778602 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:31:28.787563 INFO: === checking if optimization conditions were reached ===
6:31:28.787937 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
6:31:28.792118 INFO: Updating optimization_manager: rt_error            : 368.69663863538005 -> 315.86839832169983
6:31:28.792360 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 315.8684.
6:31:28.792445 INFO: ==============================================
6:31:28.792531 INFO: Starting optimization step 2.
6:31:28.792599 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:31:28.792695 INFO: Using rust extraction backend
6:31:28.792771 PROGRESS: Extracting batch of 5943 precursors
6:31:28.807263 INFO: === Search parameters used ===
6:31:28.807754 INFO: rt_error       : 315.86839832169983
6:31:28.807810 INFO: mobility_error : 0.1
6:31:28.807859 INFO: num_candidates : 3
6:31:28.807904 INFO: ms1_error      : 3
6:31:28.807946 INFO: ms2_error      : 10.0
6:31:28.808010 INFO: fwhm_rt        : 3.0
6:31:28.808054 INFO: quant_window   : 3
6:31:28.808097 INFO: ==============================================
6:31:28.998603 INFO: performing precursor FDR with 40 features
6:31:28.998896 INFO: Decoy channel: -1
6:31:28.998923 INFO: competitive: True
6:31:29.015035 INFO: Setting torch num_threads to 2 for FDR classification task
6:31:29.023742 INFO: Estimating optimal hyperparameters - samples: 14,240, batch_size: 128, learning_rate: 1.77e-04
6:31:29.024147 INFO: Using random state 303099 for train-test-split
6:31:31.106273 INFO: Test AUC: 0.748
6:31:31.106565 INFO: Train AUC: 0.770
6:31:31.106625 INFO: AUC difference: 2.91%
6:31:31.513145 INFO: Resetting torch num_threads to 100
6:31:31.522968 PROGRESS: === Extracted 17801 precursors and 102810 fragments ===
6:31:31.524585 INFO: === FDR correction performed with classifier version 6 ===
6:31:31.528565 PROGRESS: ============================= Precursor FDR =============================
6:31:31.529021 PROGRESS: Total precursors accumulated: 2,287
6:31:31.529116 PROGRESS: Target precursors: 2,265 (99.04%)
6:31:31.529175 PROGRESS: Decoy precursors: 22 (0.96%)
6:31:31.529227 PROGRESS: 
6:31:31.529283 PROGRESS: Precursor Summary:
6:31:31.535884 PROGRESS: Channel   0:	 0.050 FDR: 2,265; 0.010 FDR: 2,265; 0.001 FDR: 1,164
6:31:31.536533 PROGRESS: 
6:31:31.536635 PROGRESS: Protein Summary:
6:31:31.543344 PROGRESS: Channel   0:	 0.050 FDR: 1,825; 0.010 FDR: 1,825; 0.001 FDR: 1,000
6:31:31.544061 PROGRESS: =========================================================================
6:31:31.546106 INFO: Target number of precursors reached.
6:31:31.578710 INFO: fragments_df: keeping 5000 of 102810 [sum(precursor_idx_mask)=44952 sum(mass_error_mask)=102810 stop_rank=5000
6:31:31.605208 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:31:32.202385 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:31:33.187229 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:31:33.189697 INFO: Using score_cutoff 9.128376905822753 (fac=0.99, q=1)
6:31:33.190740 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:31:33.190839 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:31:33.190901 INFO: Updating optimization_manager: score_cutoff        : 9.307310698986054 -> 9.128376905822753
6:31:33.190993 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:31:33.199365 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:31:33.214061 INFO: === checking if optimization conditions were reached ===
6:31:33.215559 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
6:31:33.224900 INFO: Updating optimization_manager: rt_error            : 315.86839832169983 -> 228.686453052738
6:31:33.225946 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 228.6865.
6:31:33.226135 INFO: ==============================================
6:31:33.226238 INFO: Starting optimization step 3.
6:31:33.226348 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:31:33.226566 INFO: Using rust extraction backend
6:31:33.226734 PROGRESS: Extracting batch of 5943 precursors
6:31:33.257432 INFO: === Search parameters used ===
6:31:33.258418 INFO: rt_error       : 228.686453052738
6:31:33.258498 INFO: mobility_error : 0.1
6:31:33.258554 INFO: num_candidates : 3
6:31:33.258606 INFO: ms1_error      : 3
6:31:33.258672 INFO: ms2_error      : 10.0
6:31:33.258722 INFO: fwhm_rt        : 3.0
6:31:33.258766 INFO: quant_window   : 3
6:31:33.258811 INFO: ==============================================
6:31:33.529383 INFO: performing precursor FDR with 40 features
6:31:33.529728 INFO: Decoy channel: -1
6:31:33.529763 INFO: competitive: True
6:31:33.567326 INFO: Setting torch num_threads to 2 for FDR classification task
6:31:33.580284 INFO: Estimating optimal hyperparameters - samples: 14,236, batch_size: 128, learning_rate: 1.77e-04
6:31:33.580716 INFO: Using random state 303099 for train-test-split
6:31:35.517446 INFO: Test AUC: 0.753
6:31:35.517667 INFO: Train AUC: 0.764
6:31:35.517703 INFO: AUC difference: 1.43%
6:31:35.833544 INFO: Resetting torch num_threads to 100
6:31:35.839582 PROGRESS: === Extracted 17795 precursors and 101126 fragments ===
6:31:35.840441 INFO: === FDR correction performed with classifier version 6 ===
6:31:35.841907 PROGRESS: ============================= Precursor FDR =============================
6:31:35.842082 PROGRESS: Total precursors accumulated: 2,415
6:31:35.842147 PROGRESS: Target precursors: 2,392 (99.05%)
6:31:35.842200 PROGRESS: Decoy precursors: 23 (0.95%)
6:31:35.842267 PROGRESS: 
6:31:35.842318 PROGRESS: Precursor Summary:
6:31:35.844209 PROGRESS: Channel   0:	 0.050 FDR: 2,392; 0.010 FDR: 2,392; 0.001 FDR:     0
6:31:35.844331 PROGRESS: 
6:31:35.844388 PROGRESS: Protein Summary:
6:31:35.846622 PROGRESS: Channel   0:	 0.050 FDR: 1,915; 0.010 FDR: 1,915; 0.001 FDR:     0
6:31:35.846730 PROGRESS: =========================================================================
6:31:35.848462 INFO: Target number of precursors reached.
6:31:35.876480 INFO: fragments_df: keeping 5000 of 101126 [sum(precursor_idx_mask)=47053 sum(mass_error_mask)=101126 stop_rank=5000
6:31:35.900188 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:31:36.310880 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:31:37.242037 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:31:37.243261 INFO: Using score_cutoff 9.288623459529877 (fac=0.99, q=1)
6:31:37.243861 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:31:37.243961 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:31:37.244020 INFO: Updating optimization_manager: score_cutoff        : 9.128376905822753 -> 9.288623459529877
6:31:37.244092 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:31:37.250494 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:31:37.261804 INFO: === checking if optimization conditions were reached ===
6:31:37.262435 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
6:31:37.267845 INFO: Updating optimization_manager: rt_error            : 228.686453052738 -> 221.7691638437111
6:31:37.268345 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 221.7692.
6:31:37.268447 INFO: ==============================================
6:31:37.268538 INFO: Starting optimization step 4.
6:31:37.268621 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:31:37.268710 INFO: Using rust extraction backend
6:31:37.268804 PROGRESS: Extracting batch of 5943 precursors
6:31:37.287700 INFO: === Search parameters used ===
6:31:37.288507 INFO: rt_error       : 221.7691638437111
6:31:37.288577 INFO: mobility_error : 0.1
6:31:37.288649 INFO: num_candidates : 3
6:31:37.288696 INFO: ms1_error      : 3
6:31:37.288739 INFO: ms2_error      : 10.0
6:31:37.288785 INFO: fwhm_rt        : 3.0
6:31:37.288827 INFO: quant_window   : 3
6:31:37.288869 INFO: ==============================================
6:31:37.548484 INFO: performing precursor FDR with 40 features
6:31:37.548842 INFO: Decoy channel: -1
6:31:37.548885 INFO: competitive: True
6:31:37.582705 INFO: Setting torch num_threads to 2 for FDR classification task
6:31:37.596904 INFO: Estimating optimal hyperparameters - samples: 14,237, batch_size: 128, learning_rate: 1.77e-04
6:31:37.597392 INFO: Using random state 303099 for train-test-split
6:31:39.737531 INFO: Test AUC: 0.742
6:31:39.738187 INFO: Train AUC: 0.765
6:31:39.738239 INFO: AUC difference: 3.11%
6:31:40.228141 INFO: Resetting torch num_threads to 100
6:31:40.239123 PROGRESS: === Extracted 17797 precursors and 100976 fragments ===
6:31:40.240675 INFO: === FDR correction performed with classifier version 6 ===
6:31:40.243370 PROGRESS: ============================= Precursor FDR =============================
6:31:40.243611 PROGRESS: Total precursors accumulated: 2,401
6:31:40.243695 PROGRESS: Target precursors: 2,378 (99.04%)
6:31:40.243751 PROGRESS: Decoy precursors: 23 (0.96%)
6:31:40.243800 PROGRESS: 
6:31:40.243851 PROGRESS: Precursor Summary:
6:31:40.246285 PROGRESS: Channel   0:	 0.050 FDR: 2,378; 0.010 FDR: 2,378; 0.001 FDR:     0
6:31:40.246730 PROGRESS: 
6:31:40.246803 PROGRESS: Protein Summary:
6:31:40.249722 PROGRESS: Channel   0:	 0.050 FDR: 1,895; 0.010 FDR: 1,895; 0.001 FDR:     0
6:31:40.249941 PROGRESS: =========================================================================
6:31:40.252400 INFO: Target number of precursors reached.
6:31:40.289292 INFO: fragments_df: keeping 5000 of 100976 [sum(precursor_idx_mask)=46322 sum(mass_error_mask)=100976 stop_rank=5000
6:31:40.339406 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:31:40.949153 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:31:41.918385 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:31:41.919771 INFO: Using score_cutoff 9.075742048072813 (fac=0.99, q=1)
6:31:41.920392 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:31:41.920476 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:31:41.920529 INFO: Updating optimization_manager: score_cutoff        : 9.288623459529877 -> 9.075742048072813
6:31:41.920592 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:31:41.928047 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:31:41.940824 INFO: === checking if optimization conditions were reached ===
6:31:41.942095 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
6:31:41.944840 INFO: Updating optimization_manager: rt_error            : 221.7691638437111 -> 228.686453052738
6:31:41.945405 INFO: Updating optimization_manager: classifier_version  : 6 -> 10
6:31:41.945570 INFO: Updating optimization_manager: score_cutoff        : 9.075742048072813 -> 9.288623459529877
6:31:41.945682 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:31:41.945789 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:31:41.945938 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 228.6865 found after 5 searches.
6:31:41.946050 INFO: ==============================================
6:31:41.946221 PROGRESS: Optimization finished for rt_error.
6:31:41.988391 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:31:41.996796 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:31:42.009805 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
6:31:42.010379 PROGRESS: ==============================================
6:31:42.010477 PROGRESS: ms2_error      : 10.0000
6:31:42.010538 PROGRESS: rt_error       : 228.6865
6:31:42.010584 PROGRESS: ==============================================
6:31:42.014515 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:31:42.218303 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:31:42.792123 INFO: Using rust extraction backend
6:31:42.793775 PROGRESS: Extracting batch of 289499 precursors
6:31:43.643596 INFO: === Search parameters used ===
6:31:43.645211 INFO: rt_error       : 228.686453052738
6:31:43.645339 INFO: mobility_error : 0.1
6:31:43.645410 INFO: num_candidates : 3
6:31:43.645479 INFO: ms1_error      : 3
6:31:43.645535 INFO: ms2_error      : 10.0
6:31:43.645598 INFO: fwhm_rt        : 3.0
6:31:43.645648 INFO: quant_window   : 3
6:31:43.645691 INFO: ==============================================
6:31:44.628622 INFO: Removed 131167 precursors with score below cutoff 9.288623459529877
6:31:45.437062 INFO: performing precursor FDR with 40 features
6:31:45.437335 INFO: Decoy channel: -1
6:31:45.437362 INFO: competitive: True
6:31:45.585024 INFO: Setting torch num_threads to 2 for FDR classification task
6:31:45.676923 WARNING: FDR calculation for 393941 target and 343370 decoy PSMs
6:31:45.677270 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
6:31:46.235649 INFO: Estimating optimal hyperparameters - samples: 589,848, batch_size: 2,416, learning_rate: 7.68e-04
6:31:46.237995 INFO: Using random state 90468 for train-test-split
6:31:57.609365 INFO: Test AUC: 0.779
6:31:57.609807 INFO: Train AUC: 0.783
6:31:57.609864 INFO: AUC difference: 0.51%
6:31:58.551606 INFO: Resetting torch num_threads to 100
6:31:59.959227 PROGRESS: ============================= Precursor FDR =============================
6:31:59.960016 PROGRESS: Total precursors accumulated: 131,564
6:31:59.960113 PROGRESS: Target precursors: 130,262 (99.01%)
6:31:59.960172 PROGRESS: Decoy precursors: 1,302 (0.99%)
6:31:59.960254 PROGRESS: 
6:31:59.960304 PROGRESS: Precursor Summary:
6:32:00.106364 PROGRESS: Channel   0:	 0.050 FDR: 130,262; 0.010 FDR: 130,262; 0.001 FDR: 111,611
6:32:00.107395 PROGRESS: 
6:32:00.107469 PROGRESS: Protein Summary:
6:32:00.418970 PROGRESS: Channel   0:	 0.050 FDR: 10,638; 0.010 FDR: 10,638; 0.001 FDR: 10,471
6:32:00.419991 PROGRESS: =========================================================================
6:32:00.437722 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/psm.parquet
6:32:00.995429 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.parquet
6:32:01.733362 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
6:32:02.071809 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 
6:32:02.072426 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant
6:32:02.072664 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/figures
6:32:02.073103 INFO: Initializing TimingManager
6:32:02.074741 INFO: Initializing RawFileManager
6:32:30.304475 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.
6:32:30.319129 INFO: Determining DIA cycle
6:32:30.338254 INFO: Found cycle with start 0.00 min and length 300.
6:32:31.014529 INFO: RT (min)            : 0.0 - 26.9
6:32:31.014838 INFO: RT duration (sec)   : 1611.2
6:32:31.014875 INFO: RT duration (min)   : 26.9
6:32:31.014927 INFO: Cycle len (scans)   : 300
6:32:31.014950 INFO: Cycle len (sec)     : 1.65
6:32:31.014971 INFO: Number of cycles    : 977
6:32:31.014993 INFO: MS2 range (m/z)     : 380.4 - 980.7
6:32:31.015059 INFO: Creating DIA data object took: 28.940155506134033
6:32:32.857629 INFO: Creating DIA data NG object took: 1.842067003250122
6:32:33.038787 INFO: Initializing CalibrationManager
6:32:33.039731 INFO: Setting up calibration estimators ..
6:32:33.039800 INFO: Found 1 estimator(s) in calibration group 'fragment'
6:32:33.039928 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'}' ..
6:32:33.040047 INFO: Found 3 estimator(s) in calibration group 'precursor'
6:32:33.040112 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
6:32:33.040221 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}}' ..
6:32:33.040287 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
6:32:33.040340 INFO: Done setting up calibration estimators.
6:32:33.041319 INFO: Initializing OptimizationManager
6:32:33.041570 INFO: initial parameter: ms1_error = 3
6:32:33.041625 INFO: initial parameter: ms2_error = 10
6:32:33.041685 INFO: initial parameter: rt_error = 805.6004638671875
6:32:33.041732 INFO: initial parameter: mobility_error = 0.1
6:32:33.041775 INFO: initial parameter: num_candidates = 1
6:32:33.041816 INFO: initial parameter: fwhm_rt = 5
6:32:33.041859 INFO: initial parameter: fwhm_mobility = 0.01
6:32:33.041900 INFO: initial parameter: score_cutoff = 0
6:32:33.041940 INFO: initial parameter: classifier_version = -1
6:32:33.042050 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
6:32:33.042806 INFO: FDRManager: loading saved state not requested, will be initialized.
6:32:33.042884 INFO: Initializing FDRManager
6:32:33.042935 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
6:32:33.222923 PROGRESS: Initializing spectral library: 146,300 target precursors potentially observable (0 removed)
6:32:33.337421 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
6:32:33.338717 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
6:32:33.338943 PROGRESS: Starting initial search for precursors.
6:32:33.339094 INFO: Starting optimization step 0.
6:32:33.339172 PROGRESS: === Extracting elution groups 0 to 1000 ===
6:32:33.339297 INFO: Using rust extraction backend
6:32:33.339871 PROGRESS: Extracting batch of 1979 precursors
6:32:33.353867 INFO: === Search parameters used ===
6:32:33.355302 INFO: rt_error       : 805.6004638671875
6:32:33.355373 INFO: mobility_error : 0.1
6:32:33.355421 INFO: num_candidates : 1
6:32:33.355473 INFO: ms1_error      : 3
6:32:33.355521 INFO: ms2_error      : 10
6:32:33.355569 INFO: fwhm_rt        : 5
6:32:33.355611 INFO: quant_window   : 3
6:32:33.355655 INFO: ==============================================
6:32:33.434990 INFO: performing precursor FDR with 40 features
6:32:33.435260 INFO: Decoy channel: -1
6:32:33.435287 INFO: competitive: True
6:32:33.438530 INFO: Setting torch num_threads to 2 for FDR classification task
6:32:33.443169 INFO: Estimating optimal hyperparameters - samples: 1,583, batch_size: 128, learning_rate: 1.77e-04
6:32:33.445690 INFO: Using random state 840749 for train-test-split
6:32:33.674118 INFO: Test AUC: 0.848
6:32:33.674439 INFO: Train AUC: 0.857
6:32:33.674472 INFO: AUC difference: 1.08%
6:32:34.078800 INFO: Resetting torch num_threads to 100
6:32:34.084272 PROGRESS: === Extracted 1979 precursors and 13211 fragments ===
6:32:34.085482 INFO: === FDR correction performed with classifier version -1 ===
6:32:34.087435 PROGRESS: ============================= Precursor FDR =============================
6:32:34.087801 PROGRESS: Total precursors accumulated: 432
6:32:34.087917 PROGRESS: Target precursors: 428 (99.07%)
6:32:34.087974 PROGRESS: Decoy precursors: 4 (0.93%)
6:32:34.088020 PROGRESS: 
6:32:34.088066 PROGRESS: Precursor Summary:
6:32:34.090886 PROGRESS: Channel   0:	 0.050 FDR:   428; 0.010 FDR:   428; 0.001 FDR:   107
6:32:34.091332 PROGRESS: 
6:32:34.091418 PROGRESS: Protein Summary:
6:32:34.095034 PROGRESS: Channel   0:	 0.050 FDR:   403; 0.010 FDR:   403; 0.001 FDR:   102
6:32:34.095614 PROGRESS: =========================================================================
6:32:34.096529 INFO: Target number of precursors not reached yet.
6:32:34.117950 INFO: Starting optimization step 1.
6:32:34.118664 PROGRESS: === Extracting elution groups 1000 to 3000 ===
6:32:34.118854 INFO: Using rust extraction backend
6:32:34.118958 PROGRESS: Extracting batch of 3964 precursors
6:32:34.134334 INFO: === Search parameters used ===
6:32:34.135067 INFO: rt_error       : 805.6004638671875
6:32:34.135159 INFO: mobility_error : 0.1
6:32:34.135215 INFO: num_candidates : 1
6:32:34.135261 INFO: ms1_error      : 3
6:32:34.135300 INFO: ms2_error      : 10
6:32:34.135341 INFO: fwhm_rt        : 5
6:32:34.135379 INFO: quant_window   : 3
6:32:34.135419 INFO: ==============================================
6:32:34.216117 INFO: performing precursor FDR with 40 features
6:32:34.216346 INFO: Decoy channel: -1
6:32:34.216372 INFO: competitive: True
6:32:34.223788 INFO: Setting torch num_threads to 2 for FDR classification task
6:32:34.228562 INFO: Estimating optimal hyperparameters - samples: 4,752, batch_size: 128, learning_rate: 1.77e-04
6:32:34.228807 INFO: Using random state 299687 for train-test-split
6:32:34.713474 INFO: Test AUC: 0.872
6:32:34.713637 INFO: Train AUC: 0.881
6:32:34.713666 INFO: AUC difference: 1.12%
6:32:35.002625 INFO: Resetting torch num_threads to 100
6:32:35.008241 PROGRESS: === Extracted 5941 precursors and 39836 fragments ===
6:32:35.008904 INFO: === FDR correction performed with classifier version -1 ===
6:32:35.009987 PROGRESS: ============================= Precursor FDR =============================
6:32:35.010187 PROGRESS: Total precursors accumulated: 1,767
6:32:35.010267 PROGRESS: Target precursors: 1,750 (99.04%)
6:32:35.010318 PROGRESS: Decoy precursors: 17 (0.96%)
6:32:35.010361 PROGRESS: 
6:32:35.010405 PROGRESS: Precursor Summary:
6:32:35.012561 PROGRESS: Channel   0:	 0.050 FDR: 1,750; 0.010 FDR: 1,750; 0.001 FDR: 1,307
6:32:35.012745 PROGRESS: 
6:32:35.012807 PROGRESS: Protein Summary:
6:32:35.014955 PROGRESS: Channel   0:	 0.050 FDR: 1,451; 0.010 FDR: 1,451; 0.001 FDR: 1,109
6:32:35.015116 PROGRESS: =========================================================================
6:32:35.015831 INFO: Target number of precursors reached.
6:32:35.027426 INFO: fragments_df: keeping 5000 of 39836 [sum(precursor_idx_mask)=15853 sum(mass_error_mask)=39836 stop_rank=5000
6:32:35.049044 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:32:35.420089 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:32:36.209330 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
6:32:36.210307 INFO: Using score_cutoff 10.447785778141021 (fac=0.99, q=1)
6:32:36.210754 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
6:32:36.210839 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
6:32:36.210897 INFO: Updating optimization_manager: score_cutoff        : 0 -> 10.447785778141021
6:32:36.210962 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:32:36.216145 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:32:36.224374 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
6:32:36.224781 PROGRESS: Required number of precursors found. Starting search parameter optimization.
6:32:36.224888 INFO: Starting optimization step 2.
6:32:36.224977 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:32:36.225080 INFO: Using rust extraction backend
6:32:36.225178 PROGRESS: Extracting batch of 5943 precursors
6:32:36.239188 INFO: === Search parameters used ===
6:32:36.239779 INFO: rt_error       : 805.6004638671875
6:32:36.239840 INFO: mobility_error : 0.1
6:32:36.239889 INFO: num_candidates : 3
6:32:36.239932 INFO: ms1_error      : 3
6:32:36.239976 INFO: ms2_error      : 10
6:32:36.240018 INFO: fwhm_rt        : 3.0
6:32:36.240059 INFO: quant_window   : 3
6:32:36.240099 INFO: ==============================================
6:32:36.432709 INFO: performing precursor FDR with 40 features
6:32:36.432966 INFO: Decoy channel: -1
6:32:36.432992 INFO: competitive: True
6:32:36.442922 INFO: Setting torch num_threads to 2 for FDR classification task
6:32:36.451182 INFO: Estimating optimal hyperparameters - samples: 14,241, batch_size: 128, learning_rate: 1.77e-04
6:32:36.451530 INFO: Using random state 920849 for train-test-split
6:32:38.187946 INFO: Test AUC: 0.715
6:32:38.188162 INFO: Train AUC: 0.712
6:32:38.188200 INFO: AUC difference: 0.46%
6:32:38.486848 INFO: Resetting torch num_threads to 100
6:32:38.492163 PROGRESS: === Extracted 17802 precursors and 104291 fragments ===
6:32:38.492844 INFO: === FDR correction performed with classifier version 1 ===
6:32:38.494375 PROGRESS: ============================= Precursor FDR =============================
6:32:38.494567 PROGRESS: Total precursors accumulated: 2,067
6:32:38.494639 PROGRESS: Target precursors: 2,047 (99.03%)
6:32:38.494690 PROGRESS: Decoy precursors: 20 (0.97%)
6:32:38.494736 PROGRESS: 
6:32:38.494780 PROGRESS: Precursor Summary:
6:32:38.496899 PROGRESS: Channel   0:	 0.050 FDR: 2,047; 0.010 FDR: 2,047; 0.001 FDR: 1,265
6:32:38.497088 PROGRESS: 
6:32:38.497165 PROGRESS: Protein Summary:
6:32:38.499307 PROGRESS: Channel   0:	 0.050 FDR: 1,662; 0.010 FDR: 1,662; 0.001 FDR: 1,076
6:32:38.499444 PROGRESS: =========================================================================
6:32:38.500542 INFO: Target number of precursors reached.
6:32:38.522979 INFO: fragments_df: keeping 5000 of 104291 [sum(precursor_idx_mask)=42150 sum(mass_error_mask)=104291 stop_rank=5000
6:32:38.540600 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:32:39.029045 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:32:39.943402 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:32:39.946775 INFO: Using score_cutoff 10.117820827674866 (fac=0.99, q=1)
6:32:39.947766 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:32:39.947855 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:32:39.947908 INFO: Updating optimization_manager: score_cutoff        : 10.447785778141021 -> 10.117820827674866
6:32:39.947962 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:32:39.955396 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:32:39.968259 INFO: === checking if optimization conditions were reached ===
6:32:39.975806 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
6:32:39.976634 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
6:32:39.976746 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:32:39.976871 INFO: ==============================================
6:32:39.977144 INFO: Starting optimization step 3.
6:32:39.977277 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:32:39.977432 INFO: Using rust extraction backend
6:32:39.977604 PROGRESS: Extracting batch of 5943 precursors
6:32:40.012727 INFO: === Search parameters used ===
6:32:40.013808 INFO: rt_error       : 805.6004638671875
6:32:40.013881 INFO: mobility_error : 0.1
6:32:40.013933 INFO: num_candidates : 3
6:32:40.013979 INFO: ms1_error      : 3
6:32:40.014028 INFO: ms2_error      : 10.0
6:32:40.014068 INFO: fwhm_rt        : 3.0
6:32:40.014108 INFO: quant_window   : 3
6:32:40.014152 INFO: ==============================================
6:32:40.170487 INFO: performing precursor FDR with 40 features
6:32:40.170647 INFO: Decoy channel: -1
6:32:40.170671 INFO: competitive: True
6:32:40.176297 INFO: Setting torch num_threads to 2 for FDR classification task
6:32:40.180976 INFO: Estimating optimal hyperparameters - samples: 14,240, batch_size: 128, learning_rate: 1.77e-04
6:32:40.181134 INFO: Using random state 540085 for train-test-split
6:32:41.926895 INFO: Test AUC: 0.714
6:32:41.927204 INFO: Train AUC: 0.729
6:32:41.927241 INFO: AUC difference: 2.00%
6:32:42.249261 INFO: Resetting torch num_threads to 100
6:32:42.254982 PROGRESS: === Extracted 17801 precursors and 104313 fragments ===
6:32:42.255897 INFO: === FDR correction performed with classifier version 2 ===
6:32:42.256877 PROGRESS: ============================= Precursor FDR =============================
6:32:42.256981 PROGRESS: Total precursors accumulated: 2,154
6:32:42.257045 PROGRESS: Target precursors: 2,133 (99.03%)
6:32:42.257097 PROGRESS: Decoy precursors: 21 (0.97%)
6:32:42.257143 PROGRESS: 
6:32:42.257189 PROGRESS: Precursor Summary:
6:32:42.258857 PROGRESS: Channel   0:	 0.050 FDR: 2,133; 0.010 FDR: 2,133; 0.001 FDR: 1,283
6:32:42.258978 PROGRESS: 
6:32:42.259036 PROGRESS: Protein Summary:
6:32:42.261308 PROGRESS: Channel   0:	 0.050 FDR: 1,729; 0.010 FDR: 1,729; 0.001 FDR: 1,086
6:32:42.261425 PROGRESS: =========================================================================
6:32:42.262509 INFO: Target number of precursors reached.
6:32:42.285786 INFO: fragments_df: keeping 5000 of 104313 [sum(precursor_idx_mask)=43709 sum(mass_error_mask)=104313 stop_rank=5000
6:32:42.306476 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:32:42.828581 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:32:43.673378 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:32:43.674106 INFO: Using score_cutoff 10.26379716682434 (fac=0.99, q=1)
6:32:43.674479 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:32:43.674557 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:32:43.674613 INFO: Updating optimization_manager: score_cutoff        : 10.117820827674866 -> 10.26379716682434
6:32:43.674670 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:32:43.679272 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:32:43.687440 INFO: === checking if optimization conditions were reached ===
6:32:43.690025 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:32:43.690249 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
6:32:43.690341 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:32:43.690408 INFO: ==============================================
6:32:43.690480 INFO: Starting optimization step 4.
6:32:43.690540 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:32:43.690608 INFO: Using rust extraction backend
6:32:43.690671 PROGRESS: Extracting batch of 5943 precursors
6:32:43.702625 INFO: === Search parameters used ===
6:32:43.703171 INFO: rt_error       : 805.6004638671875
6:32:43.703231 INFO: mobility_error : 0.1
6:32:43.703294 INFO: num_candidates : 3
6:32:43.703339 INFO: ms1_error      : 3
6:32:43.703380 INFO: ms2_error      : 10.0
6:32:43.703421 INFO: fwhm_rt        : 3.0
6:32:43.703460 INFO: quant_window   : 3
6:32:43.703499 INFO: ==============================================
6:32:43.872691 INFO: performing precursor FDR with 40 features
6:32:43.872951 INFO: Decoy channel: -1
6:32:43.872977 INFO: competitive: True
6:32:43.882490 INFO: Setting torch num_threads to 2 for FDR classification task
6:32:43.890072 INFO: Estimating optimal hyperparameters - samples: 14,240, batch_size: 128, learning_rate: 1.77e-04
6:32:43.890413 INFO: Using random state 194295 for train-test-split
6:32:46.314257 INFO: Test AUC: 0.723
6:32:46.314581 INFO: Train AUC: 0.740
6:32:46.314622 INFO: AUC difference: 2.31%
6:32:46.715541 INFO: Resetting torch num_threads to 100
6:32:46.721027 PROGRESS: === Extracted 17800 precursors and 104311 fragments ===
6:32:46.721836 INFO: === FDR correction performed with classifier version 3 ===
6:32:46.722777 PROGRESS: ============================= Precursor FDR =============================
6:32:46.722891 PROGRESS: Total precursors accumulated: 2,298
6:32:46.722963 PROGRESS: Target precursors: 2,276 (99.04%)
6:32:46.723019 PROGRESS: Decoy precursors: 22 (0.96%)
6:32:46.723068 PROGRESS: 
6:32:46.723135 PROGRESS: Precursor Summary:
6:32:46.724871 PROGRESS: Channel   0:	 0.050 FDR: 2,276; 0.010 FDR: 2,276; 0.001 FDR: 1,377
6:32:46.724988 PROGRESS: 
6:32:46.725045 PROGRESS: Protein Summary:
6:32:46.727346 PROGRESS: Channel   0:	 0.050 FDR: 1,833; 0.010 FDR: 1,833; 0.001 FDR: 1,167
6:32:46.727460 PROGRESS: =========================================================================
6:32:46.728552 INFO: Target number of precursors reached.
6:32:46.756884 INFO: fragments_df: keeping 5000 of 104311 [sum(precursor_idx_mask)=45760 sum(mass_error_mask)=104311 stop_rank=5000
6:32:46.778442 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:32:47.287608 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:32:48.261270 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:32:48.262519 INFO: Using score_cutoff 9.376159665584565 (fac=0.99, q=1)
6:32:48.263114 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:32:48.263238 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:32:48.263301 INFO: Updating optimization_manager: score_cutoff        : 10.26379716682434 -> 9.376159665584565
6:32:48.263384 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:32:48.270119 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:32:48.280583 INFO: === checking if optimization conditions were reached ===
6:32:48.285058 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:32:48.285572 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
6:32:48.285682 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:32:48.285771 INFO: ==============================================
6:32:48.285870 INFO: Starting optimization step 5.
6:32:48.285941 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:32:48.286042 INFO: Using rust extraction backend
6:32:48.286151 PROGRESS: Extracting batch of 5943 precursors
6:32:48.310468 INFO: === Search parameters used ===
6:32:48.311385 INFO: rt_error       : 805.6004638671875
6:32:48.311454 INFO: mobility_error : 0.1
6:32:48.311504 INFO: num_candidates : 3
6:32:48.311547 INFO: ms1_error      : 3
6:32:48.311588 INFO: ms2_error      : 10.0
6:32:48.311630 INFO: fwhm_rt        : 3.0
6:32:48.311671 INFO: quant_window   : 3
6:32:48.311710 INFO: ==============================================
6:32:48.587278 INFO: performing precursor FDR with 40 features
6:32:48.587644 INFO: Decoy channel: -1
6:32:48.587676 INFO: competitive: True
6:32:48.611865 INFO: Setting torch num_threads to 2 for FDR classification task
6:32:48.627604 INFO: Estimating optimal hyperparameters - samples: 14,240, batch_size: 128, learning_rate: 1.77e-04
6:32:48.628113 INFO: Using random state 29739 for train-test-split
6:32:49.983027 INFO: Test AUC: 0.737
6:32:49.983609 INFO: Train AUC: 0.750
6:32:49.983653 INFO: AUC difference: 1.80%
6:32:50.498958 INFO: Resetting torch num_threads to 100
6:32:50.509688 PROGRESS: === Extracted 17800 precursors and 104306 fragments ===
6:32:50.510991 INFO: === FDR correction performed with classifier version 4 ===
6:32:50.513427 PROGRESS: ============================= Precursor FDR =============================
6:32:50.513612 PROGRESS: Total precursors accumulated: 2,364
6:32:50.513680 PROGRESS: Target precursors: 2,341 (99.03%)
6:32:50.513729 PROGRESS: Decoy precursors: 23 (0.97%)
6:32:50.513796 PROGRESS: 
6:32:50.513841 PROGRESS: Precursor Summary:
6:32:50.517374 PROGRESS: Channel   0:	 0.050 FDR: 2,341; 0.010 FDR: 2,341; 0.001 FDR: 1,472
6:32:50.517622 PROGRESS: 
6:32:50.517687 PROGRESS: Protein Summary:
6:32:50.521084 PROGRESS: Channel   0:	 0.050 FDR: 1,876; 0.010 FDR: 1,876; 0.001 FDR: 1,236
6:32:50.521232 PROGRESS: =========================================================================
6:32:50.524727 INFO: Target number of precursors reached.
6:32:50.563976 INFO: fragments_df: keeping 5000 of 104306 [sum(precursor_idx_mask)=46828 sum(mass_error_mask)=104306 stop_rank=5000
6:32:50.614851 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:32:51.196906 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:32:52.141588 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:32:52.143250 INFO: Using score_cutoff 9.297772974014281 (fac=0.99, q=1)
6:32:52.144018 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:32:52.144108 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:32:52.144174 INFO: Updating optimization_manager: score_cutoff        : 9.376159665584565 -> 9.297772974014281
6:32:52.144279 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:32:52.151547 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:32:52.163465 INFO: === checking if optimization conditions were reached ===
6:32:52.168315 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:32:52.168928 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
6:32:52.169035 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:32:52.169126 INFO: ==============================================
6:32:52.169235 INFO: Starting optimization step 6.
6:32:52.169325 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:32:52.169443 INFO: Using rust extraction backend
6:32:52.169547 PROGRESS: Extracting batch of 5943 precursors
6:32:52.200310 INFO: === Search parameters used ===
6:32:52.201456 INFO: rt_error       : 805.6004638671875
6:32:52.201520 INFO: mobility_error : 0.1
6:32:52.201575 INFO: num_candidates : 3
6:32:52.201625 INFO: ms1_error      : 3
6:32:52.201671 INFO: ms2_error      : 10.0
6:32:52.201714 INFO: fwhm_rt        : 3.0
6:32:52.201758 INFO: quant_window   : 3
6:32:52.201801 INFO: ==============================================
6:32:52.533878 INFO: performing precursor FDR with 40 features
6:32:52.534236 INFO: Decoy channel: -1
6:32:52.534273 INFO: competitive: True
6:32:52.563248 INFO: Setting torch num_threads to 2 for FDR classification task
6:32:52.582971 INFO: Estimating optimal hyperparameters - samples: 14,239, batch_size: 128, learning_rate: 1.77e-04
6:32:52.583727 INFO: Using random state 952886 for train-test-split
6:32:54.993694 INFO: Test AUC: 0.748
6:32:54.994022 INFO: Train AUC: 0.758
6:32:54.994064 INFO: AUC difference: 1.31%
6:32:55.414148 INFO: Resetting torch num_threads to 100
6:32:55.422545 PROGRESS: === Extracted 17799 precursors and 104321 fragments ===
6:32:55.424200 INFO: === FDR correction performed with classifier version 5 ===
6:32:55.426563 PROGRESS: ============================= Precursor FDR =============================
6:32:55.426796 PROGRESS: Total precursors accumulated: 2,465
6:32:55.426867 PROGRESS: Target precursors: 2,441 (99.03%)
6:32:55.426960 PROGRESS: Decoy precursors: 24 (0.97%)
6:32:55.427013 PROGRESS: 
6:32:55.427074 PROGRESS: Precursor Summary:
6:32:55.429964 PROGRESS: Channel   0:	 0.050 FDR: 2,441; 0.010 FDR: 2,441; 0.001 FDR: 1,357
6:32:55.430259 PROGRESS: 
6:32:55.430335 PROGRESS: Protein Summary:
6:32:55.433441 PROGRESS: Channel   0:	 0.050 FDR: 1,952; 0.010 FDR: 1,952; 0.001 FDR: 1,147
6:32:55.433745 PROGRESS: =========================================================================
6:32:55.435783 INFO: Target number of precursors reached.
6:32:55.470818 INFO: fragments_df: keeping 5000 of 104321 [sum(precursor_idx_mask)=48668 sum(mass_error_mask)=104321 stop_rank=5000
6:32:55.506285 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:32:56.139824 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:32:57.154947 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:32:57.156634 INFO: Using score_cutoff 9.246872440338135 (fac=0.99, q=1)
6:32:57.157261 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:32:57.157356 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:32:57.157416 INFO: Updating optimization_manager: score_cutoff        : 9.297772974014281 -> 9.246872440338135
6:32:57.157492 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:32:57.164250 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:32:57.179739 INFO: === checking if optimization conditions were reached ===
6:32:57.186408 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:32:57.186957 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
6:32:57.187044 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
6:32:57.187126 INFO: ==============================================
6:32:57.187239 PROGRESS: Optimization finished for ms2_error.
6:32:57.229659 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:32:57.241027 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:32:57.254203 INFO: Starting optimization step 0.
6:32:57.255252 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:32:57.255459 INFO: Using rust extraction backend
6:32:57.255621 PROGRESS: Extracting batch of 5943 precursors
6:32:57.286268 INFO: === Search parameters used ===
6:32:57.288067 INFO: rt_error       : 805.6004638671875
6:32:57.288138 INFO: mobility_error : 0.1
6:32:57.288192 INFO: num_candidates : 3
6:32:57.288241 INFO: ms1_error      : 3
6:32:57.288287 INFO: ms2_error      : 10.0
6:32:57.288347 INFO: fwhm_rt        : 3.0
6:32:57.288397 INFO: quant_window   : 3
6:32:57.288448 INFO: ==============================================
6:32:57.632795 INFO: performing precursor FDR with 40 features
6:32:57.633534 INFO: Decoy channel: -1
6:32:57.633570 INFO: competitive: True
6:32:57.662572 INFO: Setting torch num_threads to 2 for FDR classification task
6:32:57.682229 INFO: Estimating optimal hyperparameters - samples: 14,239, batch_size: 128, learning_rate: 1.77e-04
6:32:57.682705 INFO: Using random state 583102 for train-test-split
6:33:00.325803 INFO: Test AUC: 0.756
6:33:00.326178 INFO: Train AUC: 0.766
6:33:00.326218 INFO: AUC difference: 1.40%
6:33:00.866851 INFO: Resetting torch num_threads to 100
6:33:00.877585 PROGRESS: === Extracted 17799 precursors and 104341 fragments ===
6:33:00.879011 INFO: === FDR correction performed with classifier version 6 ===
6:33:00.881163 PROGRESS: ============================= Precursor FDR =============================
6:33:00.881377 PROGRESS: Total precursors accumulated: 2,516
6:33:00.881450 PROGRESS: Target precursors: 2,492 (99.05%)
6:33:00.881511 PROGRESS: Decoy precursors: 24 (0.95%)
6:33:00.881573 PROGRESS: 
6:33:00.881625 PROGRESS: Precursor Summary:
6:33:00.885082 PROGRESS: Channel   0:	 0.050 FDR: 2,492; 0.010 FDR: 2,492; 0.001 FDR: 1,827
6:33:00.885270 PROGRESS: 
6:33:00.885330 PROGRESS: Protein Summary:
6:33:00.890409 PROGRESS: Channel   0:	 0.050 FDR: 1,993; 0.010 FDR: 1,993; 0.001 FDR: 1,493
6:33:00.890668 PROGRESS: =========================================================================
6:33:00.893425 INFO: Target number of precursors reached.
6:33:00.934878 INFO: fragments_df: keeping 5000 of 104341 [sum(precursor_idx_mask)=49293 sum(mass_error_mask)=104341 stop_rank=5000
6:33:00.982958 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:33:01.569882 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:33:02.601808 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:33:02.603251 INFO: Using score_cutoff 9.07682104625702 (fac=0.99, q=1)
6:33:02.603987 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:33:02.604087 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:33:02.604167 INFO: Updating optimization_manager: score_cutoff        : 9.246872440338135 -> 9.07682104625702
6:33:02.604249 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:33:02.611467 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:33:02.624274 INFO: === checking if optimization conditions were reached ===
6:33:02.625009 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
6:33:02.631361 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 497.53492019673166
6:33:02.632013 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 497.5349.
6:33:02.632104 INFO: ==============================================
6:33:02.632211 INFO: Starting optimization step 1.
6:33:02.632286 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:33:02.632437 INFO: Using rust extraction backend
6:33:02.632556 PROGRESS: Extracting batch of 5943 precursors
6:33:02.658783 INFO: === Search parameters used ===
6:33:02.659976 INFO: rt_error       : 497.53492019673166
6:33:02.660062 INFO: mobility_error : 0.1
6:33:02.660131 INFO: num_candidates : 3
6:33:02.660197 INFO: ms1_error      : 3
6:33:02.660256 INFO: ms2_error      : 10.0
6:33:02.660321 INFO: fwhm_rt        : 3.0
6:33:02.660384 INFO: quant_window   : 3
6:33:02.660482 INFO: ==============================================
6:33:02.955184 INFO: performing precursor FDR with 40 features
6:33:02.955547 INFO: Decoy channel: -1
6:33:02.955580 INFO: competitive: True
6:33:02.994043 INFO: Setting torch num_threads to 2 for FDR classification task
6:33:03.019954 INFO: Estimating optimal hyperparameters - samples: 14,240, batch_size: 128, learning_rate: 1.77e-04
6:33:03.020484 INFO: Using random state 583102 for train-test-split
6:33:05.517367 INFO: Test AUC: 0.734
6:33:05.517741 INFO: Train AUC: 0.765
6:33:05.517796 INFO: AUC difference: 4.11%
6:33:05.963153 INFO: Resetting torch num_threads to 100
6:33:05.973356 PROGRESS: === Extracted 17800 precursors and 104134 fragments ===
6:33:05.974862 INFO: === FDR correction performed with classifier version 6 ===
6:33:05.976212 PROGRESS: ============================= Precursor FDR =============================
6:33:05.976385 PROGRESS: Total precursors accumulated: 2,478
6:33:05.976461 PROGRESS: Target precursors: 2,454 (99.03%)
6:33:05.976520 PROGRESS: Decoy precursors: 24 (0.97%)
6:33:05.976570 PROGRESS: 
6:33:05.976617 PROGRESS: Precursor Summary:
6:33:05.979197 PROGRESS: Channel   0:	 0.050 FDR: 2,454; 0.010 FDR: 2,454; 0.001 FDR: 1,669
6:33:05.979336 PROGRESS: 
6:33:05.979405 PROGRESS: Protein Summary:
6:33:05.982247 PROGRESS: Channel   0:	 0.050 FDR: 1,961; 0.010 FDR: 1,961; 0.001 FDR: 1,376
6:33:05.982392 PROGRESS: =========================================================================
6:33:05.983923 INFO: Target number of precursors reached.
6:33:06.017575 INFO: fragments_df: keeping 5000 of 104134 [sum(precursor_idx_mask)=48534 sum(mass_error_mask)=104134 stop_rank=5000
6:33:06.051849 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:33:06.662810 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:33:07.669408 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:33:07.670911 INFO: Using score_cutoff 9.03693618106842 (fac=0.99, q=1)
6:33:07.671683 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:33:07.671801 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:33:07.671873 INFO: Updating optimization_manager: score_cutoff        : 9.07682104625702 -> 9.03693618106842
6:33:07.672003 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:33:07.679997 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:33:07.694756 INFO: === checking if optimization conditions were reached ===
6:33:07.695461 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
6:33:07.704163 INFO: Updating optimization_manager: rt_error            : 497.53492019673166 -> 251.03952068718138
6:33:07.704794 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 251.0395.
6:33:07.704891 INFO: ==============================================
6:33:07.704996 INFO: Starting optimization step 2.
6:33:07.705077 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:33:07.705194 INFO: Using rust extraction backend
6:33:07.705288 PROGRESS: Extracting batch of 5943 precursors
6:33:07.738081 INFO: === Search parameters used ===
6:33:07.739561 INFO: rt_error       : 251.03952068718138
6:33:07.739645 INFO: mobility_error : 0.1
6:33:07.739694 INFO: num_candidates : 3
6:33:07.739742 INFO: ms1_error      : 3
6:33:07.739800 INFO: ms2_error      : 10.0
6:33:07.739875 INFO: fwhm_rt        : 3.0
6:33:07.739929 INFO: quant_window   : 3
6:33:07.739975 INFO: ==============================================
6:33:08.060829 INFO: performing precursor FDR with 40 features
6:33:08.061196 INFO: Decoy channel: -1
6:33:08.061228 INFO: competitive: True
6:33:08.100461 INFO: Setting torch num_threads to 2 for FDR classification task
6:33:08.119370 INFO: Estimating optimal hyperparameters - samples: 14,232, batch_size: 128, learning_rate: 1.77e-04
6:33:08.120471 INFO: Using random state 583102 for train-test-split
6:33:10.406271 INFO: Test AUC: 0.746
6:33:10.406652 INFO: Train AUC: 0.773
6:33:10.406691 INFO: AUC difference: 3.45%
6:33:10.899627 INFO: Resetting torch num_threads to 100
6:33:10.912487 PROGRESS: === Extracted 17791 precursors and 101924 fragments ===
6:33:10.914787 INFO: === FDR correction performed with classifier version 6 ===
6:33:10.918949 PROGRESS: ============================= Precursor FDR =============================
6:33:10.919415 PROGRESS: Total precursors accumulated: 2,597
6:33:10.919484 PROGRESS: Target precursors: 2,572 (99.04%)
6:33:10.919536 PROGRESS: Decoy precursors: 25 (0.96%)
6:33:10.919586 PROGRESS: 
6:33:10.919639 PROGRESS: Precursor Summary:
6:33:10.923505 PROGRESS: Channel   0:	 0.050 FDR: 2,572; 0.010 FDR: 2,572; 0.001 FDR: 1,931
6:33:10.923744 PROGRESS: 
6:33:10.923803 PROGRESS: Protein Summary:
6:33:10.927411 PROGRESS: Channel   0:	 0.050 FDR: 2,049; 0.010 FDR: 2,049; 0.001 FDR: 1,572
6:33:10.927680 PROGRESS: =========================================================================
6:33:10.929590 INFO: Target number of precursors reached.
6:33:10.966080 INFO: fragments_df: keeping 5000 of 101924 [sum(precursor_idx_mask)=50127 sum(mass_error_mask)=101924 stop_rank=5000
6:33:11.008931 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:33:11.614019 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:33:12.643433 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:33:12.645123 INFO: Using score_cutoff 9.154445091819763 (fac=0.99, q=1)
6:33:12.645811 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:33:12.645907 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:33:12.645965 INFO: Updating optimization_manager: score_cutoff        : 9.03693618106842 -> 9.154445091819763
6:33:12.646040 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:33:12.653215 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:33:12.665856 INFO: === checking if optimization conditions were reached ===
6:33:12.666565 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
6:33:12.673290 INFO: Updating optimization_manager: rt_error            : 251.03952068718138 -> 181.69504816891728
6:33:12.673887 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 181.6950.
6:33:12.674024 INFO: ==============================================
6:33:12.674148 INFO: Starting optimization step 3.
6:33:12.674266 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:33:12.674416 INFO: Using rust extraction backend
6:33:12.674529 PROGRESS: Extracting batch of 5943 precursors
6:33:12.705051 INFO: === Search parameters used ===
6:33:12.706225 INFO: rt_error       : 181.69504816891728
6:33:12.706287 INFO: mobility_error : 0.1
6:33:12.706337 INFO: num_candidates : 3
6:33:12.706409 INFO: ms1_error      : 3
6:33:12.706464 INFO: ms2_error      : 10.0
6:33:12.706520 INFO: fwhm_rt        : 3.0
6:33:12.706567 INFO: quant_window   : 3
6:33:12.706626 INFO: ==============================================
6:33:12.984934 INFO: performing precursor FDR with 40 features
6:33:12.985367 INFO: Decoy channel: -1
6:33:12.985415 INFO: competitive: True
6:33:13.022978 INFO: Setting torch num_threads to 2 for FDR classification task
6:33:13.040379 INFO: Estimating optimal hyperparameters - samples: 14,216, batch_size: 128, learning_rate: 1.77e-04
6:33:13.041013 INFO: Using random state 583102 for train-test-split
6:33:15.380655 INFO: Test AUC: 0.752
6:33:15.381040 INFO: Train AUC: 0.776
6:33:15.381083 INFO: AUC difference: 3.04%
6:33:15.804632 INFO: Resetting torch num_threads to 100
6:33:15.814895 PROGRESS: === Extracted 17771 precursors and 99827 fragments ===
6:33:15.817044 INFO: === FDR correction performed with classifier version 6 ===
6:33:15.820335 PROGRESS: ============================= Precursor FDR =============================
6:33:15.820595 PROGRESS: Total precursors accumulated: 2,707
6:33:15.820660 PROGRESS: Target precursors: 2,681 (99.04%)
6:33:15.820714 PROGRESS: Decoy precursors: 26 (0.96%)
6:33:15.820766 PROGRESS: 
6:33:15.820812 PROGRESS: Precursor Summary:
6:33:15.823681 PROGRESS: Channel   0:	 0.050 FDR: 2,681; 0.010 FDR: 2,681; 0.001 FDR: 2,355
6:33:15.823946 PROGRESS: 
6:33:15.824006 PROGRESS: Protein Summary:
6:33:15.828049 PROGRESS: Channel   0:	 0.050 FDR: 2,122; 0.010 FDR: 2,122; 0.001 FDR: 1,883
6:33:15.828924 PROGRESS: =========================================================================
6:33:15.831601 INFO: Target number of precursors reached.
6:33:15.873166 INFO: fragments_df: keeping 5000 of 99827 [sum(precursor_idx_mask)=51430 sum(mass_error_mask)=99827 stop_rank=5000
6:33:15.926301 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:33:16.575468 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:33:17.568886 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:33:17.571474 INFO: Using score_cutoff 8.85395750427246 (fac=0.99, q=1)
6:33:17.572656 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:33:17.572801 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:33:17.572874 INFO: Updating optimization_manager: score_cutoff        : 9.154445091819763 -> 8.85395750427246
6:33:17.573020 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:33:17.582081 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:33:17.597234 INFO: === checking if optimization conditions were reached ===
6:33:17.598064 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
6:33:17.607082 INFO: Updating optimization_manager: rt_error            : 181.69504816891728 -> 162.32378682919955
6:33:17.608507 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 162.3238.
6:33:17.608614 INFO: ==============================================
6:33:17.608778 INFO: Starting optimization step 4.
6:33:17.608886 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:33:17.609019 INFO: Using rust extraction backend
6:33:17.609129 PROGRESS: Extracting batch of 5943 precursors
6:33:17.639102 INFO: === Search parameters used ===
6:33:17.640322 INFO: rt_error       : 162.32378682919955
6:33:17.640385 INFO: mobility_error : 0.1
6:33:17.640491 INFO: num_candidates : 3
6:33:17.640542 INFO: ms1_error      : 3
6:33:17.640583 INFO: ms2_error      : 10.0
6:33:17.640626 INFO: fwhm_rt        : 3.0
6:33:17.640670 INFO: quant_window   : 3
6:33:17.640711 INFO: ==============================================
6:33:17.999654 INFO: performing precursor FDR with 40 features
6:33:18.000251 INFO: Decoy channel: -1
6:33:18.000288 INFO: competitive: True
6:33:18.046403 INFO: Setting torch num_threads to 2 for FDR classification task
6:33:18.065018 INFO: Estimating optimal hyperparameters - samples: 14,219, batch_size: 128, learning_rate: 1.77e-04
6:33:18.065866 INFO: Using random state 583102 for train-test-split
6:33:20.499101 INFO: Test AUC: 0.758
6:33:20.499420 INFO: Train AUC: 0.776
6:33:20.499462 INFO: AUC difference: 2.39%
6:33:20.872911 INFO: Resetting torch num_threads to 100
6:33:20.877000 PROGRESS: === Extracted 17774 precursors and 99028 fragments ===
6:33:20.877593 INFO: === FDR correction performed with classifier version 6 ===
6:33:20.878427 PROGRESS: ============================= Precursor FDR =============================
6:33:20.878528 PROGRESS: Total precursors accumulated: 2,637
6:33:20.878588 PROGRESS: Target precursors: 2,611 (99.01%)
6:33:20.878636 PROGRESS: Decoy precursors: 26 (0.99%)
6:33:20.878680 PROGRESS: 
6:33:20.878722 PROGRESS: Precursor Summary:
6:33:20.880463 PROGRESS: Channel   0:	 0.050 FDR: 2,611; 0.010 FDR: 2,611; 0.001 FDR: 2,238
6:33:20.880568 PROGRESS: 
6:33:20.880625 PROGRESS: Protein Summary:
6:33:20.883156 PROGRESS: Channel   0:	 0.050 FDR: 2,075; 0.010 FDR: 2,075; 0.001 FDR: 1,793
6:33:20.883275 PROGRESS: =========================================================================
6:33:20.884186 INFO: Target number of precursors reached.
6:33:20.909080 INFO: fragments_df: keeping 5000 of 99028 [sum(precursor_idx_mask)=50005 sum(mass_error_mask)=99028 stop_rank=5000
6:33:20.930904 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:33:21.538974 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:33:22.630864 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:33:22.631971 INFO: Using score_cutoff 8.923646564483642 (fac=0.99, q=1)
6:33:22.632474 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:33:22.632558 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:33:22.632615 INFO: Updating optimization_manager: score_cutoff        : 8.85395750427246 -> 8.923646564483642
6:33:22.632677 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:33:22.638050 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:33:22.646475 INFO: === checking if optimization conditions were reached ===
6:33:22.646876 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
6:33:22.651527 INFO: Updating optimization_manager: rt_error            : 162.32378682919955 -> 128.4365860663042
6:33:22.651781 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 128.4366.
6:33:22.651862 INFO: ==============================================
6:33:22.651976 INFO: Starting optimization step 5.
6:33:22.652048 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:33:22.652140 INFO: Using rust extraction backend
6:33:22.652215 PROGRESS: Extracting batch of 5943 precursors
6:33:22.666291 INFO: === Search parameters used ===
6:33:22.666935 INFO: rt_error       : 128.4365860663042
6:33:22.666995 INFO: mobility_error : 0.1
6:33:22.667044 INFO: num_candidates : 3
6:33:22.667090 INFO: ms1_error      : 3
6:33:22.667133 INFO: ms2_error      : 10.0
6:33:22.667240 INFO: fwhm_rt        : 3.0
6:33:22.667283 INFO: quant_window   : 3
6:33:22.667323 INFO: ==============================================
6:33:22.849376 INFO: performing precursor FDR with 40 features
6:33:22.849690 INFO: Decoy channel: -1
6:33:22.849718 INFO: competitive: True
6:33:22.860319 INFO: Setting torch num_threads to 2 for FDR classification task
6:33:22.868711 INFO: Estimating optimal hyperparameters - samples: 14,204, batch_size: 128, learning_rate: 1.77e-04
6:33:22.869072 INFO: Using random state 583102 for train-test-split
6:33:24.047969 INFO: Test AUC: 0.750
6:33:24.048225 INFO: Train AUC: 0.781
6:33:24.048259 INFO: AUC difference: 3.98%
6:33:24.368080 INFO: Resetting torch num_threads to 100
6:33:24.373975 PROGRESS: === Extracted 17755 precursors and 97252 fragments ===
6:33:24.374840 INFO: === FDR correction performed with classifier version 6 ===
6:33:24.377082 PROGRESS: ============================= Precursor FDR =============================
6:33:24.377330 PROGRESS: Total precursors accumulated: 2,665
6:33:24.377419 PROGRESS: Target precursors: 2,639 (99.02%)
6:33:24.377474 PROGRESS: Decoy precursors: 26 (0.98%)
6:33:24.377519 PROGRESS: 
6:33:24.377563 PROGRESS: Precursor Summary:
6:33:24.381944 PROGRESS: Channel   0:	 0.050 FDR: 2,639; 0.010 FDR: 2,639; 0.001 FDR: 2,242
6:33:24.382371 PROGRESS: 
6:33:24.382453 PROGRESS: Protein Summary:
6:33:24.387362 PROGRESS: Channel   0:	 0.050 FDR: 2,096; 0.010 FDR: 2,096; 0.001 FDR: 1,809
6:33:24.387753 PROGRESS: =========================================================================
6:33:24.388886 INFO: Target number of precursors reached.
6:33:24.414736 INFO: fragments_df: keeping 5000 of 97252 [sum(precursor_idx_mask)=50152 sum(mass_error_mask)=97252 stop_rank=5000
6:33:24.429973 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:33:25.047074 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:33:26.051307 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:33:26.053252 INFO: Using score_cutoff 8.836150106620789 (fac=0.99, q=1)
6:33:26.054741 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:33:26.055097 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:33:26.055231 INFO: Updating optimization_manager: score_cutoff        : 8.923646564483642 -> 8.836150106620789
6:33:26.055336 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:33:26.063678 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:33:26.075581 INFO: === checking if optimization conditions were reached ===
6:33:26.076133 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
6:33:26.082283 INFO: Updating optimization_manager: rt_error            : 128.4365860663042 -> 96.70664218856336
6:33:26.082873 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 96.7066.
6:33:26.083029 INFO: ==============================================
6:33:26.083161 INFO: Starting optimization step 6.
6:33:26.083329 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:33:26.083497 INFO: Using rust extraction backend
6:33:26.083626 PROGRESS: Extracting batch of 5943 precursors
6:33:26.112961 INFO: === Search parameters used ===
6:33:26.113954 INFO: rt_error       : 96.70664218856336
6:33:26.114017 INFO: mobility_error : 0.1
6:33:26.114064 INFO: num_candidates : 3
6:33:26.114109 INFO: ms1_error      : 3
6:33:26.114153 INFO: ms2_error      : 10.0
6:33:26.114264 INFO: fwhm_rt        : 3.0
6:33:26.114305 INFO: quant_window   : 3
6:33:26.114349 INFO: ==============================================
6:33:26.396891 INFO: performing precursor FDR with 40 features
6:33:26.397279 INFO: Decoy channel: -1
6:33:26.397312 INFO: competitive: True
6:33:26.426232 INFO: Setting torch num_threads to 2 for FDR classification task
6:33:26.445627 INFO: Estimating optimal hyperparameters - samples: 14,186, batch_size: 128, learning_rate: 1.77e-04
6:33:26.446148 INFO: Using random state 583102 for train-test-split
6:33:28.737883 INFO: Test AUC: 0.773
6:33:28.738104 INFO: Train AUC: 0.784
6:33:28.738137 INFO: AUC difference: 1.43%
6:33:29.133011 INFO: Resetting torch num_threads to 100
6:33:29.143430 PROGRESS: === Extracted 17733 precursors and 95046 fragments ===
6:33:29.145396 INFO: === FDR correction performed with classifier version 6 ===
6:33:29.148213 PROGRESS: ============================= Precursor FDR =============================
6:33:29.148418 PROGRESS: Total precursors accumulated: 2,629
6:33:29.148492 PROGRESS: Target precursors: 2,603 (99.01%)
6:33:29.148547 PROGRESS: Decoy precursors: 26 (0.99%)
6:33:29.148599 PROGRESS: 
6:33:29.148653 PROGRESS: Precursor Summary:
6:33:29.151960 PROGRESS: Channel   0:	 0.050 FDR: 2,603; 0.010 FDR: 2,603; 0.001 FDR: 2,234
6:33:29.152149 PROGRESS: 
6:33:29.152209 PROGRESS: Protein Summary:
6:33:29.155905 PROGRESS: Channel   0:	 0.050 FDR: 2,066; 0.010 FDR: 2,066; 0.001 FDR: 1,794
6:33:29.156160 PROGRESS: =========================================================================
6:33:29.158054 INFO: Target number of precursors reached.
6:33:29.193178 INFO: fragments_df: keeping 5000 of 95046 [sum(precursor_idx_mask)=49041 sum(mass_error_mask)=95046 stop_rank=5000
6:33:29.230094 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:33:29.796774 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:33:30.662097 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:33:30.663242 INFO: Using score_cutoff 8.860002703857422 (fac=0.99, q=1)
6:33:30.663775 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:33:30.663856 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:33:30.663911 INFO: Updating optimization_manager: score_cutoff        : 8.836150106620789 -> 8.860002703857422
6:33:30.663982 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:33:30.669470 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:33:30.678914 INFO: === checking if optimization conditions were reached ===
6:33:30.679455 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
6:33:30.684506 INFO: Updating optimization_manager: rt_error            : 96.70664218856336 -> 79.9191804517688
6:33:30.684792 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 79.9192.
6:33:30.684876 INFO: ==============================================
6:33:30.684978 INFO: Starting optimization step 7.
6:33:30.685060 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:33:30.685200 INFO: Using rust extraction backend
6:33:30.685476 PROGRESS: Extracting batch of 5943 precursors
6:33:30.700619 INFO: === Search parameters used ===
6:33:30.701326 INFO: rt_error       : 79.9191804517688
6:33:30.701393 INFO: mobility_error : 0.1
6:33:30.701454 INFO: num_candidates : 3
6:33:30.701503 INFO: ms1_error      : 3
6:33:30.701573 INFO: ms2_error      : 10.0
6:33:30.701616 INFO: fwhm_rt        : 3.0
6:33:30.701658 INFO: quant_window   : 3
6:33:30.701702 INFO: ==============================================
6:33:30.826878 INFO: performing precursor FDR with 40 features
6:33:30.827044 INFO: Decoy channel: -1
6:33:30.827070 INFO: competitive: True
6:33:30.833144 INFO: Setting torch num_threads to 2 for FDR classification task
6:33:30.839230 INFO: Estimating optimal hyperparameters - samples: 14,172, batch_size: 128, learning_rate: 1.77e-04
6:33:30.839417 INFO: Using random state 583102 for train-test-split
6:33:31.954916 INFO: Test AUC: 0.771
6:33:31.955090 INFO: Train AUC: 0.791
6:33:31.955121 INFO: AUC difference: 2.41%
6:33:32.220937 INFO: Resetting torch num_threads to 100
6:33:32.224485 PROGRESS: === Extracted 17716 precursors and 93478 fragments ===
6:33:32.224929 INFO: === FDR correction performed with classifier version 6 ===
6:33:32.225699 PROGRESS: ============================= Precursor FDR =============================
6:33:32.225785 PROGRESS: Total precursors accumulated: 2,643
6:33:32.225842 PROGRESS: Target precursors: 2,617 (99.02%)
6:33:32.225891 PROGRESS: Decoy precursors: 26 (0.98%)
6:33:32.225936 PROGRESS: 
6:33:32.225979 PROGRESS: Precursor Summary:
6:33:32.227698 PROGRESS: Channel   0:	 0.050 FDR: 2,617; 0.010 FDR: 2,617; 0.001 FDR: 2,247
6:33:32.227796 PROGRESS: 
6:33:32.227851 PROGRESS: Protein Summary:
6:33:32.230247 PROGRESS: Channel   0:	 0.050 FDR: 2,080; 0.010 FDR: 2,080; 0.001 FDR: 1,811
6:33:32.230341 PROGRESS: =========================================================================
6:33:32.231095 INFO: Target number of precursors reached.
6:33:32.254226 INFO: fragments_df: keeping 5000 of 93478 [sum(precursor_idx_mask)=48716 sum(mass_error_mask)=93478 stop_rank=5000
6:33:32.271311 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:33:32.814358 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:33:33.645539 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:33:33.646779 INFO: Using score_cutoff 8.918473106002807 (fac=0.99, q=1)
6:33:33.647361 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:33:33.647453 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:33:33.647509 INFO: Updating optimization_manager: score_cutoff        : 8.860002703857422 -> 8.918473106002807
6:33:33.647584 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:33:33.653363 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:33:33.662563 INFO: === checking if optimization conditions were reached ===
6:33:33.663193 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
6:33:33.668414 INFO: Updating optimization_manager: rt_error            : 79.9191804517688 -> 71.32382733589651
6:33:33.668708 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 71.3238.
6:33:33.668784 INFO: ==============================================
6:33:33.668899 INFO: Starting optimization step 8.
6:33:33.668975 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:33:33.669079 INFO: Using rust extraction backend
6:33:33.669302 PROGRESS: Extracting batch of 5943 precursors
6:33:33.684920 INFO: === Search parameters used ===
6:33:33.685603 INFO: rt_error       : 71.32382733589651
6:33:33.685663 INFO: mobility_error : 0.1
6:33:33.685714 INFO: num_candidates : 3
6:33:33.685760 INFO: ms1_error      : 3
6:33:33.685807 INFO: ms2_error      : 10.0
6:33:33.685851 INFO: fwhm_rt        : 3.0
6:33:33.685896 INFO: quant_window   : 3
6:33:33.685937 INFO: ==============================================
6:33:33.840971 INFO: performing precursor FDR with 40 features
6:33:33.841147 INFO: Decoy channel: -1
6:33:33.841174 INFO: competitive: True
6:33:33.847955 INFO: Setting torch num_threads to 2 for FDR classification task
6:33:33.853789 INFO: Estimating optimal hyperparameters - samples: 14,148, batch_size: 128, learning_rate: 1.77e-04
6:33:33.854113 INFO: Using random state 583102 for train-test-split
6:33:36.110839 INFO: Test AUC: 0.773
6:33:36.111212 INFO: Train AUC: 0.791
6:33:36.111263 INFO: AUC difference: 2.21%
6:33:36.590642 INFO: Resetting torch num_threads to 100
6:33:36.603766 PROGRESS: === Extracted 17686 precursors and 92181 fragments ===
6:33:36.605756 INFO: === FDR correction performed with classifier version 6 ===
6:33:36.608923 PROGRESS: ============================= Precursor FDR =============================
6:33:36.609185 PROGRESS: Total precursors accumulated: 2,614
6:33:36.609253 PROGRESS: Target precursors: 2,589 (99.04%)
6:33:36.609304 PROGRESS: Decoy precursors: 25 (0.96%)
6:33:36.609379 PROGRESS: 
6:33:36.609430 PROGRESS: Precursor Summary:
6:33:36.612808 PROGRESS: Channel   0:	 0.050 FDR: 2,589; 0.010 FDR: 2,589; 0.001 FDR: 2,229
6:33:36.613088 PROGRESS: 
6:33:36.613151 PROGRESS: Protein Summary:
6:33:36.616689 PROGRESS: Channel   0:	 0.050 FDR: 2,053; 0.010 FDR: 2,053; 0.001 FDR: 1,797
6:33:36.617050 PROGRESS: =========================================================================
6:33:36.619608 INFO: Target number of precursors reached.
6:33:36.654531 INFO: fragments_df: keeping 5000 of 92181 [sum(precursor_idx_mask)=47748 sum(mass_error_mask)=92181 stop_rank=5000
6:33:36.698055 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:33:37.289438 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:33:38.279019 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:33:38.280521 INFO: Using score_cutoff 9.073861949157713 (fac=0.99, q=1)
6:33:38.281193 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:33:38.281320 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:33:38.281381 INFO: Updating optimization_manager: score_cutoff        : 8.918473106002807 -> 9.073861949157713
6:33:38.281484 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:33:38.288644 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:33:38.301662 INFO: === checking if optimization conditions were reached ===
6:33:38.302629 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
6:33:38.309386 INFO: Updating optimization_manager: rt_error            : 71.32382733589651 -> 62.50395906946572
6:33:38.310039 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 62.5040.
6:33:38.310171 INFO: ==============================================
6:33:38.310279 INFO: Starting optimization step 9.
6:33:38.310366 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:33:38.310482 INFO: Using rust extraction backend
6:33:38.310635 PROGRESS: Extracting batch of 5943 precursors
6:33:38.334458 INFO: === Search parameters used ===
6:33:38.335258 INFO: rt_error       : 62.50395906946572
6:33:38.335319 INFO: mobility_error : 0.1
6:33:38.335366 INFO: num_candidates : 3
6:33:38.335425 INFO: ms1_error      : 3
6:33:38.335471 INFO: ms2_error      : 10.0
6:33:38.335513 INFO: fwhm_rt        : 3.0
6:33:38.335557 INFO: quant_window   : 3
6:33:38.335601 INFO: ==============================================
6:33:38.586655 INFO: performing precursor FDR with 40 features
6:33:38.586918 INFO: Decoy channel: -1
6:33:38.586945 INFO: competitive: True
6:33:38.610189 INFO: Setting torch num_threads to 2 for FDR classification task
6:33:38.631524 INFO: Estimating optimal hyperparameters - samples: 14,052, batch_size: 128, learning_rate: 1.77e-04
6:33:38.631949 INFO: Using random state 583102 for train-test-split
6:33:41.038735 INFO: Test AUC: 0.783
6:33:41.039297 INFO: Train AUC: 0.799
6:33:41.039340 INFO: AUC difference: 2.08%
6:33:41.542481 INFO: Resetting torch num_threads to 100
6:33:41.552007 PROGRESS: === Extracted 17565 precursors and 90325 fragments ===
6:33:41.554641 INFO: === FDR correction performed with classifier version 6 ===
6:33:41.558202 PROGRESS: ============================= Precursor FDR =============================
6:33:41.558442 PROGRESS: Total precursors accumulated: 2,584
6:33:41.558512 PROGRESS: Target precursors: 2,559 (99.03%)
6:33:41.558567 PROGRESS: Decoy precursors: 25 (0.97%)
6:33:41.558614 PROGRESS: 
6:33:41.558684 PROGRESS: Precursor Summary:
6:33:41.562192 PROGRESS: Channel   0:	 0.050 FDR: 2,559; 0.010 FDR: 2,559; 0.001 FDR: 1,836
6:33:41.562374 PROGRESS: 
6:33:41.562432 PROGRESS: Protein Summary:
6:33:41.567426 PROGRESS: Channel   0:	 0.050 FDR: 2,031; 0.010 FDR: 2,031; 0.001 FDR: 1,504
6:33:41.567688 PROGRESS: =========================================================================
6:33:41.570017 INFO: Target number of precursors reached.
6:33:41.605543 INFO: fragments_df: keeping 5000 of 90325 [sum(precursor_idx_mask)=46451 sum(mass_error_mask)=90325 stop_rank=5000
6:33:41.661806 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:33:42.278213 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:33:43.312315 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:33:43.314417 INFO: Using score_cutoff 8.918764164733886 (fac=0.99, q=1)
6:33:43.315686 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:33:43.315788 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:33:43.315847 INFO: Updating optimization_manager: score_cutoff        : 9.073861949157713 -> 8.918764164733886
6:33:43.315955 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:33:43.325089 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:33:43.337623 INFO: === checking if optimization conditions were reached ===
6:33:43.339797 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
6:33:43.347444 INFO: Updating optimization_manager: rt_error            : 62.50395906946572 -> 53.461906126684205
6:33:43.348378 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 53.4619.
6:33:43.348472 INFO: ==============================================
6:33:43.348589 INFO: Starting optimization step 10.
6:33:43.348674 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:33:43.348811 INFO: Using rust extraction backend
6:33:43.349391 PROGRESS: Extracting batch of 5943 precursors
6:33:43.381060 INFO: === Search parameters used ===
6:33:43.381948 INFO: rt_error       : 53.461906126684205
6:33:43.382003 INFO: mobility_error : 0.1
6:33:43.382051 INFO: num_candidates : 3
6:33:43.382154 INFO: ms1_error      : 3
6:33:43.382203 INFO: ms2_error      : 10.0
6:33:43.382249 INFO: fwhm_rt        : 3.0
6:33:43.382293 INFO: quant_window   : 3
6:33:43.382338 INFO: ==============================================
6:33:43.667528 INFO: performing precursor FDR with 40 features
6:33:43.667870 INFO: Decoy channel: -1
6:33:43.667900 INFO: competitive: True
6:33:43.701035 INFO: Setting torch num_threads to 2 for FDR classification task
6:33:43.720324 INFO: Estimating optimal hyperparameters - samples: 13,567, batch_size: 128, learning_rate: 1.77e-04
6:33:43.720909 INFO: Using random state 583102 for train-test-split
6:33:44.891726 INFO: Test AUC: 0.801
6:33:44.891962 INFO: Train AUC: 0.814
6:33:44.892001 INFO: AUC difference: 1.58%
6:33:45.178299 INFO: Resetting torch num_threads to 100
6:33:45.183214 PROGRESS: === Extracted 16959 precursors and 85971 fragments ===
6:33:45.183814 INFO: === FDR correction performed with classifier version 6 ===
6:33:45.184935 PROGRESS: ============================= Precursor FDR =============================
6:33:45.185031 PROGRESS: Total precursors accumulated: 2,599
6:33:45.185091 PROGRESS: Target precursors: 2,574 (99.04%)
6:33:45.185152 PROGRESS: Decoy precursors: 25 (0.96%)
6:33:45.185200 PROGRESS: 
6:33:45.185247 PROGRESS: Precursor Summary:
6:33:45.186956 PROGRESS: Channel   0:	 0.050 FDR: 2,574; 0.010 FDR: 2,574; 0.001 FDR: 2,175
6:33:45.187058 PROGRESS: 
6:33:45.187114 PROGRESS: Protein Summary:
6:33:45.189473 PROGRESS: Channel   0:	 0.050 FDR: 2,046; 0.010 FDR: 2,046; 0.001 FDR: 1,747
6:33:45.189571 PROGRESS: =========================================================================
6:33:45.190272 INFO: Target number of precursors reached.
6:33:45.208922 INFO: fragments_df: keeping 5000 of 85971 [sum(precursor_idx_mask)=44383 sum(mass_error_mask)=85971 stop_rank=5000
6:33:45.223878 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:33:45.761566 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:33:46.638442 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:33:46.641350 INFO: Using score_cutoff 9.07814287662506 (fac=0.99, q=1)
6:33:46.642654 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:33:46.642819 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:33:46.642951 INFO: Updating optimization_manager: score_cutoff        : 8.918764164733886 -> 9.07814287662506
6:33:46.643037 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:33:46.652312 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:33:46.669483 INFO: === checking if optimization conditions were reached ===
6:33:46.670359 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
6:33:46.678744 INFO: Updating optimization_manager: rt_error            : 53.461906126684205 -> 37.609868564270144
6:33:46.680020 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 37.6099.
6:33:46.680130 INFO: ==============================================
6:33:46.680237 INFO: Starting optimization step 11.
6:33:46.680313 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:33:46.680448 INFO: Using rust extraction backend
6:33:46.680541 PROGRESS: Extracting batch of 5943 precursors
6:33:46.717566 INFO: === Search parameters used ===
6:33:46.719158 INFO: rt_error       : 37.609868564270144
6:33:46.719221 INFO: mobility_error : 0.1
6:33:46.719268 INFO: num_candidates : 3
6:33:46.719312 INFO: ms1_error      : 3
6:33:46.719353 INFO: ms2_error      : 10.0
6:33:46.719396 INFO: fwhm_rt        : 3.0
6:33:46.719438 INFO: quant_window   : 3
6:33:46.719480 INFO: ==============================================
6:33:47.039865 INFO: performing precursor FDR with 40 features
6:33:47.040303 INFO: Decoy channel: -1
6:33:47.040333 INFO: competitive: True
6:33:47.070498 INFO: Setting torch num_threads to 2 for FDR classification task
6:33:47.086501 INFO: Estimating optimal hyperparameters - samples: 13,053, batch_size: 128, learning_rate: 1.77e-04
6:33:47.087271 INFO: Using random state 583102 for train-test-split
6:33:49.431078 INFO: Test AUC: 0.818
6:33:49.431822 INFO: Train AUC: 0.828
6:33:49.431885 INFO: AUC difference: 1.13%
6:33:49.840487 INFO: Resetting torch num_threads to 100
6:33:49.848002 PROGRESS: === Extracted 16317 precursors and 82540 fragments ===
6:33:49.849238 INFO: === FDR correction performed with classifier version 6 ===
6:33:49.851569 PROGRESS: ============================= Precursor FDR =============================
6:33:49.851779 PROGRESS: Total precursors accumulated: 2,604
6:33:49.851879 PROGRESS: Target precursors: 2,579 (99.04%)
6:33:49.851934 PROGRESS: Decoy precursors: 25 (0.96%)
6:33:49.851983 PROGRESS: 
6:33:49.852036 PROGRESS: Precursor Summary:
6:33:49.855295 PROGRESS: Channel   0:	 0.050 FDR: 2,579; 0.010 FDR: 2,579; 0.001 FDR: 1,166
6:33:49.855563 PROGRESS: 
6:33:49.855622 PROGRESS: Protein Summary:
6:33:49.858289 PROGRESS: Channel   0:	 0.050 FDR: 2,050; 0.010 FDR: 2,050; 0.001 FDR: 1,002
6:33:49.858459 PROGRESS: =========================================================================
6:33:49.859531 INFO: Target number of precursors reached.
6:33:49.884667 INFO: fragments_df: keeping 5000 of 82540 [sum(precursor_idx_mask)=42584 sum(mass_error_mask)=82540 stop_rank=5000
6:33:49.918149 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:33:50.449439 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:33:51.262944 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:33:51.263577 INFO: Using score_cutoff 8.905261109161378 (fac=0.99, q=1)
6:33:51.263917 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:33:51.263994 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:33:51.264048 INFO: Updating optimization_manager: score_cutoff        : 9.07814287662506 -> 8.905261109161378
6:33:51.264107 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:33:51.268393 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:33:51.275267 INFO: === checking if optimization conditions were reached ===
6:33:51.275383 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 5 ===
6:33:51.278433 INFO: Updating optimization_manager: rt_error            : 37.609868564270144 -> 41.733891331742
6:33:51.278547 PROGRESS: ❌ rt_error       : optimization incomplete after 12 search(es). Will search with parameter 41.7339.
6:33:51.278610 INFO: ==============================================
6:33:51.278676 INFO: Starting optimization step 12.
6:33:51.278738 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:33:51.278802 INFO: Using rust extraction backend
6:33:51.278857 PROGRESS: Extracting batch of 5943 precursors
6:33:51.288719 INFO: === Search parameters used ===
6:33:51.288843 INFO: rt_error       : 41.733891331742
6:33:51.288892 INFO: mobility_error : 0.1
6:33:51.288935 INFO: num_candidates : 3
6:33:51.288975 INFO: ms1_error      : 3
6:33:51.289014 INFO: ms2_error      : 10.0
6:33:51.289054 INFO: fwhm_rt        : 3.0
6:33:51.289093 INFO: quant_window   : 3
6:33:51.289132 INFO: ==============================================
6:33:51.413050 INFO: performing precursor FDR with 40 features
6:33:51.413207 INFO: Decoy channel: -1
6:33:51.413232 INFO: competitive: True
6:33:51.418371 INFO: Setting torch num_threads to 2 for FDR classification task
6:33:51.422618 INFO: Estimating optimal hyperparameters - samples: 13,052, batch_size: 128, learning_rate: 1.77e-04
6:33:51.422767 INFO: Using random state 583102 for train-test-split
6:33:53.323205 INFO: Test AUC: 0.807
6:33:53.323536 INFO: Train AUC: 0.830
6:33:53.323582 INFO: AUC difference: 2.76%
6:33:53.636065 INFO: Resetting torch num_threads to 100
6:33:53.641654 PROGRESS: === Extracted 16315 precursors and 82500 fragments ===
6:33:53.642451 INFO: === FDR correction performed with classifier version 6 ===
6:33:53.643587 PROGRESS: ============================= Precursor FDR =============================
6:33:53.643703 PROGRESS: Total precursors accumulated: 2,581
6:33:53.643772 PROGRESS: Target precursors: 2,556 (99.03%)
6:33:53.643825 PROGRESS: Decoy precursors: 25 (0.97%)
6:33:53.643874 PROGRESS: 
6:33:53.643923 PROGRESS: Precursor Summary:
6:33:53.645888 PROGRESS: Channel   0:	 0.050 FDR: 2,556; 0.010 FDR: 2,556; 0.001 FDR: 2,269
6:33:53.646001 PROGRESS: 
6:33:53.646056 PROGRESS: Protein Summary:
6:33:53.648825 PROGRESS: Channel   0:	 0.050 FDR: 2,030; 0.010 FDR: 2,030; 0.001 FDR: 1,825
6:33:53.648955 PROGRESS: =========================================================================
6:33:53.650248 INFO: Target number of precursors reached.
6:33:53.671613 INFO: fragments_df: keeping 5000 of 82500 [sum(precursor_idx_mask)=42378 sum(mass_error_mask)=82500 stop_rank=5000
6:33:53.694354 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:33:54.180487 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:33:55.026787 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:33:55.027552 INFO: Using score_cutoff 8.943995750427245 (fac=0.99, q=1)
6:33:55.027953 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:33:55.028029 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:33:55.028083 INFO: Updating optimization_manager: score_cutoff        : 8.905261109161378 -> 8.943995750427245
6:33:55.028147 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:33:55.032647 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:33:55.040536 INFO: === checking if optimization conditions were reached ===
6:33:55.040895 PROGRESS: === Optimization of rt_error has been performed 13 time(s); minimum number is 5 ===
6:33:55.044764 INFO: Updating optimization_manager: rt_error            : 41.733891331742 -> 34.2676952706869
6:33:55.044969 PROGRESS: ❌ rt_error       : optimization incomplete after 13 search(es). Will search with parameter 34.2677.
6:33:55.045044 INFO: ==============================================
6:33:55.045123 INFO: Starting optimization step 13.
6:33:55.045194 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:33:55.045269 INFO: Using rust extraction backend
6:33:55.045335 PROGRESS: Extracting batch of 5943 precursors
6:33:55.056170 INFO: === Search parameters used ===
6:33:55.056604 INFO: rt_error       : 34.2676952706869
6:33:55.056657 INFO: mobility_error : 0.1
6:33:55.056720 INFO: num_candidates : 3
6:33:55.056762 INFO: ms1_error      : 3
6:33:55.056803 INFO: ms2_error      : 10.0
6:33:55.056844 INFO: fwhm_rt        : 3.0
6:33:55.056882 INFO: quant_window   : 3
6:33:55.056920 INFO: ==============================================
6:33:55.325078 INFO: performing precursor FDR with 40 features
6:33:55.325503 INFO: Decoy channel: -1
6:33:55.325536 INFO: competitive: True
6:33:55.353995 INFO: Setting torch num_threads to 2 for FDR classification task
6:33:55.380032 INFO: Estimating optimal hyperparameters - samples: 13,063, batch_size: 128, learning_rate: 1.77e-04
6:33:55.380687 INFO: Using random state 583102 for train-test-split
6:33:57.441259 INFO: Test AUC: 0.816
6:33:57.441626 INFO: Train AUC: 0.826
6:33:57.441675 INFO: AUC difference: 1.17%
6:33:57.828611 INFO: Resetting torch num_threads to 100
6:33:57.834590 PROGRESS: === Extracted 16329 precursors and 82513 fragments ===
6:33:57.836274 INFO: === FDR correction performed with classifier version 6 ===
6:33:57.838092 PROGRESS: ============================= Precursor FDR =============================
6:33:57.838262 PROGRESS: Total precursors accumulated: 2,561
6:33:57.838335 PROGRESS: Target precursors: 2,536 (99.02%)
6:33:57.838387 PROGRESS: Decoy precursors: 25 (0.98%)
6:33:57.838435 PROGRESS: 
6:33:57.838484 PROGRESS: Precursor Summary:
6:33:57.840813 PROGRESS: Channel   0:	 0.050 FDR: 2,536; 0.010 FDR: 2,536; 0.001 FDR: 1,121
6:33:57.841026 PROGRESS: 
6:33:57.841199 PROGRESS: Protein Summary:
6:33:57.844632 PROGRESS: Channel   0:	 0.050 FDR: 2,014; 0.010 FDR: 2,014; 0.001 FDR:   969
6:33:57.844812 PROGRESS: =========================================================================
6:33:57.847364 INFO: Target number of precursors reached.
6:33:57.882149 INFO: fragments_df: keeping 5000 of 82513 [sum(precursor_idx_mask)=41853 sum(mass_error_mask)=82513 stop_rank=5000
6:33:57.929616 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:33:58.609376 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:33:59.531300 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:33:59.533301 INFO: Using score_cutoff 9.064234408378601 (fac=0.99, q=1)
6:33:59.534157 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:33:59.534266 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:33:59.534325 INFO: Updating optimization_manager: score_cutoff        : 8.943995750427245 -> 9.064234408378601
6:33:59.534389 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:33:59.541131 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:33:59.551759 INFO: === checking if optimization conditions were reached ===
6:33:59.552475 PROGRESS: === Optimization of rt_error has been performed 14 time(s); minimum number is 5 ===
6:33:59.559549 INFO: Updating optimization_manager: rt_error            : 34.2676952706869 -> 36.43951473610575
6:33:59.560035 PROGRESS: ❌ rt_error       : optimization incomplete after 14 search(es). Will search with parameter 36.4395.
6:33:59.560134 INFO: ==============================================
6:33:59.560234 INFO: Starting optimization step 14.
6:33:59.560316 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:33:59.560444 INFO: Using rust extraction backend
6:33:59.560549 PROGRESS: Extracting batch of 5943 precursors
6:33:59.585172 INFO: === Search parameters used ===
6:33:59.586164 INFO: rt_error       : 36.43951473610575
6:33:59.586245 INFO: mobility_error : 0.1
6:33:59.586297 INFO: num_candidates : 3
6:33:59.586344 INFO: ms1_error      : 3
6:33:59.586392 INFO: ms2_error      : 10.0
6:33:59.586434 INFO: fwhm_rt        : 3.0
6:33:59.586478 INFO: quant_window   : 3
6:33:59.586565 INFO: ==============================================
6:33:59.929363 INFO: performing precursor FDR with 40 features
6:33:59.929724 INFO: Decoy channel: -1
6:33:59.929752 INFO: competitive: True
6:33:59.953442 INFO: Setting torch num_threads to 2 for FDR classification task
6:33:59.968628 INFO: Estimating optimal hyperparameters - samples: 13,048, batch_size: 128, learning_rate: 1.77e-04
6:33:59.969622 INFO: Using random state 583102 for train-test-split
6:34:02.163628 INFO: Test AUC: 0.826
6:34:02.164005 INFO: Train AUC: 0.825
6:34:02.164062 INFO: AUC difference: 0.16%
6:34:02.562636 INFO: Resetting torch num_threads to 100
6:34:02.573880 PROGRESS: === Extracted 16310 precursors and 82469 fragments ===
6:34:02.575575 INFO: === FDR correction performed with classifier version 6 ===
6:34:02.579438 PROGRESS: ============================= Precursor FDR =============================
6:34:02.579924 PROGRESS: Total precursors accumulated: 2,587
6:34:02.580060 PROGRESS: Target precursors: 2,562 (99.03%)
6:34:02.580150 PROGRESS: Decoy precursors: 25 (0.97%)
6:34:02.580206 PROGRESS: 
6:34:02.580250 PROGRESS: Precursor Summary:
6:34:02.585850 PROGRESS: Channel   0:	 0.050 FDR: 2,562; 0.010 FDR: 2,562; 0.001 FDR: 2,171
6:34:02.586455 PROGRESS: 
6:34:02.586518 PROGRESS: Protein Summary:
6:34:02.589988 PROGRESS: Channel   0:	 0.050 FDR: 2,036; 0.010 FDR: 2,036; 0.001 FDR: 1,753
6:34:02.590369 PROGRESS: =========================================================================
6:34:02.592115 INFO: Target number of precursors reached.
6:34:02.619151 INFO: fragments_df: keeping 5000 of 82469 [sum(precursor_idx_mask)=42321 sum(mass_error_mask)=82469 stop_rank=5000
6:34:02.660743 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:34:03.190036 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:34:04.179029 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:34:04.181513 INFO: Using score_cutoff 8.91878495464325 (fac=0.99, q=1)
6:34:04.182869 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:34:04.182995 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:34:04.183055 INFO: Updating optimization_manager: score_cutoff        : 9.064234408378601 -> 8.91878495464325
6:34:04.183157 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:34:04.191086 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:34:04.205389 INFO: === checking if optimization conditions were reached ===
6:34:04.206279 PROGRESS: === Optimization of rt_error has been performed 15 time(s); minimum number is 5 ===
6:34:04.213573 INFO: Updating optimization_manager: rt_error            : 36.43951473610575 -> 33.10129671986674
6:34:04.214493 PROGRESS: ❌ rt_error       : optimization incomplete after 15 search(es). Will search with parameter 33.1013.
6:34:04.214585 INFO: ==============================================
6:34:04.214719 INFO: Starting optimization step 15.
6:34:04.214824 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:34:04.215036 INFO: Using rust extraction backend
6:34:04.215280 PROGRESS: Extracting batch of 5943 precursors
6:34:04.251293 INFO: === Search parameters used ===
6:34:04.252193 INFO: rt_error       : 33.10129671986674
6:34:04.252258 INFO: mobility_error : 0.1
6:34:04.252312 INFO: num_candidates : 3
6:34:04.252359 INFO: ms1_error      : 3
6:34:04.252402 INFO: ms2_error      : 10.0
6:34:04.252484 INFO: fwhm_rt        : 3.0
6:34:04.252529 INFO: quant_window   : 3
6:34:04.252575 INFO: ==============================================
6:34:04.542751 INFO: performing precursor FDR with 40 features
6:34:04.543094 INFO: Decoy channel: -1
6:34:04.543125 INFO: competitive: True
6:34:04.567403 INFO: Setting torch num_threads to 2 for FDR classification task
6:34:04.582662 INFO: Estimating optimal hyperparameters - samples: 13,052, batch_size: 128, learning_rate: 1.77e-04
6:34:04.583282 INFO: Using random state 583102 for train-test-split
6:34:06.776999 INFO: Test AUC: 0.813
6:34:06.777291 INFO: Train AUC: 0.828
6:34:06.777328 INFO: AUC difference: 1.72%
6:34:07.205009 INFO: Resetting torch num_threads to 100
6:34:07.213737 PROGRESS: === Extracted 16315 precursors and 82489 fragments ===
6:34:07.215462 INFO: === FDR correction performed with classifier version 6 ===
6:34:07.217241 PROGRESS: ============================= Precursor FDR =============================
6:34:07.217468 PROGRESS: Total precursors accumulated: 2,618
6:34:07.217540 PROGRESS: Target precursors: 2,593 (99.05%)
6:34:07.217612 PROGRESS: Decoy precursors: 25 (0.95%)
6:34:07.217669 PROGRESS: 
6:34:07.217719 PROGRESS: Precursor Summary:
6:34:07.220319 PROGRESS: Channel   0:	 0.050 FDR: 2,593; 0.010 FDR: 2,593; 0.001 FDR: 1,449
6:34:07.220547 PROGRESS: 
6:34:07.220609 PROGRESS: Protein Summary:
6:34:07.223843 PROGRESS: Channel   0:	 0.050 FDR: 2,055; 0.010 FDR: 2,055; 0.001 FDR: 1,228
6:34:07.224030 PROGRESS: =========================================================================
6:34:07.225448 INFO: Target number of precursors reached.
6:34:07.253274 INFO: fragments_df: keeping 5000 of 82489 [sum(precursor_idx_mask)=42718 sum(mass_error_mask)=82489 stop_rank=5000
6:34:07.286865 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:34:07.841517 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:34:08.804245 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:34:08.806795 INFO: Using score_cutoff 8.857057787704468 (fac=0.99, q=1)
6:34:08.808276 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:34:08.808407 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:34:08.808462 INFO: Updating optimization_manager: score_cutoff        : 8.91878495464325 -> 8.857057787704468
6:34:08.808537 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:34:08.817261 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:34:08.829796 INFO: === checking if optimization conditions were reached ===
6:34:08.830907 PROGRESS: === Optimization of rt_error has been performed 16 time(s); minimum number is 5 ===
6:34:08.839797 INFO: Updating optimization_manager: rt_error            : 33.10129671986674 -> 38.10701026801715
6:34:08.841017 PROGRESS: ❌ rt_error       : optimization incomplete after 16 search(es). Will search with parameter 38.1070.
6:34:08.841139 INFO: ==============================================
6:34:08.841282 INFO: Starting optimization step 16.
6:34:08.841415 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:34:08.841520 INFO: Using rust extraction backend
6:34:08.841611 PROGRESS: Extracting batch of 5943 precursors
6:34:08.876141 INFO: === Search parameters used ===
6:34:08.877535 INFO: rt_error       : 38.10701026801715
6:34:08.877590 INFO: mobility_error : 0.1
6:34:08.877637 INFO: num_candidates : 3
6:34:08.877717 INFO: ms1_error      : 3
6:34:08.877767 INFO: ms2_error      : 10.0
6:34:08.877810 INFO: fwhm_rt        : 3.0
6:34:08.877849 INFO: quant_window   : 3
6:34:08.877890 INFO: ==============================================
6:34:09.155202 INFO: performing precursor FDR with 40 features
6:34:09.155713 INFO: Decoy channel: -1
6:34:09.155755 INFO: competitive: True
6:34:09.180864 INFO: Setting torch num_threads to 2 for FDR classification task
6:34:09.203521 INFO: Estimating optimal hyperparameters - samples: 13,053, batch_size: 128, learning_rate: 1.77e-04
6:34:09.204047 INFO: Using random state 583102 for train-test-split
6:34:11.239345 INFO: Test AUC: 0.805
6:34:11.239749 INFO: Train AUC: 0.828
6:34:11.239794 INFO: AUC difference: 2.71%
6:34:11.639679 INFO: Resetting torch num_threads to 100
6:34:11.648750 PROGRESS: === Extracted 16317 precursors and 82496 fragments ===
6:34:11.650026 INFO: === FDR correction performed with classifier version 6 ===
6:34:11.651739 PROGRESS: ============================= Precursor FDR =============================
6:34:11.651881 PROGRESS: Total precursors accumulated: 2,637
6:34:11.651952 PROGRESS: Target precursors: 2,611 (99.01%)
6:34:11.652006 PROGRESS: Decoy precursors: 26 (0.99%)
6:34:11.652056 PROGRESS: 
6:34:11.652102 PROGRESS: Precursor Summary:
6:34:11.654352 PROGRESS: Channel   0:	 0.050 FDR: 2,611; 0.010 FDR: 2,611; 0.001 FDR: 2,216
6:34:11.654489 PROGRESS: 
6:34:11.654550 PROGRESS: Protein Summary:
6:34:11.658175 PROGRESS: Channel   0:	 0.050 FDR: 2,075; 0.010 FDR: 2,075; 0.001 FDR: 1,787
6:34:11.658349 PROGRESS: =========================================================================
6:34:11.660166 INFO: Target number of precursors reached.
6:34:11.690740 INFO: fragments_df: keeping 5000 of 82496 [sum(precursor_idx_mask)=43127 sum(mass_error_mask)=82496 stop_rank=5000
6:34:11.726764 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:34:12.334241 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:34:13.239383 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:34:13.241150 INFO: Using score_cutoff 9.019158353805542 (fac=0.99, q=1)
6:34:13.242366 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:34:13.242484 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:34:13.242545 INFO: Updating optimization_manager: score_cutoff        : 8.857057787704468 -> 9.019158353805542
6:34:13.242652 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:34:13.250553 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:34:13.264357 INFO: === checking if optimization conditions were reached ===
6:34:13.266068 PROGRESS: === Optimization of rt_error has been performed 17 time(s); minimum number is 5 ===
6:34:13.275534 INFO: Updating optimization_manager: rt_error            : 38.10701026801715 -> 34.95484562334539
6:34:13.276843 PROGRESS: ❌ rt_error       : optimization incomplete after 17 search(es). Will search with parameter 34.9548.
6:34:13.276936 INFO: ==============================================
6:34:13.277028 INFO: Starting optimization step 17.
6:34:13.277099 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:34:13.277298 INFO: Using rust extraction backend
6:34:13.277609 PROGRESS: Extracting batch of 5943 precursors
6:34:13.309719 INFO: === Search parameters used ===
6:34:13.310558 INFO: rt_error       : 34.95484562334539
6:34:13.310650 INFO: mobility_error : 0.1
6:34:13.310702 INFO: num_candidates : 3
6:34:13.310748 INFO: ms1_error      : 3
6:34:13.310797 INFO: ms2_error      : 10.0
6:34:13.310840 INFO: fwhm_rt        : 3.0
6:34:13.310887 INFO: quant_window   : 3
6:34:13.310927 INFO: ==============================================
6:34:13.541301 INFO: performing precursor FDR with 40 features
6:34:13.541644 INFO: Decoy channel: -1
6:34:13.541675 INFO: competitive: True
6:34:13.564131 INFO: Setting torch num_threads to 2 for FDR classification task
6:34:13.577828 INFO: Estimating optimal hyperparameters - samples: 13,052, batch_size: 128, learning_rate: 1.77e-04
6:34:13.578419 INFO: Using random state 583102 for train-test-split
6:34:15.874745 INFO: Test AUC: 0.809
6:34:15.875182 INFO: Train AUC: 0.828
6:34:15.875244 INFO: AUC difference: 2.36%
6:34:16.254069 INFO: Resetting torch num_threads to 100
6:34:16.264007 PROGRESS: === Extracted 16316 precursors and 82480 fragments ===
6:34:16.265986 INFO: === FDR correction performed with classifier version 6 ===
6:34:16.268028 PROGRESS: ============================= Precursor FDR =============================
6:34:16.268262 PROGRESS: Total precursors accumulated: 2,599
6:34:16.268356 PROGRESS: Target precursors: 2,574 (99.04%)
6:34:16.268427 PROGRESS: Decoy precursors: 25 (0.96%)
6:34:16.268493 PROGRESS: 
6:34:16.268543 PROGRESS: Precursor Summary:
6:34:16.271646 PROGRESS: Channel   0:	 0.050 FDR: 2,574; 0.010 FDR: 2,574; 0.001 FDR: 2,219
6:34:16.271820 PROGRESS: 
6:34:16.271882 PROGRESS: Protein Summary:
6:34:16.275101 PROGRESS: Channel   0:	 0.050 FDR: 2,048; 0.010 FDR: 2,048; 0.001 FDR: 1,787
6:34:16.275325 PROGRESS: =========================================================================
6:34:16.277346 INFO: Target number of precursors reached.
6:34:16.307489 INFO: fragments_df: keeping 5000 of 82480 [sum(precursor_idx_mask)=42566 sum(mass_error_mask)=82480 stop_rank=5000
6:34:16.358437 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:34:16.960316 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:34:17.845443 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:34:17.846776 INFO: Using score_cutoff 9.001509033107757 (fac=0.99, q=1)
6:34:17.847548 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:34:17.847652 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:34:17.847707 INFO: Updating optimization_manager: score_cutoff        : 9.019158353805542 -> 9.001509033107757
6:34:17.847798 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:34:17.854563 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:34:17.866391 INFO: === checking if optimization conditions were reached ===
6:34:17.867126 PROGRESS: === Optimization of rt_error has been performed 18 time(s); minimum number is 5 ===
6:34:17.873212 INFO: Updating optimization_manager: rt_error            : 34.95484562334539 -> 37.039851393162465
6:34:17.873844 PROGRESS: ❌ rt_error       : optimization incomplete after 18 search(es). Will search with parameter 37.0399.
6:34:17.873935 INFO: ==============================================
6:34:17.874051 INFO: Starting optimization step 18.
6:34:17.874126 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:34:17.874249 INFO: Using rust extraction backend
6:34:17.874383 PROGRESS: Extracting batch of 5943 precursors
6:34:17.898124 INFO: === Search parameters used ===
6:34:17.898862 INFO: rt_error       : 37.039851393162465
6:34:17.898918 INFO: mobility_error : 0.1
6:34:17.898962 INFO: num_candidates : 3
6:34:17.899005 INFO: ms1_error      : 3
6:34:17.899046 INFO: ms2_error      : 10.0
6:34:17.899086 INFO: fwhm_rt        : 3.0
6:34:17.899127 INFO: quant_window   : 3
6:34:17.899255 INFO: ==============================================
6:34:18.165262 INFO: performing precursor FDR with 40 features
6:34:18.165663 INFO: Decoy channel: -1
6:34:18.165693 INFO: competitive: True
6:34:18.188094 INFO: Setting torch num_threads to 2 for FDR classification task
6:34:18.201128 INFO: Estimating optimal hyperparameters - samples: 13,051, batch_size: 128, learning_rate: 1.77e-04
6:34:18.201636 INFO: Using random state 583102 for train-test-split
6:34:20.446464 INFO: Test AUC: 0.817
6:34:20.446832 INFO: Train AUC: 0.824
6:34:20.446891 INFO: AUC difference: 0.87%
6:34:20.857799 INFO: Resetting torch num_threads to 100
6:34:20.866249 PROGRESS: === Extracted 16314 precursors and 82483 fragments ===
6:34:20.867681 INFO: === FDR correction performed with classifier version 6 ===
6:34:20.870489 PROGRESS: ============================= Precursor FDR =============================
6:34:20.870760 PROGRESS: Total precursors accumulated: 2,564
6:34:20.870845 PROGRESS: Target precursors: 2,539 (99.02%)
6:34:20.870899 PROGRESS: Decoy precursors: 25 (0.98%)
6:34:20.870950 PROGRESS: 
6:34:20.871002 PROGRESS: Precursor Summary:
6:34:20.873732 PROGRESS: Channel   0:	 0.050 FDR: 2,539; 0.010 FDR: 2,539; 0.001 FDR: 2,311
6:34:20.873968 PROGRESS: 
6:34:20.874036 PROGRESS: Protein Summary:
6:34:20.877296 PROGRESS: Channel   0:	 0.050 FDR: 2,018; 0.010 FDR: 2,018; 0.001 FDR: 1,858
6:34:20.877577 PROGRESS: =========================================================================
6:34:20.879168 INFO: Target number of precursors reached.
6:34:20.906127 INFO: fragments_df: keeping 5000 of 82483 [sum(precursor_idx_mask)=42020 sum(mass_error_mask)=82483 stop_rank=5000
6:34:20.945725 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:34:21.462843 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:34:22.427039 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:34:22.428948 INFO: Using score_cutoff 8.983989663505554 (fac=0.99, q=1)
6:34:22.429786 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:34:22.429935 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:34:22.430002 INFO: Updating optimization_manager: score_cutoff        : 9.001509033107757 -> 8.983989663505554
6:34:22.430081 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:34:22.438659 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:34:22.453204 INFO: === checking if optimization conditions were reached ===
6:34:22.454600 PROGRESS: === Optimization of rt_error has been performed 19 time(s); minimum number is 5 ===
6:34:22.464689 INFO: Updating optimization_manager: rt_error            : 37.039851393162465 -> 34.7455988679267
6:34:22.465886 PROGRESS: ❌ rt_error       : optimization incomplete after 19 search(es). Will search with parameter 34.7456.
6:34:22.466033 INFO: ==============================================
6:34:22.466212 INFO: Starting optimization step 19.
6:34:22.466335 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:34:22.466557 INFO: Using rust extraction backend
6:34:22.466666 PROGRESS: Extracting batch of 5943 precursors
6:34:22.495931 INFO: === Search parameters used ===
6:34:22.497026 INFO: rt_error       : 34.7455988679267
6:34:22.497118 INFO: mobility_error : 0.1
6:34:22.497172 INFO: num_candidates : 3
6:34:22.497231 INFO: ms1_error      : 3
6:34:22.497287 INFO: ms2_error      : 10.0
6:34:22.497335 INFO: fwhm_rt        : 3.0
6:34:22.497377 INFO: quant_window   : 3
6:34:22.497423 INFO: ==============================================
6:34:22.822865 INFO: performing precursor FDR with 40 features
6:34:22.823337 INFO: Decoy channel: -1
6:34:22.823388 INFO: competitive: True
6:34:22.863363 INFO: Setting torch num_threads to 2 for FDR classification task
6:34:22.880489 INFO: Estimating optimal hyperparameters - samples: 13,060, batch_size: 128, learning_rate: 1.77e-04
6:34:22.881099 INFO: Using random state 583102 for train-test-split
6:34:25.238857 INFO: Test AUC: 0.823
6:34:25.239312 INFO: Train AUC: 0.824
6:34:25.239366 INFO: AUC difference: 0.03%
6:34:25.676275 INFO: Resetting torch num_threads to 100
6:34:25.684809 PROGRESS: === Extracted 16325 precursors and 82535 fragments ===
6:34:25.686174 INFO: === FDR correction performed with classifier version 6 ===
6:34:25.687787 PROGRESS: ============================= Precursor FDR =============================
6:34:25.687963 PROGRESS: Total precursors accumulated: 2,598
6:34:25.688044 PROGRESS: Target precursors: 2,573 (99.04%)
6:34:25.688108 PROGRESS: Decoy precursors: 25 (0.96%)
6:34:25.688159 PROGRESS: 
6:34:25.688209 PROGRESS: Precursor Summary:
6:34:25.690487 PROGRESS: Channel   0:	 0.050 FDR: 2,573; 0.010 FDR: 2,573; 0.001 FDR: 1,107
6:34:25.690655 PROGRESS: 
6:34:25.690713 PROGRESS: Protein Summary:
6:34:25.693964 PROGRESS: Channel   0:	 0.050 FDR: 2,043; 0.010 FDR: 2,043; 0.001 FDR:   958
6:34:25.694198 PROGRESS: =========================================================================
6:34:25.696398 INFO: Target number of precursors reached.
6:34:25.724522 INFO: fragments_df: keeping 5000 of 82535 [sum(precursor_idx_mask)=42511 sum(mass_error_mask)=82535 stop_rank=5000
6:34:25.766190 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:34:26.325888 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:34:27.292686 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:34:27.294319 INFO: Using score_cutoff 8.918861184310913 (fac=0.99, q=1)
6:34:27.294953 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:34:27.295050 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:34:27.295109 INFO: Updating optimization_manager: score_cutoff        : 8.983989663505554 -> 8.918861184310913
6:34:27.295207 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:34:27.302680 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:34:27.314452 INFO: === checking if optimization conditions were reached ===
6:34:27.315249 PROGRESS: === Optimization of rt_error has been performed 20 time(s); minimum number is 5 ===
6:34:27.321642 INFO: Updating optimization_manager: rt_error            : 34.7455988679267 -> 38.358021700479185
6:34:27.322222 PROGRESS: ❌ rt_error       : optimization incomplete after 20 search(es). Will search with parameter 38.3580.
6:34:27.322338 INFO: ==============================================
6:34:27.322503 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
6:34:27.322597 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
6:34:27.322666 PROGRESS: ==============================================
6:34:27.322754 PROGRESS: ms2_error      : 10.0000
6:34:27.322821 PROGRESS: rt_error       : 38.3580
6:34:27.322881 PROGRESS: ==============================================
6:34:27.325711 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:34:27.555595 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:34:28.207781 INFO: Using rust extraction backend
6:34:28.208727 PROGRESS: Extracting batch of 289499 precursors
6:34:29.027817 INFO: === Search parameters used ===
6:34:29.028681 INFO: rt_error       : 38.358021700479185
6:34:29.028746 INFO: mobility_error : 0.1
6:34:29.028797 INFO: num_candidates : 3
6:34:29.028840 INFO: ms1_error      : 3
6:34:29.028883 INFO: ms2_error      : 10.0
6:34:29.028936 INFO: fwhm_rt        : 3.0
6:34:29.028977 INFO: quant_window   : 3
6:34:29.029024 INFO: ==============================================
6:34:29.881120 INFO: Removed 284698 precursors with score below cutoff 8.918861184310913
6:34:30.646786 INFO: performing precursor FDR with 40 features
6:34:30.647046 INFO: Decoy channel: -1
6:34:30.647076 INFO: competitive: True
6:34:30.744098 INFO: Setting torch num_threads to 2 for FDR classification task
6:34:30.812469 WARNING: FDR calculation for 299318 target and 214947 decoy PSMs
6:34:30.812772 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
6:34:31.135077 INFO: Estimating optimal hyperparameters - samples: 411,412, batch_size: 1,685, learning_rate: 6.41e-04
6:34:31.136056 INFO: Using random state 583102 for train-test-split
6:34:40.800144 INFO: Test AUC: 0.861
6:34:40.800758 INFO: Train AUC: 0.864
6:34:40.800817 INFO: AUC difference: 0.33%
6:34:41.445122 INFO: Resetting torch num_threads to 100
6:34:42.800411 PROGRESS: ============================= Precursor FDR =============================
6:34:42.802098 PROGRESS: Total precursors accumulated: 134,682
6:34:42.802203 PROGRESS: Target precursors: 133,349 (99.01%)
6:34:42.802275 PROGRESS: Decoy precursors: 1,333 (0.99%)
6:34:42.802325 PROGRESS: 
6:34:42.802373 PROGRESS: Precursor Summary:
6:34:42.969368 PROGRESS: Channel   0:	 0.050 FDR: 133,349; 0.010 FDR: 133,349; 0.001 FDR: 118,851
6:34:42.970192 PROGRESS: 
6:34:42.970263 PROGRESS: Protein Summary:
6:34:43.352450 PROGRESS: Channel   0:	 0.050 FDR: 10,649; 0.010 FDR: 10,649; 0.001 FDR: 10,556
6:34:43.353319 PROGRESS: =========================================================================
6:34:43.365181 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/psm.parquet
6:34:44.050020 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.parquet
6:34:44.790807 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
6:34:45.141921 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 
6:34:45.142430 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant
6:34:45.142660 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/figures
6:34:45.143067 INFO: Initializing TimingManager
6:34:45.144526 INFO: Initializing RawFileManager
6:35:18.566887 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.
6:35:18.583347 INFO: Determining DIA cycle
6:35:18.602776 INFO: Found cycle with start 0.00 min and length 300.
6:35:19.398566 INFO: RT (min)            : 0.0 - 26.9
6:35:19.398836 INFO: RT duration (sec)   : 1611.2
6:35:19.398868 INFO: RT duration (min)   : 26.9
6:35:19.398899 INFO: Cycle len (scans)   : 300
6:35:19.398948 INFO: Cycle len (sec)     : 1.65
6:35:19.398971 INFO: Number of cycles    : 977
6:35:19.398992 INFO: MS2 range (m/z)     : 380.4 - 980.7
6:35:19.399053 INFO: Creating DIA data object took: 34.25436282157898
6:35:21.400641 INFO: Creating DIA data NG object took: 2.0011308193206787
6:35:21.490635 INFO: Initializing CalibrationManager
6:35:21.491191 INFO: Setting up calibration estimators ..
6:35:21.491262 INFO: Found 1 estimator(s) in calibration group 'fragment'
6:35:21.491364 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'}' ..
6:35:21.491474 INFO: Found 3 estimator(s) in calibration group 'precursor'
6:35:21.491526 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
6:35:21.491582 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}}' ..
6:35:21.491632 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
6:35:21.491677 INFO: Done setting up calibration estimators.
6:35:21.492144 INFO: Initializing OptimizationManager
6:35:21.492296 INFO: initial parameter: ms1_error = 3
6:35:21.492347 INFO: initial parameter: ms2_error = 10
6:35:21.492393 INFO: initial parameter: rt_error = 805.5982666015625
6:35:21.492435 INFO: initial parameter: mobility_error = 0.1
6:35:21.492472 INFO: initial parameter: num_candidates = 1
6:35:21.492510 INFO: initial parameter: fwhm_rt = 5
6:35:21.492555 INFO: initial parameter: fwhm_mobility = 0.01
6:35:21.492597 INFO: initial parameter: score_cutoff = 0
6:35:21.492636 INFO: initial parameter: classifier_version = -1
6:35:21.492712 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
6:35:21.493234 INFO: FDRManager: loading saved state not requested, will be initialized.
6:35:21.493269 INFO: Initializing FDRManager
6:35:21.493313 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
6:35:21.590728 PROGRESS: Initializing spectral library: 146,300 target precursors potentially observable (0 removed)
6:35:21.655199 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
6:35:21.655948 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
6:35:21.656076 PROGRESS: Starting initial search for precursors.
6:35:21.656186 INFO: Starting optimization step 0.
6:35:21.656255 PROGRESS: === Extracting elution groups 0 to 1000 ===
6:35:21.656317 INFO: Using rust extraction backend
6:35:21.656528 PROGRESS: Extracting batch of 1979 precursors
6:35:21.663821 INFO: === Search parameters used ===
6:35:21.664313 INFO: rt_error       : 805.5982666015625
6:35:21.664375 INFO: mobility_error : 0.1
6:35:21.664431 INFO: num_candidates : 1
6:35:21.664477 INFO: ms1_error      : 3
6:35:21.664525 INFO: ms2_error      : 10
6:35:21.664572 INFO: fwhm_rt        : 5
6:35:21.664612 INFO: quant_window   : 3
6:35:21.664650 INFO: ==============================================
6:35:21.703737 INFO: performing precursor FDR with 40 features
6:35:21.703855 INFO: Decoy channel: -1
6:35:21.703883 INFO: competitive: True
6:35:21.705353 INFO: Setting torch num_threads to 2 for FDR classification task
6:35:21.707425 INFO: Estimating optimal hyperparameters - samples: 1,582, batch_size: 128, learning_rate: 1.77e-04
6:35:21.708500 INFO: Using random state 94632 for train-test-split
6:35:21.830045 INFO: Test AUC: 0.844
6:35:21.830152 INFO: Train AUC: 0.858
6:35:21.830179 INFO: AUC difference: 1.64%
6:35:22.084671 INFO: Resetting torch num_threads to 100
6:35:22.086976 PROGRESS: === Extracted 1978 precursors and 13229 fragments ===
6:35:22.087402 INFO: === FDR correction performed with classifier version -1 ===
6:35:22.087958 PROGRESS: ============================= Precursor FDR =============================
6:35:22.088054 PROGRESS: Total precursors accumulated: 380
6:35:22.088112 PROGRESS: Target precursors: 377 (99.21%)
6:35:22.088160 PROGRESS: Decoy precursors: 3 (0.79%)
6:35:22.088202 PROGRESS: 
6:35:22.088253 PROGRESS: Precursor Summary:
6:35:22.089345 PROGRESS: Channel   0:	 0.050 FDR:   377; 0.010 FDR:   377; 0.001 FDR:   316
6:35:22.089427 PROGRESS: 
6:35:22.089480 PROGRESS: Protein Summary:
6:35:22.090770 PROGRESS: Channel   0:	 0.050 FDR:   355; 0.010 FDR:   355; 0.001 FDR:   301
6:35:22.090856 PROGRESS: =========================================================================
6:35:22.091152 INFO: Target number of precursors not reached yet.
6:35:22.100540 INFO: Starting optimization step 1.
6:35:22.100672 PROGRESS: === Extracting elution groups 1000 to 3000 ===
6:35:22.100754 INFO: Using rust extraction backend
6:35:22.100814 PROGRESS: Extracting batch of 3964 precursors
6:35:22.108744 INFO: === Search parameters used ===
6:35:22.108881 INFO: rt_error       : 805.5982666015625
6:35:22.108932 INFO: mobility_error : 0.1
6:35:22.108978 INFO: num_candidates : 1
6:35:22.109020 INFO: ms1_error      : 3
6:35:22.109061 INFO: ms2_error      : 10
6:35:22.109100 INFO: fwhm_rt        : 5
6:35:22.109139 INFO: quant_window   : 3
6:35:22.109178 INFO: ==============================================
6:35:22.212317 INFO: performing precursor FDR with 40 features
6:35:22.212620 INFO: Decoy channel: -1
6:35:22.212648 INFO: competitive: True
6:35:22.225456 INFO: Setting torch num_threads to 2 for FDR classification task
6:35:22.235617 INFO: Estimating optimal hyperparameters - samples: 4,751, batch_size: 128, learning_rate: 1.77e-04
6:35:22.236120 INFO: Using random state 874277 for train-test-split
6:35:22.669321 INFO: Test AUC: 0.893
6:35:22.669437 INFO: Train AUC: 0.882
6:35:22.669468 INFO: AUC difference: 1.25%
6:35:22.917137 INFO: Resetting torch num_threads to 100
6:35:22.921112 PROGRESS: === Extracted 5939 precursors and 40075 fragments ===
6:35:22.921555 INFO: === FDR correction performed with classifier version -1 ===
6:35:22.922196 PROGRESS: ============================= Precursor FDR =============================
6:35:22.922290 PROGRESS: Total precursors accumulated: 1,534
6:35:22.922353 PROGRESS: Target precursors: 1,519 (99.02%)
6:35:22.922405 PROGRESS: Decoy precursors: 15 (0.98%)
6:35:22.922453 PROGRESS: 
6:35:22.922500 PROGRESS: Precursor Summary:
6:35:22.923956 PROGRESS: Channel   0:	 0.050 FDR: 1,519; 0.010 FDR: 1,519; 0.001 FDR: 1,168
6:35:22.924058 PROGRESS: 
6:35:22.924115 PROGRESS: Protein Summary:
6:35:22.925930 PROGRESS: Channel   0:	 0.050 FDR: 1,261; 0.010 FDR: 1,261; 0.001 FDR:   994
6:35:22.926024 PROGRESS: =========================================================================
6:35:22.926393 INFO: Target number of precursors reached.
6:35:22.935081 INFO: fragments_df: keeping 5000 of 40075 [sum(precursor_idx_mask)=14111 sum(mass_error_mask)=40075 stop_rank=5000
6:35:22.946999 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:35:23.211285 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:35:23.976126 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
6:35:23.977171 INFO: Using score_cutoff 10.867777890586854 (fac=0.99, q=1)
6:35:23.977689 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
6:35:23.977770 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
6:35:23.977825 INFO: Updating optimization_manager: score_cutoff        : 0 -> 10.867777890586854
6:35:23.977882 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:35:23.982967 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:35:23.990671 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
6:35:23.991031 PROGRESS: Required number of precursors found. Starting search parameter optimization.
6:35:23.991167 INFO: Starting optimization step 2.
6:35:23.991250 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:35:23.991346 INFO: Using rust extraction backend
6:35:23.991426 PROGRESS: Extracting batch of 5943 precursors
6:35:24.007025 INFO: === Search parameters used ===
6:35:24.007776 INFO: rt_error       : 805.5982666015625
6:35:24.007839 INFO: mobility_error : 0.1
6:35:24.007887 INFO: num_candidates : 3
6:35:24.007930 INFO: ms1_error      : 3
6:35:24.007970 INFO: ms2_error      : 10
6:35:24.008010 INFO: fwhm_rt        : 3.0
6:35:24.008049 INFO: quant_window   : 3
6:35:24.008087 INFO: ==============================================
6:35:24.188457 INFO: performing precursor FDR with 40 features
6:35:24.188664 INFO: Decoy channel: -1
6:35:24.188692 INFO: competitive: True
6:35:24.199352 INFO: Setting torch num_threads to 2 for FDR classification task
6:35:24.206893 INFO: Estimating optimal hyperparameters - samples: 14,252, batch_size: 128, learning_rate: 1.77e-04
6:35:24.207248 INFO: Using random state 282015 for train-test-split
6:35:25.370915 INFO: Test AUC: 0.696
6:35:25.371135 INFO: Train AUC: 0.724
6:35:25.371183 INFO: AUC difference: 3.80%
6:35:25.682863 INFO: Resetting torch num_threads to 100
6:35:25.687787 PROGRESS: === Extracted 17816 precursors and 105221 fragments ===
6:35:25.688506 INFO: === FDR correction performed with classifier version 1 ===
6:35:25.689402 PROGRESS: ============================= Precursor FDR =============================
6:35:25.689496 PROGRESS: Total precursors accumulated: 1,794
6:35:25.689556 PROGRESS: Target precursors: 1,777 (99.05%)
6:35:25.689604 PROGRESS: Decoy precursors: 17 (0.95%)
6:35:25.689646 PROGRESS: 
6:35:25.689689 PROGRESS: Precursor Summary:
6:35:25.691241 PROGRESS: Channel   0:	 0.050 FDR: 1,777; 0.010 FDR: 1,777; 0.001 FDR: 1,281
6:35:25.691350 PROGRESS: 
6:35:25.691415 PROGRESS: Protein Summary:
6:35:25.693514 PROGRESS: Channel   0:	 0.050 FDR: 1,452; 0.010 FDR: 1,452; 0.001 FDR: 1,081
6:35:25.693615 PROGRESS: =========================================================================
6:35:25.694818 INFO: Target number of precursors reached.
6:35:25.717046 INFO: fragments_df: keeping 5000 of 105221 [sum(precursor_idx_mask)=37610 sum(mass_error_mask)=105221 stop_rank=5000
6:35:25.737281 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:35:26.822809 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:35:29.674827 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:35:29.677036 INFO: Using score_cutoff 11.077877410125732 (fac=0.99, q=1)
6:35:29.678919 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:35:29.679347 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:35:29.679681 INFO: Updating optimization_manager: score_cutoff        : 10.867777890586854 -> 11.077877410125732
6:35:29.680001 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:35:29.692565 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:35:29.709502 INFO: === checking if optimization conditions were reached ===
6:35:29.716074 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
6:35:29.716685 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
6:35:29.716827 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:35:29.716973 INFO: ==============================================
6:35:29.717190 INFO: Starting optimization step 3.
6:35:29.717363 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:35:29.717558 INFO: Using rust extraction backend
6:35:29.717754 PROGRESS: Extracting batch of 5943 precursors
6:35:29.747099 INFO: === Search parameters used ===
6:35:29.747800 INFO: rt_error       : 805.5982666015625
6:35:29.747936 INFO: mobility_error : 0.1
6:35:29.748052 INFO: num_candidates : 3
6:35:29.748129 INFO: ms1_error      : 3
6:35:29.748193 INFO: ms2_error      : 10.0
6:35:29.748259 INFO: fwhm_rt        : 3.0
6:35:29.748345 INFO: quant_window   : 3
6:35:29.748414 INFO: ==============================================
6:35:30.151077 INFO: performing precursor FDR with 40 features
6:35:30.151350 INFO: Decoy channel: -1
6:35:30.151377 INFO: competitive: True
6:35:30.177206 INFO: Setting torch num_threads to 2 for FDR classification task
6:35:30.197376 INFO: Estimating optimal hyperparameters - samples: 14,252, batch_size: 128, learning_rate: 1.77e-04
6:35:30.197805 INFO: Using random state 154899 for train-test-split
6:35:33.129913 INFO: Test AUC: 0.749
6:35:33.130322 INFO: Train AUC: 0.731
6:35:33.130465 INFO: AUC difference: 2.59%
6:35:59.571516 INFO: Resetting torch num_threads to 100
6:35:59.592016 PROGRESS: === Extracted 17815 precursors and 105196 fragments ===
6:35:59.593512 INFO: === FDR correction performed with classifier version 2 ===
6:35:59.595977 PROGRESS: ============================= Precursor FDR =============================
6:35:59.596194 PROGRESS: Total precursors accumulated: 2,003
6:35:59.596266 PROGRESS: Target precursors: 1,984 (99.05%)
6:35:59.596322 PROGRESS: Decoy precursors: 19 (0.95%)
6:35:59.596374 PROGRESS: 
6:35:59.596424 PROGRESS: Precursor Summary:
6:35:59.599415 PROGRESS: Channel   0:	 0.050 FDR: 1,984; 0.010 FDR: 1,984; 0.001 FDR: 1,422
6:35:59.599637 PROGRESS: 
6:35:59.599702 PROGRESS: Protein Summary:
6:35:59.602830 PROGRESS: Channel   0:	 0.050 FDR: 1,614; 0.010 FDR: 1,614; 0.001 FDR: 1,194
6:35:59.603085 PROGRESS: =========================================================================
6:35:59.604933 INFO: Target number of precursors reached.
6:35:59.636517 INFO: fragments_df: keeping 5000 of 105196 [sum(precursor_idx_mask)=41322 sum(mass_error_mask)=105196 stop_rank=5000
6:35:59.697043 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:36:00.225754 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:36:01.235846 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:36:01.238621 INFO: Using score_cutoff 10.626021164417267 (fac=0.99, q=1)
6:36:01.239561 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:36:01.239699 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:36:01.239764 INFO: Updating optimization_manager: score_cutoff        : 11.077877410125732 -> 10.626021164417267
6:36:01.239937 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:36:01.249393 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:36:01.264816 INFO: === checking if optimization conditions were reached ===
6:36:01.272105 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:36:01.272727 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
6:36:01.272825 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:36:01.272927 INFO: ==============================================
6:36:01.273028 INFO: Starting optimization step 4.
6:36:01.273102 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:36:01.273216 INFO: Using rust extraction backend
6:36:01.273392 PROGRESS: Extracting batch of 5943 precursors
6:36:01.308581 INFO: === Search parameters used ===
6:36:01.310172 INFO: rt_error       : 805.5982666015625
6:36:01.310262 INFO: mobility_error : 0.1
6:36:01.310332 INFO: num_candidates : 3
6:36:01.310391 INFO: ms1_error      : 3
6:36:01.310444 INFO: ms2_error      : 10.0
6:36:01.310525 INFO: fwhm_rt        : 3.0
6:36:01.310592 INFO: quant_window   : 3
6:36:01.310640 INFO: ==============================================
6:36:01.775782 INFO: performing precursor FDR with 40 features
6:36:01.776085 INFO: Decoy channel: -1
6:36:01.776111 INFO: competitive: True
6:36:01.811617 INFO: Setting torch num_threads to 2 for FDR classification task
6:36:01.829392 INFO: Estimating optimal hyperparameters - samples: 14,252, batch_size: 128, learning_rate: 1.77e-04
6:36:01.830047 INFO: Using random state 640024 for train-test-split
6:36:04.517870 INFO: Test AUC: 0.732
6:36:04.518200 INFO: Train AUC: 0.749
6:36:04.518238 INFO: AUC difference: 2.36%
6:36:04.946200 INFO: Resetting torch num_threads to 100
6:36:04.956042 PROGRESS: === Extracted 17815 precursors and 105174 fragments ===
6:36:04.957729 INFO: === FDR correction performed with classifier version 3 ===
6:36:04.960826 PROGRESS: ============================= Precursor FDR =============================
6:36:04.961087 PROGRESS: Total precursors accumulated: 2,158
6:36:04.961160 PROGRESS: Target precursors: 2,137 (99.03%)
6:36:04.961216 PROGRESS: Decoy precursors: 21 (0.97%)
6:36:04.961264 PROGRESS: 
6:36:04.961310 PROGRESS: Precursor Summary:
6:36:04.964290 PROGRESS: Channel   0:	 0.050 FDR: 2,137; 0.010 FDR: 2,137; 0.001 FDR: 1,419
6:36:04.964472 PROGRESS: 
6:36:04.964532 PROGRESS: Protein Summary:
6:36:04.968178 PROGRESS: Channel   0:	 0.050 FDR: 1,721; 0.010 FDR: 1,721; 0.001 FDR: 1,184
6:36:04.968502 PROGRESS: =========================================================================
6:36:04.970275 INFO: Target number of precursors reached.
6:36:05.002507 INFO: fragments_df: keeping 5000 of 105174 [sum(precursor_idx_mask)=43978 sum(mass_error_mask)=105174 stop_rank=5000
6:36:05.040158 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:36:05.598421 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:36:06.687082 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:36:06.688944 INFO: Using score_cutoff 10.315762347793578 (fac=0.99, q=1)
6:36:06.689664 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:36:06.689816 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:36:06.689874 INFO: Updating optimization_manager: score_cutoff        : 10.626021164417267 -> 10.315762347793578
6:36:06.689991 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:36:06.698047 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:36:06.710509 INFO: === checking if optimization conditions were reached ===
6:36:06.716506 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:36:06.716956 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
6:36:06.717084 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:36:06.717182 INFO: ==============================================
6:36:06.717275 INFO: Starting optimization step 5.
6:36:06.717351 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:36:06.717472 INFO: Using rust extraction backend
6:36:06.717627 PROGRESS: Extracting batch of 5943 precursors
6:36:06.745641 INFO: === Search parameters used ===
6:36:06.747003 INFO: rt_error       : 805.5982666015625
6:36:06.747085 INFO: mobility_error : 0.1
6:36:06.747165 INFO: num_candidates : 3
6:36:06.747220 INFO: ms1_error      : 3
6:36:06.747275 INFO: ms2_error      : 10.0
6:36:06.747322 INFO: fwhm_rt        : 3.0
6:36:06.747362 INFO: quant_window   : 3
6:36:06.747404 INFO: ==============================================
6:36:07.108354 INFO: performing precursor FDR with 40 features
6:36:07.108824 INFO: Decoy channel: -1
6:36:07.108862 INFO: competitive: True
6:36:07.140512 INFO: Setting torch num_threads to 2 for FDR classification task
6:36:07.160558 INFO: Estimating optimal hyperparameters - samples: 14,252, batch_size: 128, learning_rate: 1.77e-04
6:36:07.161434 INFO: Using random state 874513 for train-test-split
6:36:09.526370 INFO: Test AUC: 0.733
6:36:09.526726 INFO: Train AUC: 0.759
6:36:09.526774 INFO: AUC difference: 3.41%
6:36:09.955690 INFO: Resetting torch num_threads to 100
6:36:09.967858 PROGRESS: === Extracted 17815 precursors and 105162 fragments ===
6:36:09.969496 INFO: === FDR correction performed with classifier version 4 ===
6:36:09.974032 PROGRESS: ============================= Precursor FDR =============================
6:36:09.974593 PROGRESS: Total precursors accumulated: 2,241
6:36:09.974732 PROGRESS: Target precursors: 2,219 (99.02%)
6:36:09.974819 PROGRESS: Decoy precursors: 22 (0.98%)
6:36:09.974934 PROGRESS: 
6:36:09.975008 PROGRESS: Precursor Summary:
6:36:09.983635 PROGRESS: Channel   0:	 0.050 FDR: 2,219; 0.010 FDR: 2,219; 0.001 FDR: 1,512
6:36:09.984357 PROGRESS: 
6:36:09.984480 PROGRESS: Protein Summary:
6:36:09.994235 PROGRESS: Channel   0:	 0.050 FDR: 1,791; 0.010 FDR: 1,791; 0.001 FDR: 1,244
6:36:09.994994 PROGRESS: =========================================================================
6:36:09.997655 INFO: Target number of precursors reached.
6:36:10.032777 INFO: fragments_df: keeping 5000 of 105162 [sum(precursor_idx_mask)=45325 sum(mass_error_mask)=105162 stop_rank=5000
6:36:10.071741 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:36:10.614714 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:36:11.572462 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:36:11.574092 INFO: Using score_cutoff 10.08704065876007 (fac=0.99, q=1)
6:36:11.574733 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:36:11.574819 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:36:11.574877 INFO: Updating optimization_manager: score_cutoff        : 10.315762347793578 -> 10.08704065876007
6:36:11.574949 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:36:11.582369 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:36:11.594654 INFO: === checking if optimization conditions were reached ===
6:36:11.600405 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:36:11.600914 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
6:36:11.601019 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:36:11.601108 INFO: ==============================================
6:36:11.601217 INFO: Starting optimization step 6.
6:36:11.601295 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:36:11.601415 INFO: Using rust extraction backend
6:36:11.601521 PROGRESS: Extracting batch of 5943 precursors
6:36:11.626644 INFO: === Search parameters used ===
6:36:11.627754 INFO: rt_error       : 805.5982666015625
6:36:11.627822 INFO: mobility_error : 0.1
6:36:11.627871 INFO: num_candidates : 3
6:36:11.627913 INFO: ms1_error      : 3
6:36:11.627956 INFO: ms2_error      : 10.0
6:36:11.627999 INFO: fwhm_rt        : 3.0
6:36:11.628041 INFO: quant_window   : 3
6:36:11.628079 INFO: ==============================================
6:36:11.988660 INFO: performing precursor FDR with 40 features
6:36:11.989102 INFO: Decoy channel: -1
6:36:11.989132 INFO: competitive: True
6:36:12.019134 INFO: Setting torch num_threads to 2 for FDR classification task
6:36:12.040131 INFO: Estimating optimal hyperparameters - samples: 14,252, batch_size: 128, learning_rate: 1.77e-04
6:36:12.040753 INFO: Using random state 247581 for train-test-split
6:36:14.533367 INFO: Test AUC: 0.740
6:36:14.533748 INFO: Train AUC: 0.766
6:36:14.533785 INFO: AUC difference: 3.48%
6:36:15.036660 INFO: Resetting torch num_threads to 100
6:36:15.047005 PROGRESS: === Extracted 17815 precursors and 105182 fragments ===
6:36:15.048442 INFO: === FDR correction performed with classifier version 5 ===
6:36:15.051073 PROGRESS: ============================= Precursor FDR =============================
6:36:15.051316 PROGRESS: Total precursors accumulated: 2,275
6:36:15.051397 PROGRESS: Target precursors: 2,253 (99.03%)
6:36:15.051483 PROGRESS: Decoy precursors: 22 (0.97%)
6:36:15.051537 PROGRESS: 
6:36:15.051584 PROGRESS: Precursor Summary:
6:36:15.054494 PROGRESS: Channel   0:	 0.050 FDR: 2,253; 0.010 FDR: 2,253; 0.001 FDR: 1,462
6:36:15.054692 PROGRESS: 
6:36:15.054747 PROGRESS: Protein Summary:
6:36:15.057988 PROGRESS: Channel   0:	 0.050 FDR: 1,820; 0.010 FDR: 1,820; 0.001 FDR: 1,215
6:36:15.058179 PROGRESS: =========================================================================
6:36:15.060107 INFO: Target number of precursors reached.
6:36:15.095551 INFO: fragments_df: keeping 5000 of 105182 [sum(precursor_idx_mask)=45843 sum(mass_error_mask)=105182 stop_rank=5000
6:36:15.138232 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:36:15.756408 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:36:16.716892 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:36:16.718425 INFO: Using score_cutoff 9.946303074645996 (fac=0.99, q=1)
6:36:16.719562 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:36:16.719692 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:36:16.719785 INFO: Updating optimization_manager: score_cutoff        : 10.08704065876007 -> 9.946303074645996
6:36:16.719871 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:36:16.727741 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:36:16.744612 INFO: === checking if optimization conditions were reached ===
6:36:16.751076 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:36:16.751642 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
6:36:16.751736 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
6:36:16.751826 INFO: ==============================================
6:36:16.751958 PROGRESS: Optimization finished for ms2_error.
6:36:16.798056 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:36:16.809602 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:36:16.824399 INFO: Starting optimization step 0.
6:36:16.825199 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:36:16.825357 INFO: Using rust extraction backend
6:36:16.825473 PROGRESS: Extracting batch of 5943 precursors
6:36:16.851985 INFO: === Search parameters used ===
6:36:16.852996 INFO: rt_error       : 805.5982666015625
6:36:16.853061 INFO: mobility_error : 0.1
6:36:16.853111 INFO: num_candidates : 3
6:36:16.853169 INFO: ms1_error      : 3
6:36:16.853220 INFO: ms2_error      : 10.0
6:36:16.853262 INFO: fwhm_rt        : 3.0
6:36:16.853311 INFO: quant_window   : 3
6:36:16.853354 INFO: ==============================================
6:36:17.226245 INFO: performing precursor FDR with 40 features
6:36:17.226565 INFO: Decoy channel: -1
6:36:17.226595 INFO: competitive: True
6:36:17.253680 INFO: Setting torch num_threads to 2 for FDR classification task
6:36:17.274593 INFO: Estimating optimal hyperparameters - samples: 14,252, batch_size: 128, learning_rate: 1.77e-04
6:36:17.275170 INFO: Using random state 125325 for train-test-split
6:36:19.988837 INFO: Test AUC: 0.758
6:36:19.989404 INFO: Train AUC: 0.771
6:36:19.989445 INFO: AUC difference: 1.72%
6:36:20.505055 INFO: Resetting torch num_threads to 100
6:36:20.514775 PROGRESS: === Extracted 17815 precursors and 105184 fragments ===
6:36:20.516688 INFO: === FDR correction performed with classifier version 6 ===
6:36:20.518326 PROGRESS: ============================= Precursor FDR =============================
6:36:20.518526 PROGRESS: Total precursors accumulated: 2,271
6:36:20.518611 PROGRESS: Target precursors: 2,249 (99.03%)
6:36:20.518668 PROGRESS: Decoy precursors: 22 (0.97%)
6:36:20.518721 PROGRESS: 
6:36:20.518773 PROGRESS: Precursor Summary:
6:36:20.521917 PROGRESS: Channel   0:	 0.050 FDR: 2,249; 0.010 FDR: 2,249; 0.001 FDR: 1,557
6:36:20.522120 PROGRESS: 
6:36:20.522200 PROGRESS: Protein Summary:
6:36:20.525654 PROGRESS: Channel   0:	 0.050 FDR: 1,810; 0.010 FDR: 1,810; 0.001 FDR: 1,281
6:36:20.525836 PROGRESS: =========================================================================
6:36:20.527590 INFO: Target number of precursors reached.
6:36:20.561966 INFO: fragments_df: keeping 5000 of 105184 [sum(precursor_idx_mask)=45718 sum(mass_error_mask)=105184 stop_rank=5000
6:36:20.600779 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:36:21.138862 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:36:22.120819 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:36:22.122573 INFO: Using score_cutoff 9.94268755645752 (fac=0.99, q=1)
6:36:22.123329 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:36:22.123430 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:36:22.123510 INFO: Updating optimization_manager: score_cutoff        : 9.946303074645996 -> 9.94268755645752
6:36:22.123590 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:36:22.131463 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:36:22.142535 INFO: === checking if optimization conditions were reached ===
6:36:22.143307 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
6:36:22.149751 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 487.7654472093977
6:36:22.150384 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 487.7654.
6:36:22.150492 INFO: ==============================================
6:36:22.150602 INFO: Starting optimization step 1.
6:36:22.150697 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:36:22.150844 INFO: Using rust extraction backend
6:36:22.150948 PROGRESS: Extracting batch of 5943 precursors
6:36:22.175309 INFO: === Search parameters used ===
6:36:22.176545 INFO: rt_error       : 487.7654472093977
6:36:22.176612 INFO: mobility_error : 0.1
6:36:22.176662 INFO: num_candidates : 3
6:36:22.176708 INFO: ms1_error      : 3
6:36:22.176752 INFO: ms2_error      : 10.0
6:36:22.176793 INFO: fwhm_rt        : 3.0
6:36:22.176836 INFO: quant_window   : 3
6:36:22.176876 INFO: ==============================================
6:36:22.521898 INFO: performing precursor FDR with 40 features
6:36:22.522221 INFO: Decoy channel: -1
6:36:22.522251 INFO: competitive: True
6:36:22.550948 INFO: Setting torch num_threads to 2 for FDR classification task
6:36:22.582996 INFO: Estimating optimal hyperparameters - samples: 14,252, batch_size: 128, learning_rate: 1.77e-04
6:36:22.583704 INFO: Using random state 125325 for train-test-split
6:36:25.058488 INFO: Test AUC: 0.761
6:36:25.058850 INFO: Train AUC: 0.771
6:36:25.058891 INFO: AUC difference: 1.28%
6:36:25.541033 INFO: Resetting torch num_threads to 100
6:36:25.554858 PROGRESS: === Extracted 17816 precursors and 104962 fragments ===
6:36:25.556606 INFO: === FDR correction performed with classifier version 6 ===
6:36:25.558844 PROGRESS: ============================= Precursor FDR =============================
6:36:25.559062 PROGRESS: Total precursors accumulated: 2,279
6:36:25.559140 PROGRESS: Target precursors: 2,257 (99.03%)
6:36:25.559238 PROGRESS: Decoy precursors: 22 (0.97%)
6:36:25.559291 PROGRESS: 
6:36:25.559339 PROGRESS: Precursor Summary:
6:36:25.562758 PROGRESS: Channel   0:	 0.050 FDR: 2,257; 0.010 FDR: 2,257; 0.001 FDR: 1,517
6:36:25.562961 PROGRESS: 
6:36:25.563031 PROGRESS: Protein Summary:
6:36:25.567615 PROGRESS: Channel   0:	 0.050 FDR: 1,816; 0.010 FDR: 1,816; 0.001 FDR: 1,249
6:36:25.567896 PROGRESS: =========================================================================
6:36:25.570424 INFO: Target number of precursors reached.
6:36:25.612265 INFO: fragments_df: keeping 5000 of 104962 [sum(precursor_idx_mask)=45948 sum(mass_error_mask)=104962 stop_rank=5000
6:36:25.660597 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:36:26.161484 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:36:27.041920 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:36:27.043558 INFO: Using score_cutoff 10.04952763710022 (fac=0.99, q=1)
6:36:27.044219 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:36:27.044323 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:36:27.044383 INFO: Updating optimization_manager: score_cutoff        : 9.94268755645752 -> 10.04952763710022
6:36:27.044473 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:36:27.052404 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:36:27.064035 INFO: === checking if optimization conditions were reached ===
6:36:27.064750 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
6:36:27.071030 INFO: Updating optimization_manager: rt_error            : 487.7654472093977 -> 401.9735980405685
6:36:27.071678 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 401.9736.
6:36:27.071778 INFO: ==============================================
6:36:27.071890 INFO: Starting optimization step 2.
6:36:27.071981 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:36:27.072111 INFO: Using rust extraction backend
6:36:27.072195 PROGRESS: Extracting batch of 5943 precursors
6:36:27.098351 INFO: === Search parameters used ===
6:36:27.099181 INFO: rt_error       : 401.9735980405685
6:36:27.099272 INFO: mobility_error : 0.1
6:36:27.099330 INFO: num_candidates : 3
6:36:27.099385 INFO: ms1_error      : 3
6:36:27.099430 INFO: ms2_error      : 10.0
6:36:27.099473 INFO: fwhm_rt        : 3.0
6:36:27.099545 INFO: quant_window   : 3
6:36:27.099587 INFO: ==============================================
6:36:27.379362 INFO: performing precursor FDR with 40 features
6:36:27.379693 INFO: Decoy channel: -1
6:36:27.379722 INFO: competitive: True
6:36:27.408746 INFO: Setting torch num_threads to 2 for FDR classification task
6:36:27.426890 INFO: Estimating optimal hyperparameters - samples: 14,247, batch_size: 128, learning_rate: 1.77e-04
6:36:27.427630 INFO: Using random state 125325 for train-test-split
6:36:29.656824 INFO: Test AUC: 0.753
6:36:29.657195 INFO: Train AUC: 0.774
6:36:29.657238 INFO: AUC difference: 2.62%
6:36:30.178267 INFO: Resetting torch num_threads to 100
6:36:30.190124 PROGRESS: === Extracted 17809 precursors and 104637 fragments ===
6:36:30.191828 INFO: === FDR correction performed with classifier version 6 ===
6:36:30.193814 PROGRESS: ============================= Precursor FDR =============================
6:36:30.193990 PROGRESS: Total precursors accumulated: 2,257
6:36:30.194062 PROGRESS: Target precursors: 2,235 (99.03%)
6:36:30.194117 PROGRESS: Decoy precursors: 22 (0.97%)
6:36:30.194167 PROGRESS: 
6:36:30.194215 PROGRESS: Precursor Summary:
6:36:30.197146 PROGRESS: Channel   0:	 0.050 FDR: 2,235; 0.010 FDR: 2,235; 0.001 FDR: 1,593
6:36:30.197321 PROGRESS: 
6:36:30.197409 PROGRESS: Protein Summary:
6:36:30.200479 PROGRESS: Channel   0:	 0.050 FDR: 1,795; 0.010 FDR: 1,795; 0.001 FDR: 1,309
6:36:30.200660 PROGRESS: =========================================================================
6:36:30.202714 INFO: Target number of precursors reached.
6:36:30.235788 INFO: fragments_df: keeping 5000 of 104637 [sum(precursor_idx_mask)=45585 sum(mass_error_mask)=104637 stop_rank=5000
6:36:30.275975 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:36:30.937517 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:36:31.977316 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:36:31.979565 INFO: Using score_cutoff 10.201768461227417 (fac=0.99, q=1)
6:36:31.980432 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:36:31.980540 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:36:31.980598 INFO: Updating optimization_manager: score_cutoff        : 10.04952763710022 -> 10.201768461227417
6:36:31.980680 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:36:31.989061 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:36:32.005939 INFO: === checking if optimization conditions were reached ===
6:36:32.007018 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
6:36:32.016063 INFO: Updating optimization_manager: rt_error            : 401.9735980405685 -> 385.1987682218863
6:36:32.016936 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 385.1988.
6:36:32.017029 INFO: ==============================================
6:36:32.017135 INFO: Starting optimization step 3.
6:36:32.017217 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:36:32.017345 INFO: Using rust extraction backend
6:36:32.017445 PROGRESS: Extracting batch of 5943 precursors
6:36:32.053362 INFO: === Search parameters used ===
6:36:32.054457 INFO: rt_error       : 385.1987682218863
6:36:32.054527 INFO: mobility_error : 0.1
6:36:32.054579 INFO: num_candidates : 3
6:36:32.054627 INFO: ms1_error      : 3
6:36:32.054714 INFO: ms2_error      : 10.0
6:36:32.054763 INFO: fwhm_rt        : 3.0
6:36:32.054804 INFO: quant_window   : 3
6:36:32.054849 INFO: ==============================================
6:36:32.418836 INFO: performing precursor FDR with 40 features
6:36:32.419236 INFO: Decoy channel: -1
6:36:32.419265 INFO: competitive: True
6:36:32.454064 INFO: Setting torch num_threads to 2 for FDR classification task
6:36:32.477473 INFO: Estimating optimal hyperparameters - samples: 14,247, batch_size: 128, learning_rate: 1.77e-04
6:36:32.479014 INFO: Using random state 125325 for train-test-split
6:36:33.845579 INFO: Test AUC: 0.758
6:36:33.845945 INFO: Train AUC: 0.773
6:36:33.845978 INFO: AUC difference: 1.94%
6:36:34.290952 INFO: Resetting torch num_threads to 100
6:36:34.303249 PROGRESS: === Extracted 17809 precursors and 104543 fragments ===
6:36:34.304956 INFO: === FDR correction performed with classifier version 6 ===
6:36:34.309825 PROGRESS: ============================= Precursor FDR =============================
6:36:34.310692 PROGRESS: Total precursors accumulated: 2,234
6:36:34.310886 PROGRESS: Target precursors: 2,212 (99.02%)
6:36:34.310951 PROGRESS: Decoy precursors: 22 (0.98%)
6:36:34.311012 PROGRESS: 
6:36:34.311063 PROGRESS: Precursor Summary:
6:36:34.321124 PROGRESS: Channel   0:	 0.050 FDR: 2,212; 0.010 FDR: 2,212; 0.001 FDR: 1,499
6:36:34.321906 PROGRESS: 
6:36:34.322022 PROGRESS: Protein Summary:
6:36:34.333482 PROGRESS: Channel   0:	 0.050 FDR: 1,782; 0.010 FDR: 1,782; 0.001 FDR: 1,242
6:36:34.334237 PROGRESS: =========================================================================
6:36:34.337270 INFO: Target number of precursors reached.
6:36:34.377325 INFO: fragments_df: keeping 5000 of 104543 [sum(precursor_idx_mask)=45055 sum(mass_error_mask)=104543 stop_rank=5000
6:36:34.427058 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:36:35.087848 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:36:36.039042 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:36:36.040480 INFO: Using score_cutoff 10.214109358978272 (fac=0.99, q=1)
6:36:36.041138 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:36:36.041229 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:36:36.041292 INFO: Updating optimization_manager: score_cutoff        : 10.201768461227417 -> 10.214109358978272
6:36:36.041360 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:36:36.048447 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:36:36.059869 INFO: === checking if optimization conditions were reached ===
6:36:36.060570 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
6:36:36.066501 INFO: Updating optimization_manager: rt_error            : 385.1987682218863 -> 384.9194648306892
6:36:36.067079 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 384.9195.
6:36:36.067189 INFO: ==============================================
6:36:36.067304 INFO: Starting optimization step 4.
6:36:36.067378 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:36:36.067503 INFO: Using rust extraction backend
6:36:36.067594 PROGRESS: Extracting batch of 5943 precursors
6:36:36.092221 INFO: === Search parameters used ===
6:36:36.093102 INFO: rt_error       : 384.9194648306892
6:36:36.093161 INFO: mobility_error : 0.1
6:36:36.093264 INFO: num_candidates : 3
6:36:36.093311 INFO: ms1_error      : 3
6:36:36.093355 INFO: ms2_error      : 10.0
6:36:36.093400 INFO: fwhm_rt        : 3.0
6:36:36.093449 INFO: quant_window   : 3
6:36:36.093491 INFO: ==============================================
6:36:36.334734 INFO: performing precursor FDR with 40 features
6:36:36.334993 INFO: Decoy channel: -1
6:36:36.335032 INFO: competitive: True
6:36:36.357511 INFO: Setting torch num_threads to 2 for FDR classification task
6:36:36.374271 INFO: Estimating optimal hyperparameters - samples: 14,247, batch_size: 128, learning_rate: 1.77e-04
6:36:36.374861 INFO: Using random state 125325 for train-test-split
6:36:37.708682 INFO: Test AUC: 0.757
6:36:37.709018 INFO: Train AUC: 0.773
6:36:37.709053 INFO: AUC difference: 2.03%
6:36:38.188359 INFO: Resetting torch num_threads to 100
6:36:38.199786 PROGRESS: === Extracted 17809 precursors and 104535 fragments ===
6:36:38.201289 INFO: === FDR correction performed with classifier version 6 ===
6:36:38.203786 PROGRESS: ============================= Precursor FDR =============================
6:36:38.203999 PROGRESS: Total precursors accumulated: 2,259
6:36:38.204070 PROGRESS: Target precursors: 2,237 (99.03%)
6:36:38.204126 PROGRESS: Decoy precursors: 22 (0.97%)
6:36:38.204174 PROGRESS: 
6:36:38.204217 PROGRESS: Precursor Summary:
6:36:38.207177 PROGRESS: Channel   0:	 0.050 FDR: 2,237; 0.010 FDR: 2,237; 0.001 FDR: 1,549
6:36:38.207527 PROGRESS: 
6:36:38.207585 PROGRESS: Protein Summary:
6:36:38.211015 PROGRESS: Channel   0:	 0.050 FDR: 1,803; 0.010 FDR: 1,803; 0.001 FDR: 1,282
6:36:38.211586 PROGRESS: =========================================================================
6:36:38.214326 INFO: Target number of precursors reached.
6:36:38.251063 INFO: fragments_df: keeping 5000 of 104535 [sum(precursor_idx_mask)=45457 sum(mass_error_mask)=104535 stop_rank=5000
6:36:38.290215 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:36:39.299846 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:36:40.308794 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:36:40.310289 INFO: Using score_cutoff 10.02386665763855 (fac=0.99, q=1)
6:36:40.311007 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:36:40.311093 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:36:40.311155 INFO: Updating optimization_manager: score_cutoff        : 10.214109358978272 -> 10.02386665763855
6:36:40.311240 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:36:40.318384 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:36:40.330773 INFO: === checking if optimization conditions were reached ===
6:36:40.331476 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
6:36:40.333784 INFO: Updating optimization_manager: rt_error            : 384.9194648306892 -> 487.7654472093977
6:36:40.334068 INFO: Updating optimization_manager: classifier_version  : 6 -> 8
6:36:40.334168 INFO: Updating optimization_manager: score_cutoff        : 10.02386665763855 -> 10.04952763710022
6:36:40.334255 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:36:40.334344 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:36:40.334457 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 487.7654 found after 5 searches.
6:36:40.334538 INFO: ==============================================
6:36:40.334669 PROGRESS: Optimization finished for rt_error.
6:36:40.367085 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:36:40.375733 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:36:40.387845 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
6:36:40.388517 PROGRESS: ==============================================
6:36:40.388647 PROGRESS: ms2_error      : 10.0000
6:36:40.388717 PROGRESS: rt_error       : 487.7654
6:36:40.388763 PROGRESS: ==============================================
6:36:40.391570 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:36:40.614685 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:36:41.225106 INFO: Using rust extraction backend
6:36:41.226291 PROGRESS: Extracting batch of 289499 precursors
6:36:42.360964 INFO: === Search parameters used ===
6:36:42.362201 INFO: rt_error       : 487.7654472093977
6:36:42.362472 INFO: mobility_error : 0.1
6:36:42.362593 INFO: num_candidates : 3
6:36:42.362650 INFO: ms1_error      : 3
6:36:42.362705 INFO: ms2_error      : 10.0
6:36:42.362762 INFO: fwhm_rt        : 3.0
6:36:42.362806 INFO: quant_window   : 3
6:36:42.362849 INFO: ==============================================
6:36:43.529049 INFO: Removed 118375 precursors with score below cutoff 10.04952763710022
6:36:44.414977 INFO: performing precursor FDR with 40 features
6:36:44.415231 INFO: Decoy channel: -1
6:36:44.415277 INFO: competitive: True
6:36:44.532732 INFO: Setting torch num_threads to 2 for FDR classification task
6:36:44.614892 WARNING: FDR calculation for 395228 target and 354894 decoy PSMs
6:36:44.615098 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
6:36:45.005759 INFO: Estimating optimal hyperparameters - samples: 600,097, batch_size: 2,457, learning_rate: 7.75e-04
6:36:45.007821 INFO: Using random state 850098 for train-test-split
6:37:00.352510 INFO: Test AUC: 0.770
6:37:00.352920 INFO: Train AUC: 0.774
6:37:00.352980 INFO: AUC difference: 0.58%
6:37:01.362762 INFO: Resetting torch num_threads to 100
6:37:02.652896 PROGRESS: ============================= Precursor FDR =============================
6:37:02.654780 PROGRESS: Total precursors accumulated: 130,052
6:37:02.654887 PROGRESS: Target precursors: 128,765 (99.01%)
6:37:02.654946 PROGRESS: Decoy precursors: 1,287 (0.99%)
6:37:02.655000 PROGRESS: 
6:37:02.655058 PROGRESS: Precursor Summary:
6:37:02.838683 PROGRESS: Channel   0:	 0.050 FDR: 128,765; 0.010 FDR: 128,765; 0.001 FDR: 110,781
6:37:02.839612 PROGRESS: 
6:37:02.839681 PROGRESS: Protein Summary:
6:37:03.294697 PROGRESS: Channel   0:	 0.050 FDR: 10,640; 0.010 FDR: 10,640; 0.001 FDR: 10,460
6:37:03.295743 PROGRESS: =========================================================================
6:37:03.323972 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/psm.parquet
6:37:03.939543 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.parquet
6:37:04.596694 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
6:37:04.877234 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 
6:37:04.877630 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant
6:37:04.877836 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/figures
6:37:04.878185 INFO: Initializing TimingManager
6:37:04.879436 INFO: Initializing RawFileManager
6:37:31.592690 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.
6:37:31.607965 INFO: Determining DIA cycle
6:37:31.627218 INFO: Found cycle with start 0.00 min and length 300.
6:37:32.349532 INFO: RT (min)            : 0.0 - 26.9
6:37:32.349861 INFO: RT duration (sec)   : 1611.2
6:37:32.349893 INFO: RT duration (min)   : 26.9
6:37:32.349925 INFO: Cycle len (scans)   : 300
6:37:32.349947 INFO: Cycle len (sec)     : 1.65
6:37:32.349969 INFO: Number of cycles    : 977
6:37:32.349989 INFO: MS2 range (m/z)     : 380.4 - 980.7
6:37:32.350040 INFO: Creating DIA data object took: 27.470447540283203
6:37:34.173896 INFO: Creating DIA data NG object took: 1.823415756225586
6:37:34.273284 INFO: Initializing CalibrationManager
6:37:34.273849 INFO: Setting up calibration estimators ..
6:37:34.273926 INFO: Found 1 estimator(s) in calibration group 'fragment'
6:37:34.274027 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'}' ..
6:37:34.274134 INFO: Found 3 estimator(s) in calibration group 'precursor'
6:37:34.274195 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
6:37:34.274260 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}}' ..
6:37:34.274316 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
6:37:34.274375 INFO: Done setting up calibration estimators.
6:37:34.274870 INFO: Initializing OptimizationManager
6:37:34.275042 INFO: initial parameter: ms1_error = 3
6:37:34.275095 INFO: initial parameter: ms2_error = 10
6:37:34.275142 INFO: initial parameter: rt_error = 805.6002197265625
6:37:34.275221 INFO: initial parameter: mobility_error = 0.1
6:37:34.275270 INFO: initial parameter: num_candidates = 1
6:37:34.275311 INFO: initial parameter: fwhm_rt = 5
6:37:34.275350 INFO: initial parameter: fwhm_mobility = 0.01
6:37:34.275390 INFO: initial parameter: score_cutoff = 0
6:37:34.275431 INFO: initial parameter: classifier_version = -1
6:37:34.275509 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
6:37:34.276013 INFO: FDRManager: loading saved state not requested, will be initialized.
6:37:34.276047 INFO: Initializing FDRManager
6:37:34.276089 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
6:37:34.407429 PROGRESS: Initializing spectral library: 146,300 target precursors potentially observable (0 removed)
6:37:34.519923 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
6:37:34.521931 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
6:37:34.522138 PROGRESS: Starting initial search for precursors.
6:37:34.522302 INFO: Starting optimization step 0.
6:37:34.522403 PROGRESS: === Extracting elution groups 0 to 1000 ===
6:37:34.522501 INFO: Using rust extraction backend
6:37:34.522627 PROGRESS: Extracting batch of 1979 precursors
6:37:34.537663 INFO: === Search parameters used ===
6:37:34.539009 INFO: rt_error       : 805.6002197265625
6:37:34.539068 INFO: mobility_error : 0.1
6:37:34.539118 INFO: num_candidates : 1
6:37:34.539179 INFO: ms1_error      : 3
6:37:34.539225 INFO: ms2_error      : 10
6:37:34.539268 INFO: fwhm_rt        : 5
6:37:34.539311 INFO: quant_window   : 3
6:37:34.539364 INFO: ==============================================
6:37:34.623446 INFO: performing precursor FDR with 40 features
6:37:34.623737 INFO: Decoy channel: -1
6:37:34.623766 INFO: competitive: True
6:37:34.628011 INFO: Setting torch num_threads to 2 for FDR classification task
6:37:34.633801 INFO: Estimating optimal hyperparameters - samples: 1,580, batch_size: 128, learning_rate: 1.77e-04
6:37:34.636848 INFO: Using random state 481232 for train-test-split
6:37:34.823924 INFO: Test AUC: 0.836
6:37:34.824409 INFO: Train AUC: 0.860
6:37:34.824455 INFO: AUC difference: 2.76%
6:37:35.227224 INFO: Resetting torch num_threads to 100
6:37:35.230826 PROGRESS: === Extracted 1976 precursors and 13171 fragments ===
6:37:35.231548 INFO: === FDR correction performed with classifier version -1 ===
6:37:35.232393 PROGRESS: ============================= Precursor FDR =============================
6:37:35.232520 PROGRESS: Total precursors accumulated: 558
6:37:35.232582 PROGRESS: Target precursors: 553 (99.10%)
6:37:35.232630 PROGRESS: Decoy precursors: 5 (0.90%)
6:37:35.232683 PROGRESS: 
6:37:35.232728 PROGRESS: Precursor Summary:
6:37:35.234094 PROGRESS: Channel   0:	 0.050 FDR:   553; 0.010 FDR:   553; 0.001 FDR:   448
6:37:35.234192 PROGRESS: 
6:37:35.234245 PROGRESS: Protein Summary:
6:37:35.235847 PROGRESS: Channel   0:	 0.050 FDR:   510; 0.010 FDR:   510; 0.001 FDR:   418
6:37:35.235954 PROGRESS: =========================================================================
6:37:35.236609 INFO: Target number of precursors not reached yet.
6:37:35.250365 INFO: Starting optimization step 1.
6:37:35.250792 PROGRESS: === Extracting elution groups 1000 to 3000 ===
6:37:35.250913 INFO: Using rust extraction backend
6:37:35.250985 PROGRESS: Extracting batch of 3964 precursors
6:37:35.262640 INFO: === Search parameters used ===
6:37:35.263285 INFO: rt_error       : 805.6002197265625
6:37:35.263356 INFO: mobility_error : 0.1
6:37:35.263405 INFO: num_candidates : 1
6:37:35.263447 INFO: ms1_error      : 3
6:37:35.263488 INFO: ms2_error      : 10
6:37:35.263526 INFO: fwhm_rt        : 5
6:37:35.263584 INFO: quant_window   : 3
6:37:35.263628 INFO: ==============================================
6:37:35.346928 INFO: performing precursor FDR with 40 features
6:37:35.347115 INFO: Decoy channel: -1
6:37:35.347142 INFO: competitive: True
6:37:35.354633 INFO: Setting torch num_threads to 2 for FDR classification task
6:37:35.359725 INFO: Estimating optimal hyperparameters - samples: 4,748, batch_size: 128, learning_rate: 1.77e-04
6:37:35.359988 INFO: Using random state 785641 for train-test-split
6:37:35.751348 INFO: Test AUC: 0.894
6:37:35.751545 INFO: Train AUC: 0.878
6:37:35.751578 INFO: AUC difference: 1.80%
6:37:36.046971 INFO: Resetting torch num_threads to 100
6:37:36.050877 PROGRESS: === Extracted 5936 precursors and 39920 fragments ===
6:37:36.051367 INFO: === FDR correction performed with classifier version -1 ===
6:37:36.052089 PROGRESS: ============================= Precursor FDR =============================
6:37:36.052176 PROGRESS: Total precursors accumulated: 1,885
6:37:36.052235 PROGRESS: Target precursors: 1,867 (99.05%)
6:37:36.052281 PROGRESS: Decoy precursors: 18 (0.95%)
6:37:36.052326 PROGRESS: 
6:37:36.052371 PROGRESS: Precursor Summary:
6:37:36.053871 PROGRESS: Channel   0:	 0.050 FDR: 1,867; 0.010 FDR: 1,867; 0.001 FDR: 1,132
6:37:36.053964 PROGRESS: 
6:37:36.054022 PROGRESS: Protein Summary:
6:37:36.056020 PROGRESS: Channel   0:	 0.050 FDR: 1,516; 0.010 FDR: 1,516; 0.001 FDR:   974
6:37:36.056120 PROGRESS: =========================================================================
6:37:36.056458 INFO: Target number of precursors reached.
6:37:36.065709 INFO: fragments_df: keeping 5000 of 39920 [sum(precursor_idx_mask)=16725 sum(mass_error_mask)=39920 stop_rank=5000
6:37:36.077272 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:37:36.488672 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:37:37.293722 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
6:37:37.294804 INFO: Using score_cutoff 10.15898397960663 (fac=0.99, q=1)
6:37:37.295380 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
6:37:37.295470 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
6:37:37.295525 INFO: Updating optimization_manager: score_cutoff        : 0 -> 10.15898397960663
6:37:37.295592 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:37:37.301140 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:37:37.309850 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
6:37:37.310302 PROGRESS: Required number of precursors found. Starting search parameter optimization.
6:37:37.310447 INFO: Starting optimization step 2.
6:37:37.310535 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:37:37.310640 INFO: Using rust extraction backend
6:37:37.310726 PROGRESS: Extracting batch of 5943 precursors
6:37:37.326772 INFO: === Search parameters used ===
6:37:37.327561 INFO: rt_error       : 805.6002197265625
6:37:37.327624 INFO: mobility_error : 0.1
6:37:37.327673 INFO: num_candidates : 3
6:37:37.327717 INFO: ms1_error      : 3
6:37:37.327760 INFO: ms2_error      : 10
6:37:37.327800 INFO: fwhm_rt        : 3.0
6:37:37.327842 INFO: quant_window   : 3
6:37:37.327882 INFO: ==============================================
6:37:37.560745 INFO: performing precursor FDR with 40 features
6:37:37.561077 INFO: Decoy channel: -1
6:37:37.561106 INFO: competitive: True
6:37:37.584302 INFO: Setting torch num_threads to 2 for FDR classification task
6:37:37.605225 INFO: Estimating optimal hyperparameters - samples: 14,246, batch_size: 128, learning_rate: 1.77e-04
6:37:37.605777 INFO: Using random state 432723 for train-test-split
6:37:39.746778 INFO: Test AUC: 0.708
6:37:39.747225 INFO: Train AUC: 0.720
6:37:39.747270 INFO: AUC difference: 1.59%
6:37:40.218949 INFO: Resetting torch num_threads to 100
6:37:40.232459 PROGRESS: === Extracted 17808 precursors and 104864 fragments ===
6:37:40.234375 INFO: === FDR correction performed with classifier version 1 ===
6:37:40.237191 PROGRESS: ============================= Precursor FDR =============================
6:37:40.237466 PROGRESS: Total precursors accumulated: 2,025
6:37:40.237551 PROGRESS: Target precursors: 2,005 (99.01%)
6:37:40.237616 PROGRESS: Decoy precursors: 20 (0.99%)
6:37:40.237667 PROGRESS: 
6:37:40.237724 PROGRESS: Precursor Summary:
6:37:40.241617 PROGRESS: Channel   0:	 0.050 FDR: 2,005; 0.010 FDR: 2,005; 0.001 FDR: 1,215
6:37:40.241829 PROGRESS: 
6:37:40.241922 PROGRESS: Protein Summary:
6:37:40.245290 PROGRESS: Channel   0:	 0.050 FDR: 1,605; 0.010 FDR: 1,605; 0.001 FDR: 1,031
6:37:40.245709 PROGRESS: =========================================================================
6:37:40.248727 INFO: Target number of precursors reached.
6:37:40.282189 INFO: fragments_df: keeping 5000 of 104864 [sum(precursor_idx_mask)=41632 sum(mass_error_mask)=104864 stop_rank=5000
6:37:40.324197 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:37:40.802963 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:37:41.702432 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:37:41.703890 INFO: Using score_cutoff 10.503095934677125 (fac=0.99, q=1)
6:37:41.704658 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:37:41.704764 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:37:41.704819 INFO: Updating optimization_manager: score_cutoff        : 10.15898397960663 -> 10.503095934677125
6:37:41.704885 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:37:41.712037 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:37:41.724084 INFO: === checking if optimization conditions were reached ===
6:37:41.728719 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
6:37:41.729471 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
6:37:41.729573 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:37:41.729670 INFO: ==============================================
6:37:41.729797 INFO: Starting optimization step 3.
6:37:41.729879 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:37:41.729968 INFO: Using rust extraction backend
6:37:41.730040 PROGRESS: Extracting batch of 5943 precursors
6:37:41.762029 INFO: === Search parameters used ===
6:37:41.763015 INFO: rt_error       : 805.6002197265625
6:37:41.763081 INFO: mobility_error : 0.1
6:37:41.763131 INFO: num_candidates : 3
6:37:41.763197 INFO: ms1_error      : 3
6:37:41.763289 INFO: ms2_error      : 10.0
6:37:41.763341 INFO: fwhm_rt        : 3.0
6:37:41.763385 INFO: quant_window   : 3
6:37:41.763437 INFO: ==============================================
6:37:42.032901 INFO: performing precursor FDR with 40 features
6:37:42.033183 INFO: Decoy channel: -1
6:37:42.033210 INFO: competitive: True
6:37:42.055812 INFO: Setting torch num_threads to 2 for FDR classification task
6:37:42.072822 INFO: Estimating optimal hyperparameters - samples: 14,247, batch_size: 128, learning_rate: 1.77e-04
6:37:42.073478 INFO: Using random state 348116 for train-test-split
6:37:44.241538 INFO: Test AUC: 0.711
6:37:44.241964 INFO: Train AUC: 0.739
6:37:44.242003 INFO: AUC difference: 3.78%
6:37:44.743922 INFO: Resetting torch num_threads to 100
6:37:44.751134 PROGRESS: === Extracted 17809 precursors and 104885 fragments ===
6:37:44.751996 INFO: === FDR correction performed with classifier version 2 ===
6:37:44.753392 PROGRESS: ============================= Precursor FDR =============================
6:37:44.753527 PROGRESS: Total precursors accumulated: 2,190
6:37:44.753602 PROGRESS: Target precursors: 2,169 (99.04%)
6:37:44.753658 PROGRESS: Decoy precursors: 21 (0.96%)
6:37:44.753714 PROGRESS: 
6:37:44.753765 PROGRESS: Precursor Summary:
6:37:44.755787 PROGRESS: Channel   0:	 0.050 FDR: 2,169; 0.010 FDR: 2,169; 0.001 FDR: 1,231
6:37:44.755952 PROGRESS: 
6:37:44.756015 PROGRESS: Protein Summary:
6:37:44.758815 PROGRESS: Channel   0:	 0.050 FDR: 1,731; 0.010 FDR: 1,731; 0.001 FDR: 1,040
6:37:44.758974 PROGRESS: =========================================================================
6:37:44.760882 INFO: Target number of precursors reached.
6:37:44.790593 INFO: fragments_df: keeping 5000 of 104885 [sum(precursor_idx_mask)=44344 sum(mass_error_mask)=104885 stop_rank=5000
6:37:44.823059 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:37:45.417130 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:37:46.468334 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:37:46.469654 INFO: Using score_cutoff 10.103452847671509 (fac=0.99, q=1)
6:37:46.470335 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:37:46.470425 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:37:46.470481 INFO: Updating optimization_manager: score_cutoff        : 10.503095934677125 -> 10.103452847671509
6:37:46.470552 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:37:46.477951 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:37:46.490618 INFO: === checking if optimization conditions were reached ===
6:37:46.495439 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:37:46.495967 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
6:37:46.496053 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:37:46.496153 INFO: ==============================================
6:37:46.496245 INFO: Starting optimization step 4.
6:37:46.496312 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:37:46.496413 INFO: Using rust extraction backend
6:37:46.496493 PROGRESS: Extracting batch of 5943 precursors
6:37:46.521811 INFO: === Search parameters used ===
6:37:46.523382 INFO: rt_error       : 805.6002197265625
6:37:46.523468 INFO: mobility_error : 0.1
6:37:46.523518 INFO: num_candidates : 3
6:37:46.523562 INFO: ms1_error      : 3
6:37:46.523600 INFO: ms2_error      : 10.0
6:37:46.523637 INFO: fwhm_rt        : 3.0
6:37:46.523677 INFO: quant_window   : 3
6:37:46.523718 INFO: ==============================================
6:37:46.832014 INFO: performing precursor FDR with 40 features
6:37:46.832346 INFO: Decoy channel: -1
6:37:46.832372 INFO: competitive: True
6:37:46.864692 INFO: Setting torch num_threads to 2 for FDR classification task
6:37:46.881789 INFO: Estimating optimal hyperparameters - samples: 14,247, batch_size: 128, learning_rate: 1.77e-04
6:37:46.882485 INFO: Using random state 714354 for train-test-split
6:37:49.079575 INFO: Test AUC: 0.723
6:37:49.079852 INFO: Train AUC: 0.749
6:37:49.079894 INFO: AUC difference: 3.51%
6:37:49.471483 INFO: Resetting torch num_threads to 100
6:37:49.480951 PROGRESS: === Extracted 17809 precursors and 104899 fragments ===
6:37:49.482790 INFO: === FDR correction performed with classifier version 3 ===
6:37:49.485731 PROGRESS: ============================= Precursor FDR =============================
6:37:49.485940 PROGRESS: Total precursors accumulated: 2,199
6:37:49.486006 PROGRESS: Target precursors: 2,178 (99.05%)
6:37:49.486061 PROGRESS: Decoy precursors: 21 (0.95%)
6:37:49.486113 PROGRESS: 
6:37:49.486209 PROGRESS: Precursor Summary:
6:37:49.489392 PROGRESS: Channel   0:	 0.050 FDR: 2,178; 0.010 FDR: 2,178; 0.001 FDR: 1,190
6:37:49.489769 PROGRESS: 
6:37:49.489843 PROGRESS: Protein Summary:
6:37:49.493767 PROGRESS: Channel   0:	 0.050 FDR: 1,731; 0.010 FDR: 1,731; 0.001 FDR: 1,016
6:37:49.493978 PROGRESS: =========================================================================
6:37:49.496176 INFO: Target number of precursors reached.
6:37:49.530566 INFO: fragments_df: keeping 5000 of 104899 [sum(precursor_idx_mask)=44224 sum(mass_error_mask)=104899 stop_rank=5000
6:37:49.571657 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:37:50.050752 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:37:50.904823 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:37:50.905842 INFO: Using score_cutoff 9.773208942317963 (fac=0.99, q=1)
6:37:50.906336 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:37:50.906424 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:37:50.906507 INFO: Updating optimization_manager: score_cutoff        : 10.103452847671509 -> 9.773208942317963
6:37:50.906567 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:37:50.912001 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:37:50.920120 INFO: === checking if optimization conditions were reached ===
6:37:50.923090 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:37:50.923311 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
6:37:50.923407 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:37:50.923482 INFO: ==============================================
6:37:50.923565 INFO: Starting optimization step 5.
6:37:50.923628 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:37:50.923708 INFO: Using rust extraction backend
6:37:50.923781 PROGRESS: Extracting batch of 5943 precursors
6:37:50.938529 INFO: === Search parameters used ===
6:37:50.939214 INFO: rt_error       : 805.6002197265625
6:37:50.939276 INFO: mobility_error : 0.1
6:37:50.939333 INFO: num_candidates : 3
6:37:50.939379 INFO: ms1_error      : 3
6:37:50.939424 INFO: ms2_error      : 10.0
6:37:50.939466 INFO: fwhm_rt        : 3.0
6:37:50.939504 INFO: quant_window   : 3
6:37:50.939543 INFO: ==============================================
6:37:51.141751 INFO: performing precursor FDR with 40 features
6:37:51.141964 INFO: Decoy channel: -1
6:37:51.141989 INFO: competitive: True
6:37:51.152599 INFO: Setting torch num_threads to 2 for FDR classification task
6:37:51.160425 INFO: Estimating optimal hyperparameters - samples: 14,247, batch_size: 128, learning_rate: 1.77e-04
6:37:51.160888 INFO: Using random state 496551 for train-test-split
6:37:53.683758 INFO: Test AUC: 0.745
6:37:53.684115 INFO: Train AUC: 0.755
6:37:53.684156 INFO: AUC difference: 1.34%
6:37:54.080730 INFO: Resetting torch num_threads to 100
6:37:54.089363 PROGRESS: === Extracted 17809 precursors and 104917 fragments ===
6:37:54.090339 INFO: === FDR correction performed with classifier version 4 ===
6:37:54.091952 PROGRESS: ============================= Precursor FDR =============================
6:37:54.092085 PROGRESS: Total precursors accumulated: 2,278
6:37:54.092150 PROGRESS: Target precursors: 2,256 (99.03%)
6:37:54.092198 PROGRESS: Decoy precursors: 22 (0.97%)
6:37:54.092264 PROGRESS: 
6:37:54.092309 PROGRESS: Precursor Summary:
6:37:54.094330 PROGRESS: Channel   0:	 0.050 FDR: 2,256; 0.010 FDR: 2,256; 0.001 FDR: 1,223
6:37:54.094468 PROGRESS: 
6:37:54.094523 PROGRESS: Protein Summary:
6:37:54.097857 PROGRESS: Channel   0:	 0.050 FDR: 1,801; 0.010 FDR: 1,801; 0.001 FDR: 1,034
6:37:54.098019 PROGRESS: =========================================================================
6:37:54.100187 INFO: Target number of precursors reached.
6:37:54.130158 INFO: fragments_df: keeping 5000 of 104917 [sum(precursor_idx_mask)=45555 sum(mass_error_mask)=104917 stop_rank=5000
6:37:54.159308 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:37:54.745513 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:37:55.770539 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:37:55.772799 INFO: Using score_cutoff 9.717588797092438 (fac=0.99, q=1)
6:37:55.774028 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:37:55.774151 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:37:55.774217 INFO: Updating optimization_manager: score_cutoff        : 9.773208942317963 -> 9.717588797092438
6:37:55.774323 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:37:55.782870 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:37:55.795485 INFO: === checking if optimization conditions were reached ===
6:37:55.803172 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:37:55.803761 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
6:37:55.803853 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:37:55.803956 INFO: ==============================================
6:37:55.804049 INFO: Starting optimization step 6.
6:37:55.804115 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:37:55.804208 INFO: Using rust extraction backend
6:37:55.804303 PROGRESS: Extracting batch of 5943 precursors
6:37:55.835568 INFO: === Search parameters used ===
6:37:55.836430 INFO: rt_error       : 805.6002197265625
6:37:55.836492 INFO: mobility_error : 0.1
6:37:55.836540 INFO: num_candidates : 3
6:37:55.836585 INFO: ms1_error      : 3
6:37:55.836627 INFO: ms2_error      : 10.0
6:37:55.836672 INFO: fwhm_rt        : 3.0
6:37:55.836713 INFO: quant_window   : 3
6:37:55.836753 INFO: ==============================================
6:37:56.175938 INFO: performing precursor FDR with 40 features
6:37:56.176671 INFO: Decoy channel: -1
6:37:56.176712 INFO: competitive: True
6:37:56.204553 INFO: Setting torch num_threads to 2 for FDR classification task
6:37:56.224760 INFO: Estimating optimal hyperparameters - samples: 14,247, batch_size: 128, learning_rate: 1.77e-04
6:37:56.225597 INFO: Using random state 645862 for train-test-split
6:37:57.579337 INFO: Test AUC: 0.739
6:37:57.579714 INFO: Train AUC: 0.767
6:37:57.579760 INFO: AUC difference: 3.74%
6:37:58.070807 INFO: Resetting torch num_threads to 100
6:37:58.080000 PROGRESS: === Extracted 17809 precursors and 104906 fragments ===
6:37:58.081228 INFO: === FDR correction performed with classifier version 5 ===
6:37:58.083314 PROGRESS: ============================= Precursor FDR =============================
6:37:58.083625 PROGRESS: Total precursors accumulated: 2,353
6:37:58.083716 PROGRESS: Target precursors: 2,330 (99.02%)
6:37:58.083827 PROGRESS: Decoy precursors: 23 (0.98%)
6:37:58.083879 PROGRESS: 
6:37:58.083925 PROGRESS: Precursor Summary:
6:37:58.086825 PROGRESS: Channel   0:	 0.050 FDR: 2,330; 0.010 FDR: 2,330; 0.001 FDR: 1,227
6:37:58.087115 PROGRESS: 
6:37:58.087207 PROGRESS: Protein Summary:
6:37:58.091108 PROGRESS: Channel   0:	 0.050 FDR: 1,851; 0.010 FDR: 1,851; 0.001 FDR: 1,037
6:37:58.091317 PROGRESS: =========================================================================
6:37:58.093654 INFO: Target number of precursors reached.
6:37:58.134184 INFO: fragments_df: keeping 5000 of 104906 [sum(precursor_idx_mask)=46784 sum(mass_error_mask)=104906 stop_rank=5000
6:37:58.169032 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:37:58.816669 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:37:59.752149 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:37:59.753632 INFO: Using score_cutoff 9.72553725528717 (fac=0.99, q=1)
6:37:59.754253 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:37:59.754346 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:37:59.754403 INFO: Updating optimization_manager: score_cutoff        : 9.717588797092438 -> 9.72553725528717
6:37:59.754477 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:37:59.761426 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:37:59.773624 INFO: === checking if optimization conditions were reached ===
6:37:59.778440 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:37:59.778903 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
6:37:59.778980 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
6:37:59.779053 INFO: ==============================================
6:37:59.779179 PROGRESS: Optimization finished for ms2_error.
6:37:59.810379 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:37:59.818594 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:37:59.830068 INFO: Starting optimization step 0.
6:37:59.830817 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:37:59.830945 INFO: Using rust extraction backend
6:37:59.831042 PROGRESS: Extracting batch of 5943 precursors
6:37:59.856342 INFO: === Search parameters used ===
6:37:59.857281 INFO: rt_error       : 805.6002197265625
6:37:59.857342 INFO: mobility_error : 0.1
6:37:59.857418 INFO: num_candidates : 3
6:37:59.857469 INFO: ms1_error      : 3
6:37:59.857514 INFO: ms2_error      : 10.0
6:37:59.857561 INFO: fwhm_rt        : 3.0
6:37:59.857601 INFO: quant_window   : 3
6:37:59.857640 INFO: ==============================================
6:38:00.153919 INFO: performing precursor FDR with 40 features
6:38:00.154321 INFO: Decoy channel: -1
6:38:00.154355 INFO: competitive: True
6:38:00.183766 INFO: Setting torch num_threads to 2 for FDR classification task
6:38:00.201124 INFO: Estimating optimal hyperparameters - samples: 14,247, batch_size: 128, learning_rate: 1.77e-04
6:38:00.201886 INFO: Using random state 448199 for train-test-split
6:38:02.864202 INFO: Test AUC: 0.759
6:38:02.864667 INFO: Train AUC: 0.770
6:38:02.864708 INFO: AUC difference: 1.50%
6:38:03.382448 INFO: Resetting torch num_threads to 100
6:38:03.389192 PROGRESS: === Extracted 17809 precursors and 104890 fragments ===
6:38:03.390384 INFO: === FDR correction performed with classifier version 6 ===
6:38:03.392311 PROGRESS: ============================= Precursor FDR =============================
6:38:03.392538 PROGRESS: Total precursors accumulated: 2,402
6:38:03.392610 PROGRESS: Target precursors: 2,379 (99.04%)
6:38:03.392663 PROGRESS: Decoy precursors: 23 (0.96%)
6:38:03.392711 PROGRESS: 
6:38:03.392759 PROGRESS: Precursor Summary:
6:38:03.395113 PROGRESS: Channel   0:	 0.050 FDR: 2,379; 0.010 FDR: 2,379; 0.001 FDR: 1,308
6:38:03.395384 PROGRESS: 
6:38:03.395473 PROGRESS: Protein Summary:
6:38:03.398118 PROGRESS: Channel   0:	 0.050 FDR: 1,893; 0.010 FDR: 1,893; 0.001 FDR: 1,099
6:38:03.398471 PROGRESS: =========================================================================
6:38:03.399823 INFO: Target number of precursors reached.
6:38:03.423542 INFO: fragments_df: keeping 5000 of 104890 [sum(precursor_idx_mask)=47755 sum(mass_error_mask)=104890 stop_rank=5000
6:38:03.457053 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:38:03.885204 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:38:04.908803 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:38:04.911111 INFO: Using score_cutoff 9.468635589981078 (fac=0.99, q=1)
6:38:04.912635 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:38:04.912820 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:38:04.912934 INFO: Updating optimization_manager: score_cutoff        : 9.72553725528717 -> 9.468635589981078
6:38:04.913080 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:38:04.922680 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:38:04.938078 INFO: === checking if optimization conditions were reached ===
6:38:04.939266 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
6:38:04.948400 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 413.51955182846945
6:38:04.949677 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 413.5196.
6:38:04.949771 INFO: ==============================================
6:38:04.949879 INFO: Starting optimization step 1.
6:38:04.949979 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:38:04.950119 INFO: Using rust extraction backend
6:38:04.950209 PROGRESS: Extracting batch of 5943 precursors
6:38:04.996489 INFO: === Search parameters used ===
6:38:04.998057 INFO: rt_error       : 413.51955182846945
6:38:04.998138 INFO: mobility_error : 0.1
6:38:04.998198 INFO: num_candidates : 3
6:38:04.998252 INFO: ms1_error      : 3
6:38:04.998303 INFO: ms2_error      : 10.0
6:38:04.998360 INFO: fwhm_rt        : 3.0
6:38:04.998412 INFO: quant_window   : 3
6:38:04.998540 INFO: ==============================================
6:38:05.192939 INFO: performing precursor FDR with 40 features
6:38:05.193200 INFO: Decoy channel: -1
6:38:05.193227 INFO: competitive: True
6:38:05.203910 INFO: Setting torch num_threads to 2 for FDR classification task
6:38:05.211962 INFO: Estimating optimal hyperparameters - samples: 14,244, batch_size: 128, learning_rate: 1.77e-04
6:38:05.212361 INFO: Using random state 448199 for train-test-split
6:38:06.914190 INFO: Test AUC: 0.763
6:38:06.914478 INFO: Train AUC: 0.772
6:38:06.914512 INFO: AUC difference: 1.16%
6:38:07.239654 INFO: Resetting torch num_threads to 100
6:38:07.244994 PROGRESS: === Extracted 17805 precursors and 104506 fragments ===
6:38:07.245803 INFO: === FDR correction performed with classifier version 6 ===
6:38:07.246767 PROGRESS: ============================= Precursor FDR =============================
6:38:07.246876 PROGRESS: Total precursors accumulated: 2,424
6:38:07.246940 PROGRESS: Target precursors: 2,400 (99.01%)
6:38:07.247016 PROGRESS: Decoy precursors: 24 (0.99%)
6:38:07.247063 PROGRESS: 
6:38:07.247111 PROGRESS: Precursor Summary:
6:38:07.248908 PROGRESS: Channel   0:	 0.050 FDR: 2,400; 0.010 FDR: 2,396; 0.001 FDR: 1,320
6:38:07.249027 PROGRESS: 
6:38:07.249094 PROGRESS: Protein Summary:
6:38:07.251549 PROGRESS: Channel   0:	 0.050 FDR: 1,907; 0.010 FDR: 1,904; 0.001 FDR: 1,108
6:38:07.251690 PROGRESS: =========================================================================
6:38:07.252878 INFO: Target number of precursors reached.
6:38:07.281796 INFO: fragments_df: keeping 5000 of 104506 [sum(precursor_idx_mask)=47970 sum(mass_error_mask)=104506 stop_rank=5000
6:38:07.305960 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:38:07.766338 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:38:08.588950 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:38:08.590003 INFO: Using score_cutoff 9.427352976322174 (fac=0.99, q=1)
6:38:08.590534 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:38:08.590618 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:38:08.590673 INFO: Updating optimization_manager: score_cutoff        : 9.468635589981078 -> 9.427352976322174
6:38:08.590731 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:38:08.596659 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:38:08.605299 INFO: === checking if optimization conditions were reached ===
6:38:08.605778 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
6:38:08.610096 INFO: Updating optimization_manager: rt_error            : 413.51955182846945 -> 361.3690653893252
6:38:08.610383 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 361.3691.
6:38:08.610465 INFO: ==============================================
6:38:08.610548 INFO: Starting optimization step 2.
6:38:08.610632 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:38:08.610735 INFO: Using rust extraction backend
6:38:08.610813 PROGRESS: Extracting batch of 5943 precursors
6:38:08.625597 INFO: === Search parameters used ===
6:38:08.626322 INFO: rt_error       : 361.3690653893252
6:38:08.626382 INFO: mobility_error : 0.1
6:38:08.626440 INFO: num_candidates : 3
6:38:08.626487 INFO: ms1_error      : 3
6:38:08.626535 INFO: ms2_error      : 10.0
6:38:08.626595 INFO: fwhm_rt        : 3.0
6:38:08.626641 INFO: quant_window   : 3
6:38:08.626683 INFO: ==============================================
6:38:08.805958 INFO: performing precursor FDR with 40 features
6:38:08.806188 INFO: Decoy channel: -1
6:38:08.806215 INFO: competitive: True
6:38:08.816904 INFO: Setting torch num_threads to 2 for FDR classification task
6:38:08.825079 INFO: Estimating optimal hyperparameters - samples: 14,242, batch_size: 128, learning_rate: 1.77e-04
6:38:08.825440 INFO: Using random state 448199 for train-test-split
6:38:09.950490 INFO: Test AUC: 0.766
6:38:09.950663 INFO: Train AUC: 0.770
6:38:09.950694 INFO: AUC difference: 0.62%
6:38:10.215945 INFO: Resetting torch num_threads to 100
6:38:10.221686 PROGRESS: === Extracted 17803 precursors and 104218 fragments ===
6:38:10.222468 INFO: === FDR correction performed with classifier version 6 ===
6:38:10.223450 PROGRESS: ============================= Precursor FDR =============================
6:38:10.223573 PROGRESS: Total precursors accumulated: 2,427
6:38:10.223634 PROGRESS: Target precursors: 2,403 (99.01%)
6:38:10.223681 PROGRESS: Decoy precursors: 24 (0.99%)
6:38:10.223723 PROGRESS: 
6:38:10.223763 PROGRESS: Precursor Summary:
6:38:10.225405 PROGRESS: Channel   0:	 0.050 FDR: 2,403; 0.010 FDR: 2,403; 0.001 FDR: 1,372
6:38:10.225517 PROGRESS: 
6:38:10.225569 PROGRESS: Protein Summary:
6:38:10.228041 PROGRESS: Channel   0:	 0.050 FDR: 1,912; 0.010 FDR: 1,912; 0.001 FDR: 1,142
6:38:10.228149 PROGRESS: =========================================================================
6:38:10.229229 INFO: Target number of precursors reached.
6:38:10.256169 INFO: fragments_df: keeping 5000 of 104218 [sum(precursor_idx_mask)=47884 sum(mass_error_mask)=104218 stop_rank=5000
6:38:10.278353 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:38:10.772474 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:38:11.564539 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:38:11.565444 INFO: Using score_cutoff 9.390150963020325 (fac=0.99, q=1)
6:38:11.565892 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:38:11.565973 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:38:11.566027 INFO: Updating optimization_manager: score_cutoff        : 9.427352976322174 -> 9.390150963020325
6:38:11.566084 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:38:11.571171 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:38:11.579385 INFO: === checking if optimization conditions were reached ===
6:38:11.579835 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
6:38:11.584219 INFO: Updating optimization_manager: rt_error            : 361.3690653893252 -> 320.9645602349607
6:38:11.584466 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 320.9646.
6:38:11.584543 INFO: ==============================================
6:38:11.584621 INFO: Starting optimization step 3.
6:38:11.584688 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:38:11.584778 INFO: Using rust extraction backend
6:38:11.584850 PROGRESS: Extracting batch of 5943 precursors
6:38:11.599566 INFO: === Search parameters used ===
6:38:11.600718 INFO: rt_error       : 320.9645602349607
6:38:11.600785 INFO: mobility_error : 0.1
6:38:11.600837 INFO: num_candidates : 3
6:38:11.600906 INFO: ms1_error      : 3
6:38:11.600953 INFO: ms2_error      : 10.0
6:38:11.600998 INFO: fwhm_rt        : 3.0
6:38:11.601042 INFO: quant_window   : 3
6:38:11.601087 INFO: ==============================================
6:38:11.779203 INFO: performing precursor FDR with 40 features
6:38:11.779424 INFO: Decoy channel: -1
6:38:11.779454 INFO: competitive: True
6:38:11.789882 INFO: Setting torch num_threads to 2 for FDR classification task
6:38:11.798834 INFO: Estimating optimal hyperparameters - samples: 14,240, batch_size: 128, learning_rate: 1.77e-04
6:38:11.799205 INFO: Using random state 448199 for train-test-split
6:38:12.998321 INFO: Test AUC: 0.758
6:38:12.998594 INFO: Train AUC: 0.772
6:38:12.998630 INFO: AUC difference: 1.88%
6:38:13.343867 INFO: Resetting torch num_threads to 100
6:38:13.355289 PROGRESS: === Extracted 17800 precursors and 103771 fragments ===
6:38:13.357689 INFO: === FDR correction performed with classifier version 6 ===
6:38:13.363383 PROGRESS: ============================= Precursor FDR =============================
6:38:13.364076 PROGRESS: Total precursors accumulated: 2,460
6:38:13.364159 PROGRESS: Target precursors: 2,436 (99.02%)
6:38:13.364217 PROGRESS: Decoy precursors: 24 (0.98%)
6:38:13.364266 PROGRESS: 
6:38:13.364315 PROGRESS: Precursor Summary:
6:38:13.369683 PROGRESS: Channel   0:	 0.050 FDR: 2,436; 0.010 FDR: 2,436; 0.001 FDR: 1,304
6:38:13.370039 PROGRESS: 
6:38:13.370100 PROGRESS: Protein Summary:
6:38:13.375028 PROGRESS: Channel   0:	 0.050 FDR: 1,934; 0.010 FDR: 1,934; 0.001 FDR: 1,098
6:38:13.375713 PROGRESS: =========================================================================
6:38:13.379406 INFO: Target number of precursors reached.
6:38:13.418786 INFO: fragments_df: keeping 5000 of 103771 [sum(precursor_idx_mask)=48409 sum(mass_error_mask)=103771 stop_rank=5000
6:38:13.462900 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:38:14.015710 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:38:14.971384 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:38:14.972792 INFO: Using score_cutoff 9.434893378257751 (fac=0.99, q=1)
6:38:14.973446 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:38:14.973534 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:38:14.973587 INFO: Updating optimization_manager: score_cutoff        : 9.390150963020325 -> 9.434893378257751
6:38:14.973653 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:38:14.980451 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:38:14.992607 INFO: === checking if optimization conditions were reached ===
6:38:14.993329 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
6:38:14.999548 INFO: Updating optimization_manager: rt_error            : 320.9645602349607 -> 267.20894312376925
6:38:15.000187 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 267.2089.
6:38:15.000274 INFO: ==============================================
6:38:15.000364 INFO: Starting optimization step 4.
6:38:15.000441 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:38:15.000564 INFO: Using rust extraction backend
6:38:15.000653 PROGRESS: Extracting batch of 5943 precursors
6:38:15.021426 INFO: === Search parameters used ===
6:38:15.022427 INFO: rt_error       : 267.20894312376925
6:38:15.022505 INFO: mobility_error : 0.1
6:38:15.022608 INFO: num_candidates : 3
6:38:15.022660 INFO: ms1_error      : 3
6:38:15.022709 INFO: ms2_error      : 10.0
6:38:15.022756 INFO: fwhm_rt        : 3.0
6:38:15.022798 INFO: quant_window   : 3
6:38:15.022839 INFO: ==============================================
6:38:15.289169 INFO: performing precursor FDR with 40 features
6:38:15.289462 INFO: Decoy channel: -1
6:38:15.289488 INFO: competitive: True
6:38:15.310222 INFO: Setting torch num_threads to 2 for FDR classification task
6:38:15.317232 INFO: Estimating optimal hyperparameters - samples: 14,236, batch_size: 128, learning_rate: 1.77e-04
6:38:15.317501 INFO: Using random state 448199 for train-test-split
6:38:17.030951 INFO: Test AUC: 0.754
6:38:17.031180 INFO: Train AUC: 0.769
6:38:17.031213 INFO: AUC difference: 2.02%
6:38:17.371979 INFO: Resetting torch num_threads to 100
6:38:17.380598 PROGRESS: === Extracted 17796 precursors and 102876 fragments ===
6:38:17.382070 INFO: === FDR correction performed with classifier version 6 ===
6:38:17.385371 PROGRESS: ============================= Precursor FDR =============================
6:38:17.385776 PROGRESS: Total precursors accumulated: 2,475
6:38:17.385856 PROGRESS: Target precursors: 2,451 (99.03%)
6:38:17.385911 PROGRESS: Decoy precursors: 24 (0.97%)
6:38:17.385962 PROGRESS: 
6:38:17.386011 PROGRESS: Precursor Summary:
6:38:17.390024 PROGRESS: Channel   0:	 0.050 FDR: 2,451; 0.010 FDR: 2,451; 0.001 FDR: 1,351
6:38:17.390288 PROGRESS: 
6:38:17.390350 PROGRESS: Protein Summary:
6:38:17.393723 PROGRESS: Channel   0:	 0.050 FDR: 1,941; 0.010 FDR: 1,941; 0.001 FDR: 1,136
6:38:17.394028 PROGRESS: =========================================================================
6:38:17.396111 INFO: Target number of precursors reached.
6:38:17.433615 INFO: fragments_df: keeping 5000 of 102876 [sum(precursor_idx_mask)=48604 sum(mass_error_mask)=102876 stop_rank=5000
6:38:17.481633 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:38:18.050546 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:38:18.980615 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:38:18.982065 INFO: Using score_cutoff 9.462253446578979 (fac=0.99, q=1)
6:38:18.982743 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:38:18.982855 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:38:18.982911 INFO: Updating optimization_manager: score_cutoff        : 9.434893378257751 -> 9.462253446578979
6:38:18.982976 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:38:18.989592 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:38:19.000875 INFO: === checking if optimization conditions were reached ===
6:38:19.001643 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
6:38:19.008081 INFO: Updating optimization_manager: rt_error            : 267.20894312376925 -> 229.25338699318556
6:38:19.008713 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 229.2534.
6:38:19.008814 INFO: ==============================================
6:38:19.008900 INFO: Starting optimization step 5.
6:38:19.008981 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:38:19.009075 INFO: Using rust extraction backend
6:38:19.009166 PROGRESS: Extracting batch of 5943 precursors
6:38:19.033823 INFO: === Search parameters used ===
6:38:19.034599 INFO: rt_error       : 229.25338699318556
6:38:19.034667 INFO: mobility_error : 0.1
6:38:19.034720 INFO: num_candidates : 3
6:38:19.034770 INFO: ms1_error      : 3
6:38:19.034812 INFO: ms2_error      : 10.0
6:38:19.034856 INFO: fwhm_rt        : 3.0
6:38:19.034907 INFO: quant_window   : 3
6:38:19.034966 INFO: ==============================================
6:38:19.299316 INFO: performing precursor FDR with 40 features
6:38:19.299849 INFO: Decoy channel: -1
6:38:19.299884 INFO: competitive: True
6:38:19.328107 INFO: Setting torch num_threads to 2 for FDR classification task
6:38:19.346700 INFO: Estimating optimal hyperparameters - samples: 14,234, batch_size: 128, learning_rate: 1.77e-04
6:38:19.347437 INFO: Using random state 448199 for train-test-split
6:38:21.798346 INFO: Test AUC: 0.741
6:38:21.798720 INFO: Train AUC: 0.770
6:38:21.798765 INFO: AUC difference: 3.67%
6:38:22.296613 INFO: Resetting torch num_threads to 100
6:38:22.307179 PROGRESS: === Extracted 17793 precursors and 102026 fragments ===
6:38:22.308601 INFO: === FDR correction performed with classifier version 6 ===
6:38:22.310238 PROGRESS: ============================= Precursor FDR =============================
6:38:22.310407 PROGRESS: Total precursors accumulated: 2,493
6:38:22.310504 PROGRESS: Target precursors: 2,469 (99.04%)
6:38:22.310580 PROGRESS: Decoy precursors: 24 (0.96%)
6:38:22.310637 PROGRESS: 
6:38:22.310694 PROGRESS: Precursor Summary:
6:38:22.314310 PROGRESS: Channel   0:	 0.050 FDR: 2,469; 0.010 FDR: 2,469; 0.001 FDR: 1,358
6:38:22.314527 PROGRESS: 
6:38:22.314589 PROGRESS: Protein Summary:
6:38:22.318547 PROGRESS: Channel   0:	 0.050 FDR: 1,958; 0.010 FDR: 1,958; 0.001 FDR: 1,137
6:38:22.318838 PROGRESS: =========================================================================
6:38:22.321276 INFO: Target number of precursors reached.
6:38:22.360222 INFO: fragments_df: keeping 5000 of 102026 [sum(precursor_idx_mask)=48759 sum(mass_error_mask)=102026 stop_rank=5000
6:38:22.397692 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:38:22.924171 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:38:23.848846 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:38:23.851388 INFO: Using score_cutoff 9.609068803024291 (fac=0.99, q=1)
6:38:23.852540 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:38:23.852682 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:38:23.852749 INFO: Updating optimization_manager: score_cutoff        : 9.462253446578979 -> 9.609068803024291
6:38:23.852858 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:38:23.862190 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:38:23.875916 INFO: === checking if optimization conditions were reached ===
6:38:23.877295 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
6:38:23.885481 INFO: Updating optimization_manager: rt_error            : 229.25338699318556 -> 216.63979289557676
6:38:23.886007 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 216.6398.
6:38:23.886102 INFO: ==============================================
6:38:23.886194 INFO: Starting optimization step 6.
6:38:23.886272 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:38:23.886376 INFO: Using rust extraction backend
6:38:23.886471 PROGRESS: Extracting batch of 5943 precursors
6:38:23.909867 INFO: === Search parameters used ===
6:38:23.910711 INFO: rt_error       : 216.63979289557676
6:38:23.910772 INFO: mobility_error : 0.1
6:38:23.910829 INFO: num_candidates : 3
6:38:23.910876 INFO: ms1_error      : 3
6:38:23.910924 INFO: ms2_error      : 10.0
6:38:23.910965 INFO: fwhm_rt        : 3.0
6:38:23.911007 INFO: quant_window   : 3
6:38:23.911051 INFO: ==============================================
6:38:24.221403 INFO: performing precursor FDR with 40 features
6:38:24.221732 INFO: Decoy channel: -1
6:38:24.221757 INFO: competitive: True
6:38:24.241697 INFO: Setting torch num_threads to 2 for FDR classification task
6:38:24.252415 INFO: Estimating optimal hyperparameters - samples: 14,231, batch_size: 128, learning_rate: 1.77e-04
6:38:24.252939 INFO: Using random state 448199 for train-test-split
6:38:26.931721 INFO: Test AUC: 0.741
6:38:26.932117 INFO: Train AUC: 0.771
6:38:26.932160 INFO: AUC difference: 3.81%
6:38:27.327513 INFO: Resetting torch num_threads to 100
6:38:27.334471 PROGRESS: === Extracted 17789 precursors and 101661 fragments ===
6:38:27.335625 INFO: === FDR correction performed with classifier version 6 ===
6:38:27.337099 PROGRESS: ============================= Precursor FDR =============================
6:38:27.337293 PROGRESS: Total precursors accumulated: 2,484
6:38:27.337359 PROGRESS: Target precursors: 2,460 (99.03%)
6:38:27.337415 PROGRESS: Decoy precursors: 24 (0.97%)
6:38:27.337467 PROGRESS: 
6:38:27.337522 PROGRESS: Precursor Summary:
6:38:27.339782 PROGRESS: Channel   0:	 0.050 FDR: 2,460; 0.010 FDR: 2,460; 0.001 FDR: 1,334
6:38:27.339966 PROGRESS: 
6:38:27.340023 PROGRESS: Protein Summary:
6:38:27.342908 PROGRESS: Channel   0:	 0.050 FDR: 1,945; 0.010 FDR: 1,945; 0.001 FDR: 1,125
6:38:27.343160 PROGRESS: =========================================================================
6:38:27.344884 INFO: Target number of precursors reached.
6:38:27.378307 INFO: fragments_df: keeping 5000 of 101661 [sum(precursor_idx_mask)=48354 sum(mass_error_mask)=101661 stop_rank=5000
6:38:27.414926 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:38:27.980585 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:38:28.958440 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:38:28.961159 INFO: Using score_cutoff 9.543298725700378 (fac=0.99, q=1)
6:38:28.962006 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:38:28.962129 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:38:28.962200 INFO: Updating optimization_manager: score_cutoff        : 9.609068803024291 -> 9.543298725700378
6:38:28.962284 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:38:28.969043 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:38:28.981203 INFO: === checking if optimization conditions were reached ===
6:38:28.982414 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
6:38:28.990178 INFO: Updating optimization_manager: rt_error            : 216.63979289557676 -> 161.27424301991306
6:38:28.991209 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 161.2742.
6:38:28.991319 INFO: ==============================================
6:38:28.991464 INFO: Starting optimization step 7.
6:38:28.991597 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:38:28.991842 INFO: Using rust extraction backend
6:38:28.991996 PROGRESS: Extracting batch of 5943 precursors
6:38:29.022689 INFO: === Search parameters used ===
6:38:29.023473 INFO: rt_error       : 161.27424301991306
6:38:29.023538 INFO: mobility_error : 0.1
6:38:29.023623 INFO: num_candidates : 3
6:38:29.023669 INFO: ms1_error      : 3
6:38:29.023714 INFO: ms2_error      : 10.0
6:38:29.023756 INFO: fwhm_rt        : 3.0
6:38:29.023796 INFO: quant_window   : 3
6:38:29.023834 INFO: ==============================================
6:38:29.323069 INFO: performing precursor FDR with 40 features
6:38:29.323868 INFO: Decoy channel: -1
6:38:29.323969 INFO: competitive: True
6:38:29.366978 INFO: Setting torch num_threads to 2 for FDR classification task
6:38:29.384798 INFO: Estimating optimal hyperparameters - samples: 14,225, batch_size: 128, learning_rate: 1.77e-04
6:38:29.385795 INFO: Using random state 448199 for train-test-split
6:38:31.333790 INFO: Test AUC: 0.765
6:38:31.334051 INFO: Train AUC: 0.774
6:38:31.334087 INFO: AUC difference: 1.21%
6:38:31.652799 INFO: Resetting torch num_threads to 100
6:38:31.659933 PROGRESS: === Extracted 17782 precursors and 99696 fragments ===
6:38:31.660750 INFO: === FDR correction performed with classifier version 6 ===
6:38:31.661733 PROGRESS: ============================= Precursor FDR =============================
6:38:31.661863 PROGRESS: Total precursors accumulated: 2,550
6:38:31.661926 PROGRESS: Target precursors: 2,525 (99.02%)
6:38:31.661978 PROGRESS: Decoy precursors: 25 (0.98%)
6:38:31.662023 PROGRESS: 
6:38:31.662065 PROGRESS: Precursor Summary:
6:38:31.664000 PROGRESS: Channel   0:	 0.050 FDR: 2,525; 0.010 FDR: 2,525; 0.001 FDR: 1,476
6:38:31.664135 PROGRESS: 
6:38:31.664188 PROGRESS: Protein Summary:
6:38:31.666705 PROGRESS: Channel   0:	 0.050 FDR: 2,000; 0.010 FDR: 2,000; 0.001 FDR: 1,225
6:38:31.666811 PROGRESS: =========================================================================
6:38:31.668045 INFO: Target number of precursors reached.
6:38:31.694762 INFO: fragments_df: keeping 5000 of 99696 [sum(precursor_idx_mask)=49019 sum(mass_error_mask)=99696 stop_rank=5000
6:38:31.715897 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:38:32.258647 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:38:33.137598 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:38:33.139101 INFO: Using score_cutoff 9.398951439285279 (fac=0.99, q=1)
6:38:33.139760 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:38:33.139853 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:38:33.139911 INFO: Updating optimization_manager: score_cutoff        : 9.543298725700378 -> 9.398951439285279
6:38:33.140002 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:38:33.146094 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:38:33.154594 INFO: === checking if optimization conditions were reached ===
6:38:33.155193 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
6:38:33.160518 INFO: Updating optimization_manager: rt_error            : 161.27424301991306 -> 126.39222343586576
6:38:33.161071 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 126.3922.
6:38:33.161177 INFO: ==============================================
6:38:33.161341 INFO: Starting optimization step 8.
6:38:33.161452 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:38:33.161606 INFO: Using rust extraction backend
6:38:33.161731 PROGRESS: Extracting batch of 5943 precursors
6:38:33.191897 INFO: === Search parameters used ===
6:38:33.192783 INFO: rt_error       : 126.39222343586576
6:38:33.192847 INFO: mobility_error : 0.1
6:38:33.192904 INFO: num_candidates : 3
6:38:33.192971 INFO: ms1_error      : 3
6:38:33.193016 INFO: ms2_error      : 10.0
6:38:33.193062 INFO: fwhm_rt        : 3.0
6:38:33.193107 INFO: quant_window   : 3
6:38:33.193151 INFO: ==============================================
6:38:33.459613 INFO: performing precursor FDR with 40 features
6:38:33.460033 INFO: Decoy channel: -1
6:38:33.460063 INFO: competitive: True
6:38:33.495971 INFO: Setting torch num_threads to 2 for FDR classification task
6:38:33.512001 INFO: Estimating optimal hyperparameters - samples: 14,218, batch_size: 128, learning_rate: 1.77e-04
6:38:33.512522 INFO: Using random state 448199 for train-test-split
6:38:35.212008 INFO: Test AUC: 0.758
6:38:35.212368 INFO: Train AUC: 0.777
6:38:35.212423 INFO: AUC difference: 2.43%
6:38:35.643134 INFO: Resetting torch num_threads to 100
6:38:35.652699 PROGRESS: === Extracted 17773 precursors and 97870 fragments ===
6:38:35.654641 INFO: === FDR correction performed with classifier version 6 ===
6:38:35.656669 PROGRESS: ============================= Precursor FDR =============================
6:38:35.656967 PROGRESS: Total precursors accumulated: 2,537
6:38:35.657052 PROGRESS: Target precursors: 2,512 (99.01%)
6:38:35.657119 PROGRESS: Decoy precursors: 25 (0.99%)
6:38:35.657169 PROGRESS: 
6:38:35.657223 PROGRESS: Precursor Summary:
6:38:35.660876 PROGRESS: Channel   0:	 0.050 FDR: 2,512; 0.010 FDR: 2,512; 0.001 FDR: 1,678
6:38:35.661312 PROGRESS: 
6:38:35.661371 PROGRESS: Protein Summary:
6:38:35.664435 PROGRESS: Channel   0:	 0.050 FDR: 1,989; 0.010 FDR: 1,989; 0.001 FDR: 1,385
6:38:35.664773 PROGRESS: =========================================================================
6:38:35.667112 INFO: Target number of precursors reached.
6:38:35.701706 INFO: fragments_df: keeping 5000 of 97870 [sum(precursor_idx_mask)=48214 sum(mass_error_mask)=97870 stop_rank=5000
6:38:35.749503 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:38:36.373516 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:38:37.363683 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:38:37.366298 INFO: Using score_cutoff 9.247856779289245 (fac=0.99, q=1)
6:38:37.367568 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:38:37.367694 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:38:37.367759 INFO: Updating optimization_manager: score_cutoff        : 9.398951439285279 -> 9.247856779289245
6:38:37.367867 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:38:37.376383 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:38:37.388973 INFO: === checking if optimization conditions were reached ===
6:38:37.390254 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
6:38:37.398105 INFO: Updating optimization_manager: rt_error            : 126.39222343586576 -> 101.23977712990458
6:38:37.398751 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 101.2398.
6:38:37.398903 INFO: ==============================================
6:38:37.399039 INFO: Starting optimization step 9.
6:38:37.399168 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:38:37.399345 INFO: Using rust extraction backend
6:38:37.399430 PROGRESS: Extracting batch of 5943 precursors
6:38:37.432011 INFO: === Search parameters used ===
6:38:37.433581 INFO: rt_error       : 101.23977712990458
6:38:37.433654 INFO: mobility_error : 0.1
6:38:37.433710 INFO: num_candidates : 3
6:38:37.433755 INFO: ms1_error      : 3
6:38:37.433799 INFO: ms2_error      : 10.0
6:38:37.433840 INFO: fwhm_rt        : 3.0
6:38:37.433882 INFO: quant_window   : 3
6:38:37.433924 INFO: ==============================================
6:38:37.684860 INFO: performing precursor FDR with 40 features
6:38:37.685542 INFO: Decoy channel: -1
6:38:37.685582 INFO: competitive: True
6:38:37.729833 INFO: Setting torch num_threads to 2 for FDR classification task
6:38:37.749031 INFO: Estimating optimal hyperparameters - samples: 14,213, batch_size: 128, learning_rate: 1.77e-04
6:38:37.750060 INFO: Using random state 448199 for train-test-split
6:38:39.690605 INFO: Test AUC: 0.759
6:38:39.690862 INFO: Train AUC: 0.780
6:38:39.690896 INFO: AUC difference: 2.73%
6:38:40.021955 INFO: Resetting torch num_threads to 100
6:38:40.027529 PROGRESS: === Extracted 17767 precursors and 96210 fragments ===
6:38:40.028344 INFO: === FDR correction performed with classifier version 6 ===
6:38:40.029376 PROGRESS: ============================= Precursor FDR =============================
6:38:40.029480 PROGRESS: Total precursors accumulated: 2,652
6:38:40.029542 PROGRESS: Target precursors: 2,626 (99.02%)
6:38:40.029615 PROGRESS: Decoy precursors: 26 (0.98%)
6:38:40.029664 PROGRESS: 
6:38:40.029719 PROGRESS: Precursor Summary:
6:38:40.031663 PROGRESS: Channel   0:	 0.050 FDR: 2,626; 0.010 FDR: 2,626; 0.001 FDR: 1,620
6:38:40.031775 PROGRESS: 
6:38:40.031833 PROGRESS: Protein Summary:
6:38:40.034476 PROGRESS: Channel   0:	 0.050 FDR: 2,068; 0.010 FDR: 2,068; 0.001 FDR: 1,331
6:38:40.034592 PROGRESS: =========================================================================
6:38:40.035861 INFO: Target number of precursors reached.
6:38:40.062739 INFO: fragments_df: keeping 5000 of 96210 [sum(precursor_idx_mask)=49622 sum(mass_error_mask)=96210 stop_rank=5000
6:38:40.087743 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:38:40.618042 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:38:41.442302 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:38:41.443045 INFO: Using score_cutoff 9.174189519882201 (fac=0.99, q=1)
6:38:41.443447 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:38:41.443533 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:38:41.443585 INFO: Updating optimization_manager: score_cutoff        : 9.247856779289245 -> 9.174189519882201
6:38:41.443640 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:38:41.448630 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:38:41.457387 INFO: === checking if optimization conditions were reached ===
6:38:41.457794 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
6:38:41.462037 INFO: Updating optimization_manager: rt_error            : 101.23977712990458 -> 81.84357063482602
6:38:41.462468 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 81.8436.
6:38:41.462569 INFO: ==============================================
6:38:41.462649 INFO: Starting optimization step 10.
6:38:41.462720 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:38:41.462806 INFO: Using rust extraction backend
6:38:41.462877 PROGRESS: Extracting batch of 5943 precursors
6:38:41.475639 INFO: === Search parameters used ===
6:38:41.476127 INFO: rt_error       : 81.84357063482602
6:38:41.476186 INFO: mobility_error : 0.1
6:38:41.476235 INFO: num_candidates : 3
6:38:41.476277 INFO: ms1_error      : 3
6:38:41.476323 INFO: ms2_error      : 10.0
6:38:41.476362 INFO: fwhm_rt        : 3.0
6:38:41.476405 INFO: quant_window   : 3
6:38:41.476446 INFO: ==============================================
6:38:41.629468 INFO: performing precursor FDR with 40 features
6:38:41.629624 INFO: Decoy channel: -1
6:38:41.629648 INFO: competitive: True
6:38:41.637698 INFO: Setting torch num_threads to 2 for FDR classification task
6:38:41.643166 INFO: Estimating optimal hyperparameters - samples: 14,195, batch_size: 128, learning_rate: 1.77e-04
6:38:41.643365 INFO: Using random state 448199 for train-test-split
6:38:44.001006 INFO: Test AUC: 0.772
6:38:44.001400 INFO: Train AUC: 0.785
6:38:44.001444 INFO: AUC difference: 1.66%
6:38:44.475746 INFO: Resetting torch num_threads to 100
6:38:44.485460 PROGRESS: === Extracted 17744 precursors and 94431 fragments ===
6:38:44.487594 INFO: === FDR correction performed with classifier version 6 ===
6:38:44.489882 PROGRESS: ============================= Precursor FDR =============================
6:38:44.490098 PROGRESS: Total precursors accumulated: 2,556
6:38:44.490177 PROGRESS: Target precursors: 2,531 (99.02%)
6:38:44.490307 PROGRESS: Decoy precursors: 25 (0.98%)
6:38:44.490365 PROGRESS: 
6:38:44.490412 PROGRESS: Precursor Summary:
6:38:44.493329 PROGRESS: Channel   0:	 0.050 FDR: 2,531; 0.010 FDR: 2,531; 0.001 FDR: 2,009
6:38:44.493529 PROGRESS: 
6:38:44.493625 PROGRESS: Protein Summary:
6:38:44.496891 PROGRESS: Channel   0:	 0.050 FDR: 1,997; 0.010 FDR: 1,997; 0.001 FDR: 1,614
6:38:44.497280 PROGRESS: =========================================================================
6:38:44.499830 INFO: Target number of precursors reached.
6:38:44.534053 INFO: fragments_df: keeping 5000 of 94431 [sum(precursor_idx_mask)=47585 sum(mass_error_mask)=94431 stop_rank=5000
6:38:44.582395 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:38:45.141155 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:38:45.963012 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:38:45.963717 INFO: Using score_cutoff 9.136566864967346 (fac=0.99, q=1)
6:38:45.964090 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:38:45.964170 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:38:45.964235 INFO: Updating optimization_manager: score_cutoff        : 9.174189519882201 -> 9.136566864967346
6:38:45.964290 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:38:45.968731 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:38:45.976338 INFO: === checking if optimization conditions were reached ===
6:38:45.976733 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
6:38:45.980479 INFO: Updating optimization_manager: rt_error            : 81.84357063482602 -> 77.80071444834988
6:38:45.980675 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 77.8007.
6:38:45.980743 INFO: ==============================================
6:38:45.980813 INFO: Starting optimization step 11.
6:38:45.980874 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:38:45.980947 INFO: Using rust extraction backend
6:38:45.981009 PROGRESS: Extracting batch of 5943 precursors
6:38:45.992222 INFO: === Search parameters used ===
6:38:45.992641 INFO: rt_error       : 77.80071444834988
6:38:45.992692 INFO: mobility_error : 0.1
6:38:45.992738 INFO: num_candidates : 3
6:38:45.992779 INFO: ms1_error      : 3
6:38:45.992818 INFO: ms2_error      : 10.0
6:38:45.992861 INFO: fwhm_rt        : 3.0
6:38:45.992901 INFO: quant_window   : 3
6:38:45.992941 INFO: ==============================================
6:38:46.276448 INFO: performing precursor FDR with 40 features
6:38:46.276825 INFO: Decoy channel: -1
6:38:46.276857 INFO: competitive: True
6:38:46.306670 INFO: Setting torch num_threads to 2 for FDR classification task
6:38:46.332098 INFO: Estimating optimal hyperparameters - samples: 14,190, batch_size: 128, learning_rate: 1.77e-04
6:38:46.332758 INFO: Using random state 448199 for train-test-split
6:38:48.836937 INFO: Test AUC: 0.772
6:38:48.837383 INFO: Train AUC: 0.787
6:38:48.837425 INFO: AUC difference: 1.87%
6:38:49.245884 INFO: Resetting torch num_threads to 100
6:38:49.255974 PROGRESS: === Extracted 17738 precursors and 93863 fragments ===
6:38:49.258101 INFO: === FDR correction performed with classifier version 6 ===
6:38:49.261540 PROGRESS: ============================= Precursor FDR =============================
6:38:49.261819 PROGRESS: Total precursors accumulated: 2,634
6:38:49.261950 PROGRESS: Target precursors: 2,608 (99.01%)
6:38:49.262012 PROGRESS: Decoy precursors: 26 (0.99%)
6:38:49.262065 PROGRESS: 
6:38:49.262114 PROGRESS: Precursor Summary:
6:38:49.266976 PROGRESS: Channel   0:	 0.050 FDR: 2,608; 0.010 FDR: 2,608; 0.001 FDR: 2,259
6:38:49.267453 PROGRESS: 
6:38:49.267522 PROGRESS: Protein Summary:
6:38:49.271067 PROGRESS: Channel   0:	 0.050 FDR: 2,054; 0.010 FDR: 2,054; 0.001 FDR: 1,799
6:38:49.271459 PROGRESS: =========================================================================
6:38:49.273364 INFO: Target number of precursors reached.
6:38:49.306429 INFO: fragments_df: keeping 5000 of 93863 [sum(precursor_idx_mask)=48664 sum(mass_error_mask)=93863 stop_rank=5000
6:38:49.344494 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:38:50.056394 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:38:50.952621 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:38:50.954021 INFO: Using score_cutoff 9.165590059947968 (fac=0.99, q=1)
6:38:50.954674 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:38:50.954796 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:38:50.954848 INFO: Updating optimization_manager: score_cutoff        : 9.136566864967346 -> 9.165590059947968
6:38:50.954933 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:38:50.961738 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:38:50.973225 INFO: === checking if optimization conditions were reached ===
6:38:50.973978 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 5 ===
6:38:50.976185 INFO: Updating optimization_manager: rt_error            : 77.80071444834988 -> 101.23977712990458
6:38:50.976500 INFO: Updating optimization_manager: classifier_version  : 6 -> 16
6:38:50.976598 INFO: Updating optimization_manager: score_cutoff        : 9.165590059947968 -> 9.174189519882201
6:38:50.976696 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:38:50.976782 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:38:50.976892 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 101.2398 found after 12 searches.
6:38:50.976970 INFO: ==============================================
6:38:50.977113 PROGRESS: Optimization finished for rt_error.
6:38:51.006493 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:38:51.013927 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:38:51.025185 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
6:38:51.025890 PROGRESS: ==============================================
6:38:51.026031 PROGRESS: ms2_error      : 10.0000
6:38:51.026099 PROGRESS: rt_error       : 101.2398
6:38:51.026147 PROGRESS: ==============================================
6:38:51.028121 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:38:51.231639 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:38:51.683504 INFO: Using rust extraction backend
6:38:51.684421 PROGRESS: Extracting batch of 289499 precursors
6:38:52.442072 INFO: === Search parameters used ===
6:38:52.442952 INFO: rt_error       : 101.23977712990458
6:38:52.443108 INFO: mobility_error : 0.1
6:38:52.443174 INFO: num_candidates : 3
6:38:52.443236 INFO: ms1_error      : 3
6:38:52.443280 INFO: ms2_error      : 10.0
6:38:52.443323 INFO: fwhm_rt        : 3.0
6:38:52.443362 INFO: quant_window   : 3
6:38:52.443401 INFO: ==============================================
6:38:54.171049 INFO: Removed 204680 precursors with score below cutoff 9.174189519882201
6:38:55.475682 INFO: performing precursor FDR with 40 features
6:38:55.476066 INFO: Decoy channel: -1
6:38:55.476098 INFO: competitive: True
6:38:55.725157 INFO: Setting torch num_threads to 2 for FDR classification task
6:38:55.869981 WARNING: FDR calculation for 369680 target and 293608 decoy PSMs
6:38:55.870512 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
6:38:56.770310 INFO: Estimating optimal hyperparameters - samples: 530,630, batch_size: 2,173, learning_rate: 7.28e-04
6:38:56.773335 INFO: Using random state 951619 for train-test-split
6:39:24.636883 INFO: Test AUC: 0.807
6:39:24.637344 INFO: Train AUC: 0.811
6:39:24.637404 INFO: AUC difference: 0.48%
6:39:25.385663 INFO: Resetting torch num_threads to 100
6:39:26.811793 PROGRESS: ============================= Precursor FDR =============================
6:39:26.812906 PROGRESS: Total precursors accumulated: 134,810
6:39:26.812998 PROGRESS: Target precursors: 133,476 (99.01%)
6:39:26.813074 PROGRESS: Decoy precursors: 1,334 (0.99%)
6:39:26.813128 PROGRESS: 
6:39:26.813180 PROGRESS: Precursor Summary:
6:39:26.982450 PROGRESS: Channel   0:	 0.050 FDR: 133,476; 0.010 FDR: 133,476; 0.001 FDR: 120,182
6:39:26.983665 PROGRESS: 
6:39:26.983739 PROGRESS: Protein Summary:
6:39:27.328103 PROGRESS: Channel   0:	 0.050 FDR: 10,653; 0.010 FDR: 10,653; 0.001 FDR: 10,578
6:39:27.328970 PROGRESS: =========================================================================
6:39:27.348490 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/psm.parquet
6:39:28.035377 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.parquet
6:39:28.822472 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
6:39:29.228758 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 
6:39:29.229311 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant
6:39:29.229603 INFO: Creating folder /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/figures
6:39:29.230115 INFO: Initializing TimingManager
6:39:29.232249 INFO: Initializing RawFileManager
6:40:03.843532 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.
6:40:03.860410 INFO: Determining DIA cycle
6:40:03.878468 INFO: Found cycle with start 0.00 min and length 300.
6:40:04.649966 INFO: RT (min)            : 0.0 - 26.9
6:40:04.650231 INFO: RT duration (sec)   : 1611.2
6:40:04.650263 INFO: RT duration (min)   : 26.9
6:40:04.650292 INFO: Cycle len (scans)   : 300
6:40:04.650315 INFO: Cycle len (sec)     : 1.65
6:40:04.650337 INFO: Number of cycles    : 978
6:40:04.650362 INFO: MS2 range (m/z)     : 380.4 - 980.7
6:40:04.650408 INFO: Creating DIA data object took: 35.417872190475464
6:40:06.721161 INFO: Creating DIA data NG object took: 2.0703582763671875
6:40:06.853100 INFO: Initializing CalibrationManager
6:40:06.853842 INFO: Setting up calibration estimators ..
6:40:06.853916 INFO: Found 1 estimator(s) in calibration group 'fragment'
6:40:06.854035 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'}' ..
6:40:06.854128 INFO: Found 3 estimator(s) in calibration group 'precursor'
6:40:06.854192 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
6:40:06.854262 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}}' ..
6:40:06.854320 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
6:40:06.854367 INFO: Done setting up calibration estimators.
6:40:06.854947 INFO: Initializing OptimizationManager
6:40:06.855210 INFO: initial parameter: ms1_error = 3
6:40:06.855278 INFO: initial parameter: ms2_error = 10
6:40:06.855338 INFO: initial parameter: rt_error = 805.611083984375
6:40:06.855386 INFO: initial parameter: mobility_error = 0.1
6:40:06.855428 INFO: initial parameter: num_candidates = 1
6:40:06.855469 INFO: initial parameter: fwhm_rt = 5
6:40:06.855511 INFO: initial parameter: fwhm_mobility = 0.01
6:40:06.855556 INFO: initial parameter: score_cutoff = 0
6:40:06.855598 INFO: initial parameter: classifier_version = -1
6:40:06.855696 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
6:40:06.856292 INFO: FDRManager: loading saved state not requested, will be initialized.
6:40:06.856352 INFO: Initializing FDRManager
6:40:06.856408 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
6:40:06.984863 PROGRESS: Initializing spectral library: 146,300 target precursors potentially observable (0 removed)
6:40:07.069612 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
6:40:07.070734 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
6:40:07.070865 PROGRESS: Starting initial search for precursors.
6:40:07.070985 INFO: Starting optimization step 0.
6:40:07.071063 PROGRESS: === Extracting elution groups 0 to 1000 ===
6:40:07.071134 INFO: Using rust extraction backend
6:40:07.071231 PROGRESS: Extracting batch of 1979 precursors
6:40:07.080750 INFO: === Search parameters used ===
6:40:07.081474 INFO: rt_error       : 805.611083984375
6:40:07.081542 INFO: mobility_error : 0.1
6:40:07.081597 INFO: num_candidates : 1
6:40:07.081640 INFO: ms1_error      : 3
6:40:07.081681 INFO: ms2_error      : 10
6:40:07.081750 INFO: fwhm_rt        : 5
6:40:07.081795 INFO: quant_window   : 3
6:40:07.081834 INFO: ==============================================
6:40:07.152934 INFO: performing precursor FDR with 40 features
6:40:07.153260 INFO: Decoy channel: -1
6:40:07.153287 INFO: competitive: True
6:40:07.156333 INFO: Setting torch num_threads to 2 for FDR classification task
6:40:07.160427 INFO: Estimating optimal hyperparameters - samples: 1,582, batch_size: 128, learning_rate: 1.77e-04
6:40:07.162703 INFO: Using random state 83534 for train-test-split
6:40:07.400081 INFO: Test AUC: 0.849
6:40:07.400364 INFO: Train AUC: 0.859
6:40:07.400396 INFO: AUC difference: 1.20%
6:40:07.687366 INFO: Resetting torch num_threads to 100
6:40:07.692054 PROGRESS: === Extracted 1978 precursors and 13193 fragments ===
6:40:07.693003 INFO: === FDR correction performed with classifier version -1 ===
6:40:07.694454 PROGRESS: ============================= Precursor FDR =============================
6:40:07.694740 PROGRESS: Total precursors accumulated: 439
6:40:07.694831 PROGRESS: Target precursors: 435 (99.09%)
6:40:07.694886 PROGRESS: Decoy precursors: 4 (0.91%)
6:40:07.694937 PROGRESS: 
6:40:07.694987 PROGRESS: Precursor Summary:
6:40:07.696812 PROGRESS: Channel   0:	 0.050 FDR:   435; 0.010 FDR:   435; 0.001 FDR:   293
6:40:07.697032 PROGRESS: 
6:40:07.697093 PROGRESS: Protein Summary:
6:40:07.699273 PROGRESS: Channel   0:	 0.050 FDR:   411; 0.010 FDR:   411; 0.001 FDR:   278
6:40:07.699455 PROGRESS: =========================================================================
6:40:07.700198 INFO: Target number of precursors not reached yet.
6:40:07.715510 INFO: Starting optimization step 1.
6:40:07.716044 PROGRESS: === Extracting elution groups 1000 to 3000 ===
6:40:07.716177 INFO: Using rust extraction backend
6:40:07.716259 PROGRESS: Extracting batch of 3964 precursors
6:40:07.727063 INFO: === Search parameters used ===
6:40:07.727733 INFO: rt_error       : 805.611083984375
6:40:07.727791 INFO: mobility_error : 0.1
6:40:07.727843 INFO: num_candidates : 1
6:40:07.727893 INFO: ms1_error      : 3
6:40:07.727935 INFO: ms2_error      : 10
6:40:07.727979 INFO: fwhm_rt        : 5
6:40:07.728020 INFO: quant_window   : 3
6:40:07.728063 INFO: ==============================================
6:40:07.815580 INFO: performing precursor FDR with 40 features
6:40:07.815815 INFO: Decoy channel: -1
6:40:07.815845 INFO: competitive: True
6:40:07.825341 INFO: Setting torch num_threads to 2 for FDR classification task
6:40:07.829817 INFO: Estimating optimal hyperparameters - samples: 4,752, batch_size: 128, learning_rate: 1.77e-04
6:40:07.830084 INFO: Using random state 790408 for train-test-split
6:40:08.461331 INFO: Test AUC: 0.889
6:40:08.461589 INFO: Train AUC: 0.872
6:40:08.461624 INFO: AUC difference: 1.98%
6:40:08.748556 INFO: Resetting torch num_threads to 100
6:40:08.754628 PROGRESS: === Extracted 5941 precursors and 40032 fragments ===
6:40:08.755404 INFO: === FDR correction performed with classifier version -1 ===
6:40:08.756247 PROGRESS: ============================= Precursor FDR =============================
6:40:08.756348 PROGRESS: Total precursors accumulated: 1,874
6:40:08.756412 PROGRESS: Target precursors: 1,856 (99.04%)
6:40:08.756487 PROGRESS: Decoy precursors: 18 (0.96%)
6:40:08.756535 PROGRESS: 
6:40:08.756578 PROGRESS: Precursor Summary:
6:40:08.758202 PROGRESS: Channel   0:	 0.050 FDR: 1,856; 0.010 FDR: 1,856; 0.001 FDR: 1,358
6:40:08.758296 PROGRESS: 
6:40:08.758368 PROGRESS: Protein Summary:
6:40:08.760479 PROGRESS: Channel   0:	 0.050 FDR: 1,509; 0.010 FDR: 1,509; 0.001 FDR: 1,144
6:40:08.760583 PROGRESS: =========================================================================
6:40:08.761319 INFO: Target number of precursors reached.
6:40:08.772436 INFO: fragments_df: keeping 5000 of 40032 [sum(precursor_idx_mask)=16525 sum(mass_error_mask)=40032 stop_rank=5000
6:40:08.790933 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:40:09.115888 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:40:10.026574 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
6:40:10.027700 INFO: Using score_cutoff 10.130203635692597 (fac=0.99, q=1)
6:40:10.028269 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
6:40:10.028361 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
6:40:10.028420 INFO: Updating optimization_manager: score_cutoff        : 0 -> 10.130203635692597
6:40:10.028501 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:40:10.035455 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:40:10.047508 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
6:40:10.048463 PROGRESS: Required number of precursors found. Starting search parameter optimization.
6:40:10.048687 INFO: Starting optimization step 2.
6:40:10.048838 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:40:10.049007 INFO: Using rust extraction backend
6:40:10.049127 PROGRESS: Extracting batch of 5943 precursors
6:40:10.076291 INFO: === Search parameters used ===
6:40:10.076985 INFO: rt_error       : 805.611083984375
6:40:10.077043 INFO: mobility_error : 0.1
6:40:10.077092 INFO: num_candidates : 3
6:40:10.077136 INFO: ms1_error      : 3
6:40:10.077178 INFO: ms2_error      : 10
6:40:10.077219 INFO: fwhm_rt        : 3.0
6:40:10.077261 INFO: quant_window   : 3
6:40:10.077303 INFO: ==============================================
6:40:10.360064 INFO: performing precursor FDR with 40 features
6:40:10.360376 INFO: Decoy channel: -1
6:40:10.360402 INFO: competitive: True
6:40:10.383389 INFO: Setting torch num_threads to 2 for FDR classification task
6:40:10.400135 INFO: Estimating optimal hyperparameters - samples: 14,253, batch_size: 128, learning_rate: 1.77e-04
6:40:10.400667 INFO: Using random state 259421 for train-test-split
6:40:11.540122 INFO: Test AUC: 0.703
6:40:11.540334 INFO: Train AUC: 0.712
6:40:11.540365 INFO: AUC difference: 1.25%
6:40:11.847321 INFO: Resetting torch num_threads to 100
6:40:11.851953 PROGRESS: === Extracted 17817 precursors and 104854 fragments ===
6:40:11.852645 INFO: === FDR correction performed with classifier version 1 ===
6:40:11.853618 PROGRESS: ============================= Precursor FDR =============================
6:40:11.853720 PROGRESS: Total precursors accumulated: 2,282
6:40:11.853782 PROGRESS: Target precursors: 2,260 (99.04%)
6:40:11.853831 PROGRESS: Decoy precursors: 22 (0.96%)
6:40:11.853874 PROGRESS: 
6:40:11.853918 PROGRESS: Precursor Summary:
6:40:11.855675 PROGRESS: Channel   0:	 0.050 FDR: 2,260; 0.010 FDR: 2,260; 0.001 FDR: 1,740
6:40:11.855777 PROGRESS: 
6:40:11.855845 PROGRESS: Protein Summary:
6:40:11.858109 PROGRESS: Channel   0:	 0.050 FDR: 1,797; 0.010 FDR: 1,797; 0.001 FDR: 1,431
6:40:11.858206 PROGRESS: =========================================================================
6:40:11.859383 INFO: Target number of precursors reached.
6:40:11.885617 INFO: fragments_df: keeping 5000 of 104854 [sum(precursor_idx_mask)=45723 sum(mass_error_mask)=104854 stop_rank=5000
6:40:11.904389 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:40:12.398611 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:40:13.268142 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:40:13.269681 INFO: Using score_cutoff 9.962627062225343 (fac=0.99, q=1)
6:40:13.270249 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:40:13.270344 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:40:13.270404 INFO: Updating optimization_manager: score_cutoff        : 10.130203635692597 -> 9.962627062225343
6:40:13.270469 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:40:13.278161 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:40:13.291280 INFO: === checking if optimization conditions were reached ===
6:40:13.301911 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
6:40:13.302401 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
6:40:13.302498 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:40:13.302576 INFO: ==============================================
6:40:13.302714 INFO: Starting optimization step 3.
6:40:13.302808 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:40:13.302921 INFO: Using rust extraction backend
6:40:13.303030 PROGRESS: Extracting batch of 5943 precursors
6:40:13.335198 INFO: === Search parameters used ===
6:40:13.336907 INFO: rt_error       : 805.611083984375
6:40:13.336998 INFO: mobility_error : 0.1
6:40:13.337052 INFO: num_candidates : 3
6:40:13.337108 INFO: ms1_error      : 3
6:40:13.337160 INFO: ms2_error      : 10.0
6:40:13.337215 INFO: fwhm_rt        : 3.0
6:40:13.337257 INFO: quant_window   : 3
6:40:13.337311 INFO: ==============================================
6:40:13.543564 INFO: performing precursor FDR with 40 features
6:40:13.543844 INFO: Decoy channel: -1
6:40:13.543873 INFO: competitive: True
6:40:13.553971 INFO: Setting torch num_threads to 2 for FDR classification task
6:40:13.562415 INFO: Estimating optimal hyperparameters - samples: 14,252, batch_size: 128, learning_rate: 1.77e-04
6:40:13.562791 INFO: Using random state 450907 for train-test-split
6:40:15.877667 INFO: Test AUC: 0.710
6:40:15.878028 INFO: Train AUC: 0.731
6:40:15.878063 INFO: AUC difference: 2.85%
6:40:16.359876 INFO: Resetting torch num_threads to 100
6:40:16.373253 PROGRESS: === Extracted 17816 precursors and 104773 fragments ===
6:40:16.374745 INFO: === FDR correction performed with classifier version 2 ===
6:40:16.377211 PROGRESS: ============================= Precursor FDR =============================
6:40:16.377446 PROGRESS: Total precursors accumulated: 2,488
6:40:16.377524 PROGRESS: Target precursors: 2,464 (99.04%)
6:40:16.377574 PROGRESS: Decoy precursors: 24 (0.96%)
6:40:16.377620 PROGRESS: 
6:40:16.377666 PROGRESS: Precursor Summary:
6:40:16.381034 PROGRESS: Channel   0:	 0.050 FDR: 2,464; 0.010 FDR: 2,464; 0.001 FDR: 1,903
6:40:16.381404 PROGRESS: 
6:40:16.381470 PROGRESS: Protein Summary:
6:40:16.384738 PROGRESS: Channel   0:	 0.050 FDR: 1,955; 0.010 FDR: 1,955; 0.001 FDR: 1,549
6:40:16.385118 PROGRESS: =========================================================================
6:40:16.387172 INFO: Target number of precursors reached.
6:40:16.422498 INFO: fragments_df: keeping 5000 of 104773 [sum(precursor_idx_mask)=49126 sum(mass_error_mask)=104773 stop_rank=5000
6:40:16.477177 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:40:17.049602 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:40:17.946961 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:40:17.948353 INFO: Using score_cutoff 9.48147770204544 (fac=0.99, q=1)
6:40:17.948997 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:40:17.949090 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:40:17.949145 INFO: Updating optimization_manager: score_cutoff        : 9.962627062225343 -> 9.48147770204544
6:40:17.949226 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:40:17.956153 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:40:17.967787 INFO: === checking if optimization conditions were reached ===
6:40:17.972583 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:40:17.973273 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
6:40:17.973362 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:40:17.973485 INFO: ==============================================
6:40:17.973600 INFO: Starting optimization step 4.
6:40:17.973697 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:40:17.973798 INFO: Using rust extraction backend
6:40:17.973891 PROGRESS: Extracting batch of 5943 precursors
6:40:17.997008 INFO: === Search parameters used ===
6:40:17.997878 INFO: rt_error       : 805.611083984375
6:40:17.997932 INFO: mobility_error : 0.1
6:40:17.997991 INFO: num_candidates : 3
6:40:17.998036 INFO: ms1_error      : 3
6:40:17.998078 INFO: ms2_error      : 10.0
6:40:17.998118 INFO: fwhm_rt        : 3.0
6:40:17.998157 INFO: quant_window   : 3
6:40:17.998195 INFO: ==============================================
6:40:18.257601 INFO: performing precursor FDR with 40 features
6:40:18.257918 INFO: Decoy channel: -1
6:40:18.257956 INFO: competitive: True
6:40:18.279328 INFO: Setting torch num_threads to 2 for FDR classification task
6:40:18.290379 INFO: Estimating optimal hyperparameters - samples: 14,252, batch_size: 128, learning_rate: 1.77e-04
6:40:18.290714 INFO: Using random state 967536 for train-test-split
6:40:19.456567 INFO: Test AUC: 0.712
6:40:19.456847 INFO: Train AUC: 0.744
6:40:19.456880 INFO: AUC difference: 4.32%
6:40:19.772921 INFO: Resetting torch num_threads to 100
6:40:19.776538 PROGRESS: === Extracted 17816 precursors and 104773 fragments ===
6:40:19.777000 INFO: === FDR correction performed with classifier version 3 ===
6:40:19.777754 PROGRESS: ============================= Precursor FDR =============================
6:40:19.777857 PROGRESS: Total precursors accumulated: 2,557
6:40:19.777921 PROGRESS: Target precursors: 2,532 (99.02%)
6:40:19.777973 PROGRESS: Decoy precursors: 25 (0.98%)
6:40:19.778026 PROGRESS: 
6:40:19.778078 PROGRESS: Precursor Summary:
6:40:19.779836 PROGRESS: Channel   0:	 0.050 FDR: 2,532; 0.010 FDR: 2,532; 0.001 FDR: 1,872
6:40:19.779955 PROGRESS: 
6:40:19.780012 PROGRESS: Protein Summary:
6:40:19.782552 PROGRESS: Channel   0:	 0.050 FDR: 2,000; 0.010 FDR: 2,000; 0.001 FDR: 1,522
6:40:19.782665 PROGRESS: =========================================================================
6:40:19.783620 INFO: Target number of precursors reached.
6:40:19.810766 INFO: fragments_df: keeping 5000 of 104773 [sum(precursor_idx_mask)=49964 sum(mass_error_mask)=104773 stop_rank=5000
6:40:19.832866 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:40:20.312987 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:40:21.143725 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:40:21.144323 INFO: Using score_cutoff 9.134658961200714 (fac=0.99, q=1)
6:40:21.144662 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:40:21.144738 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:40:21.144791 INFO: Updating optimization_manager: score_cutoff        : 9.48147770204544 -> 9.134658961200714
6:40:21.144844 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:40:21.148990 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:40:21.155570 INFO: === checking if optimization conditions were reached ===
6:40:21.157245 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:40:21.157344 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
6:40:21.157418 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:40:21.157476 INFO: ==============================================
6:40:21.157545 INFO: Starting optimization step 5.
6:40:21.157602 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:40:21.157665 INFO: Using rust extraction backend
6:40:21.157718 PROGRESS: Extracting batch of 5943 precursors
6:40:21.167553 INFO: === Search parameters used ===
6:40:21.167686 INFO: rt_error       : 805.611083984375
6:40:21.167746 INFO: mobility_error : 0.1
6:40:21.167790 INFO: num_candidates : 3
6:40:21.167831 INFO: ms1_error      : 3
6:40:21.167872 INFO: ms2_error      : 10.0
6:40:21.167911 INFO: fwhm_rt        : 3.0
6:40:21.167950 INFO: quant_window   : 3
6:40:21.167987 INFO: ==============================================
6:40:21.313094 INFO: performing precursor FDR with 40 features
6:40:21.313253 INFO: Decoy channel: -1
6:40:21.313277 INFO: competitive: True
6:40:21.321063 INFO: Setting torch num_threads to 2 for FDR classification task
6:40:21.325419 INFO: Estimating optimal hyperparameters - samples: 14,253, batch_size: 128, learning_rate: 1.77e-04
6:40:21.325574 INFO: Using random state 174986 for train-test-split
6:40:22.493034 INFO: Test AUC: 0.742
6:40:22.493308 INFO: Train AUC: 0.751
6:40:22.493345 INFO: AUC difference: 1.25%
6:40:22.826224 INFO: Resetting torch num_threads to 100
6:40:22.831990 PROGRESS: === Extracted 17817 precursors and 104781 fragments ===
6:40:22.832840 INFO: === FDR correction performed with classifier version 4 ===
6:40:22.834966 PROGRESS: ============================= Precursor FDR =============================
6:40:22.835240 PROGRESS: Total precursors accumulated: 2,594
6:40:22.835345 PROGRESS: Target precursors: 2,569 (99.04%)
6:40:22.835402 PROGRESS: Decoy precursors: 25 (0.96%)
6:40:22.835465 PROGRESS: 
6:40:22.835518 PROGRESS: Precursor Summary:
6:40:22.839664 PROGRESS: Channel   0:	 0.050 FDR: 2,569; 0.010 FDR: 2,569; 0.001 FDR: 1,817
6:40:22.840051 PROGRESS: 
6:40:22.840137 PROGRESS: Protein Summary:
6:40:22.844640 PROGRESS: Channel   0:	 0.050 FDR: 2,028; 0.010 FDR: 2,028; 0.001 FDR: 1,484
6:40:22.845055 PROGRESS: =========================================================================
6:40:22.846201 INFO: Target number of precursors reached.
6:40:22.874781 INFO: fragments_df: keeping 5000 of 104781 [sum(precursor_idx_mask)=50794 sum(mass_error_mask)=104781 stop_rank=5000
6:40:22.894602 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:40:23.399783 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:40:24.312390 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:40:24.313551 INFO: Using score_cutoff 9.224266539001466 (fac=0.99, q=1)
6:40:24.314105 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:40:24.314203 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:40:24.314269 INFO: Updating optimization_manager: score_cutoff        : 9.134658961200714 -> 9.224266539001466
6:40:24.314337 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:40:24.319883 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:40:24.327689 INFO: === checking if optimization conditions were reached ===
6:40:24.330356 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:40:24.330552 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
6:40:24.330638 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
6:40:24.330717 INFO: ==============================================
6:40:24.330798 INFO: Starting optimization step 6.
6:40:24.330865 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:40:24.330953 INFO: Using rust extraction backend
6:40:24.331037 PROGRESS: Extracting batch of 5943 precursors
6:40:24.346550 INFO: === Search parameters used ===
6:40:24.347353 INFO: rt_error       : 805.611083984375
6:40:24.347437 INFO: mobility_error : 0.1
6:40:24.347489 INFO: num_candidates : 3
6:40:24.347533 INFO: ms1_error      : 3
6:40:24.347583 INFO: ms2_error      : 10.0
6:40:24.347627 INFO: fwhm_rt        : 3.0
6:40:24.347669 INFO: quant_window   : 3
6:40:24.347711 INFO: ==============================================
6:40:24.676436 INFO: performing precursor FDR with 40 features
6:40:24.676808 INFO: Decoy channel: -1
6:40:24.676849 INFO: competitive: True
6:40:24.713575 INFO: Setting torch num_threads to 2 for FDR classification task
6:40:24.729954 INFO: Estimating optimal hyperparameters - samples: 14,253, batch_size: 128, learning_rate: 1.77e-04
6:40:24.730609 INFO: Using random state 480990 for train-test-split
6:40:27.136181 INFO: Test AUC: 0.755
6:40:27.136606 INFO: Train AUC: 0.758
6:40:27.136641 INFO: AUC difference: 0.43%
6:40:27.568561 INFO: Resetting torch num_threads to 100
6:40:27.578205 PROGRESS: === Extracted 17817 precursors and 104786 fragments ===
6:40:27.579895 INFO: === FDR correction performed with classifier version 5 ===
6:40:27.581925 PROGRESS: ============================= Precursor FDR =============================
6:40:27.582138 PROGRESS: Total precursors accumulated: 2,593
6:40:27.582211 PROGRESS: Target precursors: 2,568 (99.04%)
6:40:27.582301 PROGRESS: Decoy precursors: 25 (0.96%)
6:40:27.582362 PROGRESS: 
6:40:27.582408 PROGRESS: Precursor Summary:
6:40:27.584898 PROGRESS: Channel   0:	 0.050 FDR: 2,568; 0.010 FDR: 2,568; 0.001 FDR: 1,938
6:40:27.585121 PROGRESS: 
6:40:27.585182 PROGRESS: Protein Summary:
6:40:27.588590 PROGRESS: Channel   0:	 0.050 FDR: 2,027; 0.010 FDR: 2,027; 0.001 FDR: 1,569
6:40:27.588765 PROGRESS: =========================================================================
6:40:27.590682 INFO: Target number of precursors reached.
6:40:27.626284 INFO: fragments_df: keeping 5000 of 104786 [sum(precursor_idx_mask)=50690 sum(mass_error_mask)=104786 stop_rank=5000
6:40:27.660230 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:40:28.272903 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:40:29.330193 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:40:29.332699 INFO: Using score_cutoff 9.170040176868438 (fac=0.99, q=1)
6:40:29.333834 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:40:29.333985 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:40:29.334055 INFO: Updating optimization_manager: score_cutoff        : 9.224266539001466 -> 9.170040176868438
6:40:29.334183 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:40:29.343976 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:40:29.357136 INFO: === checking if optimization conditions were reached ===
6:40:29.364306 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
6:40:29.365091 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
6:40:29.365193 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
6:40:29.365280 INFO: ==============================================
6:40:29.365387 PROGRESS: Optimization finished for ms2_error.
6:40:29.404789 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:40:29.417005 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:40:29.433387 INFO: Starting optimization step 0.
6:40:29.434767 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:40:29.434942 INFO: Using rust extraction backend
6:40:29.435061 PROGRESS: Extracting batch of 5943 precursors
6:40:29.475747 INFO: === Search parameters used ===
6:40:29.476789 INFO: rt_error       : 805.611083984375
6:40:29.476857 INFO: mobility_error : 0.1
6:40:29.476965 INFO: num_candidates : 3
6:40:29.477013 INFO: ms1_error      : 3
6:40:29.477055 INFO: ms2_error      : 10.0
6:40:29.477100 INFO: fwhm_rt        : 3.0
6:40:29.477143 INFO: quant_window   : 3
6:40:29.477184 INFO: ==============================================
6:40:29.840241 INFO: performing precursor FDR with 40 features
6:40:29.840650 INFO: Decoy channel: -1
6:40:29.840679 INFO: competitive: True
6:40:29.879242 INFO: Setting torch num_threads to 2 for FDR classification task
6:40:29.897931 INFO: Estimating optimal hyperparameters - samples: 14,253, batch_size: 128, learning_rate: 1.77e-04
6:40:29.898484 INFO: Using random state 850006 for train-test-split
6:40:32.134883 INFO: Test AUC: 0.761
6:40:32.135304 INFO: Train AUC: 0.765
6:40:32.135363 INFO: AUC difference: 0.53%
6:40:32.598499 INFO: Resetting torch num_threads to 100
6:40:32.610721 PROGRESS: === Extracted 17817 precursors and 104800 fragments ===
6:40:32.612041 INFO: === FDR correction performed with classifier version 6 ===
6:40:32.615329 PROGRESS: ============================= Precursor FDR =============================
6:40:32.615724 PROGRESS: Total precursors accumulated: 2,630
6:40:32.615805 PROGRESS: Target precursors: 2,604 (99.01%)
6:40:32.615860 PROGRESS: Decoy precursors: 26 (0.99%)
6:40:32.615909 PROGRESS: 
6:40:32.615955 PROGRESS: Precursor Summary:
6:40:32.619155 PROGRESS: Channel   0:	 0.050 FDR: 2,604; 0.010 FDR: 2,604; 0.001 FDR: 1,843
6:40:32.619359 PROGRESS: 
6:40:32.619422 PROGRESS: Protein Summary:
6:40:32.623093 PROGRESS: Channel   0:	 0.050 FDR: 2,058; 0.010 FDR: 2,058; 0.001 FDR: 1,500
6:40:32.623455 PROGRESS: =========================================================================
6:40:32.625929 INFO: Target number of precursors reached.
6:40:32.664623 INFO: fragments_df: keeping 5000 of 104800 [sum(precursor_idx_mask)=51387 sum(mass_error_mask)=104800 stop_rank=5000
6:40:32.705321 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:40:33.384665 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:40:34.390932 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:40:34.393705 INFO: Using score_cutoff 9.152026409626007 (fac=0.99, q=1)
6:40:34.394433 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:40:34.394538 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:40:34.394631 INFO: Updating optimization_manager: score_cutoff        : 9.170040176868438 -> 9.152026409626007
6:40:34.394737 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:40:34.405092 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:40:34.418109 INFO: === checking if optimization conditions were reached ===
6:40:34.419680 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
6:40:34.426721 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 254.1155111554907
6:40:34.427511 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 254.1155.
6:40:34.427614 INFO: ==============================================
6:40:34.427714 INFO: Starting optimization step 1.
6:40:34.427790 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:40:34.427950 INFO: Using rust extraction backend
6:40:34.428023 PROGRESS: Extracting batch of 5943 precursors
6:40:34.459700 INFO: === Search parameters used ===
6:40:34.460875 INFO: rt_error       : 254.1155111554907
6:40:34.460938 INFO: mobility_error : 0.1
6:40:34.460992 INFO: num_candidates : 3
6:40:34.461038 INFO: ms1_error      : 3
6:40:34.461091 INFO: ms2_error      : 10.0
6:40:34.461144 INFO: fwhm_rt        : 3.0
6:40:34.461195 INFO: quant_window   : 3
6:40:34.461319 INFO: ==============================================
6:40:34.790180 INFO: performing precursor FDR with 40 features
6:40:34.790556 INFO: Decoy channel: -1
6:40:34.790584 INFO: competitive: True
6:40:34.820729 INFO: Setting torch num_threads to 2 for FDR classification task
6:40:34.834329 INFO: Estimating optimal hyperparameters - samples: 14,240, batch_size: 128, learning_rate: 1.77e-04
6:40:34.834835 INFO: Using random state 850006 for train-test-split
6:40:37.391520 INFO: Test AUC: 0.756
6:40:37.391991 INFO: Train AUC: 0.772
6:40:37.392034 INFO: AUC difference: 2.07%
6:40:37.909770 INFO: Resetting torch num_threads to 100
6:40:37.918501 PROGRESS: === Extracted 17801 precursors and 102430 fragments ===
6:40:37.921358 INFO: === FDR correction performed with classifier version 6 ===
6:40:37.925557 PROGRESS: ============================= Precursor FDR =============================
6:40:37.925869 PROGRESS: Total precursors accumulated: 2,730
6:40:37.925950 PROGRESS: Target precursors: 2,703 (99.01%)
6:40:37.926008 PROGRESS: Decoy precursors: 27 (0.99%)
6:40:37.926058 PROGRESS: 
6:40:37.926106 PROGRESS: Precursor Summary:
6:40:37.929693 PROGRESS: Channel   0:	 0.050 FDR: 2,703; 0.010 FDR: 2,703; 0.001 FDR: 1,531
6:40:37.929898 PROGRESS: 
6:40:37.929965 PROGRESS: Protein Summary:
6:40:37.934964 PROGRESS: Channel   0:	 0.050 FDR: 2,124; 0.010 FDR: 2,124; 0.001 FDR: 1,264
6:40:37.935327 PROGRESS: =========================================================================
6:40:37.937467 INFO: Target number of precursors reached.
6:40:37.979808 INFO: fragments_df: keeping 5000 of 102430 [sum(precursor_idx_mask)=52280 sum(mass_error_mask)=102430 stop_rank=5000
6:40:38.026253 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:40:38.683213 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:40:39.647571 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:40:39.649185 INFO: Using score_cutoff 8.804236368370056 (fac=0.99, q=1)
6:40:39.650177 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:40:39.650326 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:40:39.650455 INFO: Updating optimization_manager: score_cutoff        : 9.152026409626007 -> 8.804236368370056
6:40:39.650563 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:40:39.659043 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:40:39.672814 INFO: === checking if optimization conditions were reached ===
6:40:39.674337 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
6:40:39.681933 INFO: Updating optimization_manager: rt_error            : 254.1155111554907 -> 211.17373385482836
6:40:39.683103 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 211.1737.
6:40:39.683239 INFO: ==============================================
6:40:39.683391 INFO: Starting optimization step 2.
6:40:39.683512 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:40:39.683730 INFO: Using rust extraction backend
6:40:39.683906 PROGRESS: Extracting batch of 5943 precursors
6:40:39.725469 INFO: === Search parameters used ===
6:40:39.726550 INFO: rt_error       : 211.17373385482836
6:40:39.726622 INFO: mobility_error : 0.1
6:40:39.726676 INFO: num_candidates : 3
6:40:39.726726 INFO: ms1_error      : 3
6:40:39.726800 INFO: ms2_error      : 10.0
6:40:39.726844 INFO: fwhm_rt        : 3.0
6:40:39.726919 INFO: quant_window   : 3
6:40:39.726963 INFO: ==============================================
6:40:40.048940 INFO: performing precursor FDR with 40 features
6:40:40.049311 INFO: Decoy channel: -1
6:40:40.049340 INFO: competitive: True
6:40:40.080990 INFO: Setting torch num_threads to 2 for FDR classification task
6:40:40.096287 INFO: Estimating optimal hyperparameters - samples: 14,235, batch_size: 128, learning_rate: 1.77e-04
6:40:40.096853 INFO: Using random state 850006 for train-test-split
6:40:42.548489 INFO: Test AUC: 0.751
6:40:42.548848 INFO: Train AUC: 0.774
6:40:42.548898 INFO: AUC difference: 2.87%
6:40:43.009107 INFO: Resetting torch num_threads to 100
6:40:43.016212 PROGRESS: === Extracted 17794 precursors and 101338 fragments ===
6:40:43.017357 INFO: === FDR correction performed with classifier version 6 ===
6:40:43.018908 PROGRESS: ============================= Precursor FDR =============================
6:40:43.019060 PROGRESS: Total precursors accumulated: 2,731
6:40:43.019128 PROGRESS: Target precursors: 2,704 (99.01%)
6:40:43.019203 PROGRESS: Decoy precursors: 27 (0.99%)
6:40:43.019255 PROGRESS: 
6:40:43.019301 PROGRESS: Precursor Summary:
6:40:43.021621 PROGRESS: Channel   0:	 0.050 FDR: 2,704; 0.010 FDR: 2,704; 0.001 FDR: 1,528
6:40:43.021770 PROGRESS: 
6:40:43.021833 PROGRESS: Protein Summary:
6:40:43.024784 PROGRESS: Channel   0:	 0.050 FDR: 2,131; 0.010 FDR: 2,131; 0.001 FDR: 1,266
6:40:43.024941 PROGRESS: =========================================================================
6:40:43.026507 INFO: Target number of precursors reached.
6:40:43.060990 INFO: fragments_df: keeping 5000 of 101338 [sum(precursor_idx_mask)=52160 sum(mass_error_mask)=101338 stop_rank=5000
6:40:43.092968 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:40:43.675255 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:40:44.683109 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:40:44.684579 INFO: Using score_cutoff 8.943333522891997 (fac=0.99, q=1)
6:40:44.685334 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:40:44.685429 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:40:44.685489 INFO: Updating optimization_manager: score_cutoff        : 8.804236368370056 -> 8.943333522891997
6:40:44.685570 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:40:44.692166 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:40:44.703532 INFO: === checking if optimization conditions were reached ===
6:40:44.704264 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
6:40:44.710956 INFO: Updating optimization_manager: rt_error            : 211.17373385482836 -> 187.4305604422202
6:40:44.711601 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 187.4306.
6:40:44.711685 INFO: ==============================================
6:40:44.711778 INFO: Starting optimization step 3.
6:40:44.711855 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:40:44.711964 INFO: Using rust extraction backend
6:40:44.712042 PROGRESS: Extracting batch of 5943 precursors
6:40:44.736891 INFO: === Search parameters used ===
6:40:44.737948 INFO: rt_error       : 187.4305604422202
6:40:44.738015 INFO: mobility_error : 0.1
6:40:44.738071 INFO: num_candidates : 3
6:40:44.738123 INFO: ms1_error      : 3
6:40:44.738222 INFO: ms2_error      : 10.0
6:40:44.738270 INFO: fwhm_rt        : 3.0
6:40:44.738314 INFO: quant_window   : 3
6:40:44.738356 INFO: ==============================================
6:40:45.016373 INFO: performing precursor FDR with 40 features
6:40:45.016681 INFO: Decoy channel: -1
6:40:45.016707 INFO: competitive: True
6:40:45.055702 INFO: Setting torch num_threads to 2 for FDR classification task
6:40:45.072906 INFO: Estimating optimal hyperparameters - samples: 14,236, batch_size: 128, learning_rate: 1.77e-04
6:40:45.073459 INFO: Using random state 850006 for train-test-split
6:40:47.378589 INFO: Test AUC: 0.763
6:40:47.378944 INFO: Train AUC: 0.774
6:40:47.378976 INFO: AUC difference: 1.42%
6:40:47.787801 INFO: Resetting torch num_threads to 100
6:40:47.795774 PROGRESS: === Extracted 17796 precursors and 100482 fragments ===
6:40:47.797042 INFO: === FDR correction performed with classifier version 6 ===
6:40:47.798766 PROGRESS: ============================= Precursor FDR =============================
6:40:47.798934 PROGRESS: Total precursors accumulated: 2,735
6:40:47.799003 PROGRESS: Target precursors: 2,708 (99.01%)
6:40:47.799056 PROGRESS: Decoy precursors: 27 (0.99%)
6:40:47.799106 PROGRESS: 
6:40:47.799175 PROGRESS: Precursor Summary:
6:40:47.802248 PROGRESS: Channel   0:	 0.050 FDR: 2,708; 0.010 FDR: 2,708; 0.001 FDR: 2,045
6:40:47.802428 PROGRESS: 
6:40:47.802483 PROGRESS: Protein Summary:
6:40:47.806055 PROGRESS: Channel   0:	 0.050 FDR: 2,135; 0.010 FDR: 2,135; 0.001 FDR: 1,652
6:40:47.806261 PROGRESS: =========================================================================
6:40:47.807836 INFO: Target number of precursors reached.
6:40:47.842593 INFO: fragments_df: keeping 5000 of 100482 [sum(precursor_idx_mask)=52005 sum(mass_error_mask)=100482 stop_rank=5000
6:40:47.882031 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:40:48.447056 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:40:49.352903 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:40:49.354299 INFO: Using score_cutoff 9.055424084758759 (fac=0.99, q=1)
6:40:49.355042 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:40:49.355165 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:40:49.355237 INFO: Updating optimization_manager: score_cutoff        : 8.943333522891997 -> 9.055424084758759
6:40:49.355329 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:40:49.361943 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:40:49.372434 INFO: === checking if optimization conditions were reached ===
6:40:49.373145 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
6:40:49.379341 INFO: Updating optimization_manager: rt_error            : 187.4305604422202 -> 126.30739735114109
6:40:49.380157 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 126.3074.
6:40:49.380250 INFO: ==============================================
6:40:49.380357 INFO: Starting optimization step 4.
6:40:49.380435 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:40:49.380555 INFO: Using rust extraction backend
6:40:49.380647 PROGRESS: Extracting batch of 5943 precursors
6:40:49.406531 INFO: === Search parameters used ===
6:40:49.407249 INFO: rt_error       : 126.30739735114109
6:40:49.407314 INFO: mobility_error : 0.1
6:40:49.407400 INFO: num_candidates : 3
6:40:49.407454 INFO: ms1_error      : 3
6:40:49.407500 INFO: ms2_error      : 10.0
6:40:49.407548 INFO: fwhm_rt        : 3.0
6:40:49.407601 INFO: quant_window   : 3
6:40:49.407654 INFO: ==============================================
6:40:49.639689 INFO: performing precursor FDR with 40 features
6:40:49.640068 INFO: Decoy channel: -1
6:40:49.640100 INFO: competitive: True
6:40:49.677364 INFO: Setting torch num_threads to 2 for FDR classification task
6:40:49.694509 INFO: Estimating optimal hyperparameters - samples: 14,222, batch_size: 128, learning_rate: 1.77e-04
6:40:49.695087 INFO: Using random state 850006 for train-test-split
6:40:51.996136 INFO: Test AUC: 0.788
6:40:51.996472 INFO: Train AUC: 0.770
6:40:51.996514 INFO: AUC difference: 2.34%
6:40:52.413552 INFO: Resetting torch num_threads to 100
6:40:52.425437 PROGRESS: === Extracted 17778 precursors and 97596 fragments ===
6:40:52.427131 INFO: === FDR correction performed with classifier version 6 ===
6:40:52.429958 PROGRESS: ============================= Precursor FDR =============================
6:40:52.430135 PROGRESS: Total precursors accumulated: 2,782
6:40:52.430206 PROGRESS: Target precursors: 2,755 (99.03%)
6:40:52.430254 PROGRESS: Decoy precursors: 27 (0.97%)
6:40:52.430300 PROGRESS: 
6:40:52.430346 PROGRESS: Precursor Summary:
6:40:52.433468 PROGRESS: Channel   0:	 0.050 FDR: 2,755; 0.010 FDR: 2,755; 0.001 FDR: 2,049
6:40:52.433639 PROGRESS: 
6:40:52.433699 PROGRESS: Protein Summary:
6:40:52.437015 PROGRESS: Channel   0:	 0.050 FDR: 2,171; 0.010 FDR: 2,171; 0.001 FDR: 1,653
6:40:52.437231 PROGRESS: =========================================================================
6:40:52.438699 INFO: Target number of precursors reached.
6:40:52.474080 INFO: fragments_df: keeping 5000 of 97596 [sum(precursor_idx_mask)=51931 sum(mass_error_mask)=97596 stop_rank=5000
6:40:52.507887 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:40:53.099910 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:40:54.085602 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:40:54.086907 INFO: Using score_cutoff 8.765147448921203 (fac=0.99, q=1)
6:40:54.087589 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:40:54.087694 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:40:54.087754 INFO: Updating optimization_manager: score_cutoff        : 9.055424084758759 -> 8.765147448921203
6:40:54.087839 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:40:54.096881 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:40:54.109103 INFO: === checking if optimization conditions were reached ===
6:40:54.109992 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
6:40:54.116821 INFO: Updating optimization_manager: rt_error            : 126.30739735114109 -> 105.23747762595549
6:40:54.117363 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 105.2375.
6:40:54.117452 INFO: ==============================================
6:40:54.117540 INFO: Starting optimization step 5.
6:40:54.117617 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:40:54.117778 INFO: Using rust extraction backend
6:40:54.117867 PROGRESS: Extracting batch of 5943 precursors
6:40:54.141324 INFO: === Search parameters used ===
6:40:54.142310 INFO: rt_error       : 105.23747762595549
6:40:54.142385 INFO: mobility_error : 0.1
6:40:54.142440 INFO: num_candidates : 3
6:40:54.142495 INFO: ms1_error      : 3
6:40:54.142569 INFO: ms2_error      : 10.0
6:40:54.142617 INFO: fwhm_rt        : 3.0
6:40:54.142660 INFO: quant_window   : 3
6:40:54.142708 INFO: ==============================================
6:40:54.420044 INFO: performing precursor FDR with 40 features
6:40:54.420655 INFO: Decoy channel: -1
6:40:54.420687 INFO: competitive: True
6:40:54.459488 INFO: Setting torch num_threads to 2 for FDR classification task
6:40:54.477725 INFO: Estimating optimal hyperparameters - samples: 14,211, batch_size: 128, learning_rate: 1.77e-04
6:40:54.478463 INFO: Using random state 850006 for train-test-split
6:40:57.137258 INFO: Test AUC: 0.773
6:40:57.137700 INFO: Train AUC: 0.775
6:40:57.137759 INFO: AUC difference: 0.31%
6:40:57.591500 INFO: Resetting torch num_threads to 100
6:40:57.601930 PROGRESS: === Extracted 17764 precursors and 96134 fragments ===
6:40:57.603531 INFO: === FDR correction performed with classifier version 6 ===
6:40:57.607861 PROGRESS: ============================= Precursor FDR =============================
6:40:57.608570 PROGRESS: Total precursors accumulated: 2,778
6:40:57.608716 PROGRESS: Target precursors: 2,751 (99.03%)
6:40:57.608789 PROGRESS: Decoy precursors: 27 (0.97%)
6:40:57.608851 PROGRESS: 
6:40:57.608912 PROGRESS: Precursor Summary:
6:40:57.617661 PROGRESS: Channel   0:	 0.050 FDR: 2,751; 0.010 FDR: 2,751; 0.001 FDR: 2,216
6:40:57.618347 PROGRESS: 
6:40:57.618463 PROGRESS: Protein Summary:
6:40:57.628057 PROGRESS: Channel   0:	 0.050 FDR: 2,166; 0.010 FDR: 2,166; 0.001 FDR: 1,772
6:40:57.628670 PROGRESS: =========================================================================
6:40:57.630661 INFO: Target number of precursors reached.
6:40:57.663136 INFO: fragments_df: keeping 5000 of 96134 [sum(precursor_idx_mask)=51465 sum(mass_error_mask)=96134 stop_rank=5000
6:40:57.688844 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:40:58.285480 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:40:59.170945 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:40:59.172639 INFO: Using score_cutoff 8.910132651329041 (fac=0.99, q=1)
6:40:59.173485 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:40:59.173614 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:40:59.173681 INFO: Updating optimization_manager: score_cutoff        : 8.765147448921203 -> 8.910132651329041
6:40:59.173782 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:40:59.181822 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:40:59.194865 INFO: === checking if optimization conditions were reached ===
6:40:59.196089 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
6:40:59.204528 INFO: Updating optimization_manager: rt_error            : 105.23747762595549 -> 87.13687529013701
6:40:59.205381 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 87.1369.
6:40:59.205473 INFO: ==============================================
6:40:59.205575 INFO: Starting optimization step 6.
6:40:59.205652 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:40:59.205773 INFO: Using rust extraction backend
6:40:59.205862 PROGRESS: Extracting batch of 5943 precursors
6:40:59.236193 INFO: === Search parameters used ===
6:40:59.237372 INFO: rt_error       : 87.13687529013701
6:40:59.237450 INFO: mobility_error : 0.1
6:40:59.237512 INFO: num_candidates : 3
6:40:59.237564 INFO: ms1_error      : 3
6:40:59.237610 INFO: ms2_error      : 10.0
6:40:59.237657 INFO: fwhm_rt        : 3.0
6:40:59.237700 INFO: quant_window   : 3
6:40:59.237748 INFO: ==============================================
6:40:59.536908 INFO: performing precursor FDR with 40 features
6:40:59.537279 INFO: Decoy channel: -1
6:40:59.537309 INFO: competitive: True
6:40:59.558584 INFO: Setting torch num_threads to 2 for FDR classification task
6:40:59.575395 INFO: Estimating optimal hyperparameters - samples: 14,204, batch_size: 128, learning_rate: 1.77e-04
6:40:59.575968 INFO: Using random state 850006 for train-test-split
6:41:02.057281 INFO: Test AUC: 0.762
6:41:02.057691 INFO: Train AUC: 0.782
6:41:02.057726 INFO: AUC difference: 2.59%
6:41:02.540975 INFO: Resetting torch num_threads to 100
6:41:02.548634 PROGRESS: === Extracted 17755 precursors and 94715 fragments ===
6:41:02.549889 INFO: === FDR correction performed with classifier version 6 ===
6:41:02.552739 PROGRESS: ============================= Precursor FDR =============================
6:41:02.553031 PROGRESS: Total precursors accumulated: 2,779
6:41:02.553118 PROGRESS: Target precursors: 2,752 (99.03%)
6:41:02.553176 PROGRESS: Decoy precursors: 27 (0.97%)
6:41:02.553223 PROGRESS: 
6:41:02.553270 PROGRESS: Precursor Summary:
6:41:02.559867 PROGRESS: Channel   0:	 0.050 FDR: 2,752; 0.010 FDR: 2,752; 0.001 FDR: 2,100
6:41:02.560617 PROGRESS: 
6:41:02.560755 PROGRESS: Protein Summary:
6:41:02.570361 PROGRESS: Channel   0:	 0.050 FDR: 2,163; 0.010 FDR: 2,163; 0.001 FDR: 1,689
6:41:02.571099 PROGRESS: =========================================================================
6:41:02.573603 INFO: Target number of precursors reached.
6:41:02.610100 INFO: fragments_df: keeping 5000 of 94715 [sum(precursor_idx_mask)=51211 sum(mass_error_mask)=94715 stop_rank=5000
6:41:02.635508 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:41:03.177208 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:41:04.108990 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:41:04.111814 INFO: Using score_cutoff 8.899051346397401 (fac=0.99, q=1)
6:41:04.113092 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:41:04.113252 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:41:04.113331 INFO: Updating optimization_manager: score_cutoff        : 8.910132651329041 -> 8.899051346397401
6:41:04.113456 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:41:04.120798 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:41:04.131093 INFO: === checking if optimization conditions were reached ===
6:41:04.131723 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
6:41:04.140395 INFO: Updating optimization_manager: rt_error            : 87.13687529013701 -> 77.12805774649948
6:41:04.140963 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 77.1281.
6:41:04.141054 INFO: ==============================================
6:41:04.141145 INFO: Starting optimization step 7.
6:41:04.141229 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:41:04.141375 INFO: Using rust extraction backend
6:41:04.141469 PROGRESS: Extracting batch of 5943 precursors
6:41:04.172841 INFO: === Search parameters used ===
6:41:04.173787 INFO: rt_error       : 77.12805774649948
6:41:04.173851 INFO: mobility_error : 0.1
6:41:04.173903 INFO: num_candidates : 3
6:41:04.173952 INFO: ms1_error      : 3
6:41:04.174000 INFO: ms2_error      : 10.0
6:41:04.174045 INFO: fwhm_rt        : 3.0
6:41:04.174088 INFO: quant_window   : 3
6:41:04.174130 INFO: ==============================================
6:41:04.373471 INFO: performing precursor FDR with 40 features
6:41:04.373773 INFO: Decoy channel: -1
6:41:04.373802 INFO: competitive: True
6:41:04.386310 INFO: Setting torch num_threads to 2 for FDR classification task
6:41:04.394540 INFO: Estimating optimal hyperparameters - samples: 14,192, batch_size: 128, learning_rate: 1.77e-04
6:41:04.394955 INFO: Using random state 850006 for train-test-split
6:41:06.199156 INFO: Test AUC: 0.785
6:41:06.199406 INFO: Train AUC: 0.780
6:41:06.199441 INFO: AUC difference: 0.66%
6:41:06.501727 INFO: Resetting torch num_threads to 100
6:41:06.507096 PROGRESS: === Extracted 17741 precursors and 93615 fragments ===
6:41:06.507903 INFO: === FDR correction performed with classifier version 6 ===
6:41:06.509196 PROGRESS: ============================= Precursor FDR =============================
6:41:06.509351 PROGRESS: Total precursors accumulated: 2,803
6:41:06.509444 PROGRESS: Target precursors: 2,776 (99.04%)
6:41:06.509504 PROGRESS: Decoy precursors: 27 (0.96%)
6:41:06.509552 PROGRESS: 
6:41:06.509600 PROGRESS: Precursor Summary:
6:41:06.511562 PROGRESS: Channel   0:	 0.050 FDR: 2,776; 0.010 FDR: 2,776; 0.001 FDR: 2,157
6:41:06.511679 PROGRESS: 
6:41:06.511735 PROGRESS: Protein Summary:
6:41:06.514376 PROGRESS: Channel   0:	 0.050 FDR: 2,177; 0.010 FDR: 2,177; 0.001 FDR: 1,731
6:41:06.514488 PROGRESS: =========================================================================
6:41:06.515541 INFO: Target number of precursors reached.
6:41:06.543303 INFO: fragments_df: keeping 5000 of 93615 [sum(precursor_idx_mask)=51115 sum(mass_error_mask)=93615 stop_rank=5000
6:41:06.564992 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:41:07.134239 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:41:08.015347 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:41:08.017095 INFO: Using score_cutoff 8.814491279125214 (fac=0.99, q=1)
6:41:08.018031 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:41:08.018151 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:41:08.018212 INFO: Updating optimization_manager: score_cutoff        : 8.899051346397401 -> 8.814491279125214
6:41:08.018304 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:41:08.025284 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:41:08.036990 INFO: === checking if optimization conditions were reached ===
6:41:08.037642 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
6:41:08.045344 INFO: Updating optimization_manager: rt_error            : 77.12805774649948 -> 64.87418274347525
6:41:08.046178 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 64.8742.
6:41:08.046304 INFO: ==============================================
6:41:08.046477 INFO: Starting optimization step 8.
6:41:08.046594 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:41:08.046734 INFO: Using rust extraction backend
6:41:08.046823 PROGRESS: Extracting batch of 5943 precursors
6:41:08.075203 INFO: === Search parameters used ===
6:41:08.076158 INFO: rt_error       : 64.87418274347525
6:41:08.076223 INFO: mobility_error : 0.1
6:41:08.076277 INFO: num_candidates : 3
6:41:08.076322 INFO: ms1_error      : 3
6:41:08.076367 INFO: ms2_error      : 10.0
6:41:08.076410 INFO: fwhm_rt        : 3.0
6:41:08.076452 INFO: quant_window   : 3
6:41:08.076493 INFO: ==============================================
6:41:08.368669 INFO: performing precursor FDR with 40 features
6:41:08.369006 INFO: Decoy channel: -1
6:41:08.369036 INFO: competitive: True
6:41:08.403683 INFO: Setting torch num_threads to 2 for FDR classification task
6:41:08.423138 INFO: Estimating optimal hyperparameters - samples: 14,121, batch_size: 128, learning_rate: 1.77e-04
6:41:08.423683 INFO: Using random state 850006 for train-test-split
6:41:10.771120 INFO: Test AUC: 0.779
6:41:10.771441 INFO: Train AUC: 0.794
6:41:10.771478 INFO: AUC difference: 1.97%
6:41:11.218556 INFO: Resetting torch num_threads to 100
6:41:11.228392 PROGRESS: === Extracted 17652 precursors and 91605 fragments ===
6:41:11.230534 INFO: === FDR correction performed with classifier version 6 ===
6:41:11.233143 PROGRESS: ============================= Precursor FDR =============================
6:41:11.233548 PROGRESS: Total precursors accumulated: 2,744
6:41:11.233644 PROGRESS: Target precursors: 2,717 (99.02%)
6:41:11.233716 PROGRESS: Decoy precursors: 27 (0.98%)
6:41:11.233776 PROGRESS: 
6:41:11.233833 PROGRESS: Precursor Summary:
6:41:11.237729 PROGRESS: Channel   0:	 0.050 FDR: 2,717; 0.010 FDR: 2,717; 0.001 FDR: 2,119
6:41:11.238142 PROGRESS: 
6:41:11.238203 PROGRESS: Protein Summary:
6:41:11.242089 PROGRESS: Channel   0:	 0.050 FDR: 2,137; 0.010 FDR: 2,137; 0.001 FDR: 1,714
6:41:11.242523 PROGRESS: =========================================================================
6:41:11.244501 INFO: Target number of precursors reached.
6:41:11.279001 INFO: fragments_df: keeping 5000 of 91605 [sum(precursor_idx_mask)=49206 sum(mass_error_mask)=91605 stop_rank=5000
6:41:11.321897 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:41:11.973446 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:41:13.003065 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:41:13.004507 INFO: Using score_cutoff 8.562192331695556 (fac=0.99, q=1)
6:41:13.005123 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:41:13.005210 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:41:13.005266 INFO: Updating optimization_manager: score_cutoff        : 8.814491279125214 -> 8.562192331695556
6:41:13.005344 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:41:13.011675 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:41:13.021276 INFO: === checking if optimization conditions were reached ===
6:41:13.021836 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
6:41:13.026441 INFO: Updating optimization_manager: rt_error            : 64.87418274347525 -> 48.514938526018824
6:41:13.026732 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 48.5149.
6:41:13.026833 INFO: ==============================================
6:41:13.026911 INFO: Starting optimization step 9.
6:41:13.026974 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:41:13.027057 INFO: Using rust extraction backend
6:41:13.027125 PROGRESS: Extracting batch of 5943 precursors
6:41:13.047936 INFO: === Search parameters used ===
6:41:13.048637 INFO: rt_error       : 48.514938526018824
6:41:13.048697 INFO: mobility_error : 0.1
6:41:13.048762 INFO: num_candidates : 3
6:41:13.048812 INFO: ms1_error      : 3
6:41:13.048861 INFO: ms2_error      : 10.0
6:41:13.048903 INFO: fwhm_rt        : 3.0
6:41:13.048944 INFO: quant_window   : 3
6:41:13.048989 INFO: ==============================================
6:41:13.331740 INFO: performing precursor FDR with 40 features
6:41:13.332152 INFO: Decoy channel: -1
6:41:13.332183 INFO: competitive: True
6:41:13.368611 INFO: Setting torch num_threads to 2 for FDR classification task
6:41:13.384910 INFO: Estimating optimal hyperparameters - samples: 13,089, batch_size: 128, learning_rate: 1.77e-04
6:41:13.385478 INFO: Using random state 850006 for train-test-split
6:41:15.479290 INFO: Test AUC: 0.814
6:41:15.479602 INFO: Train AUC: 0.823
6:41:15.479645 INFO: AUC difference: 1.08%
6:41:15.872005 INFO: Resetting torch num_threads to 100
6:41:15.879740 PROGRESS: === Extracted 16362 precursors and 82871 fragments ===
6:41:15.881067 INFO: === FDR correction performed with classifier version 6 ===
6:41:15.884166 PROGRESS: ============================= Precursor FDR =============================
6:41:15.884602 PROGRESS: Total precursors accumulated: 2,796
6:41:15.884681 PROGRESS: Target precursors: 2,769 (99.03%)
6:41:15.884741 PROGRESS: Decoy precursors: 27 (0.97%)
6:41:15.884794 PROGRESS: 
6:41:15.884877 PROGRESS: Precursor Summary:
6:41:15.888004 PROGRESS: Channel   0:	 0.050 FDR: 2,769; 0.010 FDR: 2,769; 0.001 FDR: 2,299
6:41:15.888288 PROGRESS: 
6:41:15.888350 PROGRESS: Protein Summary:
6:41:15.891897 PROGRESS: Channel   0:	 0.050 FDR: 2,168; 0.010 FDR: 2,168; 0.001 FDR: 1,829
6:41:15.892319 PROGRESS: =========================================================================
6:41:15.893734 INFO: Target number of precursors reached.
6:41:15.920013 INFO: fragments_df: keeping 5000 of 82871 [sum(precursor_idx_mask)=45233 sum(mass_error_mask)=82871 stop_rank=5000
6:41:15.949112 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:41:16.545161 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:41:17.480263 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:41:17.481817 INFO: Using score_cutoff 8.527878746795654 (fac=0.99, q=1)
6:41:17.482500 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:41:17.482589 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:41:17.482648 INFO: Updating optimization_manager: score_cutoff        : 8.562192331695556 -> 8.527878746795654
6:41:17.482742 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:41:17.489358 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:41:17.500484 INFO: === checking if optimization conditions were reached ===
6:41:17.501295 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
6:41:17.507578 INFO: Updating optimization_manager: rt_error            : 48.514938526018824 -> 46.04098569450156
6:41:17.508211 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 46.0410.
6:41:17.508297 INFO: ==============================================
6:41:17.508385 INFO: Starting optimization step 10.
6:41:17.508467 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:41:17.508562 INFO: Using rust extraction backend
6:41:17.508644 PROGRESS: Extracting batch of 5943 precursors
6:41:17.533979 INFO: === Search parameters used ===
6:41:17.534760 INFO: rt_error       : 46.04098569450156
6:41:17.534818 INFO: mobility_error : 0.1
6:41:17.534865 INFO: num_candidates : 3
6:41:17.534908 INFO: ms1_error      : 3
6:41:17.534949 INFO: ms2_error      : 10.0
6:41:17.534990 INFO: fwhm_rt        : 3.0
6:41:17.535032 INFO: quant_window   : 3
6:41:17.535072 INFO: ==============================================
6:41:17.793195 INFO: performing precursor FDR with 40 features
6:41:17.793555 INFO: Decoy channel: -1
6:41:17.793581 INFO: competitive: True
6:41:17.819217 INFO: Setting torch num_threads to 2 for FDR classification task
6:41:17.835918 INFO: Estimating optimal hyperparameters - samples: 13,088, batch_size: 128, learning_rate: 1.77e-04
6:41:17.836516 INFO: Using random state 850006 for train-test-split
6:41:19.892898 INFO: Test AUC: 0.821
6:41:19.893235 INFO: Train AUC: 0.821
6:41:19.893274 INFO: AUC difference: 0.02%
6:41:20.312943 INFO: Resetting torch num_threads to 100
6:41:20.320284 PROGRESS: === Extracted 16360 precursors and 82896 fragments ===
6:41:20.321365 INFO: === FDR correction performed with classifier version 6 ===
6:41:20.322927 PROGRESS: ============================= Precursor FDR =============================
6:41:20.323083 PROGRESS: Total precursors accumulated: 2,753
6:41:20.323186 PROGRESS: Target precursors: 2,726 (99.02%)
6:41:20.323272 PROGRESS: Decoy precursors: 27 (0.98%)
6:41:20.323323 PROGRESS: 
6:41:20.323371 PROGRESS: Precursor Summary:
6:41:20.325943 PROGRESS: Channel   0:	 0.050 FDR: 2,726; 0.010 FDR: 2,726; 0.001 FDR: 2,178
6:41:20.326081 PROGRESS: 
6:41:20.326139 PROGRESS: Protein Summary:
6:41:20.329332 PROGRESS: Channel   0:	 0.050 FDR: 2,144; 0.010 FDR: 2,144; 0.001 FDR: 1,743
6:41:20.329527 PROGRESS: =========================================================================
6:41:20.331347 INFO: Target number of precursors reached.
6:41:20.359058 INFO: fragments_df: keeping 5000 of 82896 [sum(precursor_idx_mask)=44752 sum(mass_error_mask)=82896 stop_rank=5000
6:41:20.393625 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:41:21.014682 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:41:21.952161 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:41:21.953477 INFO: Using score_cutoff 8.807288925647736 (fac=0.99, q=1)
6:41:21.954190 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:41:21.954311 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:41:21.954381 INFO: Updating optimization_manager: score_cutoff        : 8.527878746795654 -> 8.807288925647736
6:41:21.954473 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:41:21.961205 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:41:21.972470 INFO: === checking if optimization conditions were reached ===
6:41:21.973166 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
6:41:21.979209 INFO: Updating optimization_manager: rt_error            : 46.04098569450156 -> 44.58894319337802
6:41:21.979783 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 44.5889.
6:41:21.979871 INFO: ==============================================
6:41:21.979965 INFO: Starting optimization step 11.
6:41:21.980047 PROGRESS: === Extracting elution groups 0 to 3000 ===
6:41:21.980160 INFO: Using rust extraction backend
6:41:21.980243 PROGRESS: Extracting batch of 5943 precursors
6:41:22.003508 INFO: === Search parameters used ===
6:41:22.004237 INFO: rt_error       : 44.58894319337802
6:41:22.004346 INFO: mobility_error : 0.1
6:41:22.004403 INFO: num_candidates : 3
6:41:22.004452 INFO: ms1_error      : 3
6:41:22.004498 INFO: ms2_error      : 10.0
6:41:22.004542 INFO: fwhm_rt        : 3.0
6:41:22.004587 INFO: quant_window   : 3
6:41:22.004630 INFO: ==============================================
6:41:22.233076 INFO: performing precursor FDR with 40 features
6:41:22.233400 INFO: Decoy channel: -1
6:41:22.233436 INFO: competitive: True
6:41:22.256270 INFO: Setting torch num_threads to 2 for FDR classification task
6:41:22.276684 INFO: Estimating optimal hyperparameters - samples: 13,088, batch_size: 128, learning_rate: 1.77e-04
6:41:22.277301 INFO: Using random state 850006 for train-test-split
6:41:24.261687 INFO: Test AUC: 0.804
6:41:24.262247 INFO: Train AUC: 0.823
6:41:24.262302 INFO: AUC difference: 2.32%
6:41:24.687942 INFO: Resetting torch num_threads to 100
6:41:24.698584 PROGRESS: === Extracted 16360 precursors and 82909 fragments ===
6:41:24.700375 INFO: === FDR correction performed with classifier version 6 ===
6:41:24.703295 PROGRESS: ============================= Precursor FDR =============================
6:41:24.703544 PROGRESS: Total precursors accumulated: 2,783
6:41:24.703676 PROGRESS: Target precursors: 2,756 (99.03%)
6:41:24.703759 PROGRESS: Decoy precursors: 27 (0.97%)
6:41:24.703826 PROGRESS: 
6:41:24.703898 PROGRESS: Precursor Summary:
6:41:24.707400 PROGRESS: Channel   0:	 0.050 FDR: 2,756; 0.010 FDR: 2,756; 0.001 FDR: 2,103
6:41:24.707755 PROGRESS: 
6:41:24.707850 PROGRESS: Protein Summary:
6:41:24.713189 PROGRESS: Channel   0:	 0.050 FDR: 2,162; 0.010 FDR: 2,162; 0.001 FDR: 1,695
6:41:24.713516 PROGRESS: =========================================================================
6:41:24.715526 INFO: Target number of precursors reached.
6:41:24.753285 INFO: fragments_df: keeping 5000 of 82909 [sum(precursor_idx_mask)=45117 sum(mass_error_mask)=82909 stop_rank=5000
6:41:24.812385 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
6:41:25.495577 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
6:41:26.424963 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
6:41:26.426137 INFO: Using score_cutoff 8.567447108745576 (fac=0.99, q=1)
6:41:26.426687 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:41:26.426783 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:41:26.426841 INFO: Updating optimization_manager: score_cutoff        : 8.807288925647736 -> 8.567447108745576
6:41:26.426907 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:41:26.432822 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:41:26.443135 INFO: === checking if optimization conditions were reached ===
6:41:26.443740 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 5 ===
6:41:26.445669 INFO: Updating optimization_manager: rt_error            : 44.58894319337802 -> 77.12805774649948
6:41:26.445918 INFO: Updating optimization_manager: classifier_version  : 6 -> 14
6:41:26.446020 INFO: Updating optimization_manager: score_cutoff        : 8.567447108745576 -> 8.814491279125214
6:41:26.446144 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
6:41:26.446232 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
6:41:26.446336 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 77.1281 found after 12 searches.
6:41:26.446432 INFO: ==============================================
6:41:26.446541 PROGRESS: Optimization finished for rt_error.
6:41:26.475187 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:41:26.482911 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:41:26.494456 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
6:41:26.495136 PROGRESS: ==============================================
6:41:26.495270 PROGRESS: ms2_error      : 10.0000
6:41:26.495342 PROGRESS: rt_error       : 77.1281
6:41:26.495395 PROGRESS: ==============================================
6:41:26.497472 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
6:41:26.690089 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
6:41:27.241689 INFO: Using rust extraction backend
6:41:27.242564 PROGRESS: Extracting batch of 289499 precursors
6:41:28.351619 INFO: === Search parameters used ===
6:41:28.352535 INFO: rt_error       : 77.12805774649948
6:41:28.352611 INFO: mobility_error : 0.1
6:41:28.352667 INFO: num_candidates : 3
6:41:28.352715 INFO: ms1_error      : 3
6:41:28.352777 INFO: ms2_error      : 10.0
6:41:28.352836 INFO: fwhm_rt        : 3.0
6:41:28.352892 INFO: quant_window   : 3
6:41:28.352941 INFO: ==============================================
6:41:28.747636 INFO: Removed 224914 precursors with score below cutoff 8.814491279125214
6:41:29.349430 INFO: performing precursor FDR with 40 features
6:41:29.349605 INFO: Decoy channel: -1
6:41:29.349630 INFO: competitive: True
6:41:29.451335 INFO: Setting torch num_threads to 2 for FDR classification task
6:41:29.514735 WARNING: FDR calculation for 362390 target and 279724 decoy PSMs
6:41:29.514908 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
6:41:29.717565 INFO: Estimating optimal hyperparameters - samples: 513,691, batch_size: 2,104, learning_rate: 7.17e-04
6:41:29.718674 INFO: Using random state 439585 for train-test-split
6:41:38.923039 INFO: Test AUC: 0.820
6:41:38.923773 INFO: Train AUC: 0.822
6:41:38.923842 INFO: AUC difference: 0.23%
6:41:39.707856 INFO: Resetting torch num_threads to 100
6:41:41.162151 PROGRESS: ============================= Precursor FDR =============================
6:41:41.163367 PROGRESS: Total precursors accumulated: 136,315
6:41:41.163483 PROGRESS: Target precursors: 134,966 (99.01%)
6:41:41.163550 PROGRESS: Decoy precursors: 1,349 (0.99%)
6:41:41.163602 PROGRESS: 
6:41:41.163653 PROGRESS: Precursor Summary:
6:41:41.357355 PROGRESS: Channel   0:	 0.050 FDR: 134,966; 0.010 FDR: 134,966; 0.001 FDR: 120,811
6:41:41.358449 PROGRESS: 
6:41:41.358519 PROGRESS: Protein Summary:
6:41:41.691984 PROGRESS: Channel   0:	 0.050 FDR: 10,659; 0.010 FDR: 10,659; 0.001 FDR: 10,584
6:41:41.692869 PROGRESS: =========================================================================
6:41:41.708511 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/psm.parquet
6:41:42.414788 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.parquet
6:41:43.100743 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
6:41:44.698284 PROGRESS: Processing search outputs
6:41:44.698577 PROGRESS: === Performing protein grouping and FDR ===
6:41:44.698730 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
6:41:44.837799 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
6:41:45.010638 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
6:41:45.181182 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
6:41:45.338484 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
6:41:45.526190 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
6:41:45.826956 INFO: Performing protein inference
6:41:47.161779 INFO: Inference strategy: library. Using library grouping for protein inference
6:41:47.177856 INFO: Performing protein FDR
6:42:21.542712 INFO: Normalizing q-values using 10,661 targets and 4,003 decoys
6:42:21.547432 INFO: Test AUC: 1.000
6:42:21.547573 INFO: Train AUC: 1.000
6:42:21.547617 INFO: AUC difference: 0.00%
6:42:23.454628 INFO: ================ Protein FDR =================
6:42:23.455082 INFO: Unique protein groups in output
6:42:23.455134 INFO:   1% protein FDR: 10,657
6:42:23.455167 INFO: 
6:42:23.455190 INFO: Unique precursor in output
6:42:23.455215 INFO:   1% protein FDR: 145,830
6:42:23.455235 INFO: ================================================
6:42:23.642970 PROGRESS: Building search statistics
6:42:23.975331 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
6:42:23.975856 INFO: Initializing OptimizationManager
6:42:23.976372 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
6:42:23.976548 INFO: Initializing CalibrationManager
6:42:23.977054 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
6:42:23.977226 INFO: Initializing RawFileManager
6:42:24.047153 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
6:42:24.047501 INFO: Initializing OptimizationManager
6:42:24.047846 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
6:42:24.048010 INFO: Initializing CalibrationManager
6:42:24.048366 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
6:42:24.048489 INFO: Initializing RawFileManager
6:42:24.109350 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
6:42:24.109656 INFO: Initializing OptimizationManager
6:42:24.109959 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
6:42:24.110078 INFO: Initializing CalibrationManager
6:42:24.110421 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
6:42:24.110530 INFO: Initializing RawFileManager
6:42:24.167300 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
6:42:24.167578 INFO: Initializing OptimizationManager
6:42:24.167839 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
6:42:24.167920 INFO: Initializing CalibrationManager
6:42:24.168180 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
6:42:24.168267 INFO: Initializing RawFileManager
6:42:24.225047 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
6:42:24.225396 INFO: Initializing OptimizationManager
6:42:24.225723 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
6:42:24.225856 INFO: Initializing CalibrationManager
6:42:24.226221 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
6:42:24.226341 INFO: Initializing RawFileManager
6:42:24.288710 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
6:42:24.289072 INFO: Initializing OptimizationManager
6:42:24.289446 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
6:42:24.289618 INFO: Initializing CalibrationManager
6:42:24.289984 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
6:42:24.290114 INFO: Initializing RawFileManager
6:42:24.299482 INFO: Writing stat output to disk
6:42:24.299735 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/stat.tsv to disk
6:42:24.322474 PROGRESS: Building internal statistics
6:42:24.323135 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
6:42:24.323647 INFO: Initializing TimingManager
6:42:24.324458 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
6:42:24.324530 INFO: Initializing TimingManager
6:42:24.324929 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
6:42:24.324985 INFO: Initializing TimingManager
6:42:24.325300 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
6:42:24.325350 INFO: Initializing TimingManager
6:42:24.325662 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
6:42:24.325705 INFO: Initializing TimingManager
6:42:24.325981 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
6:42:24.326025 INFO: Initializing TimingManager
6:42:24.326730 INFO: Writing internal output to disk
6:42:24.326789 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/internal.tsv to disk
6:42:24.529023 INFO: Performing label free quantification
6:42:24.529476 INFO: Accumulating fragment data
6:42:24.529606 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
6:42:24.761417 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
6:42:30.049771 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
6:42:34.432550 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
6:42:39.350795 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
6:42:44.420516 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
6:42:50.843802 INFO: Performing label free quantification on the precursor level
6:42:50.844643 INFO: Filtering fragments by quality
6:42:51.958886 INFO: Performing label-free quantification with directlfq normalization
6:42:53.559683 INFO: Applying directLFQ normalization
6:42:54.630812 INFO: 145830 lfq-groups total
6:46:50.681625 INFO: using 100 processes
6:46:50.993382 INFO: lfq-object 0
6:46:51.110706 INFO: lfq-object 100
6:46:51.192072 INFO: lfq-object 400
6:46:51.222099 INFO: lfq-object 200
6:46:51.321401 INFO: lfq-object 500
6:46:51.323328 INFO: lfq-object 800
6:46:51.339441 INFO: lfq-object 300
6:46:51.365690 INFO: lfq-object 1100
6:46:51.445022 INFO: lfq-object 600
6:46:51.447099 INFO: lfq-object 900
6:46:51.485444 INFO: lfq-object 1200
6:46:51.516478 INFO: lfq-object 1500
6:46:51.557470 INFO: lfq-object 700
6:46:51.564749 INFO: lfq-object 1000
6:46:51.599966 INFO: lfq-object 1300
6:46:51.633953 INFO: lfq-object 1600
6:46:51.676084 INFO: lfq-object 1900
6:46:51.716320 INFO: lfq-object 1400
6:46:51.753842 INFO: lfq-object 1700
6:46:51.765063 INFO: lfq-object 2200
6:46:51.785423 INFO: lfq-object 2000
6:46:51.870565 INFO: lfq-object 1800
6:46:51.883281 INFO: lfq-object 2300
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6:48:52.498820 INFO: Performing label free quantification on the peptide level
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6:52:19.223339 INFO: Performing label free quantification on the pg level
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6:53:33.880015 INFO: lfq-object 9400
6:53:33.948395 INFO: lfq-object 9300
6:53:34.027138 INFO: lfq-object 9600
6:53:34.035252 INFO: lfq-object 9500
6:53:34.037236 INFO: lfq-object 9700
6:53:34.142949 INFO: lfq-object 9800
6:53:34.235709 INFO: lfq-object 10000
6:53:34.237175 INFO: lfq-object 9900
6:53:34.251443 INFO: lfq-object 10100
6:53:34.400384 INFO: lfq-object 10300
6:53:34.446654 INFO: lfq-object 10200
6:53:34.563324 INFO: lfq-object 10400
6:53:34.630654 INFO: lfq-object 10600
6:53:34.685517 INFO: lfq-object 10500
6:53:38.953439 INFO: Writing psm output to disk
6:53:39.104972 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/precursors.parquet to disk
6:53:40.253163 INFO: Writing precursor output to disk
6:53:40.264606 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/precursor.matrix.parquet to disk
6:53:40.417199 INFO: Writing peptide output to disk
6:53:40.422453 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/peptide.matrix.parquet to disk
6:53:40.539928 INFO: Writing pg output to disk
6:53:40.542737 INFO: Saving /home/robbe/PB_output/results/AstralManuscriptAlphaDIATL/HYE_Astral/alphadia_v2.1.1/pg.matrix.parquet to disk
6:53:40.673048 PROGRESS: Building MBR spectral library
6:53:40.673290 INFO: Running MbrLibraryBuilder
6:53:41.226995 INFO: MBR spectral library contains 145,830 precursors, 10,657 proteins
6:53:41.227139 INFO: Writing MBR spectral library to disk
6:53:42.192991 PROGRESS: =================== Search step 'mbr' finished ===================
6:53:42.258380 INFO: =================== Search Finished ===================
