0:00:00.000032 INFO: Moved old log file /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/log.txt to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/log.1.bkp.txt
0:00:00.000139 INFO: Output directory: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1, cwd: /home/robbe/PB_output/work/a8/b4c47e7e7ab5e0c8c0bdb4751c609a.
0:00:00.000172 INFO: User provided config file: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/alphadia_config.yaml.
0:00:00.014501 PROGRESS:           _      _         ___ ___   _   
0:00:00.014565 PROGRESS:      __ _| |_ __| |_  __ _|   \_ _| /_\  
0:00:00.014591 PROGRESS:     / _` | | '_ \ ' \/ _` | |) | | / _ \ 
0:00:00.014613 PROGRESS:     \__,_|_| .__/_||_\__,_|___/___/_/ \_\
0:00:00.014640 PROGRESS:            |_|                           
0:00:00.014664 PROGRESS: 
0:00:00.014683 PROGRESS: version: 2.1.1
0:00:00.014702 PROGRESS: Please cite: Wallmann, et al., Nature Biotechnology (2025), https://doi.org/10.1038/s41587-025-02791-w
0:00:00.014729 INFO: hostname: thestral
0:00:00.014753 PROGRESS: os: Linux 6.12.85+deb13-amd64 (x86_64)
0:00:00.014776 PROGRESS: python: 3.11.11 (CPython)
0:00:00.014826 INFO: date: 2026-07-09 13:04:31
0:00:00.014845 INFO: ================ AlphaX Environment ===============
0:00:00.014863 INFO: alphabase       : 1.8.1
0:00:00.014881 INFO: alpharaw        : 0.5.0
0:00:00.014898 INFO: alphatims       : 1.0.9
0:00:00.014915 INFO: alphapeptdeep   : 1.4.2
0:00:00.014931 INFO: directlfq       : 0.3.3
0:00:00.014946 INFO: ===================================================
0:00:00.014962 INFO: ================= Pip Environment =================
0:00:00.087223 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
0:00:00.087342 INFO: ===================================================
0:00:00.087373 INFO: =================== Running step 'library' ===================
0:00:00.087451 INFO: loading default config from /home/robbe/bin/alphadia/alphadia/constants/default.yaml
0:00:00.099884 INFO: loading additional config provided via CLI
0:00:00.099946 INFO: loading additional config provided via CLI parameters
0:00:00.100306 INFO: Updating config with 'user defined'
0:00:00.100380 INFO: Updating config with 'user defined (cli)'
0:00:00.100450 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/AstralManuscript/HYE_Astral/alphadia_v2.1.1', 'general': {'thread_count': 100, 'mbr_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}, 'output_directory': '/home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library'}]
0:00:00.100657 INFO: Updating config with 'user defined'
0:00:00.100704 INFO: Updating config with 'user defined (cli)'
0:00:00.100723 INFO: Updating config with 'multistep search'
0:00:00.100759 INFO: ├──version: None
0:00:00.100781 INFO: ├──workflow_name: None
0:00:00.100802 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library [multistep search, default: None][0m
0:00:00.100821 INFO: ├──library_path: None
0:00:00.100838 INFO: ├──raw_paths:
0:00:00.100857 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
0:00:00.100875 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
0:00:00.100892 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
0:00:00.100912 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
0:00:00.100935 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
0:00:00.100954 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
0:00:00.100973 INFO: ├──fasta_paths:
0:00:00.100991 INFO: │   [32;20m- /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta [user defined, default: None][0m
0:00:00.101010 INFO: ├──quant_directory: None
0:00:00.101027 INFO: ├──general
0:00:00.101046 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
0:00:00.101064 INFO: │   ├──transfer_step_enabled: False
0:00:00.101085 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
0:00:00.101103 INFO: │   ├──reuse_calibration: False
0:00:00.101120 INFO: │   ├──reuse_quant: False
0:00:00.101137 INFO: │   ├──log_level: INFO
0:00:00.101155 INFO: │   ├──use_gpu: True
0:00:00.101174 INFO: │   ├──save_figures: True
0:00:00.101192 INFO: │   [32;20m├──save_library: False [multistep search, default: True][0m
0:00:00.101210 INFO: │   ├──save_flat_library: False
0:00:00.101227 INFO: │   ├──input_library_type: base
0:00:00.101244 INFO: │   ├──save_mbr_library: True
0:00:00.101261 INFO: │   ├──random_state: None
0:00:00.101279 INFO: │   └──fail_fast: False
0:00:00.101297 INFO: ├──library_loading
0:00:00.101316 INFO: │   └──drop_decoys: False
0:00:00.101333 INFO: ├──library_prediction
0:00:00.101351 INFO: │   [32;20m├──enabled: True [user defined, default: False][0m
0:00:00.101369 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
0:00:00.101386 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
0:00:00.101404 INFO: │   [32;20m├──variable_modifications: Oxidation@M [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
0:00:00.101422 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
0:00:00.101440 INFO: │   ├──missed_cleavages: 1
0:00:00.101458 INFO: │   ├──precursor_len:
0:00:00.101477 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
0:00:00.101494 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
0:00:00.101511 INFO: │   ├──precursor_charge:
0:00:00.101528 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
0:00:00.101545 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
0:00:00.101561 INFO: │   ├──precursor_mz:
0:00:00.101578 INFO: │   │   [32;20m- 380.0 [user defined, default: 400][0m
0:00:00.101595 INFO: │   │   [32;20m- 980.0 [user defined, default: 1200][0m
0:00:00.101611 INFO: │   ├──fragment_mz:
0:00:00.101628 INFO: │   │   [32;20m- 150.0 [user defined, default: 200][0m
0:00:00.101644 INFO: │   │   - 2000.0
0:00:00.101662 INFO: │   ├──nce: 25.0
0:00:00.101678 INFO: │   ├──fragment_types:
0:00:00.101695 INFO: │   │   - b
0:00:00.101711 INFO: │   │   - y
0:00:00.101729 INFO: │   ├──max_fragment_charge: 2
0:00:00.101746 INFO: │   ├──instrument: Lumos
0:00:00.101763 INFO: │   ├──peptdeep_model_path: None
0:00:00.101781 INFO: │   ├──peptdeep_model_type: generic
0:00:00.101798 INFO: │   ├──predict_charge: False
0:00:00.101815 INFO: │   └──min_charge_probability: 0.1
0:00:00.101832 INFO: ├──custom_modifications:
0:00:00.101850 INFO: │   ├──name: Dimethyl:d12@K
0:00:00.101866 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.101884 INFO: │   ├──name: Dimethyl:d12@Any_N-term
0:00:00.101901 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.101918 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
0:00:00.101936 INFO: │   └──composition: H(-2)2H(8)13C(2)
0:00:00.101953 INFO: │   ├──name: mTRAQ:d12@K
0:00:00.101969 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
0:00:00.101991 INFO: │   ├──name: mTRAQ:d12@Any_N-term
0:00:00.102008 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.102027 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
0:00:00.102045 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
0:00:00.102062 INFO: │   ├──name: Label:13C(12)@K
0:00:00.102079 INFO: │   └──composition: C(12)
0:00:00.102095 INFO: ├──search
0:00:00.102112 INFO: │   ├──extraction_backend: rust
0:00:00.102129 INFO: │   [32;20m├──target_ms1_tolerance: 3 [user defined, default: 5][0m
0:00:00.102145 INFO: │   ├──target_ms2_tolerance: 10
0:00:00.102163 INFO: │   ├──target_rt_tolerance: 0.0
0:00:00.102180 INFO: │   ├──target_mobility_tolerance: 0.0
0:00:00.102197 INFO: │   ├──quant_window: 3
0:00:00.102214 INFO: │   ├──target_num_candidates: 3
0:00:00.102231 INFO: │   ├──channel_filter: 
0:00:00.102247 INFO: │   ├──compete_for_fragments: True
0:00:00.102264 INFO: │   ├──top_k_fragments_selection: 12
0:00:00.102281 INFO: │   ├──top_k_fragments_scoring: 12
0:00:00.102298 INFO: │   ├──min_fragment_intensity: 0.01
0:00:00.102315 INFO: │   ├──optimized_peak_group_score: False
0:00:00.102332 INFO: │   ├──exclude_shared_ions: True
0:00:00.102350 INFO: │   ├──quant_all: True
0:00:00.102367 INFO: │   └──experimental_xic: True
0:00:00.102385 INFO: ├──calibration
0:00:00.102403 INFO: │   ├──batch_size: 1000
0:00:00.102421 INFO: │   ├──optimization_lock_target: 1000
0:00:00.102438 INFO: │   ├──max_steps: 20
0:00:00.102456 INFO: │   ├──min_steps: 5
0:00:00.102473 INFO: │   ├──max_skips: 1
0:00:00.102490 INFO: │   ├──max_fragments: 5000
0:00:00.102509 INFO: │   └──min_correlation: 0.7
0:00:00.102525 INFO: ├──search_initial
0:00:00.102543 INFO: │   ├──num_candidates: 1
0:00:00.102560 INFO: │   [32;20m├──ms1_tolerance: 3 [user defined, default: 30][0m
0:00:00.102577 INFO: │   [32;20m├──ms2_tolerance: 10 [user defined, default: 30][0m
0:00:00.102595 INFO: │   ├──mobility_tolerance: 0.1
0:00:00.102613 INFO: │   └──rt_tolerance: 0.5
0:00:00.102630 INFO: ├──library_multiplexing
0:00:00.102648 INFO: │   ├──enabled: False
0:00:00.102665 INFO: │   ├──input_channel: 0
0:00:00.102682 INFO: │   └──multiplex_mapping:
0:00:00.102699 INFO: ├──multiplexing
0:00:00.102716 INFO: │   ├──enabled: False
0:00:00.102733 INFO: │   ├──target_channels: 4,8
0:00:00.102750 INFO: │   ├──decoy_channel: 12
0:00:00.102767 INFO: │   ├──reference_channel: 0
0:00:00.102784 INFO: │   └──competitive_scoring: True
0:00:00.102800 INFO: ├──fdr
0:00:00.102817 INFO: │   ├──fdr: 0.01
0:00:00.102834 INFO: │   ├──group_level: proteins
0:00:00.102850 INFO: │   ├──inference_strategy: heuristic
0:00:00.102867 INFO: │   ├──competitive_scoring: True
0:00:00.102884 INFO: │   ├──keep_decoys: False
0:00:00.102901 INFO: │   ├──keep_decoys_in_mbr_library: False
0:00:00.102918 INFO: │   ├──channel_wise_fdr: False
0:00:00.102935 INFO: │   └──enable_nn_hyperparameter_tuning: True
0:00:00.102951 INFO: ├──search_output
0:00:00.102968 INFO: │   ├──file_format: parquet
0:00:00.102984 INFO: │   ├──precursor_level_lfq: True
0:00:00.103001 INFO: │   ├──peptide_level_lfq: True
0:00:00.103018 INFO: │   ├──save_fragment_quant_matrix: False
0:00:00.103034 INFO: │   ├──min_k_fragments: 12
0:00:00.103051 INFO: │   ├──min_correlation: 0.9
0:00:00.103068 INFO: │   ├──num_samples_quadratic: 50
0:00:00.103085 INFO: │   ├──min_nonnan: 3
0:00:00.103103 INFO: │   ├──normalization_method: directlfq
0:00:00.103121 INFO: │   └──normalize_directlfq: True
0:00:00.103137 INFO: ├──optimization
0:00:00.103155 INFO: │   ├──order_of_optimization: None
0:00:00.103176 INFO: │   ├──ms2_error
0:00:00.103194 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.103214 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.103232 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.103250 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.103267 INFO: │   │   ├──try_narrower_values: True
0:00:00.103285 INFO: │   │   ├──maximal_decrease: 0.5
0:00:00.103302 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.103320 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.103336 INFO: │   ├──ms1_error
0:00:00.103353 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.103370 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.103388 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.103405 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.103421 INFO: │   │   ├──try_narrower_values: False
0:00:00.103439 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.103455 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.103472 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.103488 INFO: │   ├──mobility_error
0:00:00.103506 INFO: │   │   ├──targeted_update_percentile_range: 0.95
0:00:00.103523 INFO: │   │   ├──targeted_update_factor: 1.0
0:00:00.103541 INFO: │   │   ├──automatic_update_percentile_range: 0.99
0:00:00.103559 INFO: │   │   ├──automatic_update_factor: 1.1
0:00:00.103576 INFO: │   │   ├──try_narrower_values: False
0:00:00.103593 INFO: │   │   ├──maximal_decrease: 0.2
0:00:00.103611 INFO: │   │   ├──favour_narrower_optimum: False
0:00:00.103628 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
0:00:00.103645 INFO: │   └──rt_error
0:00:00.103662 INFO: │       ├──targeted_update_percentile_range: 0.95
0:00:00.103680 INFO: │       ├──targeted_update_factor: 1.0
0:00:00.103698 INFO: │       ├──automatic_update_percentile_range: 0.999
0:00:00.103715 INFO: │       ├──automatic_update_factor: 1.5
0:00:00.103733 INFO: │       ├──try_narrower_values: True
0:00:00.103750 INFO: │       ├──maximal_decrease: 0.1
0:00:00.103768 INFO: │       ├──favour_narrower_optimum: False
0:00:00.103785 INFO: │       └──maximum_decrease_from_maximum: 0.5
0:00:00.103802 INFO: ├──optimization_manager
0:00:00.103832 INFO: │   ├──fwhm_rt: 5
0:00:00.103854 INFO: │   ├──fwhm_mobility: 0.01
0:00:00.103872 INFO: │   └──score_cutoff: 0
0:00:00.103888 INFO: ├──transfer_library
0:00:00.103905 INFO: │   ├──enabled: False
0:00:00.103922 INFO: │   ├──fragment_types:
0:00:00.103938 INFO: │   │   - b
0:00:00.103955 INFO: │   │   - y
0:00:00.103972 INFO: │   ├──max_charge: 2
0:00:00.103989 INFO: │   ├──top_k_samples: 3
0:00:00.104006 INFO: │   ├──norm_delta_max: True
0:00:00.104023 INFO: │   ├──precursor_correlation_cutoff: 0.5
0:00:00.104041 INFO: │   └──fragment_correlation_ratio: 0.75
0:00:00.104057 INFO: └──transfer_learning
0:00:00.104074 INFO:     ├──enabled: False
0:00:00.104091 INFO:     ├──batch_size: 2000
0:00:00.104108 INFO:     ├──max_lr: 0.0001
0:00:00.104125 INFO:     ├──train_fraction: 0.7
0:00:00.104142 INFO:     ├──validation_fraction: 0.2
0:00:00.104159 INFO:     ├──test_fraction: 0.1
0:00:00.104176 INFO:     ├──test_interval: 1
0:00:00.104193 INFO:     ├──lr_patience: 3
0:00:00.104210 INFO:     ├──epochs: 51
0:00:00.104227 INFO:     ├──warmup_epochs: 5
0:00:00.104244 INFO:     ├──nce: 25
0:00:00.104261 INFO:     └──instrument: Lumos
0:00:00.109440 INFO: Moved existing config file /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/frozen_config.yaml to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/frozen_config.1.bkp.yaml
0:00:00.109642 INFO: Registering 7 custom modifications
0:00:00.143000 INFO: Searching 6 files:
0:00:00.143068 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
0:00:00.143092 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
0:00:00.143111 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
0:00:00.143128 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
0:00:00.143144 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
0:00:00.143160 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
0:00:00.143177 INFO: Using 1 fasta files:
0:00:00.143193 INFO:   /public/local/ProteoBench/fastas/ProteoBenchFASTA_MixedSpecies_HYE.fasta
0:00:00.143211 INFO: Using library: None
0:00:00.143227 INFO: Saving output to: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library
0:00:00.143249 PROGRESS: Loading spectral library
0:00:00.143271 PROGRESS: No library provided. Building library from fasta files.
0:00:00.143304 INFO: Running FastaDigest
0:00:00.144680 INFO: Digesting fasta file
0:00:06.975949 INFO: Adding modifications
0:01:55.026086 INFO: Removing non-canonical amino acids
0:02:01.337149 INFO: Fasta library contains 6,091,314 precursors
0:02:01.337368 PROGRESS: Predicting library properties.
0:02:01.337459 INFO: Running PeptDeepPrediction
0:02:01.338899 INFO: Device set to cpu
0:02:03.233798 INFO: Loading PeptDeep models of type generic
0:02:04.318382 INFO: Predicting RT, MS2 and mobility
0:02:04.318563 INFO: Using multiprocessing with 100 processes ...
0:02:04.688884 INFO: Predicting rt,ms2,mobility ...
0:09:37.479264 INFO: Adding fragment mz information
0:09:37.779905 INFO: Adding fragment intensity information
0:09:38.080695 INFO: Adding precursor information
0:09:38.384124 INFO: Running PrecursorInitializer
0:09:38.405110 INFO: Running AnnotateFasta
0:10:03.672279 INFO: Running IsotopeGenerator
0:10:03.673219 WARNING: Multiprocessing not compatible with custom modifications yet, falling back to single process.
0:14:45.943798 INFO: Running RTNormalization
0:14:45.944521 WARNING: Input library already contains normalized RT information. Skipping RT normalization
0:14:45.944720 INFO: Saving library to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/speclib.hdf
0:15:43.161927 INFO: Running DecoyGenerator
0:22:26.297861 INFO: Running FlattenLibrary
0:23:44.327629 INFO: Running InitFlatColumns
0:23:45.415079 INFO: Running LogFlatLibraryStats
0:23:45.415541 INFO: ============ Library Stats ============
0:23:45.415656 INFO: Number of precursors: 12,150,378
0:23:50.706910 INFO: 	thereof targets:6,091,314
0:23:50.707436 INFO: 	thereof decoys: 6,059,064
0:23:50.812572 INFO: Number of elution groups: 6,091,314
0:23:50.812936 INFO: 	average size: 1.99
0:23:51.766498 INFO: Number of proteins: 117,993
0:23:51.801503 INFO: Number of channels: 1 ([0])
0:23:51.802172 INFO: Isotopes Distribution for 4 isotopes
0:23:51.802211 INFO: =======================================
0:23:51.802352 PROGRESS: =================== Starting Search Workflows for step library ===================
0:23:51.802845 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 
0:23:51.802943 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
0:23:51.803201 INFO: Initializing TimingManager
0:23:51.805019 INFO: Initializing RawFileManager
0:24:28.589414 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.
0:24:28.608489 INFO: Determining DIA cycle
0:24:31.240046 INFO: Found cycle with start 0.00 min and length 300.
0:24:31.900099 INFO: RT (min)            : 0.0 - 26.9
0:24:31.900442 INFO: RT duration (sec)   : 1611.2
0:24:31.900473 INFO: RT duration (min)   : 26.9
0:24:31.900507 INFO: Cycle len (scans)   : 300
0:24:31.900530 INFO: Cycle len (sec)     : 1.65
0:24:31.900550 INFO: Number of cycles    : 977
0:24:31.900573 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:24:31.900693 INFO: Creating DIA data object took: 40.09550952911377
0:24:34.004995 INFO: Creating DIA data NG object took: 2.104048013687134
0:24:36.639758 INFO: Initializing CalibrationManager
0:24:36.641977 INFO: Setting up calibration estimators ..
0:24:36.642174 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:24:36.642443 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'}' ..
0:24:36.642658 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:24:36.642761 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:24:36.642872 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}}' ..
0:24:36.642979 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:24:36.643063 INFO: Done setting up calibration estimators.
0:24:36.644829 INFO: Initializing OptimizationManager
0:24:36.645549 INFO: initial parameter: ms1_error = 3
0:24:36.645657 INFO: initial parameter: ms2_error = 10
0:24:36.645775 INFO: initial parameter: rt_error = 805.5992431640625
0:24:36.645874 INFO: initial parameter: mobility_error = 0.1
0:24:36.645947 INFO: initial parameter: num_candidates = 1
0:24:36.646018 INFO: initial parameter: fwhm_rt = 5
0:24:36.646088 INFO: initial parameter: fwhm_mobility = 0.01
0:24:36.646164 INFO: initial parameter: score_cutoff = 0
0:24:36.646244 INFO: initial parameter: classifier_version = -1
0:24:36.646386 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:24:36.648921 INFO: FDRManager: loading saved state not requested, will be initialized.
0:24:36.649035 INFO: Initializing FDRManager
0:24:36.649214 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
0:24:40.988836 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
0:24:45.234344 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
0:24:45.236203 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
0:24:45.236795 PROGRESS: Starting initial search for precursors.
0:24:45.237087 INFO: Starting optimization step 0.
0:24:45.237236 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:24:45.237362 INFO: Using rust extraction backend
0:24:45.237509 PROGRESS: Extracting batch of 1970 precursors
0:24:45.256902 INFO: === Search parameters used ===
0:24:45.257899 INFO: rt_error       : 805.5992431640625
0:24:45.257969 INFO: mobility_error : 0.1
0:24:45.258020 INFO: num_candidates : 1
0:24:45.258069 INFO: ms1_error      : 3
0:24:45.258116 INFO: ms2_error      : 10
0:24:45.258160 INFO: fwhm_rt        : 5
0:24:45.258214 INFO: quant_window   : 3
0:24:45.258261 INFO: ==============================================
0:24:45.367476 INFO: performing precursor FDR with 40 features
0:24:45.367735 INFO: Decoy channel: -1
0:24:45.367764 INFO: competitive: True
0:24:45.372037 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:45.377008 INFO: Estimating optimal hyperparameters - samples: 1,572, batch_size: 128, learning_rate: 1.77e-04
0:24:45.379510 INFO: Using random state 373791 for train-test-split
0:24:45.657075 INFO: Test AUC: 0.526
0:24:45.657804 INFO: Train AUC: 0.545
0:24:45.657994 INFO: AUC difference: 3.48%
0:24:46.959546 INFO: Resetting torch num_threads to 100
0:24:46.966417 PROGRESS: === Extracted 1965 precursors and 10988 fragments ===
0:24:46.968367 INFO: === FDR correction performed with classifier version -1 ===
0:24:46.969950 PROGRESS: ============================= Precursor FDR =============================
0:24:46.970154 PROGRESS: Total precursors accumulated: 164
0:24:46.970251 PROGRESS: Target precursors: 163 (99.39%)
0:24:46.970392 PROGRESS: Decoy precursors: 1 (0.61%)
0:24:46.970467 PROGRESS: 
0:24:46.970556 PROGRESS: Precursor Summary:
0:24:46.972731 PROGRESS: Channel   0:	 0.050 FDR:   163; 0.010 FDR:   163; 0.001 FDR:   163
0:24:46.972908 PROGRESS: 
0:24:46.972981 PROGRESS: Protein Summary:
0:24:46.975141 PROGRESS: Channel   0:	 0.050 FDR:   162; 0.010 FDR:   162; 0.001 FDR:   162
0:24:46.975395 PROGRESS: =========================================================================
0:24:46.976774 INFO: Target number of precursors not reached yet.
0:24:47.105574 INFO: Starting optimization step 1.
0:24:47.106963 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:24:47.107203 INFO: Using rust extraction backend
0:24:47.107362 PROGRESS: Extracting batch of 3935 precursors
0:24:47.142050 INFO: === Search parameters used ===
0:24:47.143027 INFO: rt_error       : 805.5992431640625
0:24:47.143126 INFO: mobility_error : 0.1
0:24:47.143194 INFO: num_candidates : 1
0:24:47.143263 INFO: ms1_error      : 3
0:24:47.143325 INFO: ms2_error      : 10
0:24:47.143382 INFO: fwhm_rt        : 5
0:24:47.143436 INFO: quant_window   : 3
0:24:47.143491 INFO: ==============================================
0:24:47.243572 INFO: performing precursor FDR with 40 features
0:24:47.243850 INFO: Decoy channel: -1
0:24:47.243881 INFO: competitive: True
0:24:47.251999 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:47.256031 INFO: Estimating optimal hyperparameters - samples: 4,713, batch_size: 128, learning_rate: 1.77e-04
0:24:47.256278 INFO: Using random state 313830 for train-test-split
0:24:48.131600 INFO: Test AUC: 0.540
0:24:48.131833 INFO: Train AUC: 0.571
0:24:48.131869 INFO: AUC difference: 5.51%
0:24:48.131893 WARNING: AUC difference > 5%. This may indicate overfitting.
0:24:48.500272 INFO: Resetting torch num_threads to 100
0:24:48.510216 PROGRESS: === Extracted 5892 precursors and 32923 fragments ===
0:24:48.511242 INFO: === FDR correction performed with classifier version -1 ===
0:24:48.512515 PROGRESS: ============================= Precursor FDR =============================
0:24:48.512626 PROGRESS: Total precursors accumulated: 1,495
0:24:48.512689 PROGRESS: Target precursors: 1,481 (99.06%)
0:24:48.512738 PROGRESS: Decoy precursors: 14 (0.94%)
0:24:48.512784 PROGRESS: 
0:24:48.512828 PROGRESS: Precursor Summary:
0:24:48.514494 PROGRESS: Channel   0:	 0.050 FDR: 1,481; 0.010 FDR: 1,481; 0.001 FDR: 1,481
0:24:48.514605 PROGRESS: 
0:24:48.514660 PROGRESS: Protein Summary:
0:24:48.516681 PROGRESS: Channel   0:	 0.050 FDR: 1,419; 0.010 FDR: 1,419; 0.001 FDR: 1,419
0:24:48.516934 PROGRESS: =========================================================================
0:24:48.517711 INFO: Target number of precursors reached.
0:24:48.526362 INFO: fragments_df: keeping 2662 of 32923 [sum(precursor_idx_mask)=8581 sum(mass_error_mask)=32923 stop_rank=2662
0:24:48.663890 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:24:48.992832 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:24:49.594808 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:24:49.595706 INFO: Using score_cutoff 5.517583786010743 (fac=0.99, q=1)
0:24:49.596150 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:24:49.596240 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:24:49.596295 INFO: Updating optimization_manager: score_cutoff        : 0 -> 5.517583786010743
0:24:49.596379 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:24:49.601900 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:49.612703 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
0:24:49.613210 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:24:49.613313 INFO: Starting optimization step 2.
0:24:49.613438 PROGRESS: === Extracting elution groups 0 to 3000 ===
0:24:49.613523 INFO: Using rust extraction backend
0:24:49.613601 PROGRESS: Extracting batch of 5905 precursors
0:24:49.632413 INFO: === Search parameters used ===
0:24:49.632961 INFO: rt_error       : 805.5992431640625
0:24:49.633018 INFO: mobility_error : 0.1
0:24:49.633068 INFO: num_candidates : 3
0:24:49.633110 INFO: ms1_error      : 3
0:24:49.633149 INFO: ms2_error      : 10
0:24:49.633188 INFO: fwhm_rt        : 3.0
0:24:49.633227 INFO: quant_window   : 3
0:24:49.633265 INFO: ==============================================
0:24:49.815036 INFO: performing precursor FDR with 40 features
0:24:49.815351 INFO: Decoy channel: -1
0:24:49.815376 INFO: competitive: True
0:24:49.826402 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:49.834240 INFO: Estimating optimal hyperparameters - samples: 14,140, batch_size: 128, learning_rate: 1.77e-04
0:24:49.834635 INFO: Using random state 950877 for train-test-split
0:24:52.640931 INFO: Test AUC: 0.557
0:24:52.641413 INFO: Train AUC: 0.577
0:24:52.641454 INFO: AUC difference: 3.50%
0:24:53.160131 INFO: Resetting torch num_threads to 100
0:24:53.165735 PROGRESS: === Extracted 17676 precursors and 94444 fragments ===
0:24:53.167023 INFO: === FDR correction performed with classifier version 1 ===
0:24:53.167917 PROGRESS: ============================= Precursor FDR =============================
0:24:53.168045 PROGRESS: Total precursors accumulated: 2
0:24:53.168127 PROGRESS: Target precursors: 2 (100.00%)
0:24:53.168182 PROGRESS: Decoy precursors: 0 (0.00%)
0:24:53.168238 PROGRESS: 
0:24:53.168286 PROGRESS: Precursor Summary:
0:24:53.169795 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:24:53.169939 PROGRESS: 
0:24:53.170061 PROGRESS: Protein Summary:
0:24:53.172190 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:24:53.172338 PROGRESS: =========================================================================
0:24:53.175308 INFO: Target number of precursors not reached yet.
0:24:53.309403 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:24:53.319585 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:53.335214 INFO: === skipping optimization until target number of precursors are found ===
0:24:53.335769 INFO: Starting optimization step 3.
0:24:53.335882 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:24:53.336009 INFO: Using rust extraction backend
0:24:53.336096 PROGRESS: Extracting batch of 7881 precursors
0:24:53.370629 INFO: === Search parameters used ===
0:24:53.371312 INFO: rt_error       : 805.5992431640625
0:24:53.371377 INFO: mobility_error : 0.1
0:24:53.371434 INFO: num_candidates : 3
0:24:53.371485 INFO: ms1_error      : 3
0:24:53.371539 INFO: ms2_error      : 10
0:24:53.371598 INFO: fwhm_rt        : 3.0
0:24:53.371646 INFO: quant_window   : 3
0:24:53.371689 INFO: ==============================================
0:24:53.697664 INFO: performing precursor FDR with 40 features
0:24:53.698013 INFO: Decoy channel: -1
0:24:53.698045 INFO: competitive: True
0:24:53.743290 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:53.771721 INFO: Estimating optimal hyperparameters - samples: 33,014, batch_size: 135, learning_rate: 1.82e-04
0:24:53.772322 INFO: Using random state 950877 for train-test-split
0:24:58.997306 INFO: Test AUC: 0.567
0:24:58.997459 INFO: Train AUC: 0.593
0:24:58.997490 INFO: AUC difference: 4.31%
0:24:59.257774 INFO: Resetting torch num_threads to 100
0:24:59.264568 PROGRESS: === Extracted 41268 precursors and 221135 fragments ===
0:24:59.265237 INFO: === FDR correction performed with classifier version 1 ===
0:24:59.265843 PROGRESS: ============================= Precursor FDR =============================
0:24:59.265930 PROGRESS: Total precursors accumulated: 2
0:24:59.265988 PROGRESS: Target precursors: 2 (100.00%)
0:24:59.266037 PROGRESS: Decoy precursors: 0 (0.00%)
0:24:59.266081 PROGRESS: 
0:24:59.266126 PROGRESS: Precursor Summary:
0:24:59.267172 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:24:59.267255 PROGRESS: 
0:24:59.267308 PROGRESS: Protein Summary:
0:24:59.268477 PROGRESS: Channel   0:	 0.050 FDR:     2; 0.010 FDR:     2; 0.001 FDR:     2
0:24:59.268571 PROGRESS: =========================================================================
0:24:59.269158 INFO: Target number of precursors not reached yet.
0:24:59.373670 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:24:59.383712 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:24:59.408313 INFO: === skipping optimization until target number of precursors are found ===
0:24:59.408649 INFO: Starting optimization step 4.
0:24:59.408731 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:24:59.408816 INFO: Using rust extraction backend
0:24:59.408891 PROGRESS: Extracting batch of 15776 precursors
0:24:59.440026 INFO: === Search parameters used ===
0:24:59.440372 INFO: rt_error       : 805.5992431640625
0:24:59.440439 INFO: mobility_error : 0.1
0:24:59.440496 INFO: num_candidates : 3
0:24:59.440550 INFO: ms1_error      : 3
0:24:59.440604 INFO: ms2_error      : 10
0:24:59.440657 INFO: fwhm_rt        : 3.0
0:24:59.440715 INFO: quant_window   : 3
0:24:59.440768 INFO: ==============================================
0:24:59.693286 INFO: performing precursor FDR with 40 features
0:24:59.693412 INFO: Decoy channel: -1
0:24:59.693437 INFO: competitive: True
0:24:59.722616 INFO: Setting torch num_threads to 2 for FDR classification task
0:24:59.746054 INFO: Estimating optimal hyperparameters - samples: 70,772, batch_size: 289, learning_rate: 2.66e-04
0:24:59.746306 INFO: Using random state 950877 for train-test-split
0:25:05.024154 INFO: Test AUC: 0.586
0:25:05.024266 INFO: Train AUC: 0.596
0:25:05.024298 INFO: AUC difference: 1.66%
0:25:05.301505 INFO: Resetting torch num_threads to 100
0:25:05.312248 PROGRESS: === Extracted 88465 precursors and 473563 fragments ===
0:25:05.312874 INFO: === FDR correction performed with classifier version 1 ===
0:25:05.313411 PROGRESS: ============================= Precursor FDR =============================
0:25:05.313496 PROGRESS: Total precursors accumulated: 0
0:25:05.313555 PROGRESS: Target precursors: 0 (0.00%)
0:25:05.313606 PROGRESS: Decoy precursors: 0 (0.00%)
0:25:05.313653 PROGRESS: 
0:25:05.313699 PROGRESS: Precursor Summary:
0:25:05.313816 PROGRESS: 
0:25:05.313875 PROGRESS: Protein Summary:
0:25:05.313951 PROGRESS: =========================================================================
0:25:05.315060 INFO: Target number of precursors not reached yet.
0:25:05.438456 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:25:05.457024 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:25:05.501037 INFO: === skipping optimization until target number of precursors are found ===
0:25:05.501328 INFO: Starting optimization step 5.
0:25:05.501414 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:25:05.501506 INFO: Using rust extraction backend
0:25:05.501582 PROGRESS: Extracting batch of 31591 precursors
0:25:05.562803 INFO: === Search parameters used ===
0:25:05.563093 INFO: rt_error       : 805.5992431640625
0:25:05.563160 INFO: mobility_error : 0.1
0:25:05.563220 INFO: num_candidates : 3
0:25:05.563276 INFO: ms1_error      : 3
0:25:05.563330 INFO: ms2_error      : 10
0:25:05.563383 INFO: fwhm_rt        : 3.0
0:25:05.563438 INFO: quant_window   : 3
0:25:05.563491 INFO: ==============================================
0:25:05.968728 INFO: performing precursor FDR with 40 features
0:25:05.968850 INFO: Decoy channel: -1
0:25:05.968876 INFO: competitive: True
0:25:06.048649 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:06.100937 INFO: Estimating optimal hyperparameters - samples: 146,388, batch_size: 599, learning_rate: 3.82e-04
0:25:06.101294 INFO: Using random state 950877 for train-test-split
0:25:13.180230 INFO: Test AUC: 0.585
0:25:13.180366 INFO: Train AUC: 0.597
0:25:13.180398 INFO: AUC difference: 2.01%
0:25:13.490578 INFO: Resetting torch num_threads to 100
0:25:13.522277 PROGRESS: === Extracted 182985 precursors and 982054 fragments ===
0:25:13.522926 INFO: === FDR correction performed with classifier version 1 ===
0:25:13.523515 PROGRESS: ============================= Precursor FDR =============================
0:25:13.523601 PROGRESS: Total precursors accumulated: 160
0:25:13.523659 PROGRESS: Target precursors: 159 (99.38%)
0:25:13.523709 PROGRESS: Decoy precursors: 1 (0.62%)
0:25:13.523754 PROGRESS: 
0:25:13.523803 PROGRESS: Precursor Summary:
0:25:13.524791 PROGRESS: Channel   0:	 0.050 FDR:   159; 0.010 FDR:   159; 0.001 FDR:     5
0:25:13.524875 PROGRESS: 
0:25:13.524928 PROGRESS: Protein Summary:
0:25:13.526011 PROGRESS: Channel   0:	 0.050 FDR:   155; 0.010 FDR:   155; 0.001 FDR:     5
0:25:13.526101 PROGRESS: =========================================================================
0:25:13.528514 INFO: Target number of precursors not reached yet.
0:25:13.734147 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:25:13.772375 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:25:13.866535 INFO: === skipping optimization until target number of precursors are found ===
0:25:13.867173 INFO: Starting optimization step 6.
0:25:13.867266 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:25:13.867357 INFO: Using rust extraction backend
0:25:13.867437 PROGRESS: Extracting batch of 63056 precursors
0:25:13.979331 INFO: === Search parameters used ===
0:25:13.979568 INFO: rt_error       : 805.5992431640625
0:25:13.979624 INFO: mobility_error : 0.1
0:25:13.979689 INFO: num_candidates : 3
0:25:13.979731 INFO: ms1_error      : 3
0:25:13.979771 INFO: ms2_error      : 10
0:25:13.979810 INFO: fwhm_rt        : 3.0
0:25:13.979869 INFO: quant_window   : 3
0:25:13.979911 INFO: ==============================================
0:25:14.718149 INFO: performing precursor FDR with 40 features
0:25:14.718266 INFO: Decoy channel: -1
0:25:14.718290 INFO: competitive: True
0:25:14.874897 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:15.010620 INFO: Estimating optimal hyperparameters - samples: 297,316, batch_size: 1,217, learning_rate: 5.45e-04
0:25:15.011193 INFO: Using random state 950877 for train-test-split
0:25:25.608705 INFO: Test AUC: 0.594
0:25:25.608879 INFO: Train AUC: 0.597
0:25:25.608914 INFO: AUC difference: 0.51%
0:25:25.970882 INFO: Resetting torch num_threads to 100
0:25:26.072466 PROGRESS: === Extracted 371645 precursors and 1997874 fragments ===
0:25:26.073195 INFO: === FDR correction performed with classifier version 1 ===
0:25:26.073855 PROGRESS: ============================= Precursor FDR =============================
0:25:26.073946 PROGRESS: Total precursors accumulated: 531
0:25:26.074013 PROGRESS: Target precursors: 526 (99.06%)
0:25:26.074065 PROGRESS: Decoy precursors: 5 (0.94%)
0:25:26.074121 PROGRESS: 
0:25:26.074171 PROGRESS: Precursor Summary:
0:25:26.075282 PROGRESS: Channel   0:	 0.050 FDR:   526; 0.010 FDR:   526; 0.001 FDR:   433
0:25:26.075370 PROGRESS: 
0:25:26.075427 PROGRESS: Protein Summary:
0:25:26.076726 PROGRESS: Channel   0:	 0.050 FDR:   489; 0.010 FDR:   489; 0.001 FDR:   406
0:25:26.076823 PROGRESS: =========================================================================
0:25:26.081445 INFO: Target number of precursors not reached yet.
0:25:26.417168 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:25:26.488227 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:25:26.680895 INFO: === skipping optimization until target number of precursors are found ===
0:25:26.681188 INFO: Starting optimization step 7.
0:25:26.681278 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:25:26.681411 INFO: Using rust extraction backend
0:25:26.681515 PROGRESS: Extracting batch of 126233 precursors
0:25:26.901884 INFO: === Search parameters used ===
0:25:26.902147 INFO: rt_error       : 805.5992431640625
0:25:26.902205 INFO: mobility_error : 0.1
0:25:26.902254 INFO: num_candidates : 3
0:25:26.902298 INFO: ms1_error      : 3
0:25:26.902340 INFO: ms2_error      : 10
0:25:26.902382 INFO: fwhm_rt        : 3.0
0:25:26.902423 INFO: quant_window   : 3
0:25:26.902464 INFO: ==============================================
0:25:28.350244 INFO: performing precursor FDR with 40 features
0:25:28.350355 INFO: Decoy channel: -1
0:25:28.350380 INFO: competitive: True
0:25:28.680636 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:28.960515 INFO: Estimating optimal hyperparameters - samples: 599,492, batch_size: 2,455, learning_rate: 7.74e-04
0:25:28.961395 INFO: Using random state 950877 for train-test-split
0:25:41.645913 INFO: Test AUC: 0.594
0:25:41.646044 INFO: Train AUC: 0.600
0:25:41.646076 INFO: AUC difference: 0.95%
0:25:42.494217 INFO: Resetting torch num_threads to 100
0:25:42.602876 PROGRESS: === Extracted 749365 precursors and 4023632 fragments ===
0:25:42.603567 INFO: === FDR correction performed with classifier version 1 ===
0:25:42.604429 PROGRESS: ============================= Precursor FDR =============================
0:25:42.604522 PROGRESS: Total precursors accumulated: 1,267
0:25:42.604584 PROGRESS: Target precursors: 1,255 (99.05%)
0:25:42.604634 PROGRESS: Decoy precursors: 12 (0.95%)
0:25:42.604681 PROGRESS: 
0:25:42.604726 PROGRESS: Precursor Summary:
0:25:42.606046 PROGRESS: Channel   0:	 0.050 FDR: 1,255; 0.010 FDR: 1,255; 0.001 FDR: 1,040
0:25:42.606135 PROGRESS: 
0:25:42.606193 PROGRESS: Protein Summary:
0:25:42.607873 PROGRESS: Channel   0:	 0.050 FDR: 1,065; 0.010 FDR: 1,065; 0.001 FDR:   900
0:25:42.607971 PROGRESS: =========================================================================
0:25:42.616174 INFO: Target number of precursors reached.
0:25:43.060501 INFO: fragments_df: keeping 5000 of 4023632 [sum(precursor_idx_mask)=30166 sum(mass_error_mask)=4023632 stop_rank=5000
0:25:43.473889 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:25:43.705985 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:25:44.421039 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:25:44.421496 INFO: Using score_cutoff 12.425827117538452 (fac=0.99, q=1)
0:25:44.421814 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:25:44.421891 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:25:44.421945 INFO: Updating optimization_manager: score_cutoff        : 5.517583786010743 -> 12.425827117538452
0:25:44.422010 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:25:44.573754 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:25:44.910968 INFO: === checking if optimization conditions were reached ===
0:25:44.913596 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
0:25:44.913768 INFO: Updating optimization_manager: classifier_version  : 1 -> 7
0:25:44.913847 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:25:44.913919 INFO: ==============================================
0:25:44.913999 INFO: Starting optimization step 8.
0:25:44.914166 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:25:44.914253 INFO: Using rust extraction backend
0:25:44.914329 PROGRESS: Extracting batch of 250442 precursors
0:25:45.337330 INFO: === Search parameters used ===
0:25:45.337617 INFO: rt_error       : 805.5992431640625
0:25:45.337678 INFO: mobility_error : 0.1
0:25:45.337728 INFO: num_candidates : 3
0:25:45.337774 INFO: ms1_error      : 3
0:25:45.337817 INFO: ms2_error      : 10.0
0:25:45.337859 INFO: fwhm_rt        : 3.0
0:25:45.337900 INFO: quant_window   : 3
0:25:45.337941 INFO: ==============================================
0:25:47.757636 INFO: performing precursor FDR with 40 features
0:25:47.757761 INFO: Decoy channel: -1
0:25:47.757787 INFO: competitive: True
0:25:47.935546 INFO: Setting torch num_threads to 2 for FDR classification task
0:25:48.220899 INFO: Estimating optimal hyperparameters - samples: 599,617, batch_size: 2,456, learning_rate: 7.74e-04
0:25:48.221708 INFO: Using random state 969198 for train-test-split
0:26:00.366476 INFO: Test AUC: 0.602
0:26:00.366612 INFO: Train AUC: 0.608
0:26:00.366644 INFO: AUC difference: 1.06%
0:26:00.845679 INFO: Resetting torch num_threads to 100
0:26:00.873809 PROGRESS: === Extracted 749522 precursors and 4029142 fragments ===
0:26:00.874323 INFO: === FDR correction performed with classifier version 7 ===
0:26:00.875015 PROGRESS: ============================= Precursor FDR =============================
0:26:00.875100 PROGRESS: Total precursors accumulated: 1,382
0:26:00.875159 PROGRESS: Target precursors: 1,369 (99.06%)
0:26:00.875211 PROGRESS: Decoy precursors: 13 (0.94%)
0:26:00.875257 PROGRESS: 
0:26:00.875302 PROGRESS: Precursor Summary:
0:26:00.876617 PROGRESS: Channel   0:	 0.050 FDR: 1,369; 0.010 FDR: 1,369; 0.001 FDR:   808
0:26:00.876714 PROGRESS: 
0:26:00.876770 PROGRESS: Protein Summary:
0:26:00.878414 PROGRESS: Channel   0:	 0.050 FDR: 1,153; 0.010 FDR: 1,153; 0.001 FDR:   712
0:26:00.878500 PROGRESS: =========================================================================
0:26:00.893560 INFO: Target number of precursors reached.
0:26:01.342242 INFO: fragments_df: keeping 5000 of 4029142 [sum(precursor_idx_mask)=32889 sum(mass_error_mask)=4029142 stop_rank=5000
0:26:01.818022 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:26:02.041065 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:26:02.750014 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:26:02.750446 INFO: Using score_cutoff 12.412777890014647 (fac=0.99, q=1)
0:26:02.750767 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:26:02.750845 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:26:02.750900 INFO: Updating optimization_manager: score_cutoff        : 12.425827117538452 -> 12.412777890014647
0:26:02.750959 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:02.902449 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:03.260031 INFO: === checking if optimization conditions were reached ===
0:26:03.262603 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:26:03.262767 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:26:03.262848 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:26:03.262945 INFO: ==============================================
0:26:03.263029 INFO: Starting optimization step 9.
0:26:03.263099 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:26:03.263178 INFO: Using rust extraction backend
0:26:03.263236 PROGRESS: Extracting batch of 250442 precursors
0:26:03.683267 INFO: === Search parameters used ===
0:26:03.683533 INFO: rt_error       : 805.5992431640625
0:26:03.683589 INFO: mobility_error : 0.1
0:26:03.683638 INFO: num_candidates : 3
0:26:03.683687 INFO: ms1_error      : 3
0:26:03.683730 INFO: ms2_error      : 10.0
0:26:03.683772 INFO: fwhm_rt        : 3.0
0:26:03.683815 INFO: quant_window   : 3
0:26:03.683872 INFO: ==============================================
0:26:06.174630 INFO: performing precursor FDR with 40 features
0:26:06.174746 INFO: Decoy channel: -1
0:26:06.174792 INFO: competitive: True
0:26:06.341725 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:06.624192 INFO: Estimating optimal hyperparameters - samples: 599,619, batch_size: 2,456, learning_rate: 7.74e-04
0:26:06.625189 INFO: Using random state 26590 for train-test-split
0:26:18.930092 INFO: Test AUC: 0.604
0:26:18.930245 INFO: Train AUC: 0.613
0:26:18.930277 INFO: AUC difference: 1.44%
0:26:19.407186 INFO: Resetting torch num_threads to 100
0:26:19.435122 PROGRESS: === Extracted 749524 precursors and 4029633 fragments ===
0:26:19.435599 INFO: === FDR correction performed with classifier version 8 ===
0:26:19.436245 PROGRESS: ============================= Precursor FDR =============================
0:26:19.436339 PROGRESS: Total precursors accumulated: 1,373
0:26:19.436399 PROGRESS: Target precursors: 1,360 (99.05%)
0:26:19.436451 PROGRESS: Decoy precursors: 13 (0.95%)
0:26:19.436499 PROGRESS: 
0:26:19.436545 PROGRESS: Precursor Summary:
0:26:19.437860 PROGRESS: Channel   0:	 0.050 FDR: 1,360; 0.010 FDR: 1,360; 0.001 FDR: 1,083
0:26:19.437945 PROGRESS: 
0:26:19.438000 PROGRESS: Protein Summary:
0:26:19.439672 PROGRESS: Channel   0:	 0.050 FDR: 1,157; 0.010 FDR: 1,157; 0.001 FDR:   931
0:26:19.439765 PROGRESS: =========================================================================
0:26:19.453610 INFO: Target number of precursors reached.
0:26:19.897466 INFO: fragments_df: keeping 5000 of 4029633 [sum(precursor_idx_mask)=32416 sum(mass_error_mask)=4029633 stop_rank=5000
0:26:20.368747 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:26:20.589736 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:26:21.302361 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:26:21.302792 INFO: Using score_cutoff 12.173140082359314 (fac=0.99, q=1)
0:26:21.303104 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:26:21.303183 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:26:21.303238 INFO: Updating optimization_manager: score_cutoff        : 12.412777890014647 -> 12.173140082359314
0:26:21.303291 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:21.454784 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:21.809287 INFO: === checking if optimization conditions were reached ===
0:26:21.811876 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:26:21.812043 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:26:21.812141 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:26:21.812214 INFO: ==============================================
0:26:21.812293 INFO: Starting optimization step 10.
0:26:21.812362 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:26:21.812434 INFO: Using rust extraction backend
0:26:21.812510 PROGRESS: Extracting batch of 250442 precursors
0:26:22.233907 INFO: === Search parameters used ===
0:26:22.234170 INFO: rt_error       : 805.5992431640625
0:26:22.234226 INFO: mobility_error : 0.1
0:26:22.234275 INFO: num_candidates : 3
0:26:22.234318 INFO: ms1_error      : 3
0:26:22.234360 INFO: ms2_error      : 10.0
0:26:22.234421 INFO: fwhm_rt        : 3.0
0:26:22.234461 INFO: quant_window   : 3
0:26:22.234499 INFO: ==============================================
0:26:24.779285 INFO: performing precursor FDR with 40 features
0:26:24.779408 INFO: Decoy channel: -1
0:26:24.779435 INFO: competitive: True
0:26:24.972742 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:25.284037 INFO: Estimating optimal hyperparameters - samples: 599,628, batch_size: 2,456, learning_rate: 7.74e-04
0:26:25.285125 INFO: Using random state 461072 for train-test-split
0:26:37.827548 INFO: Test AUC: 0.608
0:26:37.827733 INFO: Train AUC: 0.616
0:26:37.827767 INFO: AUC difference: 1.28%
0:26:38.309493 INFO: Resetting torch num_threads to 100
0:26:38.338392 PROGRESS: === Extracted 749535 precursors and 4030471 fragments ===
0:26:38.338893 INFO: === FDR correction performed with classifier version 9 ===
0:26:38.339621 PROGRESS: ============================= Precursor FDR =============================
0:26:38.339708 PROGRESS: Total precursors accumulated: 1,447
0:26:38.339767 PROGRESS: Target precursors: 1,433 (99.03%)
0:26:38.339829 PROGRESS: Decoy precursors: 14 (0.97%)
0:26:38.339898 PROGRESS: 
0:26:38.339945 PROGRESS: Precursor Summary:
0:26:38.341196 PROGRESS: Channel   0:	 0.050 FDR: 1,433; 0.010 FDR: 1,433; 0.001 FDR:   425
0:26:38.341281 PROGRESS: 
0:26:38.341334 PROGRESS: Protein Summary:
0:26:38.342933 PROGRESS: Channel   0:	 0.050 FDR: 1,210; 0.010 FDR: 1,210; 0.001 FDR:   386
0:26:38.343020 PROGRESS: =========================================================================
0:26:38.357053 INFO: Target number of precursors reached.
0:26:38.797198 INFO: fragments_df: keeping 5000 of 4030471 [sum(precursor_idx_mask)=34174 sum(mass_error_mask)=4030471 stop_rank=5000
0:26:39.222401 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:26:39.454561 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:26:40.166875 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:26:40.167298 INFO: Using score_cutoff 12.294486553573607 (fac=0.99, q=1)
0:26:40.167608 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:26:40.167686 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:26:40.167742 INFO: Updating optimization_manager: score_cutoff        : 12.173140082359314 -> 12.294486553573607
0:26:40.167796 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:40.319625 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:40.647071 INFO: === checking if optimization conditions were reached ===
0:26:40.649264 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:26:40.649430 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:26:40.649499 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:26:40.649563 INFO: ==============================================
0:26:40.649632 INFO: Starting optimization step 11.
0:26:40.649689 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:26:40.649755 INFO: Using rust extraction backend
0:26:40.649812 PROGRESS: Extracting batch of 250442 precursors
0:26:41.072784 INFO: === Search parameters used ===
0:26:41.073081 INFO: rt_error       : 805.5992431640625
0:26:41.073135 INFO: mobility_error : 0.1
0:26:41.073179 INFO: num_candidates : 3
0:26:41.073222 INFO: ms1_error      : 3
0:26:41.073263 INFO: ms2_error      : 10.0
0:26:41.073303 INFO: fwhm_rt        : 3.0
0:26:41.073342 INFO: quant_window   : 3
0:26:41.073381 INFO: ==============================================
0:26:43.605342 INFO: performing precursor FDR with 40 features
0:26:43.605483 INFO: Decoy channel: -1
0:26:43.605507 INFO: competitive: True
0:26:43.781812 INFO: Setting torch num_threads to 2 for FDR classification task
0:26:44.065035 INFO: Estimating optimal hyperparameters - samples: 599,639, batch_size: 2,456, learning_rate: 7.74e-04
0:26:44.066135 INFO: Using random state 115778 for train-test-split
0:26:56.051287 INFO: Test AUC: 0.610
0:26:56.051440 INFO: Train AUC: 0.619
0:26:56.051475 INFO: AUC difference: 1.46%
0:26:56.530330 INFO: Resetting torch num_threads to 100
0:26:56.561702 PROGRESS: === Extracted 749549 precursors and 4030138 fragments ===
0:26:56.562204 INFO: === FDR correction performed with classifier version 10 ===
0:26:56.562844 PROGRESS: ============================= Precursor FDR =============================
0:26:56.562931 PROGRESS: Total precursors accumulated: 1,492
0:26:56.562990 PROGRESS: Target precursors: 1,478 (99.06%)
0:26:56.563054 PROGRESS: Decoy precursors: 14 (0.94%)
0:26:56.563103 PROGRESS: 
0:26:56.563147 PROGRESS: Precursor Summary:
0:26:56.564424 PROGRESS: Channel   0:	 0.050 FDR: 1,478; 0.010 FDR: 1,478; 0.001 FDR:   572
0:26:56.564512 PROGRESS: 
0:26:56.564567 PROGRESS: Protein Summary:
0:26:56.566210 PROGRESS: Channel   0:	 0.050 FDR: 1,246; 0.010 FDR: 1,246; 0.001 FDR:   516
0:26:56.566296 PROGRESS: =========================================================================
0:26:56.579641 INFO: Target number of precursors reached.
0:26:57.026448 INFO: fragments_df: keeping 5000 of 4030138 [sum(precursor_idx_mask)=35376 sum(mass_error_mask)=4030138 stop_rank=5000
0:26:57.455438 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:26:57.686492 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:26:58.397072 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:26:58.397501 INFO: Using score_cutoff 12.31692265176773 (fac=0.99, q=1)
0:26:58.397806 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:26:58.397883 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:26:58.397937 INFO: Updating optimization_manager: score_cutoff        : 12.294486553573607 -> 12.31692265176773
0:26:58.397989 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:58.549246 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:58.895291 INFO: === checking if optimization conditions were reached ===
0:26:58.897853 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:26:58.898025 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:26:58.898103 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:26:58.898174 INFO: ==============================================
0:26:58.898254 PROGRESS: Optimization finished for ms2_error.
0:26:59.292736 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:26:59.443463 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:26:59.787078 INFO: Starting optimization step 0.
0:26:59.787364 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:26:59.787467 INFO: Using rust extraction backend
0:26:59.787540 PROGRESS: Extracting batch of 250442 precursors
0:27:00.208458 INFO: === Search parameters used ===
0:27:00.208722 INFO: rt_error       : 805.5992431640625
0:27:00.208780 INFO: mobility_error : 0.1
0:27:00.208829 INFO: num_candidates : 3
0:27:00.208878 INFO: ms1_error      : 3
0:27:00.208924 INFO: ms2_error      : 10.0
0:27:00.208968 INFO: fwhm_rt        : 3.0
0:27:00.209012 INFO: quant_window   : 3
0:27:00.209055 INFO: ==============================================
0:27:02.701402 INFO: performing precursor FDR with 40 features
0:27:02.701522 INFO: Decoy channel: -1
0:27:02.701549 INFO: competitive: True
0:27:02.890201 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:03.179990 INFO: Estimating optimal hyperparameters - samples: 599,627, batch_size: 2,456, learning_rate: 7.74e-04
0:27:03.181087 INFO: Using random state 229027 for train-test-split
0:27:15.371964 INFO: Test AUC: 0.609
0:27:15.372103 INFO: Train AUC: 0.621
0:27:15.372136 INFO: AUC difference: 1.91%
0:27:15.840105 INFO: Resetting torch num_threads to 100
0:27:15.881255 PROGRESS: === Extracted 749534 precursors and 4030447 fragments ===
0:27:15.881741 INFO: === FDR correction performed with classifier version 11 ===
0:27:15.882375 PROGRESS: ============================= Precursor FDR =============================
0:27:15.882460 PROGRESS: Total precursors accumulated: 1,494
0:27:15.882519 PROGRESS: Target precursors: 1,480 (99.06%)
0:27:15.882570 PROGRESS: Decoy precursors: 14 (0.94%)
0:27:15.882617 PROGRESS: 
0:27:15.882662 PROGRESS: Precursor Summary:
0:27:15.883944 PROGRESS: Channel   0:	 0.050 FDR: 1,480; 0.010 FDR: 1,480; 0.001 FDR:   644
0:27:15.884033 PROGRESS: 
0:27:15.884086 PROGRESS: Protein Summary:
0:27:15.885736 PROGRESS: Channel   0:	 0.050 FDR: 1,255; 0.010 FDR: 1,255; 0.001 FDR:   576
0:27:15.885825 PROGRESS: =========================================================================
0:27:15.899277 INFO: Target number of precursors reached.
0:27:16.338454 INFO: fragments_df: keeping 5000 of 4030447 [sum(precursor_idx_mask)=35165 sum(mass_error_mask)=4030447 stop_rank=5000
0:27:16.746924 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:17.001671 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:17.722415 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:17.722850 INFO: Using score_cutoff 12.233149863052368 (fac=0.99, q=1)
0:27:17.723148 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:17.723224 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:17.723284 INFO: Updating optimization_manager: score_cutoff        : 12.31692265176773 -> 12.233149863052368
0:27:17.723339 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:17.872275 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:18.222648 INFO: === checking if optimization conditions were reached ===
0:27:18.222983 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:27:18.226039 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 822.4196136812639
0:27:18.226190 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 822.4196.
0:27:18.226266 INFO: ==============================================
0:27:18.226338 INFO: Starting optimization step 1.
0:27:18.226395 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:27:18.226464 INFO: Using rust extraction backend
0:27:18.226518 PROGRESS: Extracting batch of 250442 precursors
0:27:18.645467 INFO: === Search parameters used ===
0:27:18.645719 INFO: rt_error       : 822.4196136812639
0:27:18.645771 INFO: mobility_error : 0.1
0:27:18.645815 INFO: num_candidates : 3
0:27:18.645856 INFO: ms1_error      : 3
0:27:18.645895 INFO: ms2_error      : 10.0
0:27:18.645934 INFO: fwhm_rt        : 3.0
0:27:18.645972 INFO: quant_window   : 3
0:27:18.646029 INFO: ==============================================
0:27:21.165445 INFO: performing precursor FDR with 40 features
0:27:21.165580 INFO: Decoy channel: -1
0:27:21.165607 INFO: competitive: True
0:27:21.357381 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:21.658805 INFO: Estimating optimal hyperparameters - samples: 599,618, batch_size: 2,456, learning_rate: 7.74e-04
0:27:21.659909 INFO: Using random state 229027 for train-test-split
0:27:33.668248 INFO: Test AUC: 0.609
0:27:33.668389 INFO: Train AUC: 0.619
0:27:33.668421 INFO: AUC difference: 1.62%
0:27:34.137848 INFO: Resetting torch num_threads to 100
0:27:34.163661 PROGRESS: === Extracted 749523 precursors and 4030838 fragments ===
0:27:34.164156 INFO: === FDR correction performed with classifier version 11 ===
0:27:34.164807 PROGRESS: ============================= Precursor FDR =============================
0:27:34.164894 PROGRESS: Total precursors accumulated: 1,582
0:27:34.164953 PROGRESS: Target precursors: 1,567 (99.05%)
0:27:34.165004 PROGRESS: Decoy precursors: 15 (0.95%)
0:27:34.165051 PROGRESS: 
0:27:34.165097 PROGRESS: Precursor Summary:
0:27:34.166425 PROGRESS: Channel   0:	 0.050 FDR: 1,567; 0.010 FDR: 1,567; 0.001 FDR: 1,056
0:27:34.166512 PROGRESS: 
0:27:34.166567 PROGRESS: Protein Summary:
0:27:34.168323 PROGRESS: Channel   0:	 0.050 FDR: 1,346; 0.010 FDR: 1,346; 0.001 FDR:   917
0:27:34.168420 PROGRESS: =========================================================================
0:27:34.181784 INFO: Target number of precursors reached.
0:27:34.618800 INFO: fragments_df: keeping 5000 of 4030838 [sum(precursor_idx_mask)=36373 sum(mass_error_mask)=4030838 stop_rank=5000
0:27:35.041617 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:35.284974 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:35.999082 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:35.999511 INFO: Using score_cutoff 9.60344640712738 (fac=0.99, q=1)
0:27:35.999824 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:35.999906 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:35.999968 INFO: Updating optimization_manager: score_cutoff        : 12.233149863052368 -> 9.60344640712738
0:27:36.000020 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:36.151152 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:36.494568 INFO: === checking if optimization conditions were reached ===
0:27:36.494867 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:27:36.498118 INFO: Updating optimization_manager: rt_error            : 822.4196136812639 -> 841.1339757741016
0:27:36.498276 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 841.1340.
0:27:36.498356 INFO: ==============================================
0:27:36.498440 INFO: Starting optimization step 2.
0:27:36.498512 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:27:36.498587 INFO: Using rust extraction backend
0:27:36.498658 PROGRESS: Extracting batch of 250442 precursors
0:27:36.922257 INFO: === Search parameters used ===
0:27:36.922522 INFO: rt_error       : 841.1339757741016
0:27:36.922583 INFO: mobility_error : 0.1
0:27:36.922632 INFO: num_candidates : 3
0:27:36.922678 INFO: ms1_error      : 3
0:27:36.922724 INFO: ms2_error      : 10.0
0:27:36.922784 INFO: fwhm_rt        : 3.0
0:27:36.922827 INFO: quant_window   : 3
0:27:36.922870 INFO: ==============================================
0:27:39.424483 INFO: performing precursor FDR with 40 features
0:27:39.424605 INFO: Decoy channel: -1
0:27:39.424630 INFO: competitive: True
0:27:39.615293 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:39.921715 INFO: Estimating optimal hyperparameters - samples: 599,649, batch_size: 2,456, learning_rate: 7.74e-04
0:27:39.922554 INFO: Using random state 229027 for train-test-split
0:27:52.015884 INFO: Test AUC: 0.611
0:27:52.016023 INFO: Train AUC: 0.620
0:27:52.016057 INFO: AUC difference: 1.56%
0:27:52.939432 INFO: Resetting torch num_threads to 100
0:27:52.995939 PROGRESS: === Extracted 749562 precursors and 4031609 fragments ===
0:27:52.996411 INFO: === FDR correction performed with classifier version 11 ===
0:27:52.997057 PROGRESS: ============================= Precursor FDR =============================
0:27:52.997144 PROGRESS: Total precursors accumulated: 1,617
0:27:52.997203 PROGRESS: Target precursors: 1,601 (99.01%)
0:27:52.997258 PROGRESS: Decoy precursors: 16 (0.99%)
0:27:52.997305 PROGRESS: 
0:27:52.997352 PROGRESS: Precursor Summary:
0:27:52.998740 PROGRESS: Channel   0:	 0.050 FDR: 1,601; 0.010 FDR: 1,601; 0.001 FDR: 1,270
0:27:52.998839 PROGRESS: 
0:27:52.998897 PROGRESS: Protein Summary:
0:27:53.000716 PROGRESS: Channel   0:	 0.050 FDR: 1,357; 0.010 FDR: 1,357; 0.001 FDR: 1,082
0:27:53.000815 PROGRESS: =========================================================================
0:27:53.014632 INFO: Target number of precursors reached.
0:27:53.451886 INFO: fragments_df: keeping 5000 of 4031609 [sum(precursor_idx_mask)=37674 sum(mass_error_mask)=4031609 stop_rank=5000
0:27:53.886961 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:27:54.143195 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:27:54.856452 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:27:54.856884 INFO: Using score_cutoff 10.969222583770751 (fac=0.99, q=1)
0:27:54.857219 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:27:54.857307 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:27:54.857369 INFO: Updating optimization_manager: score_cutoff        : 9.60344640712738 -> 10.969222583770751
0:27:54.857435 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:27:55.008866 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:27:55.347429 INFO: === checking if optimization conditions were reached ===
0:27:55.347758 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:27:55.351144 INFO: Updating optimization_manager: rt_error            : 841.1339757741016 -> 631.0102974097422
0:27:55.351268 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 631.0103.
0:27:55.351344 INFO: ==============================================
0:27:55.351425 INFO: Starting optimization step 3.
0:27:55.351492 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:27:55.351563 INFO: Using rust extraction backend
0:27:55.351630 PROGRESS: Extracting batch of 250442 precursors
0:27:55.775248 INFO: === Search parameters used ===
0:27:55.775508 INFO: rt_error       : 631.0102974097422
0:27:55.775563 INFO: mobility_error : 0.1
0:27:55.775610 INFO: num_candidates : 3
0:27:55.775671 INFO: ms1_error      : 3
0:27:55.775715 INFO: ms2_error      : 10.0
0:27:55.775756 INFO: fwhm_rt        : 3.0
0:27:55.775797 INFO: quant_window   : 3
0:27:55.775848 INFO: ==============================================
0:27:58.183803 INFO: performing precursor FDR with 40 features
0:27:58.183957 INFO: Decoy channel: -1
0:27:58.183983 INFO: competitive: True
0:27:58.366702 INFO: Setting torch num_threads to 2 for FDR classification task
0:27:58.667448 INFO: Estimating optimal hyperparameters - samples: 599,597, batch_size: 2,455, learning_rate: 7.74e-04
0:27:58.668540 INFO: Using random state 229027 for train-test-split
0:28:11.618003 INFO: Test AUC: 0.611
0:28:11.618144 INFO: Train AUC: 0.619
0:28:11.618176 INFO: AUC difference: 1.37%
0:28:12.102601 INFO: Resetting torch num_threads to 100
0:28:12.133401 PROGRESS: === Extracted 749497 precursors and 4024217 fragments ===
0:28:12.133883 INFO: === FDR correction performed with classifier version 11 ===
0:28:12.134556 PROGRESS: ============================= Precursor FDR =============================
0:28:12.134642 PROGRESS: Total precursors accumulated: 1,568
0:28:12.134701 PROGRESS: Target precursors: 1,553 (99.04%)
0:28:12.134754 PROGRESS: Decoy precursors: 15 (0.96%)
0:28:12.134802 PROGRESS: 
0:28:12.134848 PROGRESS: Precursor Summary:
0:28:12.136207 PROGRESS: Channel   0:	 0.050 FDR: 1,553; 0.010 FDR: 1,553; 0.001 FDR: 1,115
0:28:12.136299 PROGRESS: 
0:28:12.136355 PROGRESS: Protein Summary:
0:28:12.138108 PROGRESS: Channel   0:	 0.050 FDR: 1,312; 0.010 FDR: 1,312; 0.001 FDR:   956
0:28:12.138197 PROGRESS: =========================================================================
0:28:12.155131 INFO: Target number of precursors reached.
0:28:12.605480 INFO: fragments_df: keeping 5000 of 4024217 [sum(precursor_idx_mask)=36923 sum(mass_error_mask)=4024217 stop_rank=5000
0:28:13.027254 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:28:13.266076 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:28:13.979325 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:28:13.979755 INFO: Using score_cutoff 12.160717630004882 (fac=0.99, q=1)
0:28:13.980397 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:28:13.980479 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:28:13.980534 INFO: Updating optimization_manager: score_cutoff        : 10.969222583770751 -> 12.160717630004882
0:28:13.980588 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:14.135736 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:14.482375 INFO: === checking if optimization conditions were reached ===
0:28:14.482681 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:28:14.486066 INFO: Updating optimization_manager: rt_error            : 631.0102974097422 -> 607.111834336466
0:28:14.486233 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 607.1118.
0:28:14.486313 INFO: ==============================================
0:28:14.486398 INFO: Starting optimization step 4.
0:28:14.486469 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:28:14.486544 INFO: Using rust extraction backend
0:28:14.486616 PROGRESS: Extracting batch of 250442 precursors
0:28:14.912241 INFO: === Search parameters used ===
0:28:14.912510 INFO: rt_error       : 607.111834336466
0:28:14.912588 INFO: mobility_error : 0.1
0:28:14.912638 INFO: num_candidates : 3
0:28:14.912683 INFO: ms1_error      : 3
0:28:14.912726 INFO: ms2_error      : 10.0
0:28:14.912768 INFO: fwhm_rt        : 3.0
0:28:14.912809 INFO: quant_window   : 3
0:28:14.912850 INFO: ==============================================
0:28:17.347477 INFO: performing precursor FDR with 40 features
0:28:17.347603 INFO: Decoy channel: -1
0:28:17.347628 INFO: competitive: True
0:28:17.533905 INFO: Setting torch num_threads to 2 for FDR classification task
0:28:17.821420 INFO: Estimating optimal hyperparameters - samples: 599,496, batch_size: 2,455, learning_rate: 7.74e-04
0:28:17.822513 INFO: Using random state 229027 for train-test-split
0:28:31.299458 INFO: Test AUC: 0.611
0:28:31.299617 INFO: Train AUC: 0.620
0:28:31.299649 INFO: AUC difference: 1.39%
0:28:31.782030 INFO: Resetting torch num_threads to 100
0:28:31.806329 PROGRESS: === Extracted 749371 precursors and 4017480 fragments ===
0:28:31.806818 INFO: === FDR correction performed with classifier version 11 ===
0:28:31.807472 PROGRESS: ============================= Precursor FDR =============================
0:28:31.807563 PROGRESS: Total precursors accumulated: 1,586
0:28:31.807623 PROGRESS: Target precursors: 1,571 (99.05%)
0:28:31.807676 PROGRESS: Decoy precursors: 15 (0.95%)
0:28:31.807725 PROGRESS: 
0:28:31.807771 PROGRESS: Precursor Summary:
0:28:31.809165 PROGRESS: Channel   0:	 0.050 FDR: 1,571; 0.010 FDR: 1,571; 0.001 FDR: 1,094
0:28:31.809264 PROGRESS: 
0:28:31.809319 PROGRESS: Protein Summary:
0:28:31.811086 PROGRESS: Channel   0:	 0.050 FDR: 1,348; 0.010 FDR: 1,348; 0.001 FDR:   942
0:28:31.811180 PROGRESS: =========================================================================
0:28:31.824847 INFO: Target number of precursors reached.
0:28:32.274754 INFO: fragments_df: keeping 5000 of 4017480 [sum(precursor_idx_mask)=36380 sum(mass_error_mask)=4017480 stop_rank=5000
0:28:32.682497 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:28:32.922799 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:28:33.635798 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:28:33.636253 INFO: Using score_cutoff 9.320729962348938 (fac=0.99, q=1)
0:28:33.636553 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:28:33.636626 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:28:33.636677 INFO: Updating optimization_manager: score_cutoff        : 12.160717630004882 -> 9.320729962348938
0:28:33.636730 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:33.788784 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:34.121494 INFO: === checking if optimization conditions were reached ===
0:28:34.121769 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:28:34.122634 INFO: Updating optimization_manager: rt_error            : 607.111834336466 -> 841.1339757741016
0:28:34.122756 INFO: Updating optimization_manager: classifier_version  : 11 -> 14
0:28:34.122849 INFO: Updating optimization_manager: score_cutoff        : 9.320729962348938 -> 10.969222583770751
0:28:34.122936 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:28:34.123021 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:28:34.123108 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 841.1340 found after 5 searches.
0:28:34.123166 INFO: ==============================================
0:28:34.123254 PROGRESS: Optimization finished for rt_error.
0:28:34.512392 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:34.664519 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:34.997087 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:28:34.997345 PROGRESS: ==============================================
0:28:34.997420 PROGRESS: ms2_error      : 10.0000
0:28:34.997477 PROGRESS: rt_error       : 841.1340
0:28:34.997525 PROGRESS: ==============================================
0:28:35.003757 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:28:42.746249 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:28:59.857903 INFO: Using rust extraction backend
0:28:59.860202 PROGRESS: Extracting batch of 11997144 precursors
0:29:16.171315 INFO: === Search parameters used ===
0:29:16.171870 INFO: rt_error       : 841.1339757741016
0:29:16.171951 INFO: mobility_error : 0.1
0:29:16.172006 INFO: num_candidates : 3
0:29:16.172054 INFO: ms1_error      : 3
0:29:16.172102 INFO: ms2_error      : 10.0
0:29:16.172148 INFO: fwhm_rt        : 3.0
0:29:16.172190 INFO: quant_window   : 3
0:29:16.172232 INFO: ==============================================
0:29:49.837528 INFO: Removed 9046646 precursors with score below cutoff 10.969222583770751
0:30:11.396560 INFO: performing precursor FDR with 40 features
0:30:11.396697 INFO: Decoy channel: -1
0:30:11.396730 INFO: competitive: True
0:30:14.315521 INFO: Setting torch num_threads to 2 for FDR classification task
0:30:25.304116 INFO: Estimating optimal hyperparameters - samples: 21,555,595, batch_size: 4,096, learning_rate: 1.00e-03
0:30:25.378496 INFO: Using random state 488850 for train-test-split
0:37:58.088634 INFO: Test AUC: 0.622
0:37:58.088965 INFO: Train AUC: 0.622
0:37:58.089015 INFO: AUC difference: 0.05%
0:38:04.689087 INFO: Resetting torch num_threads to 100
0:38:06.964002 PROGRESS: ============================= Precursor FDR =============================
0:38:06.964443 PROGRESS: Total precursors accumulated: 87,397
0:38:06.964522 PROGRESS: Target precursors: 86,532 (99.01%)
0:38:06.964579 PROGRESS: Decoy precursors: 865 (0.99%)
0:38:06.964628 PROGRESS: 
0:38:06.964676 PROGRESS: Precursor Summary:
0:38:06.990518 PROGRESS: Channel   0:	 0.050 FDR: 86,532; 0.010 FDR: 86,532; 0.001 FDR: 37,081
0:38:06.990762 PROGRESS: 
0:38:06.990834 PROGRESS: Protein Summary:
0:38:07.025519 PROGRESS: Channel   0:	 0.050 FDR: 14,177; 0.010 FDR: 14,177; 0.001 FDR: 7,484
0:38:07.025749 PROGRESS: =========================================================================
0:38:07.191880 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/psm.parquet
0:38:07.373417 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.parquet
0:38:07.587711 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
0:38:08.266706 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 
0:38:08.266888 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
0:38:08.267036 INFO: Initializing TimingManager
0:38:08.268184 INFO: Initializing RawFileManager
0:38:22.152992 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.
0:38:22.161940 INFO: Determining DIA cycle
0:38:22.179466 INFO: Found cycle with start 0.00 min and length 300.
0:38:22.346817 INFO: RT (min)            : 0.0 - 26.9
0:38:22.346926 INFO: RT duration (sec)   : 1611.2
0:38:22.346956 INFO: RT duration (min)   : 26.9
0:38:22.346978 INFO: Cycle len (scans)   : 300
0:38:22.346999 INFO: Cycle len (sec)     : 1.65
0:38:22.347018 INFO: Number of cycles    : 978
0:38:22.347039 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:38:22.347068 INFO: Creating DIA data object took: 14.078783988952637
0:38:23.017721 INFO: Creating DIA data NG object took: 0.6705269813537598
0:38:24.681085 INFO: Initializing CalibrationManager
0:38:24.681402 INFO: Setting up calibration estimators ..
0:38:24.681475 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:38:24.681562 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'}' ..
0:38:24.681664 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:38:24.681720 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:38:24.681774 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}}' ..
0:38:24.681825 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:38:24.681869 INFO: Done setting up calibration estimators.
0:38:24.682575 INFO: Initializing OptimizationManager
0:38:24.682854 INFO: initial parameter: ms1_error = 3
0:38:24.682912 INFO: initial parameter: ms2_error = 10
0:38:24.682963 INFO: initial parameter: rt_error = 805.6019897460938
0:38:24.683009 INFO: initial parameter: mobility_error = 0.1
0:38:24.683052 INFO: initial parameter: num_candidates = 1
0:38:24.683094 INFO: initial parameter: fwhm_rt = 5
0:38:24.683139 INFO: initial parameter: fwhm_mobility = 0.01
0:38:24.683185 INFO: initial parameter: score_cutoff = 0
0:38:24.683229 INFO: initial parameter: classifier_version = -1
0:38:24.683300 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:38:24.683717 INFO: FDRManager: loading saved state not requested, will be initialized.
0:38:24.683753 INFO: Initializing FDRManager
0:38:24.683809 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
0:38:26.231585 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
0:38:27.237643 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
0:38:27.238120 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
0:38:27.238250 PROGRESS: Starting initial search for precursors.
0:38:27.238346 INFO: Starting optimization step 0.
0:38:27.238411 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:38:27.238473 INFO: Using rust extraction backend
0:38:27.238532 PROGRESS: Extracting batch of 1970 precursors
0:38:27.243379 INFO: === Search parameters used ===
0:38:27.243486 INFO: rt_error       : 805.6019897460938
0:38:27.243538 INFO: mobility_error : 0.1
0:38:27.243583 INFO: num_candidates : 1
0:38:27.243625 INFO: ms1_error      : 3
0:38:27.243664 INFO: ms2_error      : 10
0:38:27.243702 INFO: fwhm_rt        : 5
0:38:27.243740 INFO: quant_window   : 3
0:38:27.243778 INFO: ==============================================
0:38:27.273950 INFO: performing precursor FDR with 40 features
0:38:27.274049 INFO: Decoy channel: -1
0:38:27.274073 INFO: competitive: True
0:38:27.275586 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:27.277704 INFO: Estimating optimal hyperparameters - samples: 1,573, batch_size: 128, learning_rate: 1.77e-04
0:38:27.278555 INFO: Using random state 127129 for train-test-split
0:38:27.433700 INFO: Test AUC: 0.505
0:38:27.433790 INFO: Train AUC: 0.588
0:38:27.433817 INFO: AUC difference: 13.99%
0:38:27.433840 WARNING: AUC difference > 5%. This may indicate overfitting.
0:38:27.677541 INFO: Resetting torch num_threads to 100
0:38:27.679267 PROGRESS: === Extracted 1967 precursors and 10879 fragments ===
0:38:27.679657 INFO: === FDR correction performed with classifier version -1 ===
0:38:27.680161 PROGRESS: ============================= Precursor FDR =============================
0:38:27.680249 PROGRESS: Total precursors accumulated: 21
0:38:27.680306 PROGRESS: Target precursors: 21 (100.00%)
0:38:27.680352 PROGRESS: Decoy precursors: 0 (0.00%)
0:38:27.680395 PROGRESS: 
0:38:27.680436 PROGRESS: Precursor Summary:
0:38:27.681484 PROGRESS: Channel   0:	 0.050 FDR:    21; 0.010 FDR:    21; 0.001 FDR:    21
0:38:27.681566 PROGRESS: 
0:38:27.681618 PROGRESS: Protein Summary:
0:38:27.682802 PROGRESS: Channel   0:	 0.050 FDR:    20; 0.010 FDR:    20; 0.001 FDR:    20
0:38:27.682887 PROGRESS: =========================================================================
0:38:27.683123 INFO: Target number of precursors not reached yet.
0:38:27.768489 INFO: Starting optimization step 1.
0:38:27.768724 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:38:27.768808 INFO: Using rust extraction backend
0:38:27.768869 PROGRESS: Extracting batch of 3935 precursors
0:38:27.777549 INFO: === Search parameters used ===
0:38:27.777683 INFO: rt_error       : 805.6019897460938
0:38:27.777735 INFO: mobility_error : 0.1
0:38:27.777779 INFO: num_candidates : 1
0:38:27.777820 INFO: ms1_error      : 3
0:38:27.777860 INFO: ms2_error      : 10
0:38:27.777900 INFO: fwhm_rt        : 5
0:38:27.777939 INFO: quant_window   : 3
0:38:27.777977 INFO: ==============================================
0:38:27.826648 INFO: performing precursor FDR with 40 features
0:38:27.826735 INFO: Decoy channel: -1
0:38:27.826758 INFO: competitive: True
0:38:27.831396 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:27.834068 INFO: Estimating optimal hyperparameters - samples: 4,711, batch_size: 128, learning_rate: 1.77e-04
0:38:27.834153 INFO: Using random state 763906 for train-test-split
0:38:28.303212 INFO: Test AUC: 0.514
0:38:28.303303 INFO: Train AUC: 0.578
0:38:28.303331 INFO: AUC difference: 10.96%
0:38:28.303351 WARNING: AUC difference > 5%. This may indicate overfitting.
0:38:28.544664 INFO: Resetting torch num_threads to 100
0:38:28.547846 PROGRESS: === Extracted 5889 precursors and 32686 fragments ===
0:38:28.548227 INFO: === FDR correction performed with classifier version -1 ===
0:38:28.548713 PROGRESS: ============================= Precursor FDR =============================
0:38:28.548794 PROGRESS: Total precursors accumulated: 24
0:38:28.548849 PROGRESS: Target precursors: 24 (100.00%)
0:38:28.548897 PROGRESS: Decoy precursors: 0 (0.00%)
0:38:28.548940 PROGRESS: 
0:38:28.548983 PROGRESS: Precursor Summary:
0:38:28.550021 PROGRESS: Channel   0:	 0.050 FDR:    24; 0.010 FDR:    24; 0.001 FDR:    24
0:38:28.550100 PROGRESS: 
0:38:28.550153 PROGRESS: Protein Summary:
0:38:28.551324 PROGRESS: Channel   0:	 0.050 FDR:    23; 0.010 FDR:    23; 0.001 FDR:    23
0:38:28.551407 PROGRESS: =========================================================================
0:38:28.551696 INFO: Target number of precursors not reached yet.
0:38:28.642558 INFO: Starting optimization step 2.
0:38:28.642784 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:38:28.642864 INFO: Using rust extraction backend
0:38:28.642920 PROGRESS: Extracting batch of 7881 precursors
0:38:28.657736 INFO: === Search parameters used ===
0:38:28.657875 INFO: rt_error       : 805.6019897460938
0:38:28.657927 INFO: mobility_error : 0.1
0:38:28.657970 INFO: num_candidates : 1
0:38:28.658010 INFO: ms1_error      : 3
0:38:28.658050 INFO: ms2_error      : 10
0:38:28.658089 INFO: fwhm_rt        : 5
0:38:28.658127 INFO: quant_window   : 3
0:38:28.658165 INFO: ==============================================
0:38:28.737274 INFO: performing precursor FDR with 40 features
0:38:28.737379 INFO: Decoy channel: -1
0:38:28.737403 INFO: competitive: True
0:38:28.743781 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:28.747650 INFO: Estimating optimal hyperparameters - samples: 10,999, batch_size: 128, learning_rate: 1.77e-04
0:38:28.747757 INFO: Using random state 914806 for train-test-split
0:38:29.872867 INFO: Test AUC: 0.573
0:38:29.872978 INFO: Train AUC: 0.587
0:38:29.873007 INFO: AUC difference: 2.38%
0:38:30.124420 INFO: Resetting torch num_threads to 100
0:38:30.128834 PROGRESS: === Extracted 13749 precursors and 76480 fragments ===
0:38:30.129251 INFO: === FDR correction performed with classifier version -1 ===
0:38:30.129765 PROGRESS: ============================= Precursor FDR =============================
0:38:30.129852 PROGRESS: Total precursors accumulated: 57
0:38:30.129906 PROGRESS: Target precursors: 57 (100.00%)
0:38:30.129954 PROGRESS: Decoy precursors: 0 (0.00%)
0:38:30.129997 PROGRESS: 
0:38:30.130038 PROGRESS: Precursor Summary:
0:38:30.131098 PROGRESS: Channel   0:	 0.050 FDR:    57; 0.010 FDR:    57; 0.001 FDR:    57
0:38:30.131177 PROGRESS: 
0:38:30.131228 PROGRESS: Protein Summary:
0:38:30.132411 PROGRESS: Channel   0:	 0.050 FDR:    56; 0.010 FDR:    56; 0.001 FDR:    56
0:38:30.132496 PROGRESS: =========================================================================
0:38:30.132869 INFO: Target number of precursors not reached yet.
0:38:30.232446 INFO: Starting optimization step 3.
0:38:30.232686 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:38:30.232767 INFO: Using rust extraction backend
0:38:30.232826 PROGRESS: Extracting batch of 15776 precursors
0:38:30.260985 INFO: === Search parameters used ===
0:38:30.261163 INFO: rt_error       : 805.6019897460938
0:38:30.261214 INFO: mobility_error : 0.1
0:38:30.261259 INFO: num_candidates : 1
0:38:30.261299 INFO: ms1_error      : 3
0:38:30.261338 INFO: ms2_error      : 10
0:38:30.261388 INFO: fwhm_rt        : 5
0:38:30.261427 INFO: quant_window   : 3
0:38:30.261465 INFO: ==============================================
0:38:30.399653 INFO: performing precursor FDR with 40 features
0:38:30.399768 INFO: Decoy channel: -1
0:38:30.399792 INFO: competitive: True
0:38:30.412941 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:30.419905 INFO: Estimating optimal hyperparameters - samples: 23,587, batch_size: 128, learning_rate: 1.77e-04
0:38:30.420088 INFO: Using random state 35551 for train-test-split
0:38:32.932053 INFO: Test AUC: 0.570
0:38:32.932167 INFO: Train AUC: 0.601
0:38:32.932195 INFO: AUC difference: 5.16%
0:38:32.932217 WARNING: AUC difference > 5%. This may indicate overfitting.
0:38:33.191547 INFO: Resetting torch num_threads to 100
0:38:33.198641 PROGRESS: === Extracted 29484 precursors and 163637 fragments ===
0:38:33.199117 INFO: === FDR correction performed with classifier version -1 ===
0:38:33.199623 PROGRESS: ============================= Precursor FDR =============================
0:38:33.199711 PROGRESS: Total precursors accumulated: 126
0:38:33.199770 PROGRESS: Target precursors: 125 (99.21%)
0:38:33.202078 PROGRESS: Decoy precursors: 1 (0.79%)
0:38:33.202157 PROGRESS: 
0:38:33.202204 PROGRESS: Precursor Summary:
0:38:33.203236 PROGRESS: Channel   0:	 0.050 FDR:   125; 0.010 FDR:   125; 0.001 FDR:   120
0:38:33.203322 PROGRESS: 
0:38:33.203376 PROGRESS: Protein Summary:
0:38:33.204485 PROGRESS: Channel   0:	 0.050 FDR:   123; 0.010 FDR:   123; 0.001 FDR:   118
0:38:33.204573 PROGRESS: =========================================================================
0:38:33.205173 INFO: Target number of precursors not reached yet.
0:38:33.328713 INFO: Starting optimization step 4.
0:38:33.328981 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:38:33.329065 INFO: Using rust extraction backend
0:38:33.329140 PROGRESS: Extracting batch of 31591 precursors
0:38:33.383701 INFO: === Search parameters used ===
0:38:33.383946 INFO: rt_error       : 805.6019897460938
0:38:33.384001 INFO: mobility_error : 0.1
0:38:33.384047 INFO: num_candidates : 1
0:38:33.384088 INFO: ms1_error      : 3
0:38:33.384128 INFO: ms2_error      : 10
0:38:33.384168 INFO: fwhm_rt        : 5
0:38:33.384206 INFO: quant_window   : 3
0:38:33.384244 INFO: ==============================================
0:38:33.612618 INFO: performing precursor FDR with 40 features
0:38:33.612736 INFO: Decoy channel: -1
0:38:33.612760 INFO: competitive: True
0:38:33.643294 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:33.660101 INFO: Estimating optimal hyperparameters - samples: 48,791, batch_size: 199, learning_rate: 2.20e-04
0:38:33.660321 INFO: Using random state 275793 for train-test-split
0:38:37.582586 INFO: Test AUC: 0.583
0:38:37.582831 INFO: Train AUC: 0.612
0:38:37.582866 INFO: AUC difference: 4.77%
0:38:37.852660 INFO: Resetting torch num_threads to 100
0:38:37.870785 PROGRESS: === Extracted 60989 precursors and 339099 fragments ===
0:38:37.871384 INFO: === FDR correction performed with classifier version -1 ===
0:38:37.872048 PROGRESS: ============================= Precursor FDR =============================
0:38:37.872147 PROGRESS: Total precursors accumulated: 286
0:38:37.872213 PROGRESS: Target precursors: 284 (99.30%)
0:38:37.872266 PROGRESS: Decoy precursors: 2 (0.70%)
0:38:37.872313 PROGRESS: 
0:38:37.872358 PROGRESS: Precursor Summary:
0:38:37.873408 PROGRESS: Channel   0:	 0.050 FDR:   284; 0.010 FDR:   284; 0.001 FDR:   191
0:38:37.873494 PROGRESS: 
0:38:37.873549 PROGRESS: Protein Summary:
0:38:37.874745 PROGRESS: Channel   0:	 0.050 FDR:   274; 0.010 FDR:   274; 0.001 FDR:   185
0:38:37.874832 PROGRESS: =========================================================================
0:38:37.876121 INFO: Target number of precursors not reached yet.
0:38:38.093496 INFO: Starting optimization step 5.
0:38:38.093763 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:38:38.093882 INFO: Using rust extraction backend
0:38:38.093971 PROGRESS: Extracting batch of 63056 precursors
0:38:38.205389 INFO: === Search parameters used ===
0:38:38.205672 INFO: rt_error       : 805.6019897460938
0:38:38.205731 INFO: mobility_error : 0.1
0:38:38.205785 INFO: num_candidates : 1
0:38:38.205834 INFO: ms1_error      : 3
0:38:38.205878 INFO: ms2_error      : 10
0:38:38.205920 INFO: fwhm_rt        : 5
0:38:38.205961 INFO: quant_window   : 3
0:38:38.206002 INFO: ==============================================
0:38:38.602780 INFO: performing precursor FDR with 40 features
0:38:38.602905 INFO: Decoy channel: -1
0:38:38.602930 INFO: competitive: True
0:38:38.658127 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:38.697406 INFO: Estimating optimal hyperparameters - samples: 99,111, batch_size: 405, learning_rate: 3.14e-04
0:38:38.697736 INFO: Using random state 163297 for train-test-split
0:38:43.536335 INFO: Test AUC: 0.588
0:38:43.536453 INFO: Train AUC: 0.615
0:38:43.536480 INFO: AUC difference: 4.28%
0:38:43.823208 INFO: Resetting torch num_threads to 100
0:38:43.846236 PROGRESS: === Extracted 123889 precursors and 689524 fragments ===
0:38:43.846899 INFO: === FDR correction performed with classifier version -1 ===
0:38:43.847540 PROGRESS: ============================= Precursor FDR =============================
0:38:43.847626 PROGRESS: Total precursors accumulated: 487
0:38:43.847682 PROGRESS: Target precursors: 483 (99.18%)
0:38:43.847730 PROGRESS: Decoy precursors: 4 (0.82%)
0:38:43.847773 PROGRESS: 
0:38:43.847951 PROGRESS: Precursor Summary:
0:38:43.849077 PROGRESS: Channel   0:	 0.050 FDR:   483; 0.010 FDR:   483; 0.001 FDR:   367
0:38:43.849159 PROGRESS: 
0:38:43.849210 PROGRESS: Protein Summary:
0:38:43.850487 PROGRESS: Channel   0:	 0.050 FDR:   456; 0.010 FDR:   456; 0.001 FDR:   345
0:38:43.850570 PROGRESS: =========================================================================
0:38:43.852917 INFO: Target number of precursors not reached yet.
0:38:44.187974 INFO: Starting optimization step 6.
0:38:44.188236 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:38:44.188316 INFO: Using rust extraction backend
0:38:44.188375 PROGRESS: Extracting batch of 126233 precursors
0:38:44.404303 INFO: === Search parameters used ===
0:38:44.404577 INFO: rt_error       : 805.6019897460938
0:38:44.404631 INFO: mobility_error : 0.1
0:38:44.404676 INFO: num_candidates : 1
0:38:44.404718 INFO: ms1_error      : 3
0:38:44.404759 INFO: ms2_error      : 10
0:38:44.404799 INFO: fwhm_rt        : 5
0:38:44.404838 INFO: quant_window   : 3
0:38:44.404876 INFO: ==============================================
0:38:45.129238 INFO: performing precursor FDR with 40 features
0:38:45.129362 INFO: Decoy channel: -1
0:38:45.129386 INFO: competitive: True
0:38:45.255946 INFO: Setting torch num_threads to 2 for FDR classification task
0:38:45.348955 INFO: Estimating optimal hyperparameters - samples: 199,851, batch_size: 818, learning_rate: 4.47e-04
0:38:45.349346 INFO: Using random state 728376 for train-test-split
0:38:53.831777 INFO: Test AUC: 0.596
0:38:53.831934 INFO: Train AUC: 0.610
0:38:53.831965 INFO: AUC difference: 2.39%
0:38:54.166117 INFO: Resetting torch num_threads to 100
0:38:54.222586 PROGRESS: === Extracted 249814 precursors and 1390725 fragments ===
0:38:54.223334 INFO: === FDR correction performed with classifier version -1 ===
0:38:54.224230 PROGRESS: ============================= Precursor FDR =============================
0:38:54.224322 PROGRESS: Total precursors accumulated: 1,251
0:38:54.224380 PROGRESS: Target precursors: 1,239 (99.04%)
0:38:54.224436 PROGRESS: Decoy precursors: 12 (0.96%)
0:38:54.224482 PROGRESS: 
0:38:54.224525 PROGRESS: Precursor Summary:
0:38:54.225836 PROGRESS: Channel   0:	 0.050 FDR: 1,239; 0.010 FDR: 1,239; 0.001 FDR:   798
0:38:54.225920 PROGRESS: 
0:38:54.225974 PROGRESS: Protein Summary:
0:38:54.227625 PROGRESS: Channel   0:	 0.050 FDR: 1,057; 0.010 FDR: 1,057; 0.001 FDR:   702
0:38:54.227712 PROGRESS: =========================================================================
0:38:54.233041 INFO: Target number of precursors reached.
0:38:54.399277 INFO: fragments_df: keeping 5000 of 1390725 [sum(precursor_idx_mask)=13223 sum(mass_error_mask)=1390725 stop_rank=5000
0:38:55.017619 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:38:55.237508 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:38:55.960941 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:38:55.961432 INFO: Using score_cutoff 12.21953660774231 (fac=0.99, q=1)
0:38:55.961794 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:38:55.961869 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:38:55.961925 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.21953660774231
0:38:55.961993 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:38:56.114579 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:38:56.471937 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
0:38:56.472203 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:38:56.472306 INFO: Starting optimization step 7.
0:38:56.472365 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:38:56.472436 INFO: Using rust extraction backend
0:38:56.472496 PROGRESS: Extracting batch of 250442 precursors
0:38:56.898408 INFO: === Search parameters used ===
0:38:56.898680 INFO: rt_error       : 805.6019897460938
0:38:56.898736 INFO: mobility_error : 0.1
0:38:56.898784 INFO: num_candidates : 3
0:38:56.898825 INFO: ms1_error      : 3
0:38:56.898865 INFO: ms2_error      : 10
0:38:56.898904 INFO: fwhm_rt        : 3.0
0:38:56.898943 INFO: quant_window   : 3
0:38:56.898981 INFO: ==============================================
0:38:59.550880 INFO: performing precursor FDR with 40 features
0:38:59.551004 INFO: Decoy channel: -1
0:38:59.551029 INFO: competitive: True
0:38:59.763973 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:00.078956 INFO: Estimating optimal hyperparameters - samples: 599,595, batch_size: 2,455, learning_rate: 7.74e-04
0:39:00.080417 INFO: Using random state 446214 for train-test-split
0:39:15.899053 INFO: Test AUC: 0.596
0:39:15.899230 INFO: Train AUC: 0.606
0:39:15.899265 INFO: AUC difference: 1.71%
0:39:17.086623 INFO: Resetting torch num_threads to 100
0:39:17.117372 PROGRESS: === Extracted 749494 precursors and 4005948 fragments ===
0:39:17.117859 INFO: === FDR correction performed with classifier version 6 ===
0:39:17.118614 PROGRESS: ============================= Precursor FDR =============================
0:39:17.118720 PROGRESS: Total precursors accumulated: 1,147
0:39:17.118782 PROGRESS: Target precursors: 1,136 (99.04%)
0:39:17.118834 PROGRESS: Decoy precursors: 11 (0.96%)
0:39:17.118881 PROGRESS: 
0:39:17.118925 PROGRESS: Precursor Summary:
0:39:17.120208 PROGRESS: Channel   0:	 0.050 FDR: 1,136; 0.010 FDR: 1,136; 0.001 FDR:     0
0:39:17.120301 PROGRESS: 
0:39:17.120357 PROGRESS: Protein Summary:
0:39:17.121829 PROGRESS: Channel   0:	 0.050 FDR:   980; 0.010 FDR:   980; 0.001 FDR:     0
0:39:17.121918 PROGRESS: =========================================================================
0:39:17.137669 INFO: Target number of precursors reached.
0:39:17.560130 INFO: fragments_df: keeping 5000 of 4005948 [sum(precursor_idx_mask)=27720 sum(mass_error_mask)=4005948 stop_rank=5000
0:39:18.061239 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:18.234516 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:18.887644 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:18.888107 INFO: Using score_cutoff 12.583949257850648 (fac=0.99, q=1)
0:39:18.888415 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:18.888490 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:18.888544 INFO: Updating optimization_manager: score_cutoff        : 12.21953660774231 -> 12.583949257850648
0:39:18.888596 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:19.048908 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:19.389740 INFO: === checking if optimization conditions were reached ===
0:39:19.392268 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
0:39:19.392375 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:39:19.392442 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:39:19.392509 INFO: ==============================================
0:39:19.392586 INFO: Starting optimization step 8.
0:39:19.392648 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:39:19.392709 INFO: Using rust extraction backend
0:39:19.392771 PROGRESS: Extracting batch of 250442 precursors
0:39:19.823501 INFO: === Search parameters used ===
0:39:19.823838 INFO: rt_error       : 805.6019897460938
0:39:19.823910 INFO: mobility_error : 0.1
0:39:19.823960 INFO: num_candidates : 3
0:39:19.824003 INFO: ms1_error      : 3
0:39:19.824042 INFO: ms2_error      : 10.0
0:39:19.824080 INFO: fwhm_rt        : 3.0
0:39:19.824119 INFO: quant_window   : 3
0:39:19.824157 INFO: ==============================================
0:39:22.507298 INFO: performing precursor FDR with 40 features
0:39:22.507485 INFO: Decoy channel: -1
0:39:22.507514 INFO: competitive: True
0:39:22.713449 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:23.018130 INFO: Estimating optimal hyperparameters - samples: 599,612, batch_size: 2,456, learning_rate: 7.74e-04
0:39:23.019080 INFO: Using random state 719250 for train-test-split
0:39:37.067235 INFO: Test AUC: 0.603
0:39:37.067425 INFO: Train AUC: 0.613
0:39:37.067472 INFO: AUC difference: 1.64%
0:39:37.547792 INFO: Resetting torch num_threads to 100
0:39:37.580833 PROGRESS: === Extracted 749516 precursors and 4006830 fragments ===
0:39:37.581370 INFO: === FDR correction performed with classifier version 7 ===
0:39:37.582084 PROGRESS: ============================= Precursor FDR =============================
0:39:37.582180 PROGRESS: Total precursors accumulated: 1,317
0:39:37.582244 PROGRESS: Target precursors: 1,304 (99.01%)
0:39:37.582296 PROGRESS: Decoy precursors: 13 (0.99%)
0:39:37.582343 PROGRESS: 
0:39:37.582386 PROGRESS: Precursor Summary:
0:39:37.583619 PROGRESS: Channel   0:	 0.050 FDR: 1,304; 0.010 FDR: 1,304; 0.001 FDR:    50
0:39:37.583705 PROGRESS: 
0:39:37.583761 PROGRESS: Protein Summary:
0:39:37.585327 PROGRESS: Channel   0:	 0.050 FDR: 1,117; 0.010 FDR: 1,117; 0.001 FDR:    49
0:39:37.585419 PROGRESS: =========================================================================
0:39:37.601874 INFO: Target number of precursors reached.
0:39:38.044792 INFO: fragments_df: keeping 5000 of 4006830 [sum(precursor_idx_mask)=31279 sum(mass_error_mask)=4006830 stop_rank=5000
0:39:38.503903 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:38.698585 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:39:39.349597 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:39:39.350065 INFO: Using score_cutoff 11.391372834205628 (fac=0.99, q=1)
0:39:39.350396 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:39:39.350472 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:39:39.350526 INFO: Updating optimization_manager: score_cutoff        : 12.583949257850648 -> 11.391372834205628
0:39:39.350587 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:39:39.508612 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:39:39.853898 INFO: === checking if optimization conditions were reached ===
0:39:39.856610 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:39:39.856735 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:39:39.856818 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:39:39.856889 INFO: ==============================================
0:39:39.856974 INFO: Starting optimization step 9.
0:39:39.857045 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:39:39.857136 INFO: Using rust extraction backend
0:39:39.857210 PROGRESS: Extracting batch of 250442 precursors
0:39:40.289170 INFO: === Search parameters used ===
0:39:40.289469 INFO: rt_error       : 805.6019897460938
0:39:40.289529 INFO: mobility_error : 0.1
0:39:40.289579 INFO: num_candidates : 3
0:39:40.289623 INFO: ms1_error      : 3
0:39:40.289665 INFO: ms2_error      : 10.0
0:39:40.289706 INFO: fwhm_rt        : 3.0
0:39:40.289746 INFO: quant_window   : 3
0:39:40.289786 INFO: ==============================================
0:39:42.950740 INFO: performing precursor FDR with 40 features
0:39:42.950862 INFO: Decoy channel: -1
0:39:42.950886 INFO: competitive: True
0:39:43.164406 INFO: Setting torch num_threads to 2 for FDR classification task
0:39:43.479915 INFO: Estimating optimal hyperparameters - samples: 599,632, batch_size: 2,456, learning_rate: 7.74e-04
0:39:43.481110 INFO: Using random state 333079 for train-test-split
0:39:57.882581 INFO: Test AUC: 0.605
0:39:57.882748 INFO: Train AUC: 0.617
0:39:57.882780 INFO: AUC difference: 2.03%
0:39:58.359934 INFO: Resetting torch num_threads to 100
0:39:58.392380 PROGRESS: === Extracted 749541 precursors and 4007079 fragments ===
0:39:58.392895 INFO: === FDR correction performed with classifier version 8 ===
0:39:58.393538 PROGRESS: ============================= Precursor FDR =============================
0:39:58.393627 PROGRESS: Total precursors accumulated: 1,361
0:39:58.393686 PROGRESS: Target precursors: 1,348 (99.04%)
0:39:58.393735 PROGRESS: Decoy precursors: 13 (0.96%)
0:39:58.393780 PROGRESS: 
0:39:58.393825 PROGRESS: Precursor Summary:
0:39:58.395070 PROGRESS: Channel   0:	 0.050 FDR: 1,348; 0.010 FDR: 1,348; 0.001 FDR:   303
0:39:58.395155 PROGRESS: 
0:39:58.395210 PROGRESS: Protein Summary:
0:39:58.396837 PROGRESS: Channel   0:	 0.050 FDR: 1,146; 0.010 FDR: 1,146; 0.001 FDR:   278
0:39:58.396928 PROGRESS: =========================================================================
0:39:58.412601 INFO: Target number of precursors reached.
0:39:58.844946 INFO: fragments_df: keeping 5000 of 4007079 [sum(precursor_idx_mask)=32235 sum(mass_error_mask)=4007079 stop_rank=5000
0:39:59.297903 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:39:59.492363 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:00.146179 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:00.146636 INFO: Using score_cutoff 11.479401153087617 (fac=0.99, q=1)
0:40:00.146951 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:00.147032 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:00.147091 INFO: Updating optimization_manager: score_cutoff        : 11.391372834205628 -> 11.479401153087617
0:40:00.147150 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:00.301493 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:00.638134 INFO: === checking if optimization conditions were reached ===
0:40:00.640395 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:40:00.640502 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:40:00.640574 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:40:00.640635 INFO: ==============================================
0:40:00.640716 INFO: Starting optimization step 10.
0:40:00.640775 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:40:00.640852 INFO: Using rust extraction backend
0:40:00.640922 PROGRESS: Extracting batch of 250442 precursors
0:40:01.066210 INFO: === Search parameters used ===
0:40:01.066494 INFO: rt_error       : 805.6019897460938
0:40:01.066554 INFO: mobility_error : 0.1
0:40:01.066603 INFO: num_candidates : 3
0:40:01.066648 INFO: ms1_error      : 3
0:40:01.066692 INFO: ms2_error      : 10.0
0:40:01.066734 INFO: fwhm_rt        : 3.0
0:40:01.066775 INFO: quant_window   : 3
0:40:01.066817 INFO: ==============================================
0:40:03.638779 INFO: performing precursor FDR with 40 features
0:40:03.638899 INFO: Decoy channel: -1
0:40:03.638926 INFO: competitive: True
0:40:03.841182 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:04.142579 INFO: Estimating optimal hyperparameters - samples: 599,616, batch_size: 2,456, learning_rate: 7.74e-04
0:40:04.143606 INFO: Using random state 579032 for train-test-split
0:40:17.063122 INFO: Test AUC: 0.610
0:40:17.063294 INFO: Train AUC: 0.621
0:40:17.063327 INFO: AUC difference: 1.79%
0:40:17.543004 INFO: Resetting torch num_threads to 100
0:40:17.574863 PROGRESS: === Extracted 749520 precursors and 4006577 fragments ===
0:40:17.575402 INFO: === FDR correction performed with classifier version 9 ===
0:40:17.576160 PROGRESS: ============================= Precursor FDR =============================
0:40:17.576263 PROGRESS: Total precursors accumulated: 1,342
0:40:17.576322 PROGRESS: Target precursors: 1,329 (99.03%)
0:40:17.576372 PROGRESS: Decoy precursors: 13 (0.97%)
0:40:17.576418 PROGRESS: 
0:40:17.576463 PROGRESS: Precursor Summary:
0:40:17.577738 PROGRESS: Channel   0:	 0.050 FDR: 1,329; 0.010 FDR: 1,329; 0.001 FDR:     0
0:40:17.577829 PROGRESS: 
0:40:17.577884 PROGRESS: Protein Summary:
0:40:17.579425 PROGRESS: Channel   0:	 0.050 FDR: 1,128; 0.010 FDR: 1,128; 0.001 FDR:     0
0:40:17.579516 PROGRESS: =========================================================================
0:40:17.594965 INFO: Target number of precursors reached.
0:40:18.037798 INFO: fragments_df: keeping 5000 of 4006577 [sum(precursor_idx_mask)=31886 sum(mass_error_mask)=4006577 stop_rank=5000
0:40:18.467896 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:18.654942 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:19.306335 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:19.306792 INFO: Using score_cutoff 11.627279976654052 (fac=0.99, q=1)
0:40:19.307105 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:19.307187 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:19.307241 INFO: Updating optimization_manager: score_cutoff        : 11.479401153087617 -> 11.627279976654052
0:40:19.307293 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:19.460159 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:19.785274 INFO: === checking if optimization conditions were reached ===
0:40:19.787496 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:40:19.787594 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:40:19.787656 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:40:19.787713 INFO: ==============================================
0:40:19.787777 INFO: Starting optimization step 11.
0:40:19.787853 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:40:19.787927 INFO: Using rust extraction backend
0:40:19.787988 PROGRESS: Extracting batch of 250442 precursors
0:40:20.216366 INFO: === Search parameters used ===
0:40:20.216620 INFO: rt_error       : 805.6019897460938
0:40:20.216678 INFO: mobility_error : 0.1
0:40:20.216724 INFO: num_candidates : 3
0:40:20.216766 INFO: ms1_error      : 3
0:40:20.216806 INFO: ms2_error      : 10.0
0:40:20.216845 INFO: fwhm_rt        : 3.0
0:40:20.216883 INFO: quant_window   : 3
0:40:20.216933 INFO: ==============================================
0:40:22.822821 INFO: performing precursor FDR with 40 features
0:40:22.822946 INFO: Decoy channel: -1
0:40:22.822972 INFO: competitive: True
0:40:23.035062 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:23.348097 INFO: Estimating optimal hyperparameters - samples: 599,620, batch_size: 2,456, learning_rate: 7.74e-04
0:40:23.349048 INFO: Using random state 597307 for train-test-split
0:40:37.844289 INFO: Test AUC: 0.608
0:40:37.844427 INFO: Train AUC: 0.623
0:40:37.844460 INFO: AUC difference: 2.31%
0:40:38.322816 INFO: Resetting torch num_threads to 100
0:40:38.356064 PROGRESS: === Extracted 749525 precursors and 4006983 fragments ===
0:40:38.356534 INFO: === FDR correction performed with classifier version 10 ===
0:40:38.357266 PROGRESS: ============================= Precursor FDR =============================
0:40:38.357363 PROGRESS: Total precursors accumulated: 1,426
0:40:38.357423 PROGRESS: Target precursors: 1,412 (99.02%)
0:40:38.357475 PROGRESS: Decoy precursors: 14 (0.98%)
0:40:38.357524 PROGRESS: 
0:40:38.357570 PROGRESS: Precursor Summary:
0:40:38.358958 PROGRESS: Channel   0:	 0.050 FDR: 1,412; 0.010 FDR: 1,412; 0.001 FDR: 1,052
0:40:38.359051 PROGRESS: 
0:40:38.359111 PROGRESS: Protein Summary:
0:40:38.360880 PROGRESS: Channel   0:	 0.050 FDR: 1,200; 0.010 FDR: 1,200; 0.001 FDR:   916
0:40:38.360976 PROGRESS: =========================================================================
0:40:38.377550 INFO: Target number of precursors reached.
0:40:38.812789 INFO: fragments_df: keeping 5000 of 4006983 [sum(precursor_idx_mask)=33801 sum(mass_error_mask)=4006983 stop_rank=5000
0:40:39.244432 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:40:39.443331 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:40:40.091070 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:40:40.091529 INFO: Using score_cutoff 11.48354949531555 (fac=0.99, q=1)
0:40:40.091856 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:40:40.091938 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:40:40.091993 INFO: Updating optimization_manager: score_cutoff        : 11.627279976654052 -> 11.48354949531555
0:40:40.092046 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:40.245416 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:40.590111 INFO: === checking if optimization conditions were reached ===
0:40:40.592354 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:40:40.592459 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:40:40.592528 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:40:40.592586 INFO: ==============================================
0:40:40.592660 PROGRESS: Optimization finished for ms2_error.
0:40:41.012333 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:40:41.165530 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:40:41.502593 INFO: Starting optimization step 0.
0:40:41.502855 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:40:41.502934 INFO: Using rust extraction backend
0:40:41.503002 PROGRESS: Extracting batch of 250442 precursors
0:40:41.928117 INFO: === Search parameters used ===
0:40:41.928410 INFO: rt_error       : 805.6019897460938
0:40:41.928468 INFO: mobility_error : 0.1
0:40:41.928528 INFO: num_candidates : 3
0:40:41.928580 INFO: ms1_error      : 3
0:40:41.928625 INFO: ms2_error      : 10.0
0:40:41.928666 INFO: fwhm_rt        : 3.0
0:40:41.928705 INFO: quant_window   : 3
0:40:41.928743 INFO: ==============================================
0:40:44.481290 INFO: performing precursor FDR with 40 features
0:40:44.481411 INFO: Decoy channel: -1
0:40:44.481436 INFO: competitive: True
0:40:44.689103 INFO: Setting torch num_threads to 2 for FDR classification task
0:40:44.998892 INFO: Estimating optimal hyperparameters - samples: 599,625, batch_size: 2,456, learning_rate: 7.74e-04
0:40:44.999866 INFO: Using random state 977614 for train-test-split
0:40:58.575709 INFO: Test AUC: 0.613
0:40:58.576000 INFO: Train AUC: 0.625
0:40:58.576037 INFO: AUC difference: 1.95%
0:40:59.053057 INFO: Resetting torch num_threads to 100
0:40:59.086956 PROGRESS: === Extracted 749532 precursors and 4006820 fragments ===
0:40:59.087494 INFO: === FDR correction performed with classifier version 11 ===
0:40:59.088273 PROGRESS: ============================= Precursor FDR =============================
0:40:59.088376 PROGRESS: Total precursors accumulated: 1,455
0:40:59.088440 PROGRESS: Target precursors: 1,441 (99.04%)
0:40:59.088495 PROGRESS: Decoy precursors: 14 (0.96%)
0:40:59.088543 PROGRESS: 
0:40:59.088591 PROGRESS: Precursor Summary:
0:40:59.089902 PROGRESS: Channel   0:	 0.050 FDR: 1,441; 0.010 FDR: 1,441; 0.001 FDR:    86
0:40:59.089995 PROGRESS: 
0:40:59.090052 PROGRESS: Protein Summary:
0:40:59.091642 PROGRESS: Channel   0:	 0.050 FDR: 1,220; 0.010 FDR: 1,220; 0.001 FDR:    84
0:40:59.091734 PROGRESS: =========================================================================
0:40:59.107722 INFO: Target number of precursors reached.
0:40:59.556125 INFO: fragments_df: keeping 5000 of 4006820 [sum(precursor_idx_mask)=34222 sum(mass_error_mask)=4006820 stop_rank=5000
0:41:00.019479 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:00.219654 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:00.869721 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:00.870182 INFO: Using score_cutoff 10.924113389968873 (fac=0.99, q=1)
0:41:00.870498 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:00.870575 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:00.870626 INFO: Updating optimization_manager: score_cutoff        : 11.48354949531555 -> 10.924113389968873
0:41:00.870682 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:01.026524 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:01.372014 INFO: === checking if optimization conditions were reached ===
0:41:01.372309 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:41:01.375063 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 770.8214175898727
0:41:01.375164 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 770.8214.
0:41:01.375228 INFO: ==============================================
0:41:01.375305 INFO: Starting optimization step 1.
0:41:01.375364 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:41:01.375451 INFO: Using rust extraction backend
0:41:01.375517 PROGRESS: Extracting batch of 250442 precursors
0:41:01.805953 INFO: === Search parameters used ===
0:41:01.806276 INFO: rt_error       : 770.8214175898727
0:41:01.806338 INFO: mobility_error : 0.1
0:41:01.806387 INFO: num_candidates : 3
0:41:01.806432 INFO: ms1_error      : 3
0:41:01.806472 INFO: ms2_error      : 10.0
0:41:01.806513 INFO: fwhm_rt        : 3.0
0:41:01.806551 INFO: quant_window   : 3
0:41:01.806590 INFO: ==============================================
0:41:04.466783 INFO: performing precursor FDR with 40 features
0:41:04.466901 INFO: Decoy channel: -1
0:41:04.466925 INFO: competitive: True
0:41:04.677271 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:04.999311 INFO: Estimating optimal hyperparameters - samples: 599,628, batch_size: 2,456, learning_rate: 7.74e-04
0:41:05.000271 INFO: Using random state 977614 for train-test-split
0:41:17.849177 INFO: Test AUC: 0.613
0:41:17.849345 INFO: Train AUC: 0.626
0:41:17.849375 INFO: AUC difference: 2.11%
0:41:18.334074 INFO: Resetting torch num_threads to 100
0:41:18.366663 PROGRESS: === Extracted 749535 precursors and 4006642 fragments ===
0:41:18.367147 INFO: === FDR correction performed with classifier version 11 ===
0:41:18.367890 PROGRESS: ============================= Precursor FDR =============================
0:41:18.367990 PROGRESS: Total precursors accumulated: 1,407
0:41:18.368051 PROGRESS: Target precursors: 1,394 (99.08%)
0:41:18.368100 PROGRESS: Decoy precursors: 13 (0.92%)
0:41:18.368145 PROGRESS: 
0:41:18.368187 PROGRESS: Precursor Summary:
0:41:18.369559 PROGRESS: Channel   0:	 0.050 FDR: 1,394; 0.010 FDR: 1,394; 0.001 FDR:   890
0:41:18.369649 PROGRESS: 
0:41:18.369701 PROGRESS: Protein Summary:
0:41:18.371383 PROGRESS: Channel   0:	 0.050 FDR: 1,193; 0.010 FDR: 1,193; 0.001 FDR:   782
0:41:18.371468 PROGRESS: =========================================================================
0:41:18.387555 INFO: Target number of precursors reached.
0:41:18.827940 INFO: fragments_df: keeping 5000 of 4006642 [sum(precursor_idx_mask)=33227 sum(mass_error_mask)=4006642 stop_rank=5000
0:41:19.282553 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:19.481164 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:20.132093 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:20.132568 INFO: Using score_cutoff 10.937304002094267 (fac=0.99, q=1)
0:41:20.132889 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:20.132968 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:20.133024 INFO: Updating optimization_manager: score_cutoff        : 10.924113389968873 -> 10.937304002094267
0:41:20.133091 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:20.286785 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:20.622509 INFO: === checking if optimization conditions were reached ===
0:41:20.622809 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:41:20.625659 INFO: Updating optimization_manager: rt_error            : 770.8214175898727 -> 699.6121833268696
0:41:20.625799 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 699.6122.
0:41:20.625866 INFO: ==============================================
0:41:20.625946 INFO: Starting optimization step 2.
0:41:20.626008 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:41:20.626082 INFO: Using rust extraction backend
0:41:20.626154 PROGRESS: Extracting batch of 250442 precursors
0:41:21.050099 INFO: === Search parameters used ===
0:41:21.050375 INFO: rt_error       : 699.6121833268696
0:41:21.050431 INFO: mobility_error : 0.1
0:41:21.050479 INFO: num_candidates : 3
0:41:21.050522 INFO: ms1_error      : 3
0:41:21.050561 INFO: ms2_error      : 10.0
0:41:21.050600 INFO: fwhm_rt        : 3.0
0:41:21.050638 INFO: quant_window   : 3
0:41:21.050675 INFO: ==============================================
0:41:23.549229 INFO: performing precursor FDR with 40 features
0:41:23.549351 INFO: Decoy channel: -1
0:41:23.549376 INFO: competitive: True
0:41:23.741257 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:24.042557 INFO: Estimating optimal hyperparameters - samples: 599,632, batch_size: 2,456, learning_rate: 7.74e-04
0:41:24.043585 INFO: Using random state 977614 for train-test-split
0:41:36.810503 INFO: Test AUC: 0.611
0:41:36.810676 INFO: Train AUC: 0.627
0:41:36.810708 INFO: AUC difference: 2.61%
0:41:37.280797 INFO: Resetting torch num_threads to 100
0:41:37.313411 PROGRESS: === Extracted 749541 precursors and 4005907 fragments ===
0:41:37.313893 INFO: === FDR correction performed with classifier version 11 ===
0:41:37.314631 PROGRESS: ============================= Precursor FDR =============================
0:41:37.314724 PROGRESS: Total precursors accumulated: 1,415
0:41:37.314781 PROGRESS: Target precursors: 1,401 (99.01%)
0:41:37.314828 PROGRESS: Decoy precursors: 14 (0.99%)
0:41:37.314872 PROGRESS: 
0:41:37.314913 PROGRESS: Precursor Summary:
0:41:37.316204 PROGRESS: Channel   0:	 0.050 FDR: 1,401; 0.010 FDR: 1,401; 0.001 FDR:     0
0:41:37.316297 PROGRESS: 
0:41:37.316350 PROGRESS: Protein Summary:
0:41:37.317929 PROGRESS: Channel   0:	 0.050 FDR: 1,188; 0.010 FDR: 1,188; 0.001 FDR:     0
0:41:37.318023 PROGRESS: =========================================================================
0:41:37.333828 INFO: Target number of precursors reached.
0:41:37.764975 INFO: fragments_df: keeping 5000 of 4005907 [sum(precursor_idx_mask)=33639 sum(mass_error_mask)=4005907 stop_rank=5000
0:41:38.197366 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:38.391224 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:39.041702 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:39.042162 INFO: Using score_cutoff 11.574208002090455 (fac=0.99, q=1)
0:41:39.042480 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:39.042551 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:39.042608 INFO: Updating optimization_manager: score_cutoff        : 10.937304002094267 -> 11.574208002090455
0:41:39.042665 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:39.195210 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:41:39.528969 INFO: === checking if optimization conditions were reached ===
0:41:39.529264 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:41:39.532200 INFO: Updating optimization_manager: rt_error            : 699.6121833268696 -> 728.0864322303851
0:41:39.532306 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 728.0864.
0:41:39.532382 INFO: ==============================================
0:41:39.532448 INFO: Starting optimization step 3.
0:41:39.532507 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:41:39.532572 INFO: Using rust extraction backend
0:41:39.532627 PROGRESS: Extracting batch of 250442 precursors
0:41:39.957622 INFO: === Search parameters used ===
0:41:39.957904 INFO: rt_error       : 728.0864322303851
0:41:39.957967 INFO: mobility_error : 0.1
0:41:39.958018 INFO: num_candidates : 3
0:41:39.958066 INFO: ms1_error      : 3
0:41:39.958111 INFO: ms2_error      : 10.0
0:41:39.958155 INFO: fwhm_rt        : 3.0
0:41:39.958199 INFO: quant_window   : 3
0:41:39.958241 INFO: ==============================================
0:41:42.466528 INFO: performing precursor FDR with 40 features
0:41:42.466648 INFO: Decoy channel: -1
0:41:42.466674 INFO: competitive: True
0:41:42.666534 INFO: Setting torch num_threads to 2 for FDR classification task
0:41:42.970402 INFO: Estimating optimal hyperparameters - samples: 599,611, batch_size: 2,456, learning_rate: 7.74e-04
0:41:42.971475 INFO: Using random state 977614 for train-test-split
0:41:57.259834 INFO: Test AUC: 0.614
0:41:57.259975 INFO: Train AUC: 0.626
0:41:57.260010 INFO: AUC difference: 1.87%
0:41:57.750777 INFO: Resetting torch num_threads to 100
0:41:57.810393 PROGRESS: === Extracted 749514 precursors and 4005011 fragments ===
0:41:57.810929 INFO: === FDR correction performed with classifier version 11 ===
0:41:57.811696 PROGRESS: ============================= Precursor FDR =============================
0:41:57.811795 PROGRESS: Total precursors accumulated: 1,456
0:41:57.811873 PROGRESS: Target precursors: 1,442 (99.04%)
0:41:57.811929 PROGRESS: Decoy precursors: 14 (0.96%)
0:41:57.811976 PROGRESS: 
0:41:57.812021 PROGRESS: Precursor Summary:
0:41:57.813322 PROGRESS: Channel   0:	 0.050 FDR: 1,442; 0.010 FDR: 1,442; 0.001 FDR:     4
0:41:57.813413 PROGRESS: 
0:41:57.813476 PROGRESS: Protein Summary:
0:41:57.815040 PROGRESS: Channel   0:	 0.050 FDR: 1,222; 0.010 FDR: 1,222; 0.001 FDR:     4
0:41:57.815132 PROGRESS: =========================================================================
0:41:57.835212 INFO: Target number of precursors reached.
0:41:58.268176 INFO: fragments_df: keeping 5000 of 4005011 [sum(precursor_idx_mask)=34418 sum(mass_error_mask)=4005011 stop_rank=5000
0:41:58.723322 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:41:58.934062 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:41:59.585041 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:41:59.585509 INFO: Using score_cutoff 11.462808737754822 (fac=0.99, q=1)
0:41:59.585828 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:41:59.585912 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:41:59.585967 INFO: Updating optimization_manager: score_cutoff        : 11.574208002090455 -> 11.462808737754822
0:41:59.586026 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:41:59.738991 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:42:00.069505 INFO: === checking if optimization conditions were reached ===
0:42:00.069783 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:42:00.072817 INFO: Updating optimization_manager: rt_error            : 728.0864322303851 -> 775.5607129742239
0:42:00.072928 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 775.5607.
0:42:00.073008 INFO: ==============================================
0:42:00.073087 INFO: Starting optimization step 4.
0:42:00.073149 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:42:00.073225 INFO: Using rust extraction backend
0:42:00.073291 PROGRESS: Extracting batch of 250442 precursors
0:42:00.500660 INFO: === Search parameters used ===
0:42:00.500915 INFO: rt_error       : 775.5607129742239
0:42:00.500983 INFO: mobility_error : 0.1
0:42:00.501033 INFO: num_candidates : 3
0:42:00.501092 INFO: ms1_error      : 3
0:42:00.501134 INFO: ms2_error      : 10.0
0:42:00.501179 INFO: fwhm_rt        : 3.0
0:42:00.501221 INFO: quant_window   : 3
0:42:00.501260 INFO: ==============================================
0:42:03.119453 INFO: performing precursor FDR with 40 features
0:42:03.119578 INFO: Decoy channel: -1
0:42:03.119605 INFO: competitive: True
0:42:03.320810 INFO: Setting torch num_threads to 2 for FDR classification task
0:42:03.637707 INFO: Estimating optimal hyperparameters - samples: 599,630, batch_size: 2,456, learning_rate: 7.74e-04
0:42:03.638713 INFO: Using random state 977614 for train-test-split
0:42:16.930017 INFO: Test AUC: 0.614
0:42:16.930205 INFO: Train AUC: 0.625
0:42:16.930239 INFO: AUC difference: 1.68%
0:42:18.103167 INFO: Resetting torch num_threads to 100
0:42:18.136367 PROGRESS: === Extracted 749538 precursors and 4006897 fragments ===
0:42:18.136858 INFO: === FDR correction performed with classifier version 11 ===
0:42:18.137618 PROGRESS: ============================= Precursor FDR =============================
0:42:18.137717 PROGRESS: Total precursors accumulated: 1,492
0:42:18.137777 PROGRESS: Target precursors: 1,478 (99.06%)
0:42:18.137828 PROGRESS: Decoy precursors: 14 (0.94%)
0:42:18.137874 PROGRESS: 
0:42:18.137918 PROGRESS: Precursor Summary:
0:42:18.139358 PROGRESS: Channel   0:	 0.050 FDR: 1,478; 0.010 FDR: 1,478; 0.001 FDR: 1,184
0:42:18.139452 PROGRESS: 
0:42:18.139504 PROGRESS: Protein Summary:
0:42:18.141341 PROGRESS: Channel   0:	 0.050 FDR: 1,250; 0.010 FDR: 1,250; 0.001 FDR: 1,014
0:42:18.141435 PROGRESS: =========================================================================
0:42:18.160397 INFO: Target number of precursors reached.
0:42:18.604717 INFO: fragments_df: keeping 5000 of 4006897 [sum(precursor_idx_mask)=35246 sum(mass_error_mask)=4006897 stop_rank=5000
0:42:19.046690 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:42:19.253556 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:42:19.905137 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:42:19.905602 INFO: Using score_cutoff 11.690306758403779 (fac=0.99, q=1)
0:42:19.905913 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:42:19.905989 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:42:19.906042 INFO: Updating optimization_manager: score_cutoff        : 11.462808737754822 -> 11.690306758403779
0:42:19.906095 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:42:20.059746 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:42:20.397830 INFO: === checking if optimization conditions were reached ===
0:42:20.398116 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:42:20.401075 INFO: Updating optimization_manager: rt_error            : 775.5607129742239 -> 702.061431946775
0:42:20.401189 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 702.0614.
0:42:20.401255 INFO: ==============================================
0:42:20.401324 INFO: Starting optimization step 5.
0:42:20.401381 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:42:20.401440 INFO: Using rust extraction backend
0:42:20.401493 PROGRESS: Extracting batch of 250442 precursors
0:42:20.827344 INFO: === Search parameters used ===
0:42:20.827623 INFO: rt_error       : 702.061431946775
0:42:20.827680 INFO: mobility_error : 0.1
0:42:20.827728 INFO: num_candidates : 3
0:42:20.827772 INFO: ms1_error      : 3
0:42:20.827815 INFO: ms2_error      : 10.0
0:42:20.827873 INFO: fwhm_rt        : 3.0
0:42:20.827914 INFO: quant_window   : 3
0:42:20.827955 INFO: ==============================================
0:42:23.358146 INFO: performing precursor FDR with 40 features
0:42:23.358266 INFO: Decoy channel: -1
0:42:23.358294 INFO: competitive: True
0:42:23.571592 INFO: Setting torch num_threads to 2 for FDR classification task
0:42:23.886787 INFO: Estimating optimal hyperparameters - samples: 599,617, batch_size: 2,456, learning_rate: 7.74e-04
0:42:23.887958 INFO: Using random state 977614 for train-test-split
0:42:36.830135 INFO: Test AUC: 0.612
0:42:36.830280 INFO: Train AUC: 0.626
0:42:36.830310 INFO: AUC difference: 2.20%
0:42:37.309513 INFO: Resetting torch num_threads to 100
0:42:37.342786 PROGRESS: === Extracted 749522 precursors and 4005459 fragments ===
0:42:37.343284 INFO: === FDR correction performed with classifier version 11 ===
0:42:37.344008 PROGRESS: ============================= Precursor FDR =============================
0:42:37.344111 PROGRESS: Total precursors accumulated: 1,481
0:42:37.344169 PROGRESS: Target precursors: 1,467 (99.05%)
0:42:37.344216 PROGRESS: Decoy precursors: 14 (0.95%)
0:42:37.344271 PROGRESS: 
0:42:37.344316 PROGRESS: Precursor Summary:
0:42:37.345688 PROGRESS: Channel   0:	 0.050 FDR: 1,467; 0.010 FDR: 1,467; 0.001 FDR:   912
0:42:37.345783 PROGRESS: 
0:42:37.345835 PROGRESS: Protein Summary:
0:42:37.347575 PROGRESS: Channel   0:	 0.050 FDR: 1,249; 0.010 FDR: 1,249; 0.001 FDR:   798
0:42:37.347660 PROGRESS: =========================================================================
0:42:37.363571 INFO: Target number of precursors reached.
0:42:37.798865 INFO: fragments_df: keeping 5000 of 4005459 [sum(precursor_idx_mask)=35155 sum(mass_error_mask)=4005459 stop_rank=5000
0:42:38.250391 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:42:38.468453 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:42:39.120090 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:42:39.120551 INFO: Using score_cutoff 11.192928768539428 (fac=0.99, q=1)
0:42:39.120858 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:42:39.120935 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:42:39.120990 INFO: Updating optimization_manager: score_cutoff        : 11.690306758403779 -> 11.192928768539428
0:42:39.121046 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:42:39.274424 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:42:39.610354 INFO: === checking if optimization conditions were reached ===
0:42:39.610647 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
0:42:39.613736 INFO: Updating optimization_manager: rt_error            : 702.061431946775 -> 653.2058932718412
0:42:39.613840 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 653.2059.
0:42:39.613906 INFO: ==============================================
0:42:39.613974 INFO: Starting optimization step 6.
0:42:39.614032 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:42:39.614093 INFO: Using rust extraction backend
0:42:39.614152 PROGRESS: Extracting batch of 250442 precursors
0:42:40.041113 INFO: === Search parameters used ===
0:42:40.041399 INFO: rt_error       : 653.2058932718412
0:42:40.041460 INFO: mobility_error : 0.1
0:42:40.041511 INFO: num_candidates : 3
0:42:40.041559 INFO: ms1_error      : 3
0:42:40.041603 INFO: ms2_error      : 10.0
0:42:40.041646 INFO: fwhm_rt        : 3.0
0:42:40.041690 INFO: quant_window   : 3
0:42:40.041733 INFO: ==============================================
0:42:42.642465 INFO: performing precursor FDR with 40 features
0:42:42.642584 INFO: Decoy channel: -1
0:42:42.642611 INFO: competitive: True
0:42:42.851844 INFO: Setting torch num_threads to 2 for FDR classification task
0:42:43.172270 INFO: Estimating optimal hyperparameters - samples: 599,564, batch_size: 2,455, learning_rate: 7.74e-04
0:42:43.173344 INFO: Using random state 977614 for train-test-split
0:42:56.847213 INFO: Test AUC: 0.614
0:42:56.847365 INFO: Train AUC: 0.625
0:42:56.847398 INFO: AUC difference: 1.77%
0:42:57.331539 INFO: Resetting torch num_threads to 100
0:42:57.365149 PROGRESS: === Extracted 749456 precursors and 4002148 fragments ===
0:42:57.365652 INFO: === FDR correction performed with classifier version 11 ===
0:42:57.366411 PROGRESS: ============================= Precursor FDR =============================
0:42:57.366515 PROGRESS: Total precursors accumulated: 1,432
0:42:57.366583 PROGRESS: Target precursors: 1,418 (99.02%)
0:42:57.366633 PROGRESS: Decoy precursors: 14 (0.98%)
0:42:57.366676 PROGRESS: 
0:42:57.366719 PROGRESS: Precursor Summary:
0:42:57.368036 PROGRESS: Channel   0:	 0.050 FDR: 1,418; 0.010 FDR: 1,418; 0.001 FDR:     0
0:42:57.368131 PROGRESS: 
0:42:57.368183 PROGRESS: Protein Summary:
0:42:57.369743 PROGRESS: Channel   0:	 0.050 FDR: 1,206; 0.010 FDR: 1,206; 0.001 FDR:     0
0:42:57.369834 PROGRESS: =========================================================================
0:42:57.388573 INFO: Target number of precursors reached.
0:42:57.828301 INFO: fragments_df: keeping 5000 of 4002148 [sum(precursor_idx_mask)=33516 sum(mass_error_mask)=4002148 stop_rank=5000
0:42:58.273026 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:42:58.473196 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:42:59.120735 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:42:59.121206 INFO: Using score_cutoff 10.294235841178894 (fac=0.99, q=1)
0:42:59.121516 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:42:59.121590 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:42:59.121641 INFO: Updating optimization_manager: score_cutoff        : 11.192928768539428 -> 10.294235841178894
0:42:59.121700 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:42:59.275140 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:42:59.618949 INFO: === checking if optimization conditions were reached ===
0:42:59.619203 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
0:42:59.622178 INFO: Updating optimization_manager: rt_error            : 653.2058932718412 -> 814.9376545990681
0:42:59.622288 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 814.9377.
0:42:59.622352 INFO: ==============================================
0:42:59.622420 INFO: Starting optimization step 7.
0:42:59.622480 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:42:59.622540 INFO: Using rust extraction backend
0:42:59.622596 PROGRESS: Extracting batch of 250442 precursors
0:43:00.050923 INFO: === Search parameters used ===
0:43:00.051200 INFO: rt_error       : 814.9376545990681
0:43:00.051259 INFO: mobility_error : 0.1
0:43:00.051307 INFO: num_candidates : 3
0:43:00.051351 INFO: ms1_error      : 3
0:43:00.051394 INFO: ms2_error      : 10.0
0:43:00.051435 INFO: fwhm_rt        : 3.0
0:43:00.051483 INFO: quant_window   : 3
0:43:00.051523 INFO: ==============================================
0:43:02.684444 INFO: performing precursor FDR with 40 features
0:43:02.684566 INFO: Decoy channel: -1
0:43:02.684591 INFO: competitive: True
0:43:02.891089 INFO: Setting torch num_threads to 2 for FDR classification task
0:43:03.198522 INFO: Estimating optimal hyperparameters - samples: 599,633, batch_size: 2,456, learning_rate: 7.74e-04
0:43:03.199612 INFO: Using random state 977614 for train-test-split
0:43:15.938216 INFO: Test AUC: 0.614
0:43:15.938351 INFO: Train AUC: 0.626
0:43:15.938384 INFO: AUC difference: 1.87%
0:43:16.416686 INFO: Resetting torch num_threads to 100
0:43:16.449964 PROGRESS: === Extracted 749542 precursors and 4007103 fragments ===
0:43:16.450449 INFO: === FDR correction performed with classifier version 11 ===
0:43:16.451150 PROGRESS: ============================= Precursor FDR =============================
0:43:16.451237 PROGRESS: Total precursors accumulated: 1,549
0:43:16.451296 PROGRESS: Target precursors: 1,534 (99.03%)
0:43:16.451346 PROGRESS: Decoy precursors: 15 (0.97%)
0:43:16.451392 PROGRESS: 
0:43:16.451435 PROGRESS: Precursor Summary:
0:43:16.452757 PROGRESS: Channel   0:	 0.050 FDR: 1,534; 0.010 FDR: 1,534; 0.001 FDR:   204
0:43:16.452847 PROGRESS: 
0:43:16.452910 PROGRESS: Protein Summary:
0:43:16.454540 PROGRESS: Channel   0:	 0.050 FDR: 1,305; 0.010 FDR: 1,305; 0.001 FDR:   190
0:43:16.454629 PROGRESS: =========================================================================
0:43:16.470316 INFO: Target number of precursors reached.
0:43:16.914306 INFO: fragments_df: keeping 5000 of 4007103 [sum(precursor_idx_mask)=35869 sum(mass_error_mask)=4007103 stop_rank=5000
0:43:17.355751 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:43:17.567324 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:43:18.224569 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:43:18.225044 INFO: Using score_cutoff 9.401220749473572 (fac=0.99, q=1)
0:43:18.225351 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:43:18.225423 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:43:18.225475 INFO: Updating optimization_manager: score_cutoff        : 10.294235841178894 -> 9.401220749473572
0:43:18.225532 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:43:18.378021 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:43:18.706020 INFO: === checking if optimization conditions were reached ===
0:43:18.706305 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
0:43:18.709313 INFO: Updating optimization_manager: rt_error            : 814.9376545990681 -> 802.4342954527667
0:43:18.709417 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 802.4343.
0:43:18.709479 INFO: ==============================================
0:43:18.709546 INFO: Starting optimization step 8.
0:43:18.709599 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:43:18.709658 INFO: Using rust extraction backend
0:43:18.709712 PROGRESS: Extracting batch of 250442 precursors
0:43:19.139631 INFO: === Search parameters used ===
0:43:19.139946 INFO: rt_error       : 802.4342954527667
0:43:19.140013 INFO: mobility_error : 0.1
0:43:19.140063 INFO: num_candidates : 3
0:43:19.140105 INFO: ms1_error      : 3
0:43:19.140145 INFO: ms2_error      : 10.0
0:43:19.140183 INFO: fwhm_rt        : 3.0
0:43:19.140222 INFO: quant_window   : 3
0:43:19.140264 INFO: ==============================================
0:43:21.684019 INFO: performing precursor FDR with 40 features
0:43:21.684135 INFO: Decoy channel: -1
0:43:21.684159 INFO: competitive: True
0:43:21.886637 INFO: Setting torch num_threads to 2 for FDR classification task
0:43:22.187658 INFO: Estimating optimal hyperparameters - samples: 599,636, batch_size: 2,456, learning_rate: 7.74e-04
0:43:22.189022 INFO: Using random state 977614 for train-test-split
0:43:36.223810 INFO: Test AUC: 0.614
0:43:36.223962 INFO: Train AUC: 0.626
0:43:36.223996 INFO: AUC difference: 1.92%
0:43:36.707963 INFO: Resetting torch num_threads to 100
0:43:36.741253 PROGRESS: === Extracted 749545 precursors and 4007093 fragments ===
0:43:36.741755 INFO: === FDR correction performed with classifier version 11 ===
0:43:36.742473 PROGRESS: ============================= Precursor FDR =============================
0:43:36.742569 PROGRESS: Total precursors accumulated: 1,568
0:43:36.742629 PROGRESS: Target precursors: 1,553 (99.04%)
0:43:36.742684 PROGRESS: Decoy precursors: 15 (0.96%)
0:43:36.742732 PROGRESS: 
0:43:36.742776 PROGRESS: Precursor Summary:
0:43:36.744074 PROGRESS: Channel   0:	 0.050 FDR: 1,553; 0.010 FDR: 1,553; 0.001 FDR:     0
0:43:36.744172 PROGRESS: 
0:43:36.744226 PROGRESS: Protein Summary:
0:43:36.745821 PROGRESS: Channel   0:	 0.050 FDR: 1,310; 0.010 FDR: 1,310; 0.001 FDR:     0
0:43:36.745908 PROGRESS: =========================================================================
0:43:36.761067 INFO: Target number of precursors reached.
0:43:37.201184 INFO: fragments_df: keeping 5000 of 4007093 [sum(precursor_idx_mask)=36457 sum(mass_error_mask)=4007093 stop_rank=5000
0:43:37.684296 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:43:37.929894 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:43:38.647810 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:43:38.648296 INFO: Using score_cutoff 10.303540600204467 (fac=0.99, q=1)
0:43:38.648617 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:43:38.648694 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:43:38.648752 INFO: Updating optimization_manager: score_cutoff        : 9.401220749473572 -> 10.303540600204467
0:43:38.648806 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:43:38.799307 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:43:39.124125 INFO: === checking if optimization conditions were reached ===
0:43:39.124393 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
0:43:39.125389 INFO: Updating optimization_manager: rt_error            : 802.4342954527667 -> 802.4342954527667
0:43:39.125510 INFO: Updating optimization_manager: classifier_version  : 11 -> 20
0:43:39.125602 INFO: Updating optimization_manager: score_cutoff        : 10.303540600204467 -> 10.303540600204467
0:43:39.125684 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:43:39.125764 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:43:39.125847 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 802.4343 found after 9 searches.
0:43:39.125903 INFO: ==============================================
0:43:39.125967 PROGRESS: Optimization finished for rt_error.
0:43:39.549387 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:43:39.701199 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:43:40.025795 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:43:40.026091 PROGRESS: ==============================================
0:43:40.026170 PROGRESS: ms2_error      : 10.0000
0:43:40.026232 PROGRESS: rt_error       : 802.4343
0:43:40.026281 PROGRESS: ==============================================
0:43:40.027147 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:43:47.516131 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:44:03.621537 INFO: Using rust extraction backend
0:44:03.621991 PROGRESS: Extracting batch of 11997144 precursors
0:44:19.648011 INFO: === Search parameters used ===
0:44:19.648511 INFO: rt_error       : 802.4342954527667
0:44:19.648586 INFO: mobility_error : 0.1
0:44:19.648640 INFO: num_candidates : 3
0:44:19.648692 INFO: ms1_error      : 3
0:44:19.648740 INFO: ms2_error      : 10.0
0:44:19.648790 INFO: fwhm_rt        : 3.0
0:44:19.648837 INFO: quant_window   : 3
0:44:19.648881 INFO: ==============================================
0:44:51.293307 INFO: Removed 7720577 precursors with score below cutoff 10.303540600204467
0:45:13.894572 INFO: performing precursor FDR with 40 features
0:45:13.894766 INFO: Decoy channel: -1
0:45:13.894799 INFO: competitive: True
0:45:16.915378 INFO: Setting torch num_threads to 2 for FDR classification task
0:45:28.368243 INFO: Estimating optimal hyperparameters - samples: 22,616,393, batch_size: 4,096, learning_rate: 1.00e-03
0:45:28.437140 INFO: Using random state 960055 for train-test-split
0:53:16.887069 INFO: Test AUC: 0.621
0:53:16.887338 INFO: Train AUC: 0.622
0:53:16.887379 INFO: AUC difference: 0.06%
0:53:23.488246 INFO: Resetting torch num_threads to 100
0:53:25.701081 PROGRESS: ============================= Precursor FDR =============================
0:53:25.701421 PROGRESS: Total precursors accumulated: 93,251
0:53:25.701494 PROGRESS: Target precursors: 92,328 (99.01%)
0:53:25.701549 PROGRESS: Decoy precursors: 923 (0.99%)
0:53:25.701598 PROGRESS: 
0:53:25.701645 PROGRESS: Precursor Summary:
0:53:25.730511 PROGRESS: Channel   0:	 0.050 FDR: 92,328; 0.010 FDR: 92,328; 0.001 FDR: 59,111
0:53:25.730760 PROGRESS: 
0:53:25.730820 PROGRESS: Protein Summary:
0:53:25.770038 PROGRESS: Channel   0:	 0.050 FDR: 14,133; 0.010 FDR: 14,133; 0.001 FDR: 9,505
0:53:25.770271 PROGRESS: =========================================================================
0:53:25.945637 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/psm.parquet
0:53:26.113730 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.parquet
0:53:26.356130 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
0:53:26.891200 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 
0:53:26.891355 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
0:53:26.891481 INFO: Initializing TimingManager
0:53:26.892340 INFO: Initializing RawFileManager
0:53:45.728636 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.
0:53:45.738209 INFO: Determining DIA cycle
0:53:45.755730 INFO: Found cycle with start 0.00 min and length 300.
0:53:45.920061 INFO: RT (min)            : 0.0 - 26.9
0:53:45.920316 INFO: RT duration (sec)   : 1611.2
0:53:45.920346 INFO: RT duration (min)   : 26.9
0:53:45.920370 INFO: Cycle len (scans)   : 300
0:53:45.920392 INFO: Cycle len (sec)     : 1.65
0:53:45.920412 INFO: Number of cycles    : 977
0:53:45.920432 INFO: MS2 range (m/z)     : 380.4 - 980.7
0:53:45.920463 INFO: Creating DIA data object took: 19.028022050857544
0:53:46.582652 INFO: Creating DIA data NG object took: 0.6620538234710693
0:53:47.930931 INFO: Initializing CalibrationManager
0:53:47.931233 INFO: Setting up calibration estimators ..
0:53:47.931299 INFO: Found 1 estimator(s) in calibration group 'fragment'
0:53:47.931389 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'}' ..
0:53:47.931520 INFO: Found 3 estimator(s) in calibration group 'precursor'
0:53:47.931573 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
0:53:47.931637 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}}' ..
0:53:47.931691 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
0:53:47.931736 INFO: Done setting up calibration estimators.
0:53:47.931938 INFO: Initializing OptimizationManager
0:53:47.932091 INFO: initial parameter: ms1_error = 3
0:53:47.932146 INFO: initial parameter: ms2_error = 10
0:53:47.932194 INFO: initial parameter: rt_error = 805.6004638671875
0:53:47.932238 INFO: initial parameter: mobility_error = 0.1
0:53:47.932281 INFO: initial parameter: num_candidates = 1
0:53:47.932325 INFO: initial parameter: fwhm_rt = 5
0:53:47.932367 INFO: initial parameter: fwhm_mobility = 0.01
0:53:47.932407 INFO: initial parameter: score_cutoff = 0
0:53:47.932446 INFO: initial parameter: classifier_version = -1
0:53:47.932513 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
0:53:47.932779 INFO: FDRManager: loading saved state not requested, will be initialized.
0:53:47.932814 INFO: Initializing FDRManager
0:53:47.932857 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
0:53:49.400048 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
0:53:50.302956 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
0:53:50.303388 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
0:53:50.303490 PROGRESS: Starting initial search for precursors.
0:53:50.303583 INFO: Starting optimization step 0.
0:53:50.303646 PROGRESS: === Extracting elution groups 0 to 1000 ===
0:53:50.303709 INFO: Using rust extraction backend
0:53:50.303770 PROGRESS: Extracting batch of 1970 precursors
0:53:50.308724 INFO: === Search parameters used ===
0:53:50.308826 INFO: rt_error       : 805.6004638671875
0:53:50.308877 INFO: mobility_error : 0.1
0:53:50.308922 INFO: num_candidates : 1
0:53:50.308963 INFO: ms1_error      : 3
0:53:50.309003 INFO: ms2_error      : 10
0:53:50.309042 INFO: fwhm_rt        : 5
0:53:50.309082 INFO: quant_window   : 3
0:53:50.309121 INFO: ==============================================
0:53:50.338795 INFO: performing precursor FDR with 40 features
0:53:50.338864 INFO: Decoy channel: -1
0:53:50.338887 INFO: competitive: True
0:53:50.340216 INFO: Setting torch num_threads to 2 for FDR classification task
0:53:50.342235 INFO: Estimating optimal hyperparameters - samples: 1,569, batch_size: 128, learning_rate: 1.77e-04
0:53:50.343042 INFO: Using random state 499592 for train-test-split
0:53:50.493518 INFO: Test AUC: 0.523
0:53:50.493596 INFO: Train AUC: 0.534
0:53:50.493623 INFO: AUC difference: 2.19%
0:53:50.740560 INFO: Resetting torch num_threads to 100
0:53:50.742250 PROGRESS: === Extracted 1962 precursors and 10815 fragments ===
0:53:50.742618 INFO: === FDR correction performed with classifier version -1 ===
0:53:50.743101 PROGRESS: ============================= Precursor FDR =============================
0:53:50.743183 PROGRESS: Total precursors accumulated: 16
0:53:50.743250 PROGRESS: Target precursors: 16 (100.00%)
0:53:50.743298 PROGRESS: Decoy precursors: 0 (0.00%)
0:53:50.743341 PROGRESS: 
0:53:50.743383 PROGRESS: Precursor Summary:
0:53:50.744441 PROGRESS: Channel   0:	 0.050 FDR:    16; 0.010 FDR:    16; 0.001 FDR:    16
0:53:50.744527 PROGRESS: 
0:53:50.744580 PROGRESS: Protein Summary:
0:53:50.745747 PROGRESS: Channel   0:	 0.050 FDR:    15; 0.010 FDR:    15; 0.001 FDR:    15
0:53:50.745828 PROGRESS: =========================================================================
0:53:50.746054 INFO: Target number of precursors not reached yet.
0:53:50.832705 INFO: Starting optimization step 1.
0:53:50.832930 PROGRESS: === Extracting elution groups 1000 to 3000 ===
0:53:50.833009 INFO: Using rust extraction backend
0:53:50.833066 PROGRESS: Extracting batch of 3935 precursors
0:53:50.842068 INFO: === Search parameters used ===
0:53:50.842213 INFO: rt_error       : 805.6004638671875
0:53:50.842265 INFO: mobility_error : 0.1
0:53:50.842310 INFO: num_candidates : 1
0:53:50.842353 INFO: ms1_error      : 3
0:53:50.842393 INFO: ms2_error      : 10
0:53:50.842432 INFO: fwhm_rt        : 5
0:53:50.842472 INFO: quant_window   : 3
0:53:50.842511 INFO: ==============================================
0:53:50.893452 INFO: performing precursor FDR with 40 features
0:53:50.893539 INFO: Decoy channel: -1
0:53:50.893563 INFO: competitive: True
0:53:50.897951 INFO: Setting torch num_threads to 2 for FDR classification task
0:53:50.900255 INFO: Estimating optimal hyperparameters - samples: 4,712, batch_size: 128, learning_rate: 1.77e-04
0:53:50.900339 INFO: Using random state 858960 for train-test-split
0:53:51.364137 INFO: Test AUC: 0.541
0:53:51.364247 INFO: Train AUC: 0.563
0:53:51.364276 INFO: AUC difference: 3.90%
0:53:51.609659 INFO: Resetting torch num_threads to 100
0:53:51.612781 PROGRESS: === Extracted 5891 precursors and 32866 fragments ===
0:53:51.613166 INFO: === FDR correction performed with classifier version -1 ===
0:53:51.613653 PROGRESS: ============================= Precursor FDR =============================
0:53:51.613737 PROGRESS: Total precursors accumulated: 32
0:53:51.613792 PROGRESS: Target precursors: 32 (100.00%)
0:53:51.613840 PROGRESS: Decoy precursors: 0 (0.00%)
0:53:51.613885 PROGRESS: 
0:53:51.613928 PROGRESS: Precursor Summary:
0:53:51.614993 PROGRESS: Channel   0:	 0.050 FDR:    32; 0.010 FDR:    32; 0.001 FDR:    32
0:53:51.615074 PROGRESS: 
0:53:51.615127 PROGRESS: Protein Summary:
0:53:51.616312 PROGRESS: Channel   0:	 0.050 FDR:    31; 0.010 FDR:    31; 0.001 FDR:    31
0:53:51.616401 PROGRESS: =========================================================================
0:53:51.616683 INFO: Target number of precursors not reached yet.
0:53:51.710037 INFO: Starting optimization step 2.
0:53:51.710258 PROGRESS: === Extracting elution groups 3000 to 7000 ===
0:53:51.710335 INFO: Using rust extraction backend
0:53:51.710390 PROGRESS: Extracting batch of 7881 precursors
0:53:51.725232 INFO: === Search parameters used ===
0:53:51.725371 INFO: rt_error       : 805.6004638671875
0:53:51.725422 INFO: mobility_error : 0.1
0:53:51.725466 INFO: num_candidates : 1
0:53:51.725507 INFO: ms1_error      : 3
0:53:51.725547 INFO: ms2_error      : 10
0:53:51.725586 INFO: fwhm_rt        : 5
0:53:51.725625 INFO: quant_window   : 3
0:53:51.725665 INFO: ==============================================
0:53:51.804806 INFO: performing precursor FDR with 40 features
0:53:51.804907 INFO: Decoy channel: -1
0:53:51.804949 INFO: competitive: True
0:53:51.812466 INFO: Setting torch num_threads to 2 for FDR classification task
0:53:51.816932 INFO: Estimating optimal hyperparameters - samples: 11,000, batch_size: 128, learning_rate: 1.77e-04
0:53:51.817053 INFO: Using random state 978531 for train-test-split
0:53:52.909191 INFO: Test AUC: 0.545
0:53:52.909307 INFO: Train AUC: 0.581
0:53:52.909338 INFO: AUC difference: 6.17%
0:53:52.909361 WARNING: AUC difference > 5%. This may indicate overfitting.
0:53:53.155348 INFO: Resetting torch num_threads to 100
0:53:53.159682 PROGRESS: === Extracted 13750 precursors and 76956 fragments ===
0:53:53.160097 INFO: === FDR correction performed with classifier version -1 ===
0:53:53.160615 PROGRESS: ============================= Precursor FDR =============================
0:53:53.160702 PROGRESS: Total precursors accumulated: 22
0:53:53.160761 PROGRESS: Target precursors: 22 (100.00%)
0:53:53.160812 PROGRESS: Decoy precursors: 0 (0.00%)
0:53:53.160860 PROGRESS: 
0:53:53.160907 PROGRESS: Precursor Summary:
0:53:53.161952 PROGRESS: Channel   0:	 0.050 FDR:    22; 0.010 FDR:    22; 0.001 FDR:    22
0:53:53.162034 PROGRESS: 
0:53:53.162092 PROGRESS: Protein Summary:
0:53:53.163275 PROGRESS: Channel   0:	 0.050 FDR:    21; 0.010 FDR:    21; 0.001 FDR:    21
0:53:53.163359 PROGRESS: =========================================================================
0:53:53.163727 INFO: Target number of precursors not reached yet.
0:53:53.266206 INFO: Starting optimization step 3.
0:53:53.266439 PROGRESS: === Extracting elution groups 7000 to 15000 ===
0:53:53.266522 INFO: Using rust extraction backend
0:53:53.266581 PROGRESS: Extracting batch of 15776 precursors
0:53:53.295015 INFO: === Search parameters used ===
0:53:53.295209 INFO: rt_error       : 805.6004638671875
0:53:53.295261 INFO: mobility_error : 0.1
0:53:53.295309 INFO: num_candidates : 1
0:53:53.295355 INFO: ms1_error      : 3
0:53:53.295399 INFO: ms2_error      : 10
0:53:53.295453 INFO: fwhm_rt        : 5
0:53:53.295498 INFO: quant_window   : 3
0:53:53.295543 INFO: ==============================================
0:53:53.422758 INFO: performing precursor FDR with 40 features
0:53:53.422874 INFO: Decoy channel: -1
0:53:53.422901 INFO: competitive: True
0:53:53.436284 INFO: Setting torch num_threads to 2 for FDR classification task
0:53:53.443748 INFO: Estimating optimal hyperparameters - samples: 23,585, batch_size: 128, learning_rate: 1.77e-04
0:53:53.443937 INFO: Using random state 310853 for train-test-split
0:53:55.849865 INFO: Test AUC: 0.566
0:53:55.849957 INFO: Train AUC: 0.588
0:53:55.849986 INFO: AUC difference: 3.82%
0:53:56.104267 INFO: Resetting torch num_threads to 100
0:53:56.110952 PROGRESS: === Extracted 29482 precursors and 164841 fragments ===
0:53:56.111387 INFO: === FDR correction performed with classifier version -1 ===
0:53:56.111904 PROGRESS: ============================= Precursor FDR =============================
0:53:56.111994 PROGRESS: Total precursors accumulated: 0
0:53:56.112053 PROGRESS: Target precursors: 0 (0.00%)
0:53:56.112104 PROGRESS: Decoy precursors: 0 (0.00%)
0:53:56.112151 PROGRESS: 
0:53:56.112197 PROGRESS: Precursor Summary:
0:53:56.112314 PROGRESS: 
0:53:56.112375 PROGRESS: Protein Summary:
0:53:56.112448 PROGRESS: =========================================================================
0:53:56.112950 INFO: Target number of precursors not reached yet.
0:53:56.236449 INFO: Starting optimization step 4.
0:53:56.236711 PROGRESS: === Extracting elution groups 15000 to 31000 ===
0:53:56.236793 INFO: Using rust extraction backend
0:53:56.236854 PROGRESS: Extracting batch of 31591 precursors
0:53:56.291525 INFO: === Search parameters used ===
0:53:56.291759 INFO: rt_error       : 805.6004638671875
0:53:56.291830 INFO: mobility_error : 0.1
0:53:56.291882 INFO: num_candidates : 1
0:53:56.291924 INFO: ms1_error      : 3
0:53:56.291965 INFO: ms2_error      : 10
0:53:56.292005 INFO: fwhm_rt        : 5
0:53:56.292044 INFO: quant_window   : 3
0:53:56.292082 INFO: ==============================================
0:53:56.515711 INFO: performing precursor FDR with 40 features
0:53:56.515842 INFO: Decoy channel: -1
0:53:56.515870 INFO: competitive: True
0:53:56.542370 INFO: Setting torch num_threads to 2 for FDR classification task
0:53:56.557315 INFO: Estimating optimal hyperparameters - samples: 48,795, batch_size: 199, learning_rate: 2.20e-04
0:53:56.557538 INFO: Using random state 854805 for train-test-split
0:54:00.194715 INFO: Test AUC: 0.582
0:54:00.194806 INFO: Train AUC: 0.603
0:54:00.194834 INFO: AUC difference: 3.33%
0:54:00.455106 INFO: Resetting torch num_threads to 100
0:54:00.466352 PROGRESS: === Extracted 60994 precursors and 342003 fragments ===
0:54:00.466831 INFO: === FDR correction performed with classifier version -1 ===
0:54:00.467354 PROGRESS: ============================= Precursor FDR =============================
0:54:00.467437 PROGRESS: Total precursors accumulated: 0
0:54:00.467493 PROGRESS: Target precursors: 0 (0.00%)
0:54:00.467540 PROGRESS: Decoy precursors: 0 (0.00%)
0:54:00.467583 PROGRESS: 
0:54:00.467625 PROGRESS: Precursor Summary:
0:54:00.467740 PROGRESS: 
0:54:00.467798 PROGRESS: Protein Summary:
0:54:00.467891 PROGRESS: =========================================================================
0:54:00.468728 INFO: Target number of precursors not reached yet.
0:54:00.630761 INFO: Starting optimization step 5.
0:54:00.631017 PROGRESS: === Extracting elution groups 31000 to 63000 ===
0:54:00.631097 INFO: Using rust extraction backend
0:54:00.631167 PROGRESS: Extracting batch of 63056 precursors
0:54:00.742960 INFO: === Search parameters used ===
0:54:00.743258 INFO: rt_error       : 805.6004638671875
0:54:00.743315 INFO: mobility_error : 0.1
0:54:00.743362 INFO: num_candidates : 1
0:54:00.743403 INFO: ms1_error      : 3
0:54:00.743442 INFO: ms2_error      : 10
0:54:00.743483 INFO: fwhm_rt        : 5
0:54:00.743529 INFO: quant_window   : 3
0:54:00.743569 INFO: ==============================================
0:54:01.132198 INFO: performing precursor FDR with 40 features
0:54:01.132326 INFO: Decoy channel: -1
0:54:01.132351 INFO: competitive: True
0:54:01.181641 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:01.217658 INFO: Estimating optimal hyperparameters - samples: 99,117, batch_size: 405, learning_rate: 3.14e-04
0:54:01.217952 INFO: Using random state 132203 for train-test-split
0:54:05.904994 INFO: Test AUC: 0.583
0:54:05.905097 INFO: Train AUC: 0.608
0:54:05.905125 INFO: AUC difference: 4.18%
0:54:06.185541 INFO: Resetting torch num_threads to 100
0:54:06.206717 PROGRESS: === Extracted 123897 precursors and 694927 fragments ===
0:54:06.207360 INFO: === FDR correction performed with classifier version -1 ===
0:54:06.208032 PROGRESS: ============================= Precursor FDR =============================
0:54:06.208130 PROGRESS: Total precursors accumulated: 586
0:54:06.208189 PROGRESS: Target precursors: 581 (99.15%)
0:54:06.208238 PROGRESS: Decoy precursors: 5 (0.85%)
0:54:06.208281 PROGRESS: 
0:54:06.208325 PROGRESS: Precursor Summary:
0:54:06.209430 PROGRESS: Channel   0:	 0.050 FDR:   581; 0.010 FDR:   581; 0.001 FDR:     0
0:54:06.209517 PROGRESS: 
0:54:06.209569 PROGRESS: Protein Summary:
0:54:06.210823 PROGRESS: Channel   0:	 0.050 FDR:   538; 0.010 FDR:   538; 0.001 FDR:     0
0:54:06.210918 PROGRESS: =========================================================================
0:54:06.212717 INFO: Target number of precursors not reached yet.
0:54:06.458741 INFO: Starting optimization step 6.
0:54:06.459021 PROGRESS: === Extracting elution groups 63000 to 127000 ===
0:54:06.459103 INFO: Using rust extraction backend
0:54:06.459166 PROGRESS: Extracting batch of 126233 precursors
0:54:06.674075 INFO: === Search parameters used ===
0:54:06.674350 INFO: rt_error       : 805.6004638671875
0:54:06.674406 INFO: mobility_error : 0.1
0:54:06.674452 INFO: num_candidates : 1
0:54:06.674497 INFO: ms1_error      : 3
0:54:06.674539 INFO: ms2_error      : 10
0:54:06.674579 INFO: fwhm_rt        : 5
0:54:06.674619 INFO: quant_window   : 3
0:54:06.674659 INFO: ==============================================
0:54:07.377435 INFO: performing precursor FDR with 40 features
0:54:07.377558 INFO: Decoy channel: -1
0:54:07.377584 INFO: competitive: True
0:54:07.490329 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:07.571949 INFO: Estimating optimal hyperparameters - samples: 199,848, batch_size: 818, learning_rate: 4.47e-04
0:54:07.572403 INFO: Using random state 888583 for train-test-split
0:54:14.252051 INFO: Test AUC: 0.588
0:54:14.252164 INFO: Train AUC: 0.609
0:54:14.252195 INFO: AUC difference: 3.47%
0:54:14.577597 INFO: Resetting torch num_threads to 100
0:54:14.622565 PROGRESS: === Extracted 249810 precursors and 1399479 fragments ===
0:54:14.623303 INFO: === FDR correction performed with classifier version -1 ===
0:54:14.624150 PROGRESS: ============================= Precursor FDR =============================
0:54:14.624241 PROGRESS: Total precursors accumulated: 1,136
0:54:14.624303 PROGRESS: Target precursors: 1,125 (99.03%)
0:54:14.624355 PROGRESS: Decoy precursors: 11 (0.97%)
0:54:14.624414 PROGRESS: 
0:54:14.624462 PROGRESS: Precursor Summary:
0:54:14.625677 PROGRESS: Channel   0:	 0.050 FDR: 1,125; 0.010 FDR: 1,125; 0.001 FDR:     0
0:54:14.625763 PROGRESS: 
0:54:14.625820 PROGRESS: Protein Summary:
0:54:14.627285 PROGRESS: Channel   0:	 0.050 FDR:   972; 0.010 FDR:   972; 0.001 FDR:     0
0:54:14.627374 PROGRESS: =========================================================================
0:54:14.631855 INFO: Target number of precursors reached.
0:54:14.795605 INFO: fragments_df: keeping 5000 of 1399479 [sum(precursor_idx_mask)=12104 sum(mass_error_mask)=1399479 stop_rank=5000
0:54:15.203810 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:54:15.382523 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:54:16.035031 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
0:54:16.035493 INFO: Using score_cutoff 12.031751496505736 (fac=0.99, q=1)
0:54:16.035815 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
0:54:16.035909 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
0:54:16.035965 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.031751496505736
0:54:16.036038 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:54:16.187273 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:54:16.535101 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
0:54:16.535444 PROGRESS: Required number of precursors found. Starting search parameter optimization.
0:54:16.535588 INFO: Starting optimization step 7.
0:54:16.535668 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:54:16.535762 INFO: Using rust extraction backend
0:54:16.535853 PROGRESS: Extracting batch of 250442 precursors
0:54:16.958272 INFO: === Search parameters used ===
0:54:16.958560 INFO: rt_error       : 805.6004638671875
0:54:16.958620 INFO: mobility_error : 0.1
0:54:16.958685 INFO: num_candidates : 3
0:54:16.958730 INFO: ms1_error      : 3
0:54:16.958775 INFO: ms2_error      : 10
0:54:16.958820 INFO: fwhm_rt        : 3.0
0:54:16.958862 INFO: quant_window   : 3
0:54:16.958903 INFO: ==============================================
0:54:19.570262 INFO: performing precursor FDR with 40 features
0:54:19.570385 INFO: Decoy channel: -1
0:54:19.570410 INFO: competitive: True
0:54:19.768537 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:20.077167 INFO: Estimating optimal hyperparameters - samples: 599,604, batch_size: 2,455, learning_rate: 7.74e-04
0:54:20.078314 INFO: Using random state 737769 for train-test-split
0:54:32.802087 INFO: Test AUC: 0.595
0:54:32.802217 INFO: Train AUC: 0.603
0:54:32.802251 INFO: AUC difference: 1.40%
0:54:33.292762 INFO: Resetting torch num_threads to 100
0:54:33.326956 PROGRESS: === Extracted 749505 precursors and 4023116 fragments ===
0:54:33.327436 INFO: === FDR correction performed with classifier version 6 ===
0:54:33.328167 PROGRESS: ============================= Precursor FDR =============================
0:54:33.328267 PROGRESS: Total precursors accumulated: 1,317
0:54:33.328327 PROGRESS: Target precursors: 1,304 (99.01%)
0:54:33.328379 PROGRESS: Decoy precursors: 13 (0.99%)
0:54:33.328426 PROGRESS: 
0:54:33.328472 PROGRESS: Precursor Summary:
0:54:33.329792 PROGRESS: Channel   0:	 0.050 FDR: 1,304; 0.010 FDR: 1,304; 0.001 FDR:   257
0:54:33.329882 PROGRESS: 
0:54:33.329936 PROGRESS: Protein Summary:
0:54:33.331503 PROGRESS: Channel   0:	 0.050 FDR: 1,114; 0.010 FDR: 1,114; 0.001 FDR:   237
0:54:33.331590 PROGRESS: =========================================================================
0:54:33.348869 INFO: Target number of precursors reached.
0:54:33.790639 INFO: fragments_df: keeping 5000 of 4023116 [sum(precursor_idx_mask)=31618 sum(mass_error_mask)=4023116 stop_rank=5000
0:54:34.332827 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:54:34.516990 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:54:35.168156 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:54:35.168628 INFO: Using score_cutoff 12.394765982723236 (fac=0.99, q=1)
0:54:35.168929 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:54:35.169006 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:54:35.169060 INFO: Updating optimization_manager: score_cutoff        : 12.031751496505736 -> 12.394765982723236
0:54:35.169113 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:54:35.322028 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:54:35.663246 INFO: === checking if optimization conditions were reached ===
0:54:35.665589 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
0:54:35.665700 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
0:54:35.665770 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:54:35.665843 INFO: ==============================================
0:54:35.665915 INFO: Starting optimization step 8.
0:54:35.665995 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:54:35.666061 INFO: Using rust extraction backend
0:54:35.666134 PROGRESS: Extracting batch of 250442 precursors
0:54:36.090761 INFO: === Search parameters used ===
0:54:36.091060 INFO: rt_error       : 805.6004638671875
0:54:36.091120 INFO: mobility_error : 0.1
0:54:36.091170 INFO: num_candidates : 3
0:54:36.091214 INFO: ms1_error      : 3
0:54:36.091261 INFO: ms2_error      : 10.0
0:54:36.091311 INFO: fwhm_rt        : 3.0
0:54:36.091357 INFO: quant_window   : 3
0:54:36.091398 INFO: ==============================================
0:54:38.681992 INFO: performing precursor FDR with 40 features
0:54:38.682120 INFO: Decoy channel: -1
0:54:38.682145 INFO: competitive: True
0:54:38.880145 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:39.189781 INFO: Estimating optimal hyperparameters - samples: 599,604, batch_size: 2,455, learning_rate: 7.74e-04
0:54:39.190727 INFO: Using random state 627134 for train-test-split
0:54:51.813849 INFO: Test AUC: 0.601
0:54:51.813980 INFO: Train AUC: 0.611
0:54:51.814015 INFO: AUC difference: 1.60%
0:54:53.060798 INFO: Resetting torch num_threads to 100
0:54:53.091763 PROGRESS: === Extracted 749505 precursors and 4022720 fragments ===
0:54:53.092264 INFO: === FDR correction performed with classifier version 7 ===
0:54:53.092978 PROGRESS: ============================= Precursor FDR =============================
0:54:53.093079 PROGRESS: Total precursors accumulated: 1,447
0:54:53.093140 PROGRESS: Target precursors: 1,433 (99.03%)
0:54:53.093192 PROGRESS: Decoy precursors: 14 (0.97%)
0:54:53.093239 PROGRESS: 
0:54:53.093292 PROGRESS: Precursor Summary:
0:54:53.094642 PROGRESS: Channel   0:	 0.050 FDR: 1,433; 0.010 FDR: 1,433; 0.001 FDR:   836
0:54:53.094729 PROGRESS: 
0:54:53.094784 PROGRESS: Protein Summary:
0:54:53.096511 PROGRESS: Channel   0:	 0.050 FDR: 1,219; 0.010 FDR: 1,219; 0.001 FDR:   727
0:54:53.096606 PROGRESS: =========================================================================
0:54:53.112888 INFO: Target number of precursors reached.
0:54:53.547207 INFO: fragments_df: keeping 5000 of 4022720 [sum(precursor_idx_mask)=34382 sum(mass_error_mask)=4022720 stop_rank=5000
0:54:53.972527 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:54:54.183419 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:54:54.842645 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:54:54.843113 INFO: Using score_cutoff 11.802317795562743 (fac=0.99, q=1)
0:54:54.843423 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:54:54.843500 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:54:54.843555 INFO: Updating optimization_manager: score_cutoff        : 12.394765982723236 -> 11.802317795562743
0:54:54.843608 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:54:54.995352 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:54:55.337413 INFO: === checking if optimization conditions were reached ===
0:54:55.339667 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:54:55.339766 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
0:54:55.339853 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:54:55.339924 INFO: ==============================================
0:54:55.339990 INFO: Starting optimization step 9.
0:54:55.340044 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:54:55.340102 INFO: Using rust extraction backend
0:54:55.340157 PROGRESS: Extracting batch of 250442 precursors
0:54:55.763939 INFO: === Search parameters used ===
0:54:55.764210 INFO: rt_error       : 805.6004638671875
0:54:55.764268 INFO: mobility_error : 0.1
0:54:55.764315 INFO: num_candidates : 3
0:54:55.764356 INFO: ms1_error      : 3
0:54:55.764396 INFO: ms2_error      : 10.0
0:54:55.764436 INFO: fwhm_rt        : 3.0
0:54:55.764474 INFO: quant_window   : 3
0:54:55.764511 INFO: ==============================================
0:54:58.306114 INFO: performing precursor FDR with 40 features
0:54:58.306230 INFO: Decoy channel: -1
0:54:58.306255 INFO: competitive: True
0:54:58.494079 INFO: Setting torch num_threads to 2 for FDR classification task
0:54:58.788118 INFO: Estimating optimal hyperparameters - samples: 599,618, batch_size: 2,456, learning_rate: 7.74e-04
0:54:58.789227 INFO: Using random state 5996 for train-test-split
0:55:11.268210 INFO: Test AUC: 0.604
0:55:11.268353 INFO: Train AUC: 0.616
0:55:11.268386 INFO: AUC difference: 1.92%
0:55:11.756676 INFO: Resetting torch num_threads to 100
0:55:11.789038 PROGRESS: === Extracted 749523 precursors and 4023135 fragments ===
0:55:11.789557 INFO: === FDR correction performed with classifier version 8 ===
0:55:11.790349 PROGRESS: ============================= Precursor FDR =============================
0:55:11.790453 PROGRESS: Total precursors accumulated: 1,419
0:55:11.790518 PROGRESS: Target precursors: 1,405 (99.01%)
0:55:11.790572 PROGRESS: Decoy precursors: 14 (0.99%)
0:55:11.790632 PROGRESS: 
0:55:11.790678 PROGRESS: Precursor Summary:
0:55:11.792009 PROGRESS: Channel   0:	 0.050 FDR: 1,405; 0.010 FDR: 1,405; 0.001 FDR:    17
0:55:11.792104 PROGRESS: 
0:55:11.792159 PROGRESS: Protein Summary:
0:55:11.793755 PROGRESS: Channel   0:	 0.050 FDR: 1,201; 0.010 FDR: 1,201; 0.001 FDR:    17
0:55:11.793847 PROGRESS: =========================================================================
0:55:11.808825 INFO: Target number of precursors reached.
0:55:12.232581 INFO: fragments_df: keeping 5000 of 4023135 [sum(precursor_idx_mask)=33303 sum(mass_error_mask)=4023135 stop_rank=5000
0:55:12.686162 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:55:12.891181 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:55:13.542557 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:55:13.543013 INFO: Using score_cutoff 10.433331003570558 (fac=0.99, q=1)
0:55:13.543316 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:55:13.543391 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:55:13.543444 INFO: Updating optimization_manager: score_cutoff        : 11.802317795562743 -> 10.433331003570558
0:55:13.543496 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:55:13.701768 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:55:14.056227 INFO: === checking if optimization conditions were reached ===
0:55:14.058493 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:55:14.058601 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
0:55:14.058665 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:55:14.058720 INFO: ==============================================
0:55:14.058785 INFO: Starting optimization step 10.
0:55:14.058843 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:55:14.058901 INFO: Using rust extraction backend
0:55:14.058954 PROGRESS: Extracting batch of 250442 precursors
0:55:14.483445 INFO: === Search parameters used ===
0:55:14.483726 INFO: rt_error       : 805.6004638671875
0:55:14.483782 INFO: mobility_error : 0.1
0:55:14.483844 INFO: num_candidates : 3
0:55:14.483893 INFO: ms1_error      : 3
0:55:14.483937 INFO: ms2_error      : 10.0
0:55:14.483976 INFO: fwhm_rt        : 3.0
0:55:14.484014 INFO: quant_window   : 3
0:55:14.484051 INFO: ==============================================
0:55:17.035142 INFO: performing precursor FDR with 40 features
0:55:17.035264 INFO: Decoy channel: -1
0:55:17.035288 INFO: competitive: True
0:55:17.231429 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:17.542235 INFO: Estimating optimal hyperparameters - samples: 599,620, batch_size: 2,456, learning_rate: 7.74e-04
0:55:17.543338 INFO: Using random state 764464 for train-test-split
0:55:29.919457 INFO: Test AUC: 0.607
0:55:29.919592 INFO: Train AUC: 0.619
0:55:29.919624 INFO: AUC difference: 1.83%
0:55:30.404260 INFO: Resetting torch num_threads to 100
0:55:30.438477 PROGRESS: === Extracted 749526 precursors and 4023233 fragments ===
0:55:30.438997 INFO: === FDR correction performed with classifier version 9 ===
0:55:30.439775 PROGRESS: ============================= Precursor FDR =============================
0:55:30.439897 PROGRESS: Total precursors accumulated: 1,555
0:55:30.439976 PROGRESS: Target precursors: 1,540 (99.04%)
0:55:30.440029 PROGRESS: Decoy precursors: 15 (0.96%)
0:55:30.440077 PROGRESS: 
0:55:30.440125 PROGRESS: Precursor Summary:
0:55:30.441714 PROGRESS: Channel   0:	 0.050 FDR: 1,540; 0.010 FDR: 1,540; 0.001 FDR: 1,029
0:55:30.441820 PROGRESS: 
0:55:30.441885 PROGRESS: Protein Summary:
0:55:30.443866 PROGRESS: Channel   0:	 0.050 FDR: 1,290; 0.010 FDR: 1,290; 0.001 FDR:   888
0:55:30.443969 PROGRESS: =========================================================================
0:55:30.459457 INFO: Target number of precursors reached.
0:55:30.898976 INFO: fragments_df: keeping 5000 of 4023233 [sum(precursor_idx_mask)=36529 sum(mass_error_mask)=4023233 stop_rank=5000
0:55:31.338759 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:55:31.544736 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:55:32.197567 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:55:32.198036 INFO: Using score_cutoff 11.633124858570099 (fac=0.99, q=1)
0:55:32.198348 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:55:32.198435 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:55:32.198488 INFO: Updating optimization_manager: score_cutoff        : 10.433331003570558 -> 11.633124858570099
0:55:32.198544 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:55:32.350887 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:55:32.690994 INFO: === checking if optimization conditions were reached ===
0:55:32.693260 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:55:32.693360 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
0:55:32.693424 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
0:55:32.693481 INFO: ==============================================
0:55:32.693547 INFO: Starting optimization step 11.
0:55:32.693602 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:55:32.693661 INFO: Using rust extraction backend
0:55:32.693714 PROGRESS: Extracting batch of 250442 precursors
0:55:33.116102 INFO: === Search parameters used ===
0:55:33.116389 INFO: rt_error       : 805.6004638671875
0:55:33.116450 INFO: mobility_error : 0.1
0:55:33.116503 INFO: num_candidates : 3
0:55:33.116548 INFO: ms1_error      : 3
0:55:33.116590 INFO: ms2_error      : 10.0
0:55:33.116629 INFO: fwhm_rt        : 3.0
0:55:33.116668 INFO: quant_window   : 3
0:55:33.116706 INFO: ==============================================
0:55:35.654292 INFO: performing precursor FDR with 40 features
0:55:35.654410 INFO: Decoy channel: -1
0:55:35.654434 INFO: competitive: True
0:55:35.852864 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:36.163460 INFO: Estimating optimal hyperparameters - samples: 599,608, batch_size: 2,455, learning_rate: 7.74e-04
0:55:36.164687 INFO: Using random state 894947 for train-test-split
0:55:49.310042 INFO: Test AUC: 0.609
0:55:49.310175 INFO: Train AUC: 0.621
0:55:49.310208 INFO: AUC difference: 1.93%
0:55:49.795743 INFO: Resetting torch num_threads to 100
0:55:49.856449 PROGRESS: === Extracted 749511 precursors and 4022490 fragments ===
0:55:49.856932 INFO: === FDR correction performed with classifier version 10 ===
0:55:49.857625 PROGRESS: ============================= Precursor FDR =============================
0:55:49.857726 PROGRESS: Total precursors accumulated: 1,641
0:55:49.857786 PROGRESS: Target precursors: 1,625 (99.02%)
0:55:49.857836 PROGRESS: Decoy precursors: 16 (0.98%)
0:55:49.857883 PROGRESS: 
0:55:49.857928 PROGRESS: Precursor Summary:
0:55:49.859300 PROGRESS: Channel   0:	 0.050 FDR: 1,625; 0.010 FDR: 1,625; 0.001 FDR: 1,101
0:55:49.859386 PROGRESS: 
0:55:49.859442 PROGRESS: Protein Summary:
0:55:49.861231 PROGRESS: Channel   0:	 0.050 FDR: 1,370; 0.010 FDR: 1,370; 0.001 FDR:   947
0:55:49.861324 PROGRESS: =========================================================================
0:55:49.875951 INFO: Target number of precursors reached.
0:55:50.309996 INFO: fragments_df: keeping 5000 of 4022490 [sum(precursor_idx_mask)=37951 sum(mass_error_mask)=4022490 stop_rank=5000
0:55:50.750872 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:55:50.971501 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:55:51.624389 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:55:51.624863 INFO: Using score_cutoff 10.43683356513977 (fac=0.99, q=1)
0:55:51.625182 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:55:51.625267 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:55:51.625321 INFO: Updating optimization_manager: score_cutoff        : 11.633124858570099 -> 10.43683356513977
0:55:51.625374 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:55:51.775254 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:55:52.089048 INFO: === checking if optimization conditions were reached ===
0:55:52.091225 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
0:55:52.091328 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
0:55:52.091405 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
0:55:52.091468 INFO: ==============================================
0:55:52.091539 PROGRESS: Optimization finished for ms2_error.
0:55:52.495148 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:55:52.645849 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:55:52.958005 INFO: Starting optimization step 0.
0:55:52.958269 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:55:52.958345 INFO: Using rust extraction backend
0:55:52.958406 PROGRESS: Extracting batch of 250442 precursors
0:55:53.381437 INFO: === Search parameters used ===
0:55:53.381713 INFO: rt_error       : 805.6004638671875
0:55:53.381769 INFO: mobility_error : 0.1
0:55:53.381815 INFO: num_candidates : 3
0:55:53.381857 INFO: ms1_error      : 3
0:55:53.381897 INFO: ms2_error      : 10.0
0:55:53.381936 INFO: fwhm_rt        : 3.0
0:55:53.381974 INFO: quant_window   : 3
0:55:53.382023 INFO: ==============================================
0:55:55.965623 INFO: performing precursor FDR with 40 features
0:55:55.965745 INFO: Decoy channel: -1
0:55:55.965771 INFO: competitive: True
0:55:56.166170 INFO: Setting torch num_threads to 2 for FDR classification task
0:55:56.480010 INFO: Estimating optimal hyperparameters - samples: 599,609, batch_size: 2,455, learning_rate: 7.74e-04
0:55:56.481107 INFO: Using random state 552462 for train-test-split
0:56:09.478531 INFO: Test AUC: 0.609
0:56:09.478662 INFO: Train AUC: 0.623
0:56:09.478696 INFO: AUC difference: 2.21%
0:56:09.955173 INFO: Resetting torch num_threads to 100
0:56:09.989890 PROGRESS: === Extracted 749512 precursors and 4022869 fragments ===
0:56:09.990394 INFO: === FDR correction performed with classifier version 11 ===
0:56:09.991151 PROGRESS: ============================= Precursor FDR =============================
0:56:09.991252 PROGRESS: Total precursors accumulated: 1,640
0:56:09.991313 PROGRESS: Target precursors: 1,624 (99.02%)
0:56:09.991364 PROGRESS: Decoy precursors: 16 (0.98%)
0:56:09.991411 PROGRESS: 
0:56:09.991456 PROGRESS: Precursor Summary:
0:56:09.992849 PROGRESS: Channel   0:	 0.050 FDR: 1,624; 0.010 FDR: 1,624; 0.001 FDR: 1,142
0:56:09.992941 PROGRESS: 
0:56:09.992998 PROGRESS: Protein Summary:
0:56:09.994781 PROGRESS: Channel   0:	 0.050 FDR: 1,388; 0.010 FDR: 1,388; 0.001 FDR:   983
0:56:09.994873 PROGRESS: =========================================================================
0:56:10.011012 INFO: Target number of precursors reached.
0:56:10.455011 INFO: fragments_df: keeping 5000 of 4022869 [sum(precursor_idx_mask)=37143 sum(mass_error_mask)=4022869 stop_rank=5000
0:56:10.884664 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:56:11.106181 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:56:11.760007 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:56:11.760474 INFO: Using score_cutoff 8.267965197658539 (fac=0.99, q=1)
0:56:11.760795 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:56:11.760874 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:56:11.760929 INFO: Updating optimization_manager: score_cutoff        : 10.43683356513977 -> 8.267965197658539
0:56:11.760985 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:56:11.913451 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:56:12.262795 INFO: === checking if optimization conditions were reached ===
0:56:12.263065 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
0:56:12.265850 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 616.730959766498
0:56:12.265951 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 616.7310.
0:56:12.266015 INFO: ==============================================
0:56:12.266083 INFO: Starting optimization step 1.
0:56:12.266140 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:56:12.266206 INFO: Using rust extraction backend
0:56:12.266263 PROGRESS: Extracting batch of 250442 precursors
0:56:12.688962 INFO: === Search parameters used ===
0:56:12.689230 INFO: rt_error       : 616.730959766498
0:56:12.689289 INFO: mobility_error : 0.1
0:56:12.689336 INFO: num_candidates : 3
0:56:12.689380 INFO: ms1_error      : 3
0:56:12.689422 INFO: ms2_error      : 10.0
0:56:12.689473 INFO: fwhm_rt        : 3.0
0:56:12.689514 INFO: quant_window   : 3
0:56:12.689554 INFO: ==============================================
0:56:15.189213 INFO: performing precursor FDR with 40 features
0:56:15.189335 INFO: Decoy channel: -1
0:56:15.189361 INFO: competitive: True
0:56:15.386331 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:15.696858 INFO: Estimating optimal hyperparameters - samples: 599,608, batch_size: 2,455, learning_rate: 7.74e-04
0:56:15.697988 INFO: Using random state 552462 for train-test-split
0:56:28.698698 INFO: Test AUC: 0.612
0:56:28.698827 INFO: Train AUC: 0.622
0:56:28.698864 INFO: AUC difference: 1.63%
0:56:29.182461 INFO: Resetting torch num_threads to 100
0:56:29.210570 PROGRESS: === Extracted 749511 precursors and 4020856 fragments ===
0:56:29.211047 INFO: === FDR correction performed with classifier version 11 ===
0:56:29.211713 PROGRESS: ============================= Precursor FDR =============================
0:56:29.211801 PROGRESS: Total precursors accumulated: 1,675
0:56:29.211876 PROGRESS: Target precursors: 1,659 (99.04%)
0:56:29.211929 PROGRESS: Decoy precursors: 16 (0.96%)
0:56:29.211978 PROGRESS: 
0:56:29.212024 PROGRESS: Precursor Summary:
0:56:29.213380 PROGRESS: Channel   0:	 0.050 FDR: 1,659; 0.010 FDR: 1,659; 0.001 FDR: 1,080
0:56:29.213469 PROGRESS: 
0:56:29.213526 PROGRESS: Protein Summary:
0:56:29.215306 PROGRESS: Channel   0:	 0.050 FDR: 1,390; 0.010 FDR: 1,390; 0.001 FDR:   929
0:56:29.215405 PROGRESS: =========================================================================
0:56:29.230829 INFO: Target number of precursors reached.
0:56:29.652673 INFO: fragments_df: keeping 5000 of 4020856 [sum(precursor_idx_mask)=38693 sum(mass_error_mask)=4020856 stop_rank=5000
0:56:30.081398 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:56:30.309479 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:56:30.976514 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:56:30.976974 INFO: Using score_cutoff 10.398847851562499 (fac=0.99, q=1)
0:56:30.977283 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:56:30.977359 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:56:30.977412 INFO: Updating optimization_manager: score_cutoff        : 8.267965197658539 -> 10.398847851562499
0:56:30.977465 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:56:31.129278 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:56:31.470258 INFO: === checking if optimization conditions were reached ===
0:56:31.470523 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
0:56:31.473436 INFO: Updating optimization_manager: rt_error            : 616.730959766498 -> 506.9928639019454
0:56:31.473540 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 506.9929.
0:56:31.473615 INFO: ==============================================
0:56:31.473685 INFO: Starting optimization step 2.
0:56:31.473742 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:56:31.473801 INFO: Using rust extraction backend
0:56:31.473856 PROGRESS: Extracting batch of 250442 precursors
0:56:31.895665 INFO: === Search parameters used ===
0:56:31.895945 INFO: rt_error       : 506.9928639019454
0:56:31.896006 INFO: mobility_error : 0.1
0:56:31.896055 INFO: num_candidates : 3
0:56:31.896114 INFO: ms1_error      : 3
0:56:31.896161 INFO: ms2_error      : 10.0
0:56:31.896203 INFO: fwhm_rt        : 3.0
0:56:31.896244 INFO: quant_window   : 3
0:56:31.896283 INFO: ==============================================
0:56:34.375711 INFO: performing precursor FDR with 40 features
0:56:34.375853 INFO: Decoy channel: -1
0:56:34.375891 INFO: competitive: True
0:56:34.576052 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:34.890523 INFO: Estimating optimal hyperparameters - samples: 599,116, batch_size: 2,453, learning_rate: 7.74e-04
0:56:34.891489 INFO: Using random state 552462 for train-test-split
0:56:47.613996 INFO: Test AUC: 0.610
0:56:47.614128 INFO: Train AUC: 0.621
0:56:47.614161 INFO: AUC difference: 1.73%
0:56:48.093712 INFO: Resetting torch num_threads to 100
0:56:48.121433 PROGRESS: === Extracted 748896 precursors and 3983154 fragments ===
0:56:48.121922 INFO: === FDR correction performed with classifier version 11 ===
0:56:48.122606 PROGRESS: ============================= Precursor FDR =============================
0:56:48.122699 PROGRESS: Total precursors accumulated: 1,581
0:56:48.122758 PROGRESS: Target precursors: 1,566 (99.05%)
0:56:48.122811 PROGRESS: Decoy precursors: 15 (0.95%)
0:56:48.122872 PROGRESS: 
0:56:48.122918 PROGRESS: Precursor Summary:
0:56:48.124196 PROGRESS: Channel   0:	 0.050 FDR: 1,566; 0.010 FDR: 1,566; 0.001 FDR:     1
0:56:48.124290 PROGRESS: 
0:56:48.124345 PROGRESS: Protein Summary:
0:56:48.125930 PROGRESS: Channel   0:	 0.050 FDR: 1,321; 0.010 FDR: 1,321; 0.001 FDR:     1
0:56:48.126019 PROGRESS: =========================================================================
0:56:48.140684 INFO: Target number of precursors reached.
0:56:48.588180 INFO: fragments_df: keeping 5000 of 3983154 [sum(precursor_idx_mask)=36995 sum(mass_error_mask)=3983154 stop_rank=5000
0:56:49.016212 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:56:49.247127 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:56:49.904303 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:56:49.904759 INFO: Using score_cutoff 10.924134916305542 (fac=0.99, q=1)
0:56:49.905063 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:56:49.905138 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:56:49.905191 INFO: Updating optimization_manager: score_cutoff        : 10.398847851562499 -> 10.924134916305542
0:56:49.905245 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:56:50.056102 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:56:50.390686 INFO: === checking if optimization conditions were reached ===
0:56:50.390944 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
0:56:50.393900 INFO: Updating optimization_manager: rt_error            : 506.9928639019454 -> 567.8431654351778
0:56:50.394010 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 567.8432.
0:56:50.394073 INFO: ==============================================
0:56:50.394141 INFO: Starting optimization step 3.
0:56:50.394200 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:56:50.394260 INFO: Using rust extraction backend
0:56:50.394315 PROGRESS: Extracting batch of 250442 precursors
0:56:50.818105 INFO: === Search parameters used ===
0:56:50.818381 INFO: rt_error       : 567.8431654351778
0:56:50.818450 INFO: mobility_error : 0.1
0:56:50.818500 INFO: num_candidates : 3
0:56:50.818544 INFO: ms1_error      : 3
0:56:50.818584 INFO: ms2_error      : 10.0
0:56:50.818625 INFO: fwhm_rt        : 3.0
0:56:50.818665 INFO: quant_window   : 3
0:56:50.818705 INFO: ==============================================
0:56:53.291666 INFO: performing precursor FDR with 40 features
0:56:53.291793 INFO: Decoy channel: -1
0:56:53.291835 INFO: competitive: True
0:56:53.499283 INFO: Setting torch num_threads to 2 for FDR classification task
0:56:53.810307 INFO: Estimating optimal hyperparameters - samples: 599,250, batch_size: 2,454, learning_rate: 7.74e-04
0:56:53.811544 INFO: Using random state 552462 for train-test-split
0:57:06.627577 INFO: Test AUC: 0.610
0:57:06.627721 INFO: Train AUC: 0.621
0:57:06.627753 INFO: AUC difference: 1.78%
0:57:07.112612 INFO: Resetting torch num_threads to 100
0:57:07.143928 PROGRESS: === Extracted 749063 precursors and 3997184 fragments ===
0:57:07.144448 INFO: === FDR correction performed with classifier version 11 ===
0:57:07.145208 PROGRESS: ============================= Precursor FDR =============================
0:57:07.145307 PROGRESS: Total precursors accumulated: 1,667
0:57:07.145367 PROGRESS: Target precursors: 1,651 (99.04%)
0:57:07.145416 PROGRESS: Decoy precursors: 16 (0.96%)
0:57:07.145461 PROGRESS: 
0:57:07.145505 PROGRESS: Precursor Summary:
0:57:07.146959 PROGRESS: Channel   0:	 0.050 FDR: 1,651; 0.010 FDR: 1,651; 0.001 FDR: 1,190
0:57:07.147049 PROGRESS: 
0:57:07.147104 PROGRESS: Protein Summary:
0:57:07.148960 PROGRESS: Channel   0:	 0.050 FDR: 1,404; 0.010 FDR: 1,404; 0.001 FDR: 1,023
0:57:07.149060 PROGRESS: =========================================================================
0:57:07.163993 INFO: Target number of precursors reached.
0:57:07.587310 INFO: fragments_df: keeping 5000 of 3997184 [sum(precursor_idx_mask)=37597 sum(mass_error_mask)=3997184 stop_rank=5000
0:57:08.011028 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:57:08.225957 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:57:08.881105 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:57:08.881556 INFO: Using score_cutoff 6.951001160144806 (fac=0.99, q=1)
0:57:08.881851 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:57:08.881924 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:57:08.881975 INFO: Updating optimization_manager: score_cutoff        : 10.924134916305542 -> 6.951001160144806
0:57:08.882024 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:57:09.033087 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:57:09.378032 INFO: === checking if optimization conditions were reached ===
0:57:09.378300 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
0:57:09.381284 INFO: Updating optimization_manager: rt_error            : 567.8431654351778 -> 533.9892911720135
0:57:09.381388 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 533.9893.
0:57:09.381452 INFO: ==============================================
0:57:09.381519 INFO: Starting optimization step 4.
0:57:09.381576 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:57:09.381637 INFO: Using rust extraction backend
0:57:09.381691 PROGRESS: Extracting batch of 250442 precursors
0:57:09.803243 INFO: === Search parameters used ===
0:57:09.803531 INFO: rt_error       : 533.9892911720135
0:57:09.803589 INFO: mobility_error : 0.1
0:57:09.803634 INFO: num_candidates : 3
0:57:09.803675 INFO: ms1_error      : 3
0:57:09.803715 INFO: ms2_error      : 10.0
0:57:09.803753 INFO: fwhm_rt        : 3.0
0:57:09.803792 INFO: quant_window   : 3
0:57:09.803854 INFO: ==============================================
0:57:12.247856 INFO: performing precursor FDR with 40 features
0:57:12.247978 INFO: Decoy channel: -1
0:57:12.248003 INFO: competitive: True
0:57:12.453933 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:12.766299 INFO: Estimating optimal hyperparameters - samples: 599,371, batch_size: 2,455, learning_rate: 7.74e-04
0:57:12.767433 INFO: Using random state 552462 for train-test-split
0:57:25.854674 INFO: Test AUC: 0.608
0:57:25.854805 INFO: Train AUC: 0.620
0:57:25.854837 INFO: AUC difference: 1.97%
0:57:26.336994 INFO: Resetting torch num_threads to 100
0:57:26.365626 PROGRESS: === Extracted 749214 precursors and 4001592 fragments ===
0:57:26.366112 INFO: === FDR correction performed with classifier version 11 ===
0:57:26.366807 PROGRESS: ============================= Precursor FDR =============================
0:57:26.366910 PROGRESS: Total precursors accumulated: 1,640
0:57:26.366975 PROGRESS: Target precursors: 1,624 (99.02%)
0:57:26.367026 PROGRESS: Decoy precursors: 16 (0.98%)
0:57:26.367072 PROGRESS: 
0:57:26.367117 PROGRESS: Precursor Summary:
0:57:26.368480 PROGRESS: Channel   0:	 0.050 FDR: 1,624; 0.010 FDR: 1,624; 0.001 FDR:   649
0:57:26.368590 PROGRESS: 
0:57:26.368645 PROGRESS: Protein Summary:
0:57:26.370367 PROGRESS: Channel   0:	 0.050 FDR: 1,367; 0.010 FDR: 1,367; 0.001 FDR:   576
0:57:26.370454 PROGRESS: =========================================================================
0:57:26.384770 INFO: Target number of precursors reached.
0:57:26.814033 INFO: fragments_df: keeping 5000 of 4001592 [sum(precursor_idx_mask)=38180 sum(mass_error_mask)=4001592 stop_rank=5000
0:57:27.244452 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:57:27.458942 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:57:28.110842 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:57:28.111319 INFO: Using score_cutoff 10.754892468738557 (fac=0.99, q=1)
0:57:28.111633 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:57:28.111711 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:57:28.111769 INFO: Updating optimization_manager: score_cutoff        : 6.951001160144806 -> 10.754892468738557
0:57:28.111834 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:57:28.264246 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:57:28.609384 INFO: === checking if optimization conditions were reached ===
0:57:28.609644 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
0:57:28.612631 INFO: Updating optimization_manager: rt_error            : 533.9892911720135 -> 527.0490319987969
0:57:28.612741 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 527.0490.
0:57:28.612808 INFO: ==============================================
0:57:28.612877 INFO: Starting optimization step 5.
0:57:28.612937 PROGRESS: === Extracting elution groups 0 to 127000 ===
0:57:28.613012 INFO: Using rust extraction backend
0:57:28.613070 PROGRESS: Extracting batch of 250442 precursors
0:57:29.034871 INFO: === Search parameters used ===
0:57:29.035156 INFO: rt_error       : 527.0490319987969
0:57:29.035217 INFO: mobility_error : 0.1
0:57:29.035266 INFO: num_candidates : 3
0:57:29.035311 INFO: ms1_error      : 3
0:57:29.035353 INFO: ms2_error      : 10.0
0:57:29.035394 INFO: fwhm_rt        : 3.0
0:57:29.035434 INFO: quant_window   : 3
0:57:29.035473 INFO: ==============================================
0:57:31.507803 INFO: performing precursor FDR with 40 features
0:57:31.507937 INFO: Decoy channel: -1
0:57:31.507964 INFO: competitive: True
0:57:31.710727 INFO: Setting torch num_threads to 2 for FDR classification task
0:57:32.026444 INFO: Estimating optimal hyperparameters - samples: 599,219, batch_size: 2,454, learning_rate: 7.74e-04
0:57:32.027584 INFO: Using random state 552462 for train-test-split
0:57:44.851867 INFO: Test AUC: 0.608
0:57:44.852006 INFO: Train AUC: 0.621
0:57:44.852041 INFO: AUC difference: 2.02%
0:57:45.338929 INFO: Resetting torch num_threads to 100
0:57:45.366981 PROGRESS: === Extracted 749024 precursors and 3991577 fragments ===
0:57:45.367490 INFO: === FDR correction performed with classifier version 11 ===
0:57:45.368250 PROGRESS: ============================= Precursor FDR =============================
0:57:45.368354 PROGRESS: Total precursors accumulated: 1,629
0:57:45.368417 PROGRESS: Target precursors: 1,613 (99.02%)
0:57:45.368469 PROGRESS: Decoy precursors: 16 (0.98%)
0:57:45.368520 PROGRESS: 
0:57:45.368567 PROGRESS: Precursor Summary:
0:57:45.369891 PROGRESS: Channel   0:	 0.050 FDR: 1,613; 0.010 FDR: 1,613; 0.001 FDR:     9
0:57:45.369985 PROGRESS: 
0:57:45.370043 PROGRESS: Protein Summary:
0:57:45.371697 PROGRESS: Channel   0:	 0.050 FDR: 1,359; 0.010 FDR: 1,359; 0.001 FDR:     9
0:57:45.371789 PROGRESS: =========================================================================
0:57:45.386579 INFO: Target number of precursors reached.
0:57:45.816567 INFO: fragments_df: keeping 5000 of 3991577 [sum(precursor_idx_mask)=37538 sum(mass_error_mask)=3991577 stop_rank=5000
0:57:46.247251 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
0:57:46.467344 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
0:57:47.116039 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
0:57:47.116503 INFO: Using score_cutoff 9.83201446609497 (fac=0.99, q=1)
0:57:47.116802 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:57:47.116877 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:57:47.116929 INFO: Updating optimization_manager: score_cutoff        : 10.754892468738557 -> 9.83201446609497
0:57:47.116981 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:57:47.268604 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:57:47.603106 INFO: === checking if optimization conditions were reached ===
0:57:47.603366 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
0:57:47.604326 INFO: Updating optimization_manager: rt_error            : 527.0490319987969 -> 616.730959766498
0:57:47.604456 INFO: Updating optimization_manager: classifier_version  : 11 -> 13
0:57:47.604551 INFO: Updating optimization_manager: score_cutoff        : 9.83201446609497 -> 10.398847851562499
0:57:47.604647 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
0:57:47.604733 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
0:57:47.604819 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 616.7310 found after 6 searches.
0:57:47.604880 INFO: ==============================================
0:57:47.604947 PROGRESS: Optimization finished for rt_error.
0:57:48.011286 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:57:48.161740 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:57:48.503012 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
0:57:48.503266 PROGRESS: ==============================================
0:57:48.503340 PROGRESS: ms2_error      : 10.0000
0:57:48.503396 PROGRESS: rt_error       : 616.7310
0:57:48.503443 PROGRESS: ==============================================
0:57:48.504271 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
0:57:56.124856 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
0:58:12.619533 INFO: Using rust extraction backend
0:58:12.619832 PROGRESS: Extracting batch of 11997144 precursors
0:58:28.676281 INFO: === Search parameters used ===
0:58:28.676589 INFO: rt_error       : 616.730959766498
0:58:28.676652 INFO: mobility_error : 0.1
0:58:28.676704 INFO: num_candidates : 3
0:58:28.676760 INFO: ms1_error      : 3
0:58:28.676804 INFO: ms2_error      : 10.0
0:58:28.676845 INFO: fwhm_rt        : 3.0
0:58:28.676885 INFO: quant_window   : 3
0:58:28.676925 INFO: ==============================================
0:58:57.287757 INFO: Removed 8009739 precursors with score below cutoff 10.398847851562499
0:59:19.518329 INFO: performing precursor FDR with 40 features
0:59:19.518453 INFO: Decoy channel: -1
0:59:19.518480 INFO: competitive: True
0:59:22.465268 INFO: Setting torch num_threads to 2 for FDR classification task
0:59:33.704042 INFO: Estimating optimal hyperparameters - samples: 22,384,778, batch_size: 4,096, learning_rate: 1.00e-03
0:59:33.772638 INFO: Using random state 620210 for train-test-split
1:06:41.163007 INFO: Test AUC: 0.622
1:06:41.163252 INFO: Train AUC: 0.622
1:06:41.163292 INFO: AUC difference: 0.05%
1:06:47.728651 INFO: Resetting torch num_threads to 100
1:06:49.852712 PROGRESS: ============================= Precursor FDR =============================
1:06:49.853108 PROGRESS: Total precursors accumulated: 90,318
1:06:49.853178 PROGRESS: Target precursors: 89,424 (99.01%)
1:06:49.853234 PROGRESS: Decoy precursors: 894 (0.99%)
1:06:49.853282 PROGRESS: 
1:06:49.853327 PROGRESS: Precursor Summary:
1:06:49.879619 PROGRESS: Channel   0:	 0.050 FDR: 89,424; 0.010 FDR: 89,424; 0.001 FDR: 54,248
1:06:49.879881 PROGRESS: 
1:06:49.879946 PROGRESS: Protein Summary:
1:06:49.915678 PROGRESS: Channel   0:	 0.050 FDR: 13,027; 0.010 FDR: 13,027; 0.001 FDR: 8,866
1:06:49.915950 PROGRESS: =========================================================================
1:06:50.085388 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/psm.parquet
1:06:50.252641 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.parquet
1:06:50.495445 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
1:06:51.047318 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 
1:06:51.047463 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
1:06:51.047565 INFO: Initializing TimingManager
1:06:51.048185 INFO: Initializing RawFileManager
1:07:07.028176 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.
1:07:07.037148 INFO: Determining DIA cycle
1:07:07.053433 INFO: Found cycle with start 0.00 min and length 300.
1:07:07.229214 INFO: RT (min)            : 0.0 - 26.9
1:07:07.229311 INFO: RT duration (sec)   : 1611.2
1:07:07.229340 INFO: RT duration (min)   : 26.9
1:07:07.229362 INFO: Cycle len (scans)   : 300
1:07:07.229383 INFO: Cycle len (sec)     : 1.65
1:07:07.229402 INFO: Number of cycles    : 977
1:07:07.229422 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:07:07.229454 INFO: Creating DIA data object took: 16.181174993515015
1:07:07.929340 INFO: Creating DIA data NG object took: 0.6997616291046143
1:07:09.284637 INFO: Initializing CalibrationManager
1:07:09.284923 INFO: Setting up calibration estimators ..
1:07:09.284984 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:07:09.285093 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'}' ..
1:07:09.285196 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:07:09.285253 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:07:09.285307 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}}' ..
1:07:09.285369 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:07:09.285414 INFO: Done setting up calibration estimators.
1:07:09.285622 INFO: Initializing OptimizationManager
1:07:09.285755 INFO: initial parameter: ms1_error = 3
1:07:09.285807 INFO: initial parameter: ms2_error = 10
1:07:09.285855 INFO: initial parameter: rt_error = 805.5982666015625
1:07:09.285898 INFO: initial parameter: mobility_error = 0.1
1:07:09.285938 INFO: initial parameter: num_candidates = 1
1:07:09.285977 INFO: initial parameter: fwhm_rt = 5
1:07:09.286017 INFO: initial parameter: fwhm_mobility = 0.01
1:07:09.286056 INFO: initial parameter: score_cutoff = 0
1:07:09.286095 INFO: initial parameter: classifier_version = -1
1:07:09.286164 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:07:09.286429 INFO: FDRManager: loading saved state not requested, will be initialized.
1:07:09.286461 INFO: Initializing FDRManager
1:07:09.286493 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
1:07:10.735723 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
1:07:11.624642 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
1:07:11.625065 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
1:07:11.625163 PROGRESS: Starting initial search for precursors.
1:07:11.625267 INFO: Starting optimization step 0.
1:07:11.625328 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:07:11.625383 INFO: Using rust extraction backend
1:07:11.625440 PROGRESS: Extracting batch of 1970 precursors
1:07:11.630515 INFO: === Search parameters used ===
1:07:11.630632 INFO: rt_error       : 805.5982666015625
1:07:11.630684 INFO: mobility_error : 0.1
1:07:11.630731 INFO: num_candidates : 1
1:07:11.630774 INFO: ms1_error      : 3
1:07:11.630815 INFO: ms2_error      : 10
1:07:11.630856 INFO: fwhm_rt        : 5
1:07:11.630898 INFO: quant_window   : 3
1:07:11.630938 INFO: ==============================================
1:07:11.665695 INFO: performing precursor FDR with 40 features
1:07:11.665770 INFO: Decoy channel: -1
1:07:11.665794 INFO: competitive: True
1:07:11.667119 INFO: Setting torch num_threads to 2 for FDR classification task
1:07:11.669030 INFO: Estimating optimal hyperparameters - samples: 1,572, batch_size: 128, learning_rate: 1.77e-04
1:07:11.669854 INFO: Using random state 743435 for train-test-split
1:07:11.821246 INFO: Test AUC: 0.521
1:07:11.821337 INFO: Train AUC: 0.589
1:07:11.821372 INFO: AUC difference: 11.51%
1:07:11.821394 WARNING: AUC difference > 5%. This may indicate overfitting.
1:07:12.063012 INFO: Resetting torch num_threads to 100
1:07:12.064673 PROGRESS: === Extracted 1965 precursors and 11015 fragments ===
1:07:12.065030 INFO: === FDR correction performed with classifier version -1 ===
1:07:12.065526 PROGRESS: ============================= Precursor FDR =============================
1:07:12.065613 PROGRESS: Total precursors accumulated: 24
1:07:12.065672 PROGRESS: Target precursors: 24 (100.00%)
1:07:12.065722 PROGRESS: Decoy precursors: 0 (0.00%)
1:07:12.065768 PROGRESS: 
1:07:12.065813 PROGRESS: Precursor Summary:
1:07:12.066849 PROGRESS: Channel   0:	 0.050 FDR:    24; 0.010 FDR:    24; 0.001 FDR:    24
1:07:12.066934 PROGRESS: 
1:07:12.066988 PROGRESS: Protein Summary:
1:07:12.068159 PROGRESS: Channel   0:	 0.050 FDR:    23; 0.010 FDR:    23; 0.001 FDR:    23
1:07:12.068247 PROGRESS: =========================================================================
1:07:12.068480 INFO: Target number of precursors not reached yet.
1:07:12.153017 INFO: Starting optimization step 1.
1:07:12.153241 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:07:12.153318 INFO: Using rust extraction backend
1:07:12.153377 PROGRESS: Extracting batch of 3935 precursors
1:07:12.161662 INFO: === Search parameters used ===
1:07:12.161827 INFO: rt_error       : 805.5982666015625
1:07:12.161877 INFO: mobility_error : 0.1
1:07:12.161922 INFO: num_candidates : 1
1:07:12.161963 INFO: ms1_error      : 3
1:07:12.162005 INFO: ms2_error      : 10
1:07:12.162045 INFO: fwhm_rt        : 5
1:07:12.162084 INFO: quant_window   : 3
1:07:12.162123 INFO: ==============================================
1:07:12.209215 INFO: performing precursor FDR with 40 features
1:07:12.209302 INFO: Decoy channel: -1
1:07:12.209327 INFO: competitive: True
1:07:12.213924 INFO: Setting torch num_threads to 2 for FDR classification task
1:07:12.216216 INFO: Estimating optimal hyperparameters - samples: 4,713, batch_size: 128, learning_rate: 1.77e-04
1:07:12.216300 INFO: Using random state 546069 for train-test-split
1:07:12.676993 INFO: Test AUC: 0.561
1:07:12.677084 INFO: Train AUC: 0.575
1:07:12.677112 INFO: AUC difference: 2.36%
1:07:12.926955 INFO: Resetting torch num_threads to 100
1:07:12.930217 PROGRESS: === Extracted 5892 precursors and 33078 fragments ===
1:07:12.930580 INFO: === FDR correction performed with classifier version -1 ===
1:07:12.931062 PROGRESS: ============================= Precursor FDR =============================
1:07:12.931144 PROGRESS: Total precursors accumulated: 26
1:07:12.931199 PROGRESS: Target precursors: 26 (100.00%)
1:07:12.931246 PROGRESS: Decoy precursors: 0 (0.00%)
1:07:12.931288 PROGRESS: 
1:07:12.931329 PROGRESS: Precursor Summary:
1:07:12.932381 PROGRESS: Channel   0:	 0.050 FDR:    26; 0.010 FDR:    26; 0.001 FDR:    26
1:07:12.932466 PROGRESS: 
1:07:12.932518 PROGRESS: Protein Summary:
1:07:12.933699 PROGRESS: Channel   0:	 0.050 FDR:    26; 0.010 FDR:    26; 0.001 FDR:    26
1:07:12.933780 PROGRESS: =========================================================================
1:07:12.934062 INFO: Target number of precursors not reached yet.
1:07:13.025966 INFO: Starting optimization step 2.
1:07:13.026199 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:07:13.026278 INFO: Using rust extraction backend
1:07:13.026335 PROGRESS: Extracting batch of 7881 precursors
1:07:13.041294 INFO: === Search parameters used ===
1:07:13.041444 INFO: rt_error       : 805.5982666015625
1:07:13.041495 INFO: mobility_error : 0.1
1:07:13.041546 INFO: num_candidates : 1
1:07:13.041590 INFO: ms1_error      : 3
1:07:13.041631 INFO: ms2_error      : 10
1:07:13.041670 INFO: fwhm_rt        : 5
1:07:13.041708 INFO: quant_window   : 3
1:07:13.041748 INFO: ==============================================
1:07:13.122870 INFO: performing precursor FDR with 40 features
1:07:13.122973 INFO: Decoy channel: -1
1:07:13.122997 INFO: competitive: True
1:07:13.129644 INFO: Setting torch num_threads to 2 for FDR classification task
1:07:13.133187 INFO: Estimating optimal hyperparameters - samples: 11,007, batch_size: 128, learning_rate: 1.77e-04
1:07:13.133294 INFO: Using random state 840443 for train-test-split
1:07:14.211863 INFO: Test AUC: 0.552
1:07:14.211965 INFO: Train AUC: 0.580
1:07:14.211994 INFO: AUC difference: 4.72%
1:07:14.461517 INFO: Resetting torch num_threads to 100
1:07:14.465853 PROGRESS: === Extracted 13759 precursors and 77440 fragments ===
1:07:14.466264 INFO: === FDR correction performed with classifier version -1 ===
1:07:14.466790 PROGRESS: ============================= Precursor FDR =============================
1:07:14.466873 PROGRESS: Total precursors accumulated: 49
1:07:14.466930 PROGRESS: Target precursors: 49 (100.00%)
1:07:14.466978 PROGRESS: Decoy precursors: 0 (0.00%)
1:07:14.467022 PROGRESS: 
1:07:14.467064 PROGRESS: Precursor Summary:
1:07:14.468144 PROGRESS: Channel   0:	 0.050 FDR:    49; 0.010 FDR:    49; 0.001 FDR:    49
1:07:14.468231 PROGRESS: 
1:07:14.468284 PROGRESS: Protein Summary:
1:07:14.469442 PROGRESS: Channel   0:	 0.050 FDR:    49; 0.010 FDR:    49; 0.001 FDR:    49
1:07:14.469522 PROGRESS: =========================================================================
1:07:14.469884 INFO: Target number of precursors not reached yet.
1:07:14.570494 INFO: Starting optimization step 3.
1:07:14.570745 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:07:14.570824 INFO: Using rust extraction backend
1:07:14.570882 PROGRESS: Extracting batch of 15776 precursors
1:07:14.599221 INFO: === Search parameters used ===
1:07:14.599433 INFO: rt_error       : 805.5982666015625
1:07:14.599485 INFO: mobility_error : 0.1
1:07:14.599530 INFO: num_candidates : 1
1:07:14.599571 INFO: ms1_error      : 3
1:07:14.599610 INFO: ms2_error      : 10
1:07:14.599662 INFO: fwhm_rt        : 5
1:07:14.599702 INFO: quant_window   : 3
1:07:14.599741 INFO: ==============================================
1:07:14.737227 INFO: performing precursor FDR with 40 features
1:07:14.737339 INFO: Decoy channel: -1
1:07:14.737363 INFO: competitive: True
1:07:14.748663 INFO: Setting torch num_threads to 2 for FDR classification task
1:07:14.755508 INFO: Estimating optimal hyperparameters - samples: 23,601, batch_size: 128, learning_rate: 1.77e-04
1:07:14.755680 INFO: Using random state 40935 for train-test-split
1:07:17.143175 INFO: Test AUC: 0.577
1:07:17.143291 INFO: Train AUC: 0.596
1:07:17.143322 INFO: AUC difference: 3.14%
1:07:18.277027 INFO: Resetting torch num_threads to 100
1:07:18.283765 PROGRESS: === Extracted 29502 precursors and 165736 fragments ===
1:07:18.284231 INFO: === FDR correction performed with classifier version -1 ===
1:07:18.284758 PROGRESS: ============================= Precursor FDR =============================
1:07:18.284848 PROGRESS: Total precursors accumulated: 145
1:07:18.284908 PROGRESS: Target precursors: 144 (99.31%)
1:07:18.284961 PROGRESS: Decoy precursors: 1 (0.69%)
1:07:18.285019 PROGRESS: 
1:07:18.285066 PROGRESS: Precursor Summary:
1:07:18.286044 PROGRESS: Channel   0:	 0.050 FDR:   144; 0.010 FDR:   144; 0.001 FDR:   142
1:07:18.286129 PROGRESS: 
1:07:18.286184 PROGRESS: Protein Summary:
1:07:18.287287 PROGRESS: Channel   0:	 0.050 FDR:   140; 0.010 FDR:   140; 0.001 FDR:   138
1:07:18.287371 PROGRESS: =========================================================================
1:07:18.287891 INFO: Target number of precursors not reached yet.
1:07:18.406253 INFO: Starting optimization step 4.
1:07:18.406520 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:07:18.406603 INFO: Using rust extraction backend
1:07:18.406665 PROGRESS: Extracting batch of 31591 precursors
1:07:18.461475 INFO: === Search parameters used ===
1:07:18.461725 INFO: rt_error       : 805.5982666015625
1:07:18.461778 INFO: mobility_error : 0.1
1:07:18.461823 INFO: num_candidates : 1
1:07:18.461865 INFO: ms1_error      : 3
1:07:18.461906 INFO: ms2_error      : 10
1:07:18.461946 INFO: fwhm_rt        : 5
1:07:18.461985 INFO: quant_window   : 3
1:07:18.462025 INFO: ==============================================
1:07:18.686219 INFO: performing precursor FDR with 40 features
1:07:18.686336 INFO: Decoy channel: -1
1:07:18.686361 INFO: competitive: True
1:07:18.710638 INFO: Setting torch num_threads to 2 for FDR classification task
1:07:18.724778 INFO: Estimating optimal hyperparameters - samples: 48,815, batch_size: 199, learning_rate: 2.20e-04
1:07:18.724997 INFO: Using random state 982760 for train-test-split
1:07:22.401823 INFO: Test AUC: 0.574
1:07:22.401939 INFO: Train AUC: 0.610
1:07:22.401970 INFO: AUC difference: 5.91%
1:07:22.401992 WARNING: AUC difference > 5%. This may indicate overfitting.
1:07:22.662159 INFO: Resetting torch num_threads to 100
1:07:22.673241 PROGRESS: === Extracted 61019 precursors and 343346 fragments ===
1:07:22.673694 INFO: === FDR correction performed with classifier version -1 ===
1:07:22.674225 PROGRESS: ============================= Precursor FDR =============================
1:07:22.674317 PROGRESS: Total precursors accumulated: 310
1:07:22.674382 PROGRESS: Target precursors: 307 (99.03%)
1:07:22.674435 PROGRESS: Decoy precursors: 3 (0.97%)
1:07:22.674483 PROGRESS: 
1:07:22.674529 PROGRESS: Precursor Summary:
1:07:22.675563 PROGRESS: Channel   0:	 0.050 FDR:   307; 0.010 FDR:   307; 0.001 FDR:   243
1:07:22.675652 PROGRESS: 
1:07:22.675710 PROGRESS: Protein Summary:
1:07:22.676910 PROGRESS: Channel   0:	 0.050 FDR:   294; 0.010 FDR:   294; 0.001 FDR:   233
1:07:22.677006 PROGRESS: =========================================================================
1:07:22.677848 INFO: Target number of precursors not reached yet.
1:07:22.837751 INFO: Starting optimization step 5.
1:07:22.838018 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:07:22.838101 INFO: Using rust extraction backend
1:07:22.838163 PROGRESS: Extracting batch of 63056 precursors
1:07:22.945495 INFO: === Search parameters used ===
1:07:22.945764 INFO: rt_error       : 805.5982666015625
1:07:22.945817 INFO: mobility_error : 0.1
1:07:22.945864 INFO: num_candidates : 1
1:07:22.945906 INFO: ms1_error      : 3
1:07:22.945964 INFO: ms2_error      : 10
1:07:22.946004 INFO: fwhm_rt        : 5
1:07:22.946044 INFO: quant_window   : 3
1:07:22.946083 INFO: ==============================================
1:07:23.328311 INFO: performing precursor FDR with 40 features
1:07:23.328434 INFO: Decoy channel: -1
1:07:23.328459 INFO: competitive: True
1:07:23.377112 INFO: Setting torch num_threads to 2 for FDR classification task
1:07:23.408917 INFO: Estimating optimal hyperparameters - samples: 99,144, batch_size: 406, learning_rate: 3.15e-04
1:07:23.409223 INFO: Using random state 500240 for train-test-split
1:07:28.004648 INFO: Test AUC: 0.592
1:07:28.004770 INFO: Train AUC: 0.610
1:07:28.004802 INFO: AUC difference: 2.94%
1:07:28.280848 INFO: Resetting torch num_threads to 100
1:07:28.302608 PROGRESS: === Extracted 123930 precursors and 697642 fragments ===
1:07:28.303193 INFO: === FDR correction performed with classifier version -1 ===
1:07:28.303921 PROGRESS: ============================= Precursor FDR =============================
1:07:28.304021 PROGRESS: Total precursors accumulated: 713
1:07:28.304083 PROGRESS: Target precursors: 706 (99.02%)
1:07:28.304135 PROGRESS: Decoy precursors: 7 (0.98%)
1:07:28.304195 PROGRESS: 
1:07:28.304249 PROGRESS: Precursor Summary:
1:07:28.305459 PROGRESS: Channel   0:	 0.050 FDR:   706; 0.010 FDR:   706; 0.001 FDR:   492
1:07:28.305549 PROGRESS: 
1:07:28.305603 PROGRESS: Protein Summary:
1:07:28.307001 PROGRESS: Channel   0:	 0.050 FDR:   647; 0.010 FDR:   647; 0.001 FDR:   460
1:07:28.307089 PROGRESS: =========================================================================
1:07:28.308831 INFO: Target number of precursors not reached yet.
1:07:28.552610 INFO: Starting optimization step 6.
1:07:28.552882 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:07:28.552964 INFO: Using rust extraction backend
1:07:28.553029 PROGRESS: Extracting batch of 126233 precursors
1:07:28.767662 INFO: === Search parameters used ===
1:07:28.767950 INFO: rt_error       : 805.5982666015625
1:07:28.768011 INFO: mobility_error : 0.1
1:07:28.768061 INFO: num_candidates : 1
1:07:28.768108 INFO: ms1_error      : 3
1:07:28.768153 INFO: ms2_error      : 10
1:07:28.768197 INFO: fwhm_rt        : 5
1:07:28.768238 INFO: quant_window   : 3
1:07:28.768279 INFO: ==============================================
1:07:29.477761 INFO: performing precursor FDR with 40 features
1:07:29.477892 INFO: Decoy channel: -1
1:07:29.477925 INFO: competitive: True
1:07:29.582809 INFO: Setting torch num_threads to 2 for FDR classification task
1:07:29.667239 INFO: Estimating optimal hyperparameters - samples: 199,892, batch_size: 818, learning_rate: 4.47e-04
1:07:29.667803 INFO: Using random state 626294 for train-test-split
1:07:35.980749 INFO: Test AUC: 0.596
1:07:35.980874 INFO: Train AUC: 0.611
1:07:35.980906 INFO: AUC difference: 2.53%
1:07:36.308224 INFO: Resetting torch num_threads to 100
1:07:36.352878 PROGRESS: === Extracted 249865 precursors and 1405729 fragments ===
1:07:36.353569 INFO: === FDR correction performed with classifier version -1 ===
1:07:36.354464 PROGRESS: ============================= Precursor FDR =============================
1:07:36.354552 PROGRESS: Total precursors accumulated: 1,379
1:07:36.354612 PROGRESS: Target precursors: 1,366 (99.06%)
1:07:36.354663 PROGRESS: Decoy precursors: 13 (0.94%)
1:07:36.354709 PROGRESS: 
1:07:36.354752 PROGRESS: Precursor Summary:
1:07:36.356120 PROGRESS: Channel   0:	 0.050 FDR: 1,366; 0.010 FDR: 1,366; 0.001 FDR: 1,039
1:07:36.356214 PROGRESS: 
1:07:36.356267 PROGRESS: Protein Summary:
1:07:36.357972 PROGRESS: Channel   0:	 0.050 FDR: 1,148; 0.010 FDR: 1,148; 0.001 FDR:   899
1:07:36.358061 PROGRESS: =========================================================================
1:07:36.362446 INFO: Target number of precursors reached.
1:07:36.523519 INFO: fragments_df: keeping 5000 of 1405729 [sum(precursor_idx_mask)=14581 sum(mass_error_mask)=1405729 stop_rank=5000
1:07:36.926274 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:07:37.117565 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:07:37.766582 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:07:37.767047 INFO: Using score_cutoff 12.295543506145478 (fac=0.99, q=1)
1:07:37.767366 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:07:37.767443 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:07:37.767499 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.295543506145478
1:07:37.767561 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:07:37.917536 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:07:38.250209 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
1:07:38.251506 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:07:38.251643 INFO: Starting optimization step 7.
1:07:38.251715 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:07:38.251801 INFO: Using rust extraction backend
1:07:38.251873 PROGRESS: Extracting batch of 250442 precursors
1:07:38.673427 INFO: === Search parameters used ===
1:07:38.673745 INFO: rt_error       : 805.5982666015625
1:07:38.673802 INFO: mobility_error : 0.1
1:07:38.673849 INFO: num_candidates : 3
1:07:38.673892 INFO: ms1_error      : 3
1:07:38.673934 INFO: ms2_error      : 10
1:07:38.673973 INFO: fwhm_rt        : 3.0
1:07:38.674014 INFO: quant_window   : 3
1:07:38.674058 INFO: ==============================================
1:07:41.246916 INFO: performing precursor FDR with 40 features
1:07:41.247034 INFO: Decoy channel: -1
1:07:41.247059 INFO: competitive: True
1:07:41.451257 INFO: Setting torch num_threads to 2 for FDR classification task
1:07:41.759590 INFO: Estimating optimal hyperparameters - samples: 599,837, batch_size: 2,456, learning_rate: 7.74e-04
1:07:41.760778 INFO: Using random state 577325 for train-test-split
1:07:54.101853 INFO: Test AUC: 0.600
1:07:54.101990 INFO: Train AUC: 0.607
1:07:54.102024 INFO: AUC difference: 1.16%
1:07:54.584062 INFO: Resetting torch num_threads to 100
1:07:54.618036 PROGRESS: === Extracted 749797 precursors and 4047915 fragments ===
1:07:54.618515 INFO: === FDR correction performed with classifier version 6 ===
1:07:54.619217 PROGRESS: ============================= Precursor FDR =============================
1:07:54.619317 PROGRESS: Total precursors accumulated: 1,545
1:07:54.619379 PROGRESS: Target precursors: 1,530 (99.03%)
1:07:54.619431 PROGRESS: Decoy precursors: 15 (0.97%)
1:07:54.619479 PROGRESS: 
1:07:54.619528 PROGRESS: Precursor Summary:
1:07:54.620907 PROGRESS: Channel   0:	 0.050 FDR: 1,530; 0.010 FDR: 1,530; 0.001 FDR: 1,064
1:07:54.620998 PROGRESS: 
1:07:54.621056 PROGRESS: Protein Summary:
1:07:54.622810 PROGRESS: Channel   0:	 0.050 FDR: 1,280; 0.010 FDR: 1,280; 0.001 FDR:   918
1:07:54.622900 PROGRESS: =========================================================================
1:07:54.638200 INFO: Target number of precursors reached.
1:07:55.091421 INFO: fragments_df: keeping 5000 of 4047915 [sum(precursor_idx_mask)=36867 sum(mass_error_mask)=4047915 stop_rank=5000
1:07:55.531088 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:07:55.739143 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:07:56.389115 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:07:56.389563 INFO: Using score_cutoff 12.48984980392456 (fac=0.99, q=1)
1:07:56.389863 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:07:56.389939 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:07:56.389993 INFO: Updating optimization_manager: score_cutoff        : 12.295543506145478 -> 12.48984980392456
1:07:56.390048 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:07:56.543552 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:07:56.880272 INFO: === checking if optimization conditions were reached ===
1:07:56.882526 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
1:07:56.882626 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1:07:56.882691 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:07:56.882751 INFO: ==============================================
1:07:56.882816 INFO: Starting optimization step 8.
1:07:56.882874 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:07:56.882936 INFO: Using rust extraction backend
1:07:56.882993 PROGRESS: Extracting batch of 250442 precursors
1:07:57.307647 INFO: === Search parameters used ===
1:07:57.307933 INFO: rt_error       : 805.5982666015625
1:07:57.307993 INFO: mobility_error : 0.1
1:07:57.308042 INFO: num_candidates : 3
1:07:57.308087 INFO: ms1_error      : 3
1:07:57.308130 INFO: ms2_error      : 10.0
1:07:57.308172 INFO: fwhm_rt        : 3.0
1:07:57.308213 INFO: quant_window   : 3
1:07:57.308255 INFO: ==============================================
1:07:59.883342 INFO: performing precursor FDR with 40 features
1:07:59.883466 INFO: Decoy channel: -1
1:07:59.883505 INFO: competitive: True
1:08:00.086344 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:00.396180 INFO: Estimating optimal hyperparameters - samples: 599,837, batch_size: 2,456, learning_rate: 7.74e-04
1:08:00.397110 INFO: Using random state 933370 for train-test-split
1:08:12.746014 INFO: Test AUC: 0.602
1:08:12.746160 INFO: Train AUC: 0.614
1:08:12.746195 INFO: AUC difference: 1.95%
1:08:13.233509 INFO: Resetting torch num_threads to 100
1:08:13.265291 PROGRESS: === Extracted 749797 precursors and 4047756 fragments ===
1:08:13.265765 INFO: === FDR correction performed with classifier version 7 ===
1:08:13.266567 PROGRESS: ============================= Precursor FDR =============================
1:08:13.266663 PROGRESS: Total precursors accumulated: 1,608
1:08:13.266723 PROGRESS: Target precursors: 1,593 (99.07%)
1:08:13.266778 PROGRESS: Decoy precursors: 15 (0.93%)
1:08:13.266825 PROGRESS: 
1:08:13.266871 PROGRESS: Precursor Summary:
1:08:13.268351 PROGRESS: Channel   0:	 0.050 FDR: 1,593; 0.010 FDR: 1,593; 0.001 FDR: 1,275
1:08:13.268448 PROGRESS: 
1:08:13.268504 PROGRESS: Protein Summary:
1:08:13.270391 PROGRESS: Channel   0:	 0.050 FDR: 1,339; 0.010 FDR: 1,339; 0.001 FDR: 1,083
1:08:13.270487 PROGRESS: =========================================================================
1:08:13.286412 INFO: Target number of precursors reached.
1:08:13.721082 INFO: fragments_df: keeping 5000 of 4047756 [sum(precursor_idx_mask)=37815 sum(mass_error_mask)=4047756 stop_rank=5000
1:08:14.257891 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:08:14.476528 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:08:15.125993 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:08:15.126441 INFO: Using score_cutoff 10.619678759765625 (fac=0.99, q=1)
1:08:15.126751 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:08:15.126831 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:08:15.126888 INFO: Updating optimization_manager: score_cutoff        : 12.48984980392456 -> 10.619678759765625
1:08:15.126951 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:08:15.276681 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:08:15.617826 INFO: === checking if optimization conditions were reached ===
1:08:15.620526 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:08:15.620696 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:08:15.620776 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:08:15.620856 INFO: ==============================================
1:08:15.620937 INFO: Starting optimization step 9.
1:08:15.621006 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:08:15.621081 INFO: Using rust extraction backend
1:08:15.621152 PROGRESS: Extracting batch of 250442 precursors
1:08:16.054301 INFO: === Search parameters used ===
1:08:16.054578 INFO: rt_error       : 805.5982666015625
1:08:16.054638 INFO: mobility_error : 0.1
1:08:16.054689 INFO: num_candidates : 3
1:08:16.054734 INFO: ms1_error      : 3
1:08:16.054778 INFO: ms2_error      : 10.0
1:08:16.054819 INFO: fwhm_rt        : 3.0
1:08:16.054860 INFO: quant_window   : 3
1:08:16.054900 INFO: ==============================================
1:08:18.602825 INFO: performing precursor FDR with 40 features
1:08:18.602946 INFO: Decoy channel: -1
1:08:18.602974 INFO: competitive: True
1:08:18.804526 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:19.090275 INFO: Estimating optimal hyperparameters - samples: 599,843, batch_size: 2,456, learning_rate: 7.74e-04
1:08:19.091375 INFO: Using random state 474352 for train-test-split
1:08:31.453178 INFO: Test AUC: 0.609
1:08:31.453319 INFO: Train AUC: 0.617
1:08:31.453353 INFO: AUC difference: 1.24%
1:08:31.927654 INFO: Resetting torch num_threads to 100
1:08:31.955259 PROGRESS: === Extracted 749804 precursors and 4048230 fragments ===
1:08:31.955740 INFO: === FDR correction performed with classifier version 8 ===
1:08:31.956542 PROGRESS: ============================= Precursor FDR =============================
1:08:31.956644 PROGRESS: Total precursors accumulated: 1,697
1:08:31.956703 PROGRESS: Target precursors: 1,681 (99.06%)
1:08:31.956753 PROGRESS: Decoy precursors: 16 (0.94%)
1:08:31.956798 PROGRESS: 
1:08:31.956843 PROGRESS: Precursor Summary:
1:08:31.958293 PROGRESS: Channel   0:	 0.050 FDR: 1,681; 0.010 FDR: 1,681; 0.001 FDR: 1,166
1:08:31.958383 PROGRESS: 
1:08:31.958437 PROGRESS: Protein Summary:
1:08:31.960283 PROGRESS: Channel   0:	 0.050 FDR: 1,407; 0.010 FDR: 1,407; 0.001 FDR:   996
1:08:31.960377 PROGRESS: =========================================================================
1:08:31.975245 INFO: Target number of precursors reached.
1:08:32.411239 INFO: fragments_df: keeping 5000 of 4048230 [sum(precursor_idx_mask)=39665 sum(mass_error_mask)=4048230 stop_rank=5000
1:08:32.868109 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:08:33.089507 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:08:33.737981 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:08:33.738445 INFO: Using score_cutoff 10.870126092910766 (fac=0.99, q=1)
1:08:33.738750 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:08:33.738826 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:08:33.738886 INFO: Updating optimization_manager: score_cutoff        : 10.619678759765625 -> 10.870126092910766
1:08:33.738947 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:08:33.886379 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:08:34.196593 INFO: === checking if optimization conditions were reached ===
1:08:34.198814 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:08:34.198953 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:08:34.199022 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:08:34.199084 INFO: ==============================================
1:08:34.199150 INFO: Starting optimization step 10.
1:08:34.199211 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:08:34.199273 INFO: Using rust extraction backend
1:08:34.199331 PROGRESS: Extracting batch of 250442 precursors
1:08:34.622479 INFO: === Search parameters used ===
1:08:34.622768 INFO: rt_error       : 805.5982666015625
1:08:34.622828 INFO: mobility_error : 0.1
1:08:34.622880 INFO: num_candidates : 3
1:08:34.622926 INFO: ms1_error      : 3
1:08:34.622972 INFO: ms2_error      : 10.0
1:08:34.623016 INFO: fwhm_rt        : 3.0
1:08:34.623059 INFO: quant_window   : 3
1:08:34.623102 INFO: ==============================================
1:08:37.123172 INFO: performing precursor FDR with 40 features
1:08:37.123298 INFO: Decoy channel: -1
1:08:37.123324 INFO: competitive: True
1:08:37.310528 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:37.592969 INFO: Estimating optimal hyperparameters - samples: 599,840, batch_size: 2,456, learning_rate: 7.74e-04
1:08:37.594011 INFO: Using random state 780672 for train-test-split
1:08:49.792036 INFO: Test AUC: 0.609
1:08:49.792202 INFO: Train AUC: 0.620
1:08:49.792239 INFO: AUC difference: 1.76%
1:08:50.271028 INFO: Resetting torch num_threads to 100
1:08:50.299378 PROGRESS: === Extracted 749801 precursors and 4048496 fragments ===
1:08:50.299870 INFO: === FDR correction performed with classifier version 9 ===
1:08:50.300639 PROGRESS: ============================= Precursor FDR =============================
1:08:50.300740 PROGRESS: Total precursors accumulated: 1,725
1:08:50.300802 PROGRESS: Target precursors: 1,708 (99.01%)
1:08:50.300852 PROGRESS: Decoy precursors: 17 (0.99%)
1:08:50.300906 PROGRESS: 
1:08:50.300954 PROGRESS: Precursor Summary:
1:08:50.302414 PROGRESS: Channel   0:	 0.050 FDR: 1,708; 0.010 FDR: 1,708; 0.001 FDR: 1,225
1:08:50.302509 PROGRESS: 
1:08:50.302565 PROGRESS: Protein Summary:
1:08:50.304444 PROGRESS: Channel   0:	 0.050 FDR: 1,443; 0.010 FDR: 1,443; 0.001 FDR: 1,045
1:08:50.304548 PROGRESS: =========================================================================
1:08:50.318889 INFO: Target number of precursors reached.
1:08:50.755990 INFO: fragments_df: keeping 5000 of 4048496 [sum(precursor_idx_mask)=39563 sum(mass_error_mask)=4048496 stop_rank=5000
1:08:51.176423 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:08:51.406989 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:08:52.058082 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:08:52.058534 INFO: Using score_cutoff 9.597542006778717 (fac=0.99, q=1)
1:08:52.058849 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:08:52.058934 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:08:52.058989 INFO: Updating optimization_manager: score_cutoff        : 10.870126092910766 -> 9.597542006778717
1:08:52.059043 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:08:52.207930 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:08:52.540721 INFO: === checking if optimization conditions were reached ===
1:08:52.543039 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:08:52.543190 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:08:52.543259 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:08:52.543318 INFO: ==============================================
1:08:52.543384 INFO: Starting optimization step 11.
1:08:52.543441 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:08:52.543512 INFO: Using rust extraction backend
1:08:52.543575 PROGRESS: Extracting batch of 250442 precursors
1:08:52.964030 INFO: === Search parameters used ===
1:08:52.964319 INFO: rt_error       : 805.5982666015625
1:08:52.964377 INFO: mobility_error : 0.1
1:08:52.964425 INFO: num_candidates : 3
1:08:52.964473 INFO: ms1_error      : 3
1:08:52.964522 INFO: ms2_error      : 10.0
1:08:52.964566 INFO: fwhm_rt        : 3.0
1:08:52.964606 INFO: quant_window   : 3
1:08:52.964658 INFO: ==============================================
1:08:55.444574 INFO: performing precursor FDR with 40 features
1:08:55.444698 INFO: Decoy channel: -1
1:08:55.444726 INFO: competitive: True
1:08:55.642061 INFO: Setting torch num_threads to 2 for FDR classification task
1:08:55.926481 INFO: Estimating optimal hyperparameters - samples: 599,852, batch_size: 2,456, learning_rate: 7.74e-04
1:08:55.927712 INFO: Using random state 273140 for train-test-split
1:09:08.335670 INFO: Test AUC: 0.612
1:09:08.335802 INFO: Train AUC: 0.622
1:09:08.335858 INFO: AUC difference: 1.64%
1:09:08.814096 INFO: Resetting torch num_threads to 100
1:09:08.843737 PROGRESS: === Extracted 749815 precursors and 4048835 fragments ===
1:09:08.844216 INFO: === FDR correction performed with classifier version 10 ===
1:09:08.844949 PROGRESS: ============================= Precursor FDR =============================
1:09:08.845048 PROGRESS: Total precursors accumulated: 1,755
1:09:08.845109 PROGRESS: Target precursors: 1,738 (99.03%)
1:09:08.845160 PROGRESS: Decoy precursors: 17 (0.97%)
1:09:08.845207 PROGRESS: 
1:09:08.845253 PROGRESS: Precursor Summary:
1:09:08.846717 PROGRESS: Channel   0:	 0.050 FDR: 1,738; 0.010 FDR: 1,738; 0.001 FDR: 1,213
1:09:08.846814 PROGRESS: 
1:09:08.846869 PROGRESS: Protein Summary:
1:09:08.848757 PROGRESS: Channel   0:	 0.050 FDR: 1,473; 0.010 FDR: 1,473; 0.001 FDR: 1,036
1:09:08.848858 PROGRESS: =========================================================================
1:09:08.865263 INFO: Target number of precursors reached.
1:09:09.300374 INFO: fragments_df: keeping 5000 of 4048835 [sum(precursor_idx_mask)=40198 sum(mass_error_mask)=4048835 stop_rank=5000
1:09:09.777689 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:09:10.011064 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:09:10.659383 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:09:10.659843 INFO: Using score_cutoff 9.034409782218933 (fac=0.99, q=1)
1:09:10.660158 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:09:10.660242 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:09:10.660297 INFO: Updating optimization_manager: score_cutoff        : 9.597542006778717 -> 9.034409782218933
1:09:10.660351 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:09:10.811135 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:09:11.139921 INFO: === checking if optimization conditions were reached ===
1:09:11.142119 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:09:11.142222 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:09:11.142288 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:09:11.142345 INFO: ==============================================
1:09:11.142411 PROGRESS: Optimization finished for ms2_error.
1:09:11.691036 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:09:11.838573 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:09:12.164307 INFO: Starting optimization step 0.
1:09:12.164568 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:09:12.164650 INFO: Using rust extraction backend
1:09:12.164732 PROGRESS: Extracting batch of 250442 precursors
1:09:12.588817 INFO: === Search parameters used ===
1:09:12.589087 INFO: rt_error       : 805.5982666015625
1:09:12.589147 INFO: mobility_error : 0.1
1:09:12.589212 INFO: num_candidates : 3
1:09:12.589260 INFO: ms1_error      : 3
1:09:12.589305 INFO: ms2_error      : 10.0
1:09:12.589347 INFO: fwhm_rt        : 3.0
1:09:12.589388 INFO: quant_window   : 3
1:09:12.589429 INFO: ==============================================
1:09:15.089378 INFO: performing precursor FDR with 40 features
1:09:15.089499 INFO: Decoy channel: -1
1:09:15.089525 INFO: competitive: True
1:09:15.289417 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:15.595694 INFO: Estimating optimal hyperparameters - samples: 599,847, batch_size: 2,456, learning_rate: 7.74e-04
1:09:15.596780 INFO: Using random state 887166 for train-test-split
1:09:28.033017 INFO: Test AUC: 0.612
1:09:28.033187 INFO: Train AUC: 0.624
1:09:28.033223 INFO: AUC difference: 1.96%
1:09:28.518744 INFO: Resetting torch num_threads to 100
1:09:28.549732 PROGRESS: === Extracted 749809 precursors and 4048868 fragments ===
1:09:28.550211 INFO: === FDR correction performed with classifier version 11 ===
1:09:28.550984 PROGRESS: ============================= Precursor FDR =============================
1:09:28.551085 PROGRESS: Total precursors accumulated: 1,702
1:09:28.551148 PROGRESS: Target precursors: 1,686 (99.06%)
1:09:28.551202 PROGRESS: Decoy precursors: 16 (0.94%)
1:09:28.551250 PROGRESS: 
1:09:28.551296 PROGRESS: Precursor Summary:
1:09:28.552798 PROGRESS: Channel   0:	 0.050 FDR: 1,686; 0.010 FDR: 1,686; 0.001 FDR: 1,333
1:09:28.552898 PROGRESS: 
1:09:28.552956 PROGRESS: Protein Summary:
1:09:28.554826 PROGRESS: Channel   0:	 0.050 FDR: 1,406; 0.010 FDR: 1,406; 0.001 FDR: 1,129
1:09:28.554920 PROGRESS: =========================================================================
1:09:28.569445 INFO: Target number of precursors reached.
1:09:29.011822 INFO: fragments_df: keeping 5000 of 4048868 [sum(precursor_idx_mask)=39643 sum(mass_error_mask)=4048868 stop_rank=5000
1:09:29.436684 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:09:29.685559 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:09:30.348363 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:09:30.348801 INFO: Using score_cutoff 10.361867663383485 (fac=0.99, q=1)
1:09:30.349113 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:09:30.349190 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:09:30.349245 INFO: Updating optimization_manager: score_cutoff        : 9.034409782218933 -> 10.361867663383485
1:09:30.349300 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:09:30.498739 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:09:30.834257 INFO: === checking if optimization conditions were reached ===
1:09:30.834530 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:09:30.837306 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 676.1145580821978
1:09:30.837409 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 676.1146.
1:09:30.837489 INFO: ==============================================
1:09:30.837558 INFO: Starting optimization step 1.
1:09:30.837619 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:09:30.837682 INFO: Using rust extraction backend
1:09:30.837737 PROGRESS: Extracting batch of 250442 precursors
1:09:31.259156 INFO: === Search parameters used ===
1:09:31.259445 INFO: rt_error       : 676.1145580821978
1:09:31.259501 INFO: mobility_error : 0.1
1:09:31.259555 INFO: num_candidates : 3
1:09:31.259599 INFO: ms1_error      : 3
1:09:31.259639 INFO: ms2_error      : 10.0
1:09:31.259678 INFO: fwhm_rt        : 3.0
1:09:31.259717 INFO: quant_window   : 3
1:09:31.259755 INFO: ==============================================
1:09:33.830229 INFO: performing precursor FDR with 40 features
1:09:33.830352 INFO: Decoy channel: -1
1:09:33.830379 INFO: competitive: True
1:09:34.028191 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:34.331394 INFO: Estimating optimal hyperparameters - samples: 599,720, batch_size: 2,456, learning_rate: 7.74e-04
1:09:34.332514 INFO: Using random state 887166 for train-test-split
1:09:50.124834 INFO: Test AUC: 0.612
1:09:50.125063 INFO: Train AUC: 0.624
1:09:50.125106 INFO: AUC difference: 2.07%
1:09:50.752501 INFO: Resetting torch num_threads to 100
1:09:50.795664 PROGRESS: === Extracted 749651 precursors and 4040384 fragments ===
1:09:50.798601 INFO: === FDR correction performed with classifier version 11 ===
1:09:50.799742 PROGRESS: ============================= Precursor FDR =============================
1:09:50.799867 PROGRESS: Total precursors accumulated: 1,776
1:09:50.799943 PROGRESS: Target precursors: 1,759 (99.04%)
1:09:50.800004 PROGRESS: Decoy precursors: 17 (0.96%)
1:09:50.800061 PROGRESS: 
1:09:50.800117 PROGRESS: Precursor Summary:
1:09:50.802051 PROGRESS: Channel   0:	 0.050 FDR: 1,759; 0.010 FDR: 1,759; 0.001 FDR: 1,277
1:09:50.802166 PROGRESS: 
1:09:50.802237 PROGRESS: Protein Summary:
1:09:50.804947 PROGRESS: Channel   0:	 0.050 FDR: 1,486; 0.010 FDR: 1,486; 0.001 FDR: 1,086
1:09:50.805089 PROGRESS: =========================================================================
1:09:50.831932 INFO: Target number of precursors reached.
1:09:51.497970 INFO: fragments_df: keeping 5000 of 4040384 [sum(precursor_idx_mask)=40660 sum(mass_error_mask)=4040384 stop_rank=5000
1:09:52.105318 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:09:52.579037 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:09:53.546705 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:09:53.547220 INFO: Using score_cutoff 9.573853698921205 (fac=0.99, q=1)
1:09:53.547549 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:09:53.547626 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:09:53.547682 INFO: Updating optimization_manager: score_cutoff        : 10.361867663383485 -> 9.573853698921205
1:09:53.547737 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:09:53.698624 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:09:54.055276 INFO: === checking if optimization conditions were reached ===
1:09:54.055726 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:09:54.059475 INFO: Updating optimization_manager: rt_error            : 676.1145580821978 -> 851.2323666920361
1:09:54.059608 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 851.2324.
1:09:54.059685 INFO: ==============================================
1:09:54.059770 INFO: Starting optimization step 2.
1:09:54.059852 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:09:54.059949 INFO: Using rust extraction backend
1:09:54.060028 PROGRESS: Extracting batch of 250442 precursors
1:09:54.491068 INFO: === Search parameters used ===
1:09:54.491451 INFO: rt_error       : 851.2323666920361
1:09:54.491507 INFO: mobility_error : 0.1
1:09:54.491553 INFO: num_candidates : 3
1:09:54.491596 INFO: ms1_error      : 3
1:09:54.491640 INFO: ms2_error      : 10.0
1:09:54.491680 INFO: fwhm_rt        : 3.0
1:09:54.491719 INFO: quant_window   : 3
1:09:54.491758 INFO: ==============================================
1:09:58.318435 INFO: performing precursor FDR with 40 features
1:09:58.318597 INFO: Decoy channel: -1
1:09:58.318624 INFO: competitive: True
1:09:58.586802 INFO: Setting torch num_threads to 2 for FDR classification task
1:09:59.034581 INFO: Estimating optimal hyperparameters - samples: 599,841, batch_size: 2,456, learning_rate: 7.74e-04
1:09:59.036566 INFO: Using random state 887166 for train-test-split
1:10:24.068543 INFO: Test AUC: 0.613
1:10:24.068949 INFO: Train AUC: 0.624
1:10:24.069004 INFO: AUC difference: 1.65%
1:10:24.879107 INFO: Resetting torch num_threads to 100
1:10:24.958251 PROGRESS: === Extracted 749802 precursors and 4048855 fragments ===
1:10:24.959734 INFO: === FDR correction performed with classifier version 11 ===
1:10:24.962303 PROGRESS: ============================= Precursor FDR =============================
1:10:24.962517 PROGRESS: Total precursors accumulated: 1,795
1:10:24.962597 PROGRESS: Target precursors: 1,778 (99.05%)
1:10:24.962662 PROGRESS: Decoy precursors: 17 (0.95%)
1:10:24.962718 PROGRESS: 
1:10:24.962768 PROGRESS: Precursor Summary:
1:10:24.965368 PROGRESS: Channel   0:	 0.050 FDR: 1,778; 0.010 FDR: 1,778; 0.001 FDR: 1,329
1:10:24.965596 PROGRESS: 
1:10:24.965659 PROGRESS: Protein Summary:
1:10:24.968217 PROGRESS: Channel   0:	 0.050 FDR: 1,483; 0.010 FDR: 1,483; 0.001 FDR: 1,119
1:10:24.968496 PROGRESS: =========================================================================
1:10:25.023133 INFO: Target number of precursors reached.
1:10:25.500550 INFO: fragments_df: keeping 5000 of 4048855 [sum(precursor_idx_mask)=41590 sum(mass_error_mask)=4048855 stop_rank=5000
1:10:26.749388 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:10:27.178265 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:10:28.180475 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:10:28.182177 INFO: Using score_cutoff 11.095469213962554 (fac=0.99, q=1)
1:10:28.183310 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:10:28.183514 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:10:28.183600 INFO: Updating optimization_manager: score_cutoff        : 9.573853698921205 -> 11.095469213962554
1:10:28.183695 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:10:28.388175 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:10:28.940078 INFO: === checking if optimization conditions were reached ===
1:10:28.941291 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:10:28.951561 INFO: Updating optimization_manager: rt_error            : 851.2323666920361 -> 416.7011626719453
1:10:28.952399 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 416.7012.
1:10:28.952590 INFO: ==============================================
1:10:28.952766 INFO: Starting optimization step 3.
1:10:28.953133 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:10:28.953294 INFO: Using rust extraction backend
1:10:28.953412 PROGRESS: Extracting batch of 250442 precursors
1:10:30.154801 INFO: === Search parameters used ===
1:10:30.155725 INFO: rt_error       : 416.7011626719453
1:10:30.156090 INFO: mobility_error : 0.1
1:10:30.156168 INFO: num_candidates : 3
1:10:30.156223 INFO: ms1_error      : 3
1:10:30.156270 INFO: ms2_error      : 10.0
1:10:30.156316 INFO: fwhm_rt        : 3.0
1:10:30.156363 INFO: quant_window   : 3
1:10:30.156413 INFO: ==============================================
1:10:37.250467 INFO: performing precursor FDR with 40 features
1:10:37.250896 INFO: Decoy channel: -1
1:10:37.250930 INFO: competitive: True
1:10:37.948919 INFO: Setting torch num_threads to 2 for FDR classification task
1:10:38.678425 INFO: Estimating optimal hyperparameters - samples: 598,415, batch_size: 2,451, learning_rate: 7.74e-04
1:10:38.681785 INFO: Using random state 887166 for train-test-split
1:11:08.504752 INFO: Test AUC: 0.610
1:11:08.505188 INFO: Train AUC: 0.621
1:11:08.505242 INFO: AUC difference: 1.73%
1:11:09.286626 INFO: Resetting torch num_threads to 100
1:11:09.373338 PROGRESS: === Extracted 748019 precursors and 3914559 fragments ===
1:11:09.374823 INFO: === FDR correction performed with classifier version 11 ===
1:11:09.377209 PROGRESS: ============================= Precursor FDR =============================
1:11:09.377458 PROGRESS: Total precursors accumulated: 1,781
1:11:09.377538 PROGRESS: Target precursors: 1,764 (99.05%)
1:11:09.377595 PROGRESS: Decoy precursors: 17 (0.95%)
1:11:09.377645 PROGRESS: 
1:11:09.377692 PROGRESS: Precursor Summary:
1:11:09.379995 PROGRESS: Channel   0:	 0.050 FDR: 1,764; 0.010 FDR: 1,764; 0.001 FDR: 1,397
1:11:09.380137 PROGRESS: 
1:11:09.380221 PROGRESS: Protein Summary:
1:11:09.382660 PROGRESS: Channel   0:	 0.050 FDR: 1,480; 0.010 FDR: 1,480; 0.001 FDR: 1,181
1:11:09.382893 PROGRESS: =========================================================================
1:11:09.437778 INFO: Target number of precursors reached.
1:11:09.908436 INFO: fragments_df: keeping 5000 of 3914559 [sum(precursor_idx_mask)=40738 sum(mass_error_mask)=3914559 stop_rank=5000
1:11:11.163448 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:11:11.700274 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:11:12.568968 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:11:12.570427 INFO: Using score_cutoff 9.402797978496551 (fac=0.99, q=1)
1:11:12.571044 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:11:12.571132 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:11:12.571190 INFO: Updating optimization_manager: score_cutoff        : 11.095469213962554 -> 9.402797978496551
1:11:12.571256 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:11:12.793071 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:11:13.401791 INFO: === checking if optimization conditions were reached ===
1:11:13.402539 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:11:13.407602 INFO: Updating optimization_manager: rt_error            : 416.7011626719453 -> 507.59950838741696
1:11:13.407977 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 507.5995.
1:11:13.408102 INFO: ==============================================
1:11:13.408187 INFO: Starting optimization step 4.
1:11:13.408260 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:11:13.408357 INFO: Using rust extraction backend
1:11:13.408434 PROGRESS: Extracting batch of 250442 precursors
1:11:14.515546 INFO: === Search parameters used ===
1:11:14.516882 INFO: rt_error       : 507.59950838741696
1:11:14.516948 INFO: mobility_error : 0.1
1:11:14.516999 INFO: num_candidates : 3
1:11:14.517050 INFO: ms1_error      : 3
1:11:14.517097 INFO: ms2_error      : 10.0
1:11:14.517152 INFO: fwhm_rt        : 3.0
1:11:14.517194 INFO: quant_window   : 3
1:11:14.517235 INFO: ==============================================
1:11:22.206111 INFO: performing precursor FDR with 40 features
1:11:22.206435 INFO: Decoy channel: -1
1:11:22.206470 INFO: competitive: True
1:11:22.918837 INFO: Setting torch num_threads to 2 for FDR classification task
1:11:24.058228 INFO: Estimating optimal hyperparameters - samples: 599,149, batch_size: 2,454, learning_rate: 7.74e-04
1:11:24.064539 INFO: Using random state 887166 for train-test-split
1:11:54.908320 INFO: Test AUC: 0.612
1:11:54.908816 INFO: Train AUC: 0.622
1:11:54.908908 INFO: AUC difference: 1.58%
1:11:55.707798 INFO: Resetting torch num_threads to 100
1:11:55.799334 PROGRESS: === Extracted 748937 precursors and 3994500 fragments ===
1:11:55.800925 INFO: === FDR correction performed with classifier version 11 ===
1:11:55.803307 PROGRESS: ============================= Precursor FDR =============================
1:11:55.803486 PROGRESS: Total precursors accumulated: 1,769
1:11:55.803558 PROGRESS: Target precursors: 1,752 (99.04%)
1:11:55.803613 PROGRESS: Decoy precursors: 17 (0.96%)
1:11:55.803664 PROGRESS: 
1:11:55.803713 PROGRESS: Precursor Summary:
1:11:55.806057 PROGRESS: Channel   0:	 0.050 FDR: 1,752; 0.010 FDR: 1,752; 0.001 FDR: 1,287
1:11:55.806241 PROGRESS: 
1:11:55.806304 PROGRESS: Protein Summary:
1:11:55.808883 PROGRESS: Channel   0:	 0.050 FDR: 1,462; 0.010 FDR: 1,462; 0.001 FDR: 1,091
1:11:55.809153 PROGRESS: =========================================================================
1:11:55.872595 INFO: Target number of precursors reached.
1:11:56.344261 INFO: fragments_df: keeping 5000 of 3994500 [sum(precursor_idx_mask)=40310 sum(mass_error_mask)=3994500 stop_rank=5000
1:11:57.576427 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:11:58.074277 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:11:59.090348 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:11:59.091588 INFO: Using score_cutoff 9.42409025402069 (fac=0.99, q=1)
1:11:59.092201 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:11:59.092301 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:11:59.092357 INFO: Updating optimization_manager: score_cutoff        : 9.402797978496551 -> 9.42409025402069
1:11:59.092433 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:11:59.296146 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:11:59.871676 INFO: === checking if optimization conditions were reached ===
1:11:59.872488 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:11:59.878287 INFO: Updating optimization_manager: rt_error            : 507.59950838741696 -> 666.6076243319649
1:11:59.878683 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 666.6076.
1:11:59.878772 INFO: ==============================================
1:11:59.878868 INFO: Starting optimization step 5.
1:11:59.878943 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:11:59.879046 INFO: Using rust extraction backend
1:11:59.879128 PROGRESS: Extracting batch of 250442 precursors
1:12:00.835167 INFO: === Search parameters used ===
1:12:00.836139 INFO: rt_error       : 666.6076243319649
1:12:00.836210 INFO: mobility_error : 0.1
1:12:00.836264 INFO: num_candidates : 3
1:12:00.836316 INFO: ms1_error      : 3
1:12:00.836364 INFO: ms2_error      : 10.0
1:12:00.836415 INFO: fwhm_rt        : 3.0
1:12:00.836462 INFO: quant_window   : 3
1:12:00.836509 INFO: ==============================================
1:12:08.461561 INFO: performing precursor FDR with 40 features
1:12:08.461987 INFO: Decoy channel: -1
1:12:08.462023 INFO: competitive: True
1:12:09.150358 INFO: Setting torch num_threads to 2 for FDR classification task
1:12:10.281439 INFO: Estimating optimal hyperparameters - samples: 599,685, batch_size: 2,456, learning_rate: 7.74e-04
1:12:10.292534 INFO: Using random state 887166 for train-test-split
1:12:40.528229 INFO: Test AUC: 0.613
1:12:40.528684 INFO: Train AUC: 0.624
1:12:40.528736 INFO: AUC difference: 1.82%
1:12:41.341128 INFO: Resetting torch num_threads to 100
1:12:41.478487 PROGRESS: === Extracted 749607 precursors and 4038440 fragments ===
1:12:41.479985 INFO: === FDR correction performed with classifier version 11 ===
1:12:41.482541 PROGRESS: ============================= Precursor FDR =============================
1:12:41.482769 PROGRESS: Total precursors accumulated: 1,796
1:12:41.482847 PROGRESS: Target precursors: 1,779 (99.05%)
1:12:41.482908 PROGRESS: Decoy precursors: 17 (0.95%)
1:12:41.482983 PROGRESS: 
1:12:41.483050 PROGRESS: Precursor Summary:
1:12:41.485551 PROGRESS: Channel   0:	 0.050 FDR: 1,779; 0.010 FDR: 1,779; 0.001 FDR: 1,416
1:12:41.485776 PROGRESS: 
1:12:41.485839 PROGRESS: Protein Summary:
1:12:41.488549 PROGRESS: Channel   0:	 0.050 FDR: 1,501; 0.010 FDR: 1,501; 0.001 FDR: 1,189
1:12:41.488758 PROGRESS: =========================================================================
1:12:41.571656 INFO: Target number of precursors reached.
1:12:42.068934 INFO: fragments_df: keeping 5000 of 4038440 [sum(precursor_idx_mask)=40850 sum(mass_error_mask)=4038440 stop_rank=5000
1:12:43.529671 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:12:44.149898 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:12:44.997064 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:12:44.998564 INFO: Using score_cutoff 8.299544758415223 (fac=0.99, q=1)
1:12:44.999311 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:12:44.999399 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:12:44.999459 INFO: Updating optimization_manager: score_cutoff        : 9.42409025402069 -> 8.299544758415223
1:12:44.999542 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:12:45.213304 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:12:45.803720 INFO: === checking if optimization conditions were reached ===
1:12:45.804797 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
1:12:45.811502 INFO: Updating optimization_manager: rt_error            : 666.6076243319649 -> 745.9225838551724
1:12:45.812250 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 745.9226.
1:12:45.812353 INFO: ==============================================
1:12:45.812483 INFO: Starting optimization step 6.
1:12:45.812570 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:12:45.812734 INFO: Using rust extraction backend
1:12:45.812832 PROGRESS: Extracting batch of 250442 precursors
1:12:46.869934 INFO: === Search parameters used ===
1:12:46.870656 INFO: rt_error       : 745.9225838551724
1:12:46.870722 INFO: mobility_error : 0.1
1:12:46.870776 INFO: num_candidates : 3
1:12:46.870821 INFO: ms1_error      : 3
1:12:46.870867 INFO: ms2_error      : 10.0
1:12:46.870924 INFO: fwhm_rt        : 3.0
1:12:46.870981 INFO: quant_window   : 3
1:12:46.871025 INFO: ==============================================
1:12:54.621798 INFO: performing precursor FDR with 40 features
1:12:54.622354 INFO: Decoy channel: -1
1:12:54.622386 INFO: competitive: True
1:12:55.392987 INFO: Setting torch num_threads to 2 for FDR classification task
1:12:56.555021 INFO: Estimating optimal hyperparameters - samples: 599,838, batch_size: 2,456, learning_rate: 7.74e-04
1:12:56.562891 INFO: Using random state 887166 for train-test-split
1:13:26.027178 INFO: Test AUC: 0.611
1:13:26.027606 INFO: Train AUC: 0.625
1:13:26.027662 INFO: AUC difference: 2.20%
1:13:26.787009 INFO: Resetting torch num_threads to 100
1:13:26.862961 PROGRESS: === Extracted 749798 precursors and 4047623 fragments ===
1:13:26.864284 INFO: === FDR correction performed with classifier version 11 ===
1:13:26.866297 PROGRESS: ============================= Precursor FDR =============================
1:13:26.866485 PROGRESS: Total precursors accumulated: 1,760
1:13:26.866588 PROGRESS: Target precursors: 1,743 (99.03%)
1:13:26.866644 PROGRESS: Decoy precursors: 17 (0.97%)
1:13:26.866694 PROGRESS: 
1:13:26.866741 PROGRESS: Precursor Summary:
1:13:26.869089 PROGRESS: Channel   0:	 0.050 FDR: 1,743; 0.010 FDR: 1,743; 0.001 FDR: 1,397
1:13:26.869246 PROGRESS: 
1:13:26.869307 PROGRESS: Protein Summary:
1:13:26.871620 PROGRESS: Channel   0:	 0.050 FDR: 1,482; 0.010 FDR: 1,482; 0.001 FDR: 1,189
1:13:26.871776 PROGRESS: =========================================================================
1:13:26.921094 INFO: Target number of precursors reached.
1:13:27.393472 INFO: fragments_df: keeping 5000 of 4047623 [sum(precursor_idx_mask)=39904 sum(mass_error_mask)=4047623 stop_rank=5000
1:13:28.591456 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:13:29.135425 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:13:30.083608 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:13:30.085130 INFO: Using score_cutoff 8.833961010360719 (fac=0.99, q=1)
1:13:30.085796 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:13:30.085879 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:13:30.085935 INFO: Updating optimization_manager: score_cutoff        : 8.299544758415223 -> 8.833961010360719
1:13:30.086006 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:13:30.306225 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:13:30.892261 INFO: === checking if optimization conditions were reached ===
1:13:30.893222 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
1:13:30.898867 INFO: Updating optimization_manager: rt_error            : 745.9225838551724 -> 912.7181611854181
1:13:30.899236 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 912.7182.
1:13:30.899323 INFO: ==============================================
1:13:30.899414 INFO: Starting optimization step 7.
1:13:30.899488 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:13:30.899599 INFO: Using rust extraction backend
1:13:30.899679 PROGRESS: Extracting batch of 250442 precursors
1:13:31.821270 INFO: === Search parameters used ===
1:13:31.822087 INFO: rt_error       : 912.7181611854181
1:13:31.822154 INFO: mobility_error : 0.1
1:13:31.822212 INFO: num_candidates : 3
1:13:31.822263 INFO: ms1_error      : 3
1:13:31.822308 INFO: ms2_error      : 10.0
1:13:31.822353 INFO: fwhm_rt        : 3.0
1:13:31.822397 INFO: quant_window   : 3
1:13:31.822445 INFO: ==============================================
1:13:38.365784 INFO: performing precursor FDR with 40 features
1:13:38.366160 INFO: Decoy channel: -1
1:13:38.366194 INFO: competitive: True
1:13:39.133106 INFO: Setting torch num_threads to 2 for FDR classification task
1:13:40.286828 INFO: Estimating optimal hyperparameters - samples: 599,846, batch_size: 2,456, learning_rate: 7.74e-04
1:13:40.292450 INFO: Using random state 887166 for train-test-split
1:14:10.575849 INFO: Test AUC: 0.614
1:14:10.576254 INFO: Train AUC: 0.624
1:14:10.576306 INFO: AUC difference: 1.57%
1:14:11.364214 INFO: Resetting torch num_threads to 100
1:14:11.448460 PROGRESS: === Extracted 749808 precursors and 4049028 fragments ===
1:14:11.449850 INFO: === FDR correction performed with classifier version 11 ===
1:14:11.452478 PROGRESS: ============================= Precursor FDR =============================
1:14:11.452755 PROGRESS: Total precursors accumulated: 1,777
1:14:11.452836 PROGRESS: Target precursors: 1,760 (99.04%)
1:14:11.452893 PROGRESS: Decoy precursors: 17 (0.96%)
1:14:11.452947 PROGRESS: 
1:14:11.452995 PROGRESS: Precursor Summary:
1:14:11.455397 PROGRESS: Channel   0:	 0.050 FDR: 1,760; 0.010 FDR: 1,760; 0.001 FDR: 1,280
1:14:11.455583 PROGRESS: 
1:14:11.455641 PROGRESS: Protein Summary:
1:14:11.458217 PROGRESS: Channel   0:	 0.050 FDR: 1,480; 0.010 FDR: 1,480; 0.001 FDR: 1,088
1:14:11.458454 PROGRESS: =========================================================================
1:14:11.514296 INFO: Target number of precursors reached.
1:14:11.995834 INFO: fragments_df: keeping 5000 of 4049028 [sum(precursor_idx_mask)=41015 sum(mass_error_mask)=4049028 stop_rank=5000
1:14:13.158229 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:14:13.602066 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:14:14.543226 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:14:14.545162 INFO: Using score_cutoff 9.065158681297303 (fac=0.99, q=1)
1:14:14.546306 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:14:14.546665 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:14:14.546874 INFO: Updating optimization_manager: score_cutoff        : 8.833961010360719 -> 9.065158681297303
1:14:14.547019 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:14:14.791321 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:14:15.447512 INFO: === checking if optimization conditions were reached ===
1:14:15.448377 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
1:14:15.454473 INFO: Updating optimization_manager: rt_error            : 912.7181611854181 -> 963.0491821864936
1:14:15.454818 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 963.0492.
1:14:15.454909 INFO: ==============================================
1:14:15.455021 INFO: Starting optimization step 8.
1:14:15.455110 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:14:15.455229 INFO: Using rust extraction backend
1:14:15.455315 PROGRESS: Extracting batch of 250442 precursors
1:14:16.502454 INFO: === Search parameters used ===
1:14:16.503554 INFO: rt_error       : 963.0491821864936
1:14:16.503620 INFO: mobility_error : 0.1
1:14:16.503671 INFO: num_candidates : 3
1:14:16.503718 INFO: ms1_error      : 3
1:14:16.503763 INFO: ms2_error      : 10.0
1:14:16.503804 INFO: fwhm_rt        : 3.0
1:14:16.503863 INFO: quant_window   : 3
1:14:16.503906 INFO: ==============================================
1:14:22.961769 INFO: performing precursor FDR with 40 features
1:14:22.962179 INFO: Decoy channel: -1
1:14:22.962209 INFO: competitive: True
1:14:23.527489 INFO: Setting torch num_threads to 2 for FDR classification task
1:14:24.583249 INFO: Estimating optimal hyperparameters - samples: 599,848, batch_size: 2,456, learning_rate: 7.74e-04
1:14:24.590236 INFO: Using random state 887166 for train-test-split
1:14:53.978976 INFO: Test AUC: 0.612
1:14:53.979302 INFO: Train AUC: 0.624
1:14:53.979348 INFO: AUC difference: 1.79%
1:14:59.095958 INFO: Resetting torch num_threads to 100
1:14:59.185589 PROGRESS: === Extracted 749811 precursors and 4048775 fragments ===
1:14:59.187028 INFO: === FDR correction performed with classifier version 11 ===
1:14:59.189717 PROGRESS: ============================= Precursor FDR =============================
1:14:59.189934 PROGRESS: Total precursors accumulated: 1,761
1:14:59.190012 PROGRESS: Target precursors: 1,744 (99.03%)
1:14:59.190072 PROGRESS: Decoy precursors: 17 (0.97%)
1:14:59.190124 PROGRESS: 
1:14:59.190174 PROGRESS: Precursor Summary:
1:14:59.192733 PROGRESS: Channel   0:	 0.050 FDR: 1,744; 0.010 FDR: 1,744; 0.001 FDR: 1,297
1:14:59.192892 PROGRESS: 
1:14:59.192958 PROGRESS: Protein Summary:
1:14:59.195762 PROGRESS: Channel   0:	 0.050 FDR: 1,488; 0.010 FDR: 1,488; 0.001 FDR: 1,110
1:14:59.195984 PROGRESS: =========================================================================
1:14:59.252669 INFO: Target number of precursors reached.
1:14:59.750606 INFO: fragments_df: keeping 5000 of 4048775 [sum(precursor_idx_mask)=39785 sum(mass_error_mask)=4048775 stop_rank=5000
1:15:01.067433 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:15:01.673489 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:15:02.649595 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:15:02.651306 INFO: Using score_cutoff 8.040796548843385 (fac=0.99, q=1)
1:15:02.652351 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:15:02.652638 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:15:02.652738 INFO: Updating optimization_manager: score_cutoff        : 9.065158681297303 -> 8.040796548843385
1:15:02.652843 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:15:02.889492 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:15:03.491987 INFO: === checking if optimization conditions were reached ===
1:15:03.493121 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
1:15:03.499470 INFO: Updating optimization_manager: rt_error            : 963.0491821864936 -> 873.9252465184693
1:15:03.500111 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 873.9252.
1:15:03.500203 INFO: ==============================================
1:15:03.500311 INFO: Starting optimization step 9.
1:15:03.500401 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:15:03.500523 INFO: Using rust extraction backend
1:15:03.500620 PROGRESS: Extracting batch of 250442 precursors
1:15:04.556950 INFO: === Search parameters used ===
1:15:04.558081 INFO: rt_error       : 873.9252465184693
1:15:04.558156 INFO: mobility_error : 0.1
1:15:04.558215 INFO: num_candidates : 3
1:15:04.558271 INFO: ms1_error      : 3
1:15:04.558318 INFO: ms2_error      : 10.0
1:15:04.558365 INFO: fwhm_rt        : 3.0
1:15:04.558408 INFO: quant_window   : 3
1:15:04.558492 INFO: ==============================================
1:15:09.545501 INFO: performing precursor FDR with 40 features
1:15:09.545735 INFO: Decoy channel: -1
1:15:09.545765 INFO: competitive: True
1:15:09.938209 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:10.419533 INFO: Estimating optimal hyperparameters - samples: 599,856, batch_size: 2,457, learning_rate: 7.75e-04
1:15:10.420891 INFO: Using random state 887166 for train-test-split
1:15:42.077998 INFO: Test AUC: 0.611
1:15:42.078487 INFO: Train AUC: 0.625
1:15:42.078544 INFO: AUC difference: 2.14%
1:15:42.952523 INFO: Resetting torch num_threads to 100
1:15:43.050696 PROGRESS: === Extracted 749820 precursors and 4049315 fragments ===
1:15:43.053254 INFO: === FDR correction performed with classifier version 11 ===
1:15:43.056339 PROGRESS: ============================= Precursor FDR =============================
1:15:43.056801 PROGRESS: Total precursors accumulated: 1,617
1:15:43.056880 PROGRESS: Target precursors: 1,601 (99.01%)
1:15:43.056937 PROGRESS: Decoy precursors: 16 (0.99%)
1:15:43.056990 PROGRESS: 
1:15:43.057041 PROGRESS: Precursor Summary:
1:15:43.060794 PROGRESS: Channel   0:	 0.050 FDR: 1,601; 0.010 FDR: 1,601; 0.001 FDR: 1,321
1:15:43.061308 PROGRESS: 
1:15:43.061378 PROGRESS: Protein Summary:
1:15:43.064467 PROGRESS: Channel   0:	 0.050 FDR: 1,388; 0.010 FDR: 1,388; 0.001 FDR: 1,141
1:15:43.064751 PROGRESS: =========================================================================
1:15:43.124668 INFO: Target number of precursors reached.
1:15:43.610244 INFO: fragments_df: keeping 5000 of 4049315 [sum(precursor_idx_mask)=36302 sum(mass_error_mask)=4049315 stop_rank=5000
1:15:44.831770 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:15:45.359440 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:15:46.676817 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:15:46.678294 INFO: Using score_cutoff 7.803652038574219 (fac=0.99, q=1)
1:15:46.679136 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:15:46.679242 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:15:46.679310 INFO: Updating optimization_manager: score_cutoff        : 8.040796548843385 -> 7.803652038574219
1:15:46.679389 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:15:46.895709 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:15:47.466962 INFO: === checking if optimization conditions were reached ===
1:15:47.468050 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
1:15:47.476174 INFO: Updating optimization_manager: rt_error            : 873.9252465184693 -> 1059.1436925655066
1:15:47.476970 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 1059.1437.
1:15:47.477238 INFO: ==============================================
1:15:47.477392 INFO: Starting optimization step 10.
1:15:47.477488 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:15:47.477609 INFO: Using rust extraction backend
1:15:47.477704 PROGRESS: Extracting batch of 250442 precursors
1:15:49.515152 INFO: === Search parameters used ===
1:15:49.516160 INFO: rt_error       : 1059.1436925655066
1:15:49.516267 INFO: mobility_error : 0.1
1:15:49.516320 INFO: num_candidates : 3
1:15:49.516368 INFO: ms1_error      : 3
1:15:49.516413 INFO: ms2_error      : 10.0
1:15:49.516466 INFO: fwhm_rt        : 3.0
1:15:49.516507 INFO: quant_window   : 3
1:15:49.516548 INFO: ==============================================
1:15:57.525543 INFO: performing precursor FDR with 40 features
1:15:57.525907 INFO: Decoy channel: -1
1:15:57.525939 INFO: competitive: True
1:15:58.269203 INFO: Setting torch num_threads to 2 for FDR classification task
1:15:59.760761 INFO: Estimating optimal hyperparameters - samples: 599,843, batch_size: 2,456, learning_rate: 7.74e-04
1:15:59.772663 INFO: Using random state 887166 for train-test-split
1:16:35.778648 INFO: Test AUC: 0.611
1:16:35.779185 INFO: Train AUC: 0.624
1:16:35.779241 INFO: AUC difference: 1.99%
1:16:36.680686 INFO: Resetting torch num_threads to 100
1:16:36.775722 PROGRESS: === Extracted 749804 precursors and 4048426 fragments ===
1:16:36.777193 INFO: === FDR correction performed with classifier version 11 ===
1:16:36.780142 PROGRESS: ============================= Precursor FDR =============================
1:16:36.780376 PROGRESS: Total precursors accumulated: 1,667
1:16:36.780454 PROGRESS: Target precursors: 1,651 (99.04%)
1:16:36.780515 PROGRESS: Decoy precursors: 16 (0.96%)
1:16:36.780585 PROGRESS: 
1:16:36.780637 PROGRESS: Precursor Summary:
1:16:36.782976 PROGRESS: Channel   0:	 0.050 FDR: 1,651; 0.010 FDR: 1,651; 0.001 FDR: 1,395
1:16:36.783222 PROGRESS: 
1:16:36.783296 PROGRESS: Protein Summary:
1:16:36.786037 PROGRESS: Channel   0:	 0.050 FDR: 1,395; 0.010 FDR: 1,395; 0.001 FDR: 1,178
1:16:36.786219 PROGRESS: =========================================================================
1:16:36.841378 INFO: Target number of precursors reached.
1:16:37.323461 INFO: fragments_df: keeping 5000 of 4048426 [sum(precursor_idx_mask)=38724 sum(mass_error_mask)=4048426 stop_rank=5000
1:16:38.542706 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:16:38.983345 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:16:39.937614 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:16:39.938970 INFO: Using score_cutoff 10.31772753238678 (fac=0.99, q=1)
1:16:39.940060 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:16:39.940279 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:16:39.940337 INFO: Updating optimization_manager: score_cutoff        : 7.803652038574219 -> 10.31772753238678
1:16:39.940406 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:16:40.157767 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:16:40.806171 INFO: === checking if optimization conditions were reached ===
1:16:40.806980 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
1:16:40.814665 INFO: Updating optimization_manager: rt_error            : 1059.1436925655066 -> 1148.71395545526
1:16:40.815506 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 1148.7140.
1:16:40.815705 INFO: ==============================================
1:16:40.815881 INFO: Starting optimization step 11.
1:16:40.816004 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:16:40.816136 INFO: Using rust extraction backend
1:16:40.816217 PROGRESS: Extracting batch of 250442 precursors
1:16:41.892302 INFO: === Search parameters used ===
1:16:41.893211 INFO: rt_error       : 1148.71395545526
1:16:41.893278 INFO: mobility_error : 0.1
1:16:41.893329 INFO: num_candidates : 3
1:16:41.893376 INFO: ms1_error      : 3
1:16:41.893463 INFO: ms2_error      : 10.0
1:16:41.893511 INFO: fwhm_rt        : 3.0
1:16:41.893556 INFO: quant_window   : 3
1:16:41.893612 INFO: ==============================================
1:16:49.398023 INFO: performing precursor FDR with 40 features
1:16:49.398418 INFO: Decoy channel: -1
1:16:49.398450 INFO: competitive: True
1:16:50.053408 INFO: Setting torch num_threads to 2 for FDR classification task
1:16:51.159480 INFO: Estimating optimal hyperparameters - samples: 599,824, batch_size: 2,456, learning_rate: 7.74e-04
1:16:51.167582 INFO: Using random state 887166 for train-test-split
1:17:22.212690 INFO: Test AUC: 0.613
1:17:22.213048 INFO: Train AUC: 0.624
1:17:22.213105 INFO: AUC difference: 1.79%
1:17:23.063480 INFO: Resetting torch num_threads to 100
1:17:23.158486 PROGRESS: === Extracted 749781 precursors and 4047757 fragments ===
1:17:23.159961 INFO: === FDR correction performed with classifier version 11 ===
1:17:23.162508 PROGRESS: ============================= Precursor FDR =============================
1:17:23.162704 PROGRESS: Total precursors accumulated: 1,673
1:17:23.162780 PROGRESS: Target precursors: 1,657 (99.04%)
1:17:23.162840 PROGRESS: Decoy precursors: 16 (0.96%)
1:17:23.162895 PROGRESS: 
1:17:23.162948 PROGRESS: Precursor Summary:
1:17:23.165741 PROGRESS: Channel   0:	 0.050 FDR: 1,657; 0.010 FDR: 1,657; 0.001 FDR: 1,328
1:17:23.165962 PROGRESS: 
1:17:23.166024 PROGRESS: Protein Summary:
1:17:23.168600 PROGRESS: Channel   0:	 0.050 FDR: 1,398; 0.010 FDR: 1,398; 0.001 FDR: 1,126
1:17:23.168772 PROGRESS: =========================================================================
1:17:23.230300 INFO: Target number of precursors reached.
1:17:23.712347 INFO: fragments_df: keeping 5000 of 4047757 [sum(precursor_idx_mask)=38381 sum(mass_error_mask)=4047757 stop_rank=5000
1:17:24.888696 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:17:25.500600 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:17:28.575154 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:17:28.577687 INFO: Using score_cutoff 9.399780165481568 (fac=0.99, q=1)
1:17:28.579389 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:17:28.579568 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:17:28.579676 INFO: Updating optimization_manager: score_cutoff        : 10.31772753238678 -> 9.399780165481568
1:17:28.579896 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:17:28.880532 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:17:29.522829 INFO: === checking if optimization conditions were reached ===
1:17:29.524039 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 5 ===
1:17:29.529853 INFO: Updating optimization_manager: rt_error            : 1148.71395545526 -> 868.5203649966311
1:17:29.530228 PROGRESS: ❌ rt_error       : optimization incomplete after 12 search(es). Will search with parameter 868.5204.
1:17:29.530317 INFO: ==============================================
1:17:29.530406 INFO: Starting optimization step 12.
1:17:29.530478 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:17:29.530577 INFO: Using rust extraction backend
1:17:29.530654 PROGRESS: Extracting batch of 250442 precursors
1:17:30.469721 INFO: === Search parameters used ===
1:17:30.470764 INFO: rt_error       : 868.5203649966311
1:17:30.470831 INFO: mobility_error : 0.1
1:17:30.470916 INFO: num_candidates : 3
1:17:30.470967 INFO: ms1_error      : 3
1:17:30.471012 INFO: ms2_error      : 10.0
1:17:30.471054 INFO: fwhm_rt        : 3.0
1:17:30.471098 INFO: quant_window   : 3
1:17:30.471140 INFO: ==============================================
1:17:38.176985 INFO: performing precursor FDR with 40 features
1:17:38.177556 INFO: Decoy channel: -1
1:17:38.177611 INFO: competitive: True
1:17:38.921088 INFO: Setting torch num_threads to 2 for FDR classification task
1:17:40.062751 INFO: Estimating optimal hyperparameters - samples: 599,845, batch_size: 2,456, learning_rate: 7.74e-04
1:17:40.068470 INFO: Using random state 887166 for train-test-split
1:18:10.035942 INFO: Test AUC: 0.614
1:18:10.036575 INFO: Train AUC: 0.624
1:18:10.036645 INFO: AUC difference: 1.65%
1:18:11.012977 INFO: Resetting torch num_threads to 100
1:18:11.104651 PROGRESS: === Extracted 749807 precursors and 4048960 fragments ===
1:18:11.106503 INFO: === FDR correction performed with classifier version 11 ===
1:18:11.109918 PROGRESS: ============================= Precursor FDR =============================
1:18:11.110358 PROGRESS: Total precursors accumulated: 1,803
1:18:11.110449 PROGRESS: Target precursors: 1,786 (99.06%)
1:18:11.110505 PROGRESS: Decoy precursors: 17 (0.94%)
1:18:11.110565 PROGRESS: 
1:18:11.110624 PROGRESS: Precursor Summary:
1:18:11.114477 PROGRESS: Channel   0:	 0.050 FDR: 1,786; 0.010 FDR: 1,786; 0.001 FDR: 1,298
1:18:11.115007 PROGRESS: 
1:18:11.115086 PROGRESS: Protein Summary:
1:18:11.118623 PROGRESS: Channel   0:	 0.050 FDR: 1,504; 0.010 FDR: 1,504; 0.001 FDR: 1,103
1:18:11.119125 PROGRESS: =========================================================================
1:18:11.186212 INFO: Target number of precursors reached.
1:18:11.663368 INFO: fragments_df: keeping 5000 of 4048960 [sum(precursor_idx_mask)=40931 sum(mass_error_mask)=4048960 stop_rank=5000
1:18:12.909697 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:18:13.428071 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:18:14.573607 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:18:14.575204 INFO: Using score_cutoff 9.073466091156005 (fac=0.99, q=1)
1:18:14.576634 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:18:14.576946 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:18:14.577021 INFO: Updating optimization_manager: score_cutoff        : 9.399780165481568 -> 9.073466091156005
1:18:14.577105 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:18:14.788470 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:18:15.372714 INFO: === checking if optimization conditions were reached ===
1:18:15.373547 PROGRESS: === Optimization of rt_error has been performed 13 time(s); minimum number is 5 ===
1:18:15.380097 INFO: Updating optimization_manager: rt_error            : 868.5203649966311 -> 1147.6308557988536
1:18:15.380498 PROGRESS: ❌ rt_error       : optimization incomplete after 13 search(es). Will search with parameter 1147.6309.
1:18:15.380630 INFO: ==============================================
1:18:15.380737 INFO: Starting optimization step 13.
1:18:15.380815 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:18:15.380945 INFO: Using rust extraction backend
1:18:15.381040 PROGRESS: Extracting batch of 250442 precursors
1:18:16.414777 INFO: === Search parameters used ===
1:18:16.415941 INFO: rt_error       : 1147.6308557988536
1:18:16.416019 INFO: mobility_error : 0.1
1:18:16.416077 INFO: num_candidates : 3
1:18:16.416123 INFO: ms1_error      : 3
1:18:16.416168 INFO: ms2_error      : 10.0
1:18:16.416210 INFO: fwhm_rt        : 3.0
1:18:16.416251 INFO: quant_window   : 3
1:18:16.416292 INFO: ==============================================
1:18:24.614614 INFO: performing precursor FDR with 40 features
1:18:24.614954 INFO: Decoy channel: -1
1:18:24.614984 INFO: competitive: True
1:18:25.365736 INFO: Setting torch num_threads to 2 for FDR classification task
1:18:26.565070 INFO: Estimating optimal hyperparameters - samples: 599,824, batch_size: 2,456, learning_rate: 7.74e-04
1:18:26.572200 INFO: Using random state 887166 for train-test-split
1:18:56.041747 INFO: Test AUC: 0.613
1:18:56.042215 INFO: Train AUC: 0.624
1:18:56.042272 INFO: AUC difference: 1.79%
1:18:56.870954 INFO: Resetting torch num_threads to 100
1:18:56.972506 PROGRESS: === Extracted 749781 precursors and 4047896 fragments ===
1:18:56.974385 INFO: === FDR correction performed with classifier version 11 ===
1:18:56.978112 PROGRESS: ============================= Precursor FDR =============================
1:18:56.978740 PROGRESS: Total precursors accumulated: 1,732
1:18:56.978817 PROGRESS: Target precursors: 1,715 (99.02%)
1:18:56.978892 PROGRESS: Decoy precursors: 17 (0.98%)
1:18:56.978957 PROGRESS: 
1:18:56.979025 PROGRESS: Precursor Summary:
1:18:56.983714 PROGRESS: Channel   0:	 0.050 FDR: 1,715; 0.010 FDR: 1,715; 0.001 FDR: 1,313
1:18:56.984435 PROGRESS: 
1:18:56.984524 PROGRESS: Protein Summary:
1:18:56.988583 PROGRESS: Channel   0:	 0.050 FDR: 1,438; 0.010 FDR: 1,438; 0.001 FDR: 1,114
1:18:56.989367 PROGRESS: =========================================================================
1:18:57.053292 INFO: Target number of precursors reached.
1:18:57.548595 INFO: fragments_df: keeping 5000 of 4047896 [sum(precursor_idx_mask)=40080 sum(mass_error_mask)=4047896 stop_rank=5000
1:18:58.780293 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:18:59.237122 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:19:00.106760 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:19:00.108391 INFO: Using score_cutoff 10.055159342193603 (fac=0.99, q=1)
1:19:00.109253 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:19:00.109353 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:19:00.109414 INFO: Updating optimization_manager: score_cutoff        : 9.073466091156005 -> 10.055159342193603
1:19:00.109497 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:19:00.323992 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:19:00.850857 INFO: === checking if optimization conditions were reached ===
1:19:00.852133 PROGRESS: === Optimization of rt_error has been performed 14 time(s); minimum number is 5 ===
1:19:00.861616 INFO: Updating optimization_manager: rt_error            : 1147.6308557988536 -> 1033.1101806564948
1:19:00.862859 PROGRESS: ❌ rt_error       : optimization incomplete after 14 search(es). Will search with parameter 1033.1102.
1:19:00.862983 INFO: ==============================================
1:19:00.863116 INFO: Starting optimization step 14.
1:19:00.863217 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:19:00.863415 INFO: Using rust extraction backend
1:19:00.863572 PROGRESS: Extracting batch of 250442 precursors
1:19:02.019434 INFO: === Search parameters used ===
1:19:02.020624 INFO: rt_error       : 1033.1101806564948
1:19:02.020781 INFO: mobility_error : 0.1
1:19:02.020875 INFO: num_candidates : 3
1:19:02.020950 INFO: ms1_error      : 3
1:19:02.021004 INFO: ms2_error      : 10.0
1:19:02.021061 INFO: fwhm_rt        : 3.0
1:19:02.021117 INFO: quant_window   : 3
1:19:02.021162 INFO: ==============================================
1:19:23.928530 INFO: performing precursor FDR with 40 features
1:19:23.928686 INFO: Decoy channel: -1
1:19:23.928724 INFO: competitive: True
1:19:27.481063 INFO: Setting torch num_threads to 2 for FDR classification task
1:19:34.236520 INFO: Estimating optimal hyperparameters - samples: 599,839, batch_size: 2,456, learning_rate: 7.74e-04
1:19:34.237880 INFO: Using random state 887166 for train-test-split
1:21:03.230136 INFO: Test AUC: 0.611
1:21:03.230687 INFO: Train AUC: 0.624
1:21:03.230745 INFO: AUC difference: 2.10%
1:21:03.992194 INFO: Resetting torch num_threads to 100
1:21:04.080849 PROGRESS: === Extracted 749799 precursors and 4048347 fragments ===
1:21:04.082391 INFO: === FDR correction performed with classifier version 11 ===
1:21:04.085009 PROGRESS: ============================= Precursor FDR =============================
1:21:04.085249 PROGRESS: Total precursors accumulated: 1,778
1:21:04.085319 PROGRESS: Target precursors: 1,761 (99.04%)
1:21:04.085373 PROGRESS: Decoy precursors: 17 (0.96%)
1:21:04.085423 PROGRESS: 
1:21:04.085471 PROGRESS: Precursor Summary:
1:21:04.088144 PROGRESS: Channel   0:	 0.050 FDR: 1,761; 0.010 FDR: 1,761; 0.001 FDR: 1,361
1:21:04.088373 PROGRESS: 
1:21:04.088435 PROGRESS: Protein Summary:
1:21:04.091079 PROGRESS: Channel   0:	 0.050 FDR: 1,488; 0.010 FDR: 1,488; 0.001 FDR: 1,150
1:21:04.091338 PROGRESS: =========================================================================
1:21:04.148709 INFO: Target number of precursors reached.
1:21:04.703551 INFO: fragments_df: keeping 5000 of 4048347 [sum(precursor_idx_mask)=40727 sum(mass_error_mask)=4048347 stop_rank=5000
1:21:06.103255 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:21:06.733171 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:21:07.771755 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:21:07.773161 INFO: Using score_cutoff 8.982335666656494 (fac=0.99, q=1)
1:21:07.773845 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:21:07.773944 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:21:07.774002 INFO: Updating optimization_manager: score_cutoff        : 10.055159342193603 -> 8.982335666656494
1:21:07.774088 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:21:07.989217 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:21:08.576936 INFO: === checking if optimization conditions were reached ===
1:21:08.577963 PROGRESS: === Optimization of rt_error has been performed 15 time(s); minimum number is 5 ===
1:21:08.584506 INFO: Updating optimization_manager: rt_error            : 1033.1101806564948 -> 925.8374266832326
1:21:08.584965 PROGRESS: ❌ rt_error       : optimization incomplete after 15 search(es). Will search with parameter 925.8374.
1:21:08.585073 INFO: ==============================================
1:21:08.585164 INFO: Starting optimization step 15.
1:21:08.585242 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:21:08.585396 INFO: Using rust extraction backend
1:21:08.585497 PROGRESS: Extracting batch of 250442 precursors
1:21:09.672662 INFO: === Search parameters used ===
1:21:09.673679 INFO: rt_error       : 925.8374266832326
1:21:09.673847 INFO: mobility_error : 0.1
1:21:09.673909 INFO: num_candidates : 3
1:21:09.673955 INFO: ms1_error      : 3
1:21:09.674002 INFO: ms2_error      : 10.0
1:21:09.674046 INFO: fwhm_rt        : 3.0
1:21:09.674088 INFO: quant_window   : 3
1:21:09.674129 INFO: ==============================================
1:21:17.892625 INFO: performing precursor FDR with 40 features
1:21:17.893030 INFO: Decoy channel: -1
1:21:17.893064 INFO: competitive: True
1:21:18.613972 INFO: Setting torch num_threads to 2 for FDR classification task
1:21:19.757312 INFO: Estimating optimal hyperparameters - samples: 599,840, batch_size: 2,456, learning_rate: 7.74e-04
1:21:19.766406 INFO: Using random state 887166 for train-test-split
1:21:47.671436 INFO: Test AUC: 0.612
1:21:47.671940 INFO: Train AUC: 0.624
1:21:47.671994 INFO: AUC difference: 2.03%
1:21:48.496068 INFO: Resetting torch num_threads to 100
1:21:48.583664 PROGRESS: === Extracted 749801 precursors and 4048597 fragments ===
1:21:48.585409 INFO: === FDR correction performed with classifier version 11 ===
1:21:48.587993 PROGRESS: ============================= Precursor FDR =============================
1:21:48.588231 PROGRESS: Total precursors accumulated: 1,837
1:21:48.588309 PROGRESS: Target precursors: 1,819 (99.02%)
1:21:48.588365 PROGRESS: Decoy precursors: 18 (0.98%)
1:21:48.588417 PROGRESS: 
1:21:48.588466 PROGRESS: Precursor Summary:
1:21:48.590930 PROGRESS: Channel   0:	 0.050 FDR: 1,819; 0.010 FDR: 1,819; 0.001 FDR: 1,244
1:21:48.591080 PROGRESS: 
1:21:48.591168 PROGRESS: Protein Summary:
1:21:48.593912 PROGRESS: Channel   0:	 0.050 FDR: 1,550; 0.010 FDR: 1,550; 0.001 FDR: 1,065
1:21:48.594086 PROGRESS: =========================================================================
1:21:48.660218 INFO: Target number of precursors reached.
1:21:49.146254 INFO: fragments_df: keeping 5000 of 4048597 [sum(precursor_idx_mask)=41264 sum(mass_error_mask)=4048597 stop_rank=5000
1:21:50.345015 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:21:51.075592 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:21:52.072597 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:21:52.074082 INFO: Using score_cutoff 8.176788576507569 (fac=0.99, q=1)
1:21:52.075222 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:21:52.075557 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:21:52.075651 INFO: Updating optimization_manager: score_cutoff        : 8.982335666656494 -> 8.176788576507569
1:21:52.075739 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:21:52.304293 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:21:52.914062 INFO: === checking if optimization conditions were reached ===
1:21:52.914889 PROGRESS: === Optimization of rt_error has been performed 16 time(s); minimum number is 5 ===
1:21:52.922609 INFO: Updating optimization_manager: rt_error            : 925.8374266832326 -> 1130.5911546203124
1:21:52.923456 PROGRESS: ❌ rt_error       : optimization incomplete after 16 search(es). Will search with parameter 1130.5912.
1:21:52.923605 INFO: ==============================================
1:21:52.923744 INFO: Starting optimization step 16.
1:21:52.923862 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:21:52.924003 INFO: Using rust extraction backend
1:21:52.924101 PROGRESS: Extracting batch of 250442 precursors
1:21:53.985065 INFO: === Search parameters used ===
1:21:53.986661 INFO: rt_error       : 1130.5911546203124
1:21:53.986734 INFO: mobility_error : 0.1
1:21:53.986784 INFO: num_candidates : 3
1:21:53.986831 INFO: ms1_error      : 3
1:21:53.986874 INFO: ms2_error      : 10.0
1:21:53.986915 INFO: fwhm_rt        : 3.0
1:21:53.986963 INFO: quant_window   : 3
1:21:53.987009 INFO: ==============================================
1:21:57.635257 INFO: performing precursor FDR with 40 features
1:21:57.635444 INFO: Decoy channel: -1
1:21:57.635479 INFO: competitive: True
1:21:57.885613 INFO: Setting torch num_threads to 2 for FDR classification task
1:21:58.320847 INFO: Estimating optimal hyperparameters - samples: 599,828, batch_size: 2,456, learning_rate: 7.74e-04
1:21:58.322446 INFO: Using random state 887166 for train-test-split
1:22:23.367872 INFO: Test AUC: 0.612
1:22:23.368479 INFO: Train AUC: 0.624
1:22:23.368541 INFO: AUC difference: 1.87%
1:22:24.189267 INFO: Resetting torch num_threads to 100
1:22:24.315650 PROGRESS: === Extracted 749786 precursors and 4048197 fragments ===
1:22:24.317187 INFO: === FDR correction performed with classifier version 11 ===
1:22:24.319537 PROGRESS: ============================= Precursor FDR =============================
1:22:24.319760 PROGRESS: Total precursors accumulated: 1,780
1:22:24.319852 PROGRESS: Target precursors: 1,763 (99.04%)
1:22:24.319920 PROGRESS: Decoy precursors: 17 (0.96%)
1:22:24.319980 PROGRESS: 
1:22:24.320030 PROGRESS: Precursor Summary:
1:22:24.322609 PROGRESS: Channel   0:	 0.050 FDR: 1,763; 0.010 FDR: 1,763; 0.001 FDR: 1,366
1:22:24.322871 PROGRESS: 
1:22:24.322947 PROGRESS: Protein Summary:
1:22:24.326020 PROGRESS: Channel   0:	 0.050 FDR: 1,516; 0.010 FDR: 1,516; 0.001 FDR: 1,176
1:22:24.326281 PROGRESS: =========================================================================
1:22:24.390699 INFO: Target number of precursors reached.
1:22:24.871581 INFO: fragments_df: keeping 5000 of 4048197 [sum(precursor_idx_mask)=38970 sum(mass_error_mask)=4048197 stop_rank=5000
1:22:26.176422 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:22:26.722395 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:22:27.714182 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:22:27.715662 INFO: Using score_cutoff 7.709992307281493 (fac=0.99, q=1)
1:22:27.716924 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:22:27.717203 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:22:27.717322 INFO: Updating optimization_manager: score_cutoff        : 8.176788576507569 -> 7.709992307281493
1:22:27.717417 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:22:27.915250 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:22:28.416196 INFO: === checking if optimization conditions were reached ===
1:22:28.417434 PROGRESS: === Optimization of rt_error has been performed 17 time(s); minimum number is 5 ===
1:22:28.425841 INFO: Updating optimization_manager: rt_error            : 1130.5911546203124 -> 1199.3969369337428
1:22:28.426486 PROGRESS: ❌ rt_error       : optimization incomplete after 17 search(es). Will search with parameter 1199.3969.
1:22:28.426576 INFO: ==============================================
1:22:28.426679 INFO: Starting optimization step 17.
1:22:28.426766 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:22:28.426877 INFO: Using rust extraction backend
1:22:28.426971 PROGRESS: Extracting batch of 250442 precursors
1:22:29.642042 INFO: === Search parameters used ===
1:22:29.643026 INFO: rt_error       : 1199.3969369337428
1:22:29.643213 INFO: mobility_error : 0.1
1:22:29.643284 INFO: num_candidates : 3
1:22:29.643338 INFO: ms1_error      : 3
1:22:29.643398 INFO: ms2_error      : 10.0
1:22:29.643451 INFO: fwhm_rt        : 3.0
1:22:29.643495 INFO: quant_window   : 3
1:22:29.643541 INFO: ==============================================
1:22:38.218653 INFO: performing precursor FDR with 40 features
1:22:38.219008 INFO: Decoy channel: -1
1:22:38.219043 INFO: competitive: True
1:22:38.979132 INFO: Setting torch num_threads to 2 for FDR classification task
1:22:40.124809 INFO: Estimating optimal hyperparameters - samples: 599,812, batch_size: 2,456, learning_rate: 7.74e-04
1:22:40.131677 INFO: Using random state 887166 for train-test-split
1:23:09.788738 INFO: Test AUC: 0.614
1:23:09.789243 INFO: Train AUC: 0.624
1:23:09.789304 INFO: AUC difference: 1.74%
1:23:10.574755 INFO: Resetting torch num_threads to 100
1:23:10.677979 PROGRESS: === Extracted 749766 precursors and 4047776 fragments ===
1:23:10.679787 INFO: === FDR correction performed with classifier version 11 ===
1:23:10.682377 PROGRESS: ============================= Precursor FDR =============================
1:23:10.682622 PROGRESS: Total precursors accumulated: 1,789
1:23:10.682695 PROGRESS: Target precursors: 1,772 (99.05%)
1:23:10.682754 PROGRESS: Decoy precursors: 17 (0.95%)
1:23:10.682814 PROGRESS: 
1:23:10.682893 PROGRESS: Precursor Summary:
1:23:10.685150 PROGRESS: Channel   0:	 0.050 FDR: 1,772; 0.010 FDR: 1,772; 0.001 FDR: 1,242
1:23:10.685332 PROGRESS: 
1:23:10.685394 PROGRESS: Protein Summary:
1:23:10.688126 PROGRESS: Channel   0:	 0.050 FDR: 1,486; 0.010 FDR: 1,486; 0.001 FDR: 1,056
1:23:10.688287 PROGRESS: =========================================================================
1:23:10.746985 INFO: Target number of precursors reached.
1:23:11.229400 INFO: fragments_df: keeping 5000 of 4047776 [sum(precursor_idx_mask)=41293 sum(mass_error_mask)=4047776 stop_rank=5000
1:23:12.550064 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:23:13.037647 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:23:14.020341 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:23:14.022140 INFO: Using score_cutoff 9.878043013858795 (fac=0.99, q=1)
1:23:14.022813 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:23:14.022910 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:23:14.022966 INFO: Updating optimization_manager: score_cutoff        : 7.709992307281493 -> 9.878043013858795
1:23:14.023039 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:23:14.245684 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:23:14.838811 INFO: === checking if optimization conditions were reached ===
1:23:14.839694 PROGRESS: === Optimization of rt_error has been performed 18 time(s); minimum number is 5 ===
1:23:14.846382 INFO: Updating optimization_manager: rt_error            : 1199.3969369337428 -> 966.3149021959559
1:23:14.847068 PROGRESS: ❌ rt_error       : optimization incomplete after 18 search(es). Will search with parameter 966.3149.
1:23:14.847186 INFO: ==============================================
1:23:14.847311 INFO: Starting optimization step 18.
1:23:14.847409 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:23:14.847598 INFO: Using rust extraction backend
1:23:14.847712 PROGRESS: Extracting batch of 250442 precursors
1:23:15.979216 INFO: === Search parameters used ===
1:23:15.980184 INFO: rt_error       : 966.3149021959559
1:23:15.980259 INFO: mobility_error : 0.1
1:23:15.980314 INFO: num_candidates : 3
1:23:15.980366 INFO: ms1_error      : 3
1:23:15.980420 INFO: ms2_error      : 10.0
1:23:15.980467 INFO: fwhm_rt        : 3.0
1:23:15.980525 INFO: quant_window   : 3
1:23:15.980639 INFO: ==============================================
1:23:24.283594 INFO: performing precursor FDR with 40 features
1:23:24.284190 INFO: Decoy channel: -1
1:23:24.284230 INFO: competitive: True
1:23:25.037180 INFO: Setting torch num_threads to 2 for FDR classification task
1:23:26.746377 INFO: Estimating optimal hyperparameters - samples: 599,849, batch_size: 2,456, learning_rate: 7.74e-04
1:23:26.747629 INFO: Using random state 887166 for train-test-split
1:36:42.098978 INFO: Test AUC: 0.612
1:36:42.100314 INFO: Train AUC: 0.624
1:36:42.100607 INFO: AUC difference: 1.91%
1:36:44.034307 INFO: Resetting torch num_threads to 100
1:36:44.141637 PROGRESS: === Extracted 749812 precursors and 4048760 fragments ===
1:36:44.143063 INFO: === FDR correction performed with classifier version 11 ===
1:36:44.145355 PROGRESS: ============================= Precursor FDR =============================
1:36:44.145548 PROGRESS: Total precursors accumulated: 1,821
1:36:44.145654 PROGRESS: Target precursors: 1,803 (99.01%)
1:36:44.145720 PROGRESS: Decoy precursors: 18 (0.99%)
1:36:44.145769 PROGRESS: 
1:36:44.145818 PROGRESS: Precursor Summary:
1:36:44.148989 PROGRESS: Channel   0:	 0.050 FDR: 1,803; 0.010 FDR: 1,803; 0.001 FDR: 1,281
1:36:44.149170 PROGRESS: 
1:36:44.149229 PROGRESS: Protein Summary:
1:36:44.151768 PROGRESS: Channel   0:	 0.050 FDR: 1,516; 0.010 FDR: 1,516; 0.001 FDR: 1,084
1:36:44.152014 PROGRESS: =========================================================================
1:36:44.212072 INFO: Target number of precursors reached.
1:36:44.696971 INFO: fragments_df: keeping 5000 of 4048760 [sum(precursor_idx_mask)=41569 sum(mass_error_mask)=4048760 stop_rank=5000
1:36:46.157659 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:36:47.474553 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:36:48.802207 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:36:48.803694 INFO: Using score_cutoff 9.411239389801025 (fac=0.99, q=1)
1:36:48.804848 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:36:48.805133 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:36:48.805218 INFO: Updating optimization_manager: score_cutoff        : 9.878043013858795 -> 9.411239389801025
1:36:48.805308 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:36:49.011175 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:36:49.496631 INFO: === checking if optimization conditions were reached ===
1:36:49.497494 PROGRESS: === Optimization of rt_error has been performed 19 time(s); minimum number is 5 ===
1:36:49.503049 INFO: Updating optimization_manager: rt_error            : 966.3149021959559 -> 914.1652949445936
1:36:49.503301 PROGRESS: ❌ rt_error       : optimization incomplete after 19 search(es). Will search with parameter 914.1653.
1:36:49.503402 INFO: ==============================================
1:36:49.503499 INFO: Starting optimization step 19.
1:36:49.503569 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:36:49.503682 INFO: Using rust extraction backend
1:36:49.503773 PROGRESS: Extracting batch of 250442 precursors
1:36:50.690198 INFO: === Search parameters used ===
1:36:50.690992 INFO: rt_error       : 914.1652949445936
1:36:50.691066 INFO: mobility_error : 0.1
1:36:50.691124 INFO: num_candidates : 3
1:36:50.691180 INFO: ms1_error      : 3
1:36:50.691234 INFO: ms2_error      : 10.0
1:36:50.691286 INFO: fwhm_rt        : 3.0
1:36:50.691343 INFO: quant_window   : 3
1:36:50.691393 INFO: ==============================================
1:37:01.985358 INFO: performing precursor FDR with 40 features
1:37:01.985749 INFO: Decoy channel: -1
1:37:01.985780 INFO: competitive: True
1:37:02.963312 INFO: Setting torch num_threads to 2 for FDR classification task
1:37:05.063491 INFO: Estimating optimal hyperparameters - samples: 599,838, batch_size: 2,456, learning_rate: 7.74e-04
1:37:05.076148 INFO: Using random state 887166 for train-test-split
1:37:56.162291 INFO: Test AUC: 0.611
1:37:56.162817 INFO: Train AUC: 0.624
1:37:56.162915 INFO: AUC difference: 1.94%
1:37:56.990133 INFO: Resetting torch num_threads to 100
1:37:57.076489 PROGRESS: === Extracted 749798 precursors and 4048649 fragments ===
1:37:57.077947 INFO: === FDR correction performed with classifier version 11 ===
1:37:57.080514 PROGRESS: ============================= Precursor FDR =============================
1:37:57.080775 PROGRESS: Total precursors accumulated: 1,780
1:37:57.080850 PROGRESS: Target precursors: 1,763 (99.04%)
1:37:57.080903 PROGRESS: Decoy precursors: 17 (0.96%)
1:37:57.080950 PROGRESS: 
1:37:57.080994 PROGRESS: Precursor Summary:
1:37:57.083374 PROGRESS: Channel   0:	 0.050 FDR: 1,763; 0.010 FDR: 1,763; 0.001 FDR: 1,309
1:37:57.083598 PROGRESS: 
1:37:57.083657 PROGRESS: Protein Summary:
1:37:57.086248 PROGRESS: Channel   0:	 0.050 FDR: 1,499; 0.010 FDR: 1,499; 0.001 FDR: 1,117
1:37:57.086463 PROGRESS: =========================================================================
1:37:57.141199 INFO: Target number of precursors reached.
1:37:57.620394 INFO: fragments_df: keeping 5000 of 4048649 [sum(precursor_idx_mask)=40181 sum(mass_error_mask)=4048649 stop_rank=5000
1:37:58.850893 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:37:59.433777 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:38:00.750190 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:38:00.752212 INFO: Using score_cutoff 8.220142240905762 (fac=0.99, q=1)
1:38:00.753247 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:38:00.753363 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:38:00.753428 INFO: Updating optimization_manager: score_cutoff        : 9.411239389801025 -> 8.220142240905762
1:38:00.753518 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:38:00.997935 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:38:01.525495 INFO: === checking if optimization conditions were reached ===
1:38:01.526577 PROGRESS: === Optimization of rt_error has been performed 20 time(s); minimum number is 5 ===
1:38:01.534923 INFO: Updating optimization_manager: rt_error            : 914.1652949445936 -> 1121.945684586382
1:38:01.535526 PROGRESS: ❌ rt_error       : optimization incomplete after 20 search(es). Will search with parameter 1121.9457.
1:38:01.535733 INFO: ==============================================
1:38:01.535857 WARNING: Optimization did not converge within the maximum number of steps, which is 20.
1:38:01.535975 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:38:01.536036 PROGRESS: ==============================================
1:38:01.536105 PROGRESS: ms2_error      : 10.0000
1:38:01.536168 PROGRESS: rt_error       : 1121.9457
1:38:01.536216 PROGRESS: ==============================================
1:38:01.540677 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:38:14.319330 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:39:00.806597 INFO: Using rust extraction backend
1:39:00.807096 PROGRESS: Extracting batch of 11997144 precursors
1:39:19.159543 INFO: === Search parameters used ===
1:39:19.160217 INFO: rt_error       : 1121.945684586382
1:39:19.160305 INFO: mobility_error : 0.1
1:39:19.160393 INFO: num_candidates : 3
1:39:19.160452 INFO: ms1_error      : 3
1:39:19.160514 INFO: ms2_error      : 10.0
1:39:19.160569 INFO: fwhm_rt        : 3.0
1:39:19.160622 INFO: quant_window   : 3
1:39:19.160680 INFO: ==============================================
1:40:27.908010 INFO: Removed 3389722 precursors with score below cutoff 8.220142240905762
1:41:05.397885 INFO: performing precursor FDR with 40 features
1:41:05.398163 INFO: Decoy channel: -1
1:41:05.398204 INFO: competitive: True
1:41:09.474068 INFO: Setting torch num_threads to 2 for FDR classification task
1:41:32.837618 INFO: Estimating optimal hyperparameters - samples: 26,081,210, batch_size: 4,096, learning_rate: 1.00e-03
1:41:32.933738 INFO: Using random state 887166 for train-test-split
1:51:21.248661 INFO: Test AUC: 0.621
1:51:21.248958 INFO: Train AUC: 0.622
1:51:21.249004 INFO: AUC difference: 0.12%
1:51:29.704170 INFO: Resetting torch num_threads to 100
1:51:32.770705 PROGRESS: ============================= Precursor FDR =============================
1:51:32.771115 PROGRESS: Total precursors accumulated: 94,160
1:51:32.771214 PROGRESS: Target precursors: 93,228 (99.01%)
1:51:32.771286 PROGRESS: Decoy precursors: 932 (0.99%)
1:51:32.771351 PROGRESS: 
1:51:32.771420 PROGRESS: Precursor Summary:
1:51:32.804799 PROGRESS: Channel   0:	 0.050 FDR: 93,228; 0.010 FDR: 93,228; 0.001 FDR: 60,361
1:51:32.805034 PROGRESS: 
1:51:32.805106 PROGRESS: Protein Summary:
1:51:32.863542 PROGRESS: Channel   0:	 0.050 FDR: 13,836; 0.010 FDR: 13,836; 0.001 FDR: 9,075
1:51:32.863846 PROGRESS: =========================================================================
1:51:33.092572 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/psm.parquet
1:51:33.308190 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.parquet
1:51:33.610844 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
1:51:34.388539 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 
1:51:34.388728 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
1:51:34.388842 INFO: Initializing TimingManager
1:51:34.389852 INFO: Initializing RawFileManager
1:51:54.513518 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
1:51:54.527299 INFO: Determining DIA cycle
1:51:54.546723 INFO: Found cycle with start 0.00 min and length 300.
1:51:54.758406 INFO: RT (min)            : 0.0 - 26.9
1:51:54.758525 INFO: RT duration (sec)   : 1611.2
1:51:54.758563 INFO: RT duration (min)   : 26.9
1:51:54.758592 INFO: Cycle len (scans)   : 300
1:51:54.758619 INFO: Cycle len (sec)     : 1.65
1:51:54.758643 INFO: Number of cycles    : 977
1:51:54.758667 INFO: MS2 range (m/z)     : 380.4 - 980.7
1:51:54.758710 INFO: Creating DIA data object took: 20.36873698234558
1:51:56.323625 INFO: Creating DIA data NG object took: 1.5647470951080322
1:51:58.055722 INFO: Initializing CalibrationManager
1:51:58.056059 INFO: Setting up calibration estimators ..
1:51:58.056136 INFO: Found 1 estimator(s) in calibration group 'fragment'
1:51:58.056227 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
1:51:58.056306 INFO: Found 3 estimator(s) in calibration group 'precursor'
1:51:58.056377 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
1:51:58.056441 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
1:51:58.056514 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
1:51:58.056574 INFO: Done setting up calibration estimators.
1:51:58.056819 INFO: Initializing OptimizationManager
1:51:58.056994 INFO: initial parameter: ms1_error = 3
1:51:58.057056 INFO: initial parameter: ms2_error = 10
1:51:58.057118 INFO: initial parameter: rt_error = 805.6002197265625
1:51:58.057174 INFO: initial parameter: mobility_error = 0.1
1:51:58.057225 INFO: initial parameter: num_candidates = 1
1:51:58.057274 INFO: initial parameter: fwhm_rt = 5
1:51:58.057333 INFO: initial parameter: fwhm_mobility = 0.01
1:51:58.057383 INFO: initial parameter: score_cutoff = 0
1:51:58.057441 INFO: initial parameter: classifier_version = -1
1:51:58.057531 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
1:51:58.057867 INFO: FDRManager: loading saved state not requested, will be initialized.
1:51:58.057909 INFO: Initializing FDRManager
1:51:58.057957 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
1:51:59.831034 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
1:52:01.074084 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
1:52:01.074778 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
1:52:01.074942 PROGRESS: Starting initial search for precursors.
1:52:01.075074 INFO: Starting optimization step 0.
1:52:01.075162 PROGRESS: === Extracting elution groups 0 to 1000 ===
1:52:01.075252 INFO: Using rust extraction backend
1:52:01.075344 PROGRESS: Extracting batch of 1970 precursors
1:52:01.081120 INFO: === Search parameters used ===
1:52:01.081330 INFO: rt_error       : 805.6002197265625
1:52:01.081404 INFO: mobility_error : 0.1
1:52:01.081471 INFO: num_candidates : 1
1:52:01.081534 INFO: ms1_error      : 3
1:52:01.081594 INFO: ms2_error      : 10
1:52:01.081651 INFO: fwhm_rt        : 5
1:52:01.081710 INFO: quant_window   : 3
1:52:01.081767 INFO: ==============================================
1:52:01.169038 INFO: performing precursor FDR with 40 features
1:52:01.169161 INFO: Decoy channel: -1
1:52:01.169193 INFO: competitive: True
1:52:01.171043 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:01.173444 INFO: Estimating optimal hyperparameters - samples: 1,572, batch_size: 128, learning_rate: 1.77e-04
1:52:01.174778 INFO: Using random state 147895 for train-test-split
1:52:01.372436 INFO: Test AUC: 0.495
1:52:01.372541 INFO: Train AUC: 0.612
1:52:01.372576 INFO: AUC difference: 19.17%
1:52:01.372604 WARNING: AUC difference > 5%. This may indicate overfitting.
1:52:01.726206 INFO: Resetting torch num_threads to 100
1:52:01.728308 PROGRESS: === Extracted 1965 precursors and 11111 fragments ===
1:52:01.728757 INFO: === FDR correction performed with classifier version -1 ===
1:52:01.729388 PROGRESS: ============================= Precursor FDR =============================
1:52:01.729489 PROGRESS: Total precursors accumulated: 15
1:52:01.729569 PROGRESS: Target precursors: 15 (100.00%)
1:52:01.729635 PROGRESS: Decoy precursors: 0 (0.00%)
1:52:01.729692 PROGRESS: 
1:52:01.729755 PROGRESS: Precursor Summary:
1:52:01.731164 PROGRESS: Channel   0:	 0.050 FDR:    15; 0.010 FDR:    15; 0.001 FDR:    15
1:52:01.731265 PROGRESS: 
1:52:01.731329 PROGRESS: Protein Summary:
1:52:01.732860 PROGRESS: Channel   0:	 0.050 FDR:    14; 0.010 FDR:    14; 0.001 FDR:    14
1:52:01.732961 PROGRESS: =========================================================================
1:52:01.733296 INFO: Target number of precursors not reached yet.
1:52:01.832301 INFO: Starting optimization step 1.
1:52:01.832581 PROGRESS: === Extracting elution groups 1000 to 3000 ===
1:52:01.832684 INFO: Using rust extraction backend
1:52:01.832758 PROGRESS: Extracting batch of 3935 precursors
1:52:01.841783 INFO: === Search parameters used ===
1:52:01.842015 INFO: rt_error       : 805.6002197265625
1:52:01.842079 INFO: mobility_error : 0.1
1:52:01.842144 INFO: num_candidates : 1
1:52:01.842198 INFO: ms1_error      : 3
1:52:01.842249 INFO: ms2_error      : 10
1:52:01.842302 INFO: fwhm_rt        : 5
1:52:01.842360 INFO: quant_window   : 3
1:52:01.842412 INFO: ==============================================
1:52:01.999371 INFO: performing precursor FDR with 40 features
1:52:01.999492 INFO: Decoy channel: -1
1:52:01.999524 INFO: competitive: True
1:52:02.005432 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:02.008607 INFO: Estimating optimal hyperparameters - samples: 4,713, batch_size: 128, learning_rate: 1.77e-04
1:52:02.008716 INFO: Using random state 103920 for train-test-split
1:52:02.588639 INFO: Test AUC: 0.532
1:52:02.588772 INFO: Train AUC: 0.590
1:52:02.588810 INFO: AUC difference: 9.71%
1:52:02.588838 WARNING: AUC difference > 5%. This may indicate overfitting.
1:52:02.933083 INFO: Resetting torch num_threads to 100
1:52:02.937403 PROGRESS: === Extracted 5892 precursors and 33166 fragments ===
1:52:02.937893 INFO: === FDR correction performed with classifier version -1 ===
1:52:02.938519 PROGRESS: ============================= Precursor FDR =============================
1:52:02.938622 PROGRESS: Total precursors accumulated: 19
1:52:02.938697 PROGRESS: Target precursors: 19 (100.00%)
1:52:02.938758 PROGRESS: Decoy precursors: 0 (0.00%)
1:52:02.938811 PROGRESS: 
1:52:02.938870 PROGRESS: Precursor Summary:
1:52:02.940279 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
1:52:02.940379 PROGRESS: 
1:52:02.940445 PROGRESS: Protein Summary:
1:52:02.942008 PROGRESS: Channel   0:	 0.050 FDR:    18; 0.010 FDR:    18; 0.001 FDR:    18
1:52:02.942107 PROGRESS: =========================================================================
1:52:02.942511 INFO: Target number of precursors not reached yet.
1:52:03.048641 INFO: Starting optimization step 2.
1:52:03.048931 PROGRESS: === Extracting elution groups 3000 to 7000 ===
1:52:03.049027 INFO: Using rust extraction backend
1:52:03.049098 PROGRESS: Extracting batch of 7881 precursors
1:52:03.065530 INFO: === Search parameters used ===
1:52:03.065798 INFO: rt_error       : 805.6002197265625
1:52:03.065895 INFO: mobility_error : 0.1
1:52:03.065952 INFO: num_candidates : 1
1:52:03.066005 INFO: ms1_error      : 3
1:52:03.066061 INFO: ms2_error      : 10
1:52:03.066111 INFO: fwhm_rt        : 5
1:52:03.066160 INFO: quant_window   : 3
1:52:03.066214 INFO: ==============================================
1:52:03.242741 INFO: performing precursor FDR with 40 features
1:52:03.242872 INFO: Decoy channel: -1
1:52:03.242904 INFO: competitive: True
1:52:03.253854 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:03.258859 INFO: Estimating optimal hyperparameters - samples: 11,010, batch_size: 128, learning_rate: 1.77e-04
1:52:03.259046 INFO: Using random state 181544 for train-test-split
1:52:04.606806 INFO: Test AUC: 0.546
1:52:04.606945 INFO: Train AUC: 0.599
1:52:04.606987 INFO: AUC difference: 8.91%
1:52:04.607019 WARNING: AUC difference > 5%. This may indicate overfitting.
1:52:04.932478 INFO: Resetting torch num_threads to 100
1:52:04.938036 PROGRESS: === Extracted 13763 precursors and 77052 fragments ===
1:52:04.938521 INFO: === FDR correction performed with classifier version -1 ===
1:52:04.939098 PROGRESS: ============================= Precursor FDR =============================
1:52:04.939193 PROGRESS: Total precursors accumulated: 54
1:52:04.939253 PROGRESS: Target precursors: 54 (100.00%)
1:52:04.939305 PROGRESS: Decoy precursors: 0 (0.00%)
1:52:04.939353 PROGRESS: 
1:52:04.939399 PROGRESS: Precursor Summary:
1:52:04.940533 PROGRESS: Channel   0:	 0.050 FDR:    54; 0.010 FDR:    54; 0.001 FDR:    54
1:52:04.940635 PROGRESS: 
1:52:04.940695 PROGRESS: Protein Summary:
1:52:04.941912 PROGRESS: Channel   0:	 0.050 FDR:    52; 0.010 FDR:    52; 0.001 FDR:    52
1:52:04.942000 PROGRESS: =========================================================================
1:52:04.942379 INFO: Target number of precursors not reached yet.
1:52:05.052185 INFO: Starting optimization step 3.
1:52:05.052438 PROGRESS: === Extracting elution groups 7000 to 15000 ===
1:52:05.052522 INFO: Using rust extraction backend
1:52:05.052588 PROGRESS: Extracting batch of 15776 precursors
1:52:05.081598 INFO: === Search parameters used ===
1:52:05.081832 INFO: rt_error       : 805.6002197265625
1:52:05.081888 INFO: mobility_error : 0.1
1:52:05.081936 INFO: num_candidates : 1
1:52:05.081980 INFO: ms1_error      : 3
1:52:05.082022 INFO: ms2_error      : 10
1:52:05.082075 INFO: fwhm_rt        : 5
1:52:05.082118 INFO: quant_window   : 3
1:52:05.082159 INFO: ==============================================
1:52:05.394936 INFO: performing precursor FDR with 40 features
1:52:05.395070 INFO: Decoy channel: -1
1:52:05.395120 INFO: competitive: True
1:52:05.411636 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:05.422850 INFO: Estimating optimal hyperparameters - samples: 23,605, batch_size: 128, learning_rate: 1.77e-04
1:52:05.423048 INFO: Using random state 897185 for train-test-split
1:52:08.250851 INFO: Test AUC: 0.573
1:52:08.250963 INFO: Train AUC: 0.612
1:52:08.250993 INFO: AUC difference: 6.25%
1:52:08.251016 WARNING: AUC difference > 5%. This may indicate overfitting.
1:52:08.535564 INFO: Resetting torch num_threads to 100
1:52:08.543491 PROGRESS: === Extracted 29507 precursors and 164810 fragments ===
1:52:08.544202 INFO: === FDR correction performed with classifier version -1 ===
1:52:08.544878 PROGRESS: ============================= Precursor FDR =============================
1:52:08.544997 PROGRESS: Total precursors accumulated: 157
1:52:08.545069 PROGRESS: Target precursors: 156 (99.36%)
1:52:08.545132 PROGRESS: Decoy precursors: 1 (0.64%)
1:52:08.545197 PROGRESS: 
1:52:08.545254 PROGRESS: Precursor Summary:
1:52:08.546600 PROGRESS: Channel   0:	 0.050 FDR:   156; 0.010 FDR:   156; 0.001 FDR:    41
1:52:08.546699 PROGRESS: 
1:52:08.546766 PROGRESS: Protein Summary:
1:52:08.548298 PROGRESS: Channel   0:	 0.050 FDR:   151; 0.010 FDR:   151; 0.001 FDR:    41
1:52:08.548409 PROGRESS: =========================================================================
1:52:08.549336 INFO: Target number of precursors not reached yet.
1:52:08.685187 INFO: Starting optimization step 4.
1:52:08.685448 PROGRESS: === Extracting elution groups 15000 to 31000 ===
1:52:08.685530 INFO: Using rust extraction backend
1:52:08.685593 PROGRESS: Extracting batch of 31591 precursors
1:52:08.743999 INFO: === Search parameters used ===
1:52:08.744285 INFO: rt_error       : 805.6002197265625
1:52:08.744355 INFO: mobility_error : 0.1
1:52:08.744406 INFO: num_candidates : 1
1:52:08.744450 INFO: ms1_error      : 3
1:52:08.744490 INFO: ms2_error      : 10
1:52:08.744529 INFO: fwhm_rt        : 5
1:52:08.744567 INFO: quant_window   : 3
1:52:08.744606 INFO: ==============================================
1:52:09.144183 INFO: performing precursor FDR with 40 features
1:52:09.144296 INFO: Decoy channel: -1
1:52:09.144320 INFO: competitive: True
1:52:09.173086 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:09.197845 INFO: Estimating optimal hyperparameters - samples: 48,830, batch_size: 200, learning_rate: 2.21e-04
1:52:09.198148 INFO: Using random state 519623 for train-test-split
1:52:13.697506 INFO: Test AUC: 0.596
1:52:13.697634 INFO: Train AUC: 0.617
1:52:13.697674 INFO: AUC difference: 3.42%
1:52:14.063555 INFO: Resetting torch num_threads to 100
1:52:14.085274 PROGRESS: === Extracted 61038 precursors and 341553 fragments ===
1:52:14.086064 INFO: === FDR correction performed with classifier version -1 ===
1:52:14.086859 PROGRESS: ============================= Precursor FDR =============================
1:52:14.086969 PROGRESS: Total precursors accumulated: 304
1:52:14.087042 PROGRESS: Target precursors: 301 (99.01%)
1:52:14.087108 PROGRESS: Decoy precursors: 3 (0.99%)
1:52:14.087171 PROGRESS: 
1:52:14.087227 PROGRESS: Precursor Summary:
1:52:14.088625 PROGRESS: Channel   0:	 0.050 FDR:   301; 0.010 FDR:   301; 0.001 FDR:   176
1:52:14.088729 PROGRESS: 
1:52:14.088801 PROGRESS: Protein Summary:
1:52:14.090379 PROGRESS: Channel   0:	 0.050 FDR:   284; 0.010 FDR:   284; 0.001 FDR:   168
1:52:14.090482 PROGRESS: =========================================================================
1:52:14.093067 INFO: Target number of precursors not reached yet.
1:52:14.308769 INFO: Starting optimization step 5.
1:52:14.309084 PROGRESS: === Extracting elution groups 31000 to 63000 ===
1:52:14.309183 INFO: Using rust extraction backend
1:52:14.309269 PROGRESS: Extracting batch of 63056 precursors
1:52:14.431181 INFO: === Search parameters used ===
1:52:14.431546 INFO: rt_error       : 805.6002197265625
1:52:14.431648 INFO: mobility_error : 0.1
1:52:14.431734 INFO: num_candidates : 1
1:52:14.431829 INFO: ms1_error      : 3
1:52:14.431923 INFO: ms2_error      : 10
1:52:14.431999 INFO: fwhm_rt        : 5
1:52:14.432071 INFO: quant_window   : 3
1:52:14.432141 INFO: ==============================================
1:52:15.233937 INFO: performing precursor FDR with 40 features
1:52:15.234089 INFO: Decoy channel: -1
1:52:15.234119 INFO: competitive: True
1:52:15.320655 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:15.370310 INFO: Estimating optimal hyperparameters - samples: 99,156, batch_size: 406, learning_rate: 3.15e-04
1:52:15.370684 INFO: Using random state 311647 for train-test-split
1:52:21.095797 INFO: Test AUC: 0.594
1:52:21.095948 INFO: Train AUC: 0.614
1:52:21.095985 INFO: AUC difference: 3.38%
1:52:21.432308 INFO: Resetting torch num_threads to 100
1:52:21.472593 PROGRESS: === Extracted 123945 precursors and 694613 fragments ===
1:52:21.473387 INFO: === FDR correction performed with classifier version -1 ===
1:52:21.474267 PROGRESS: ============================= Precursor FDR =============================
1:52:21.474373 PROGRESS: Total precursors accumulated: 577
1:52:21.474452 PROGRESS: Target precursors: 572 (99.13%)
1:52:21.474516 PROGRESS: Decoy precursors: 5 (0.87%)
1:52:21.474573 PROGRESS: 
1:52:21.474652 PROGRESS: Precursor Summary:
1:52:21.476139 PROGRESS: Channel   0:	 0.050 FDR:   572; 0.010 FDR:   572; 0.001 FDR:   229
1:52:21.476241 PROGRESS: 
1:52:21.476314 PROGRESS: Protein Summary:
1:52:21.478021 PROGRESS: Channel   0:	 0.050 FDR:   514; 0.010 FDR:   514; 0.001 FDR:   218
1:52:21.478128 PROGRESS: =========================================================================
1:52:21.482636 INFO: Target number of precursors not reached yet.
1:52:21.811864 INFO: Starting optimization step 6.
1:52:21.812163 PROGRESS: === Extracting elution groups 63000 to 127000 ===
1:52:21.812260 INFO: Using rust extraction backend
1:52:21.812341 PROGRESS: Extracting batch of 126233 precursors
1:52:22.044590 INFO: === Search parameters used ===
1:52:22.044913 INFO: rt_error       : 805.6002197265625
1:52:22.044998 INFO: mobility_error : 0.1
1:52:22.045062 INFO: num_candidates : 1
1:52:22.045124 INFO: ms1_error      : 3
1:52:22.045180 INFO: ms2_error      : 10
1:52:22.045231 INFO: fwhm_rt        : 5
1:52:22.045282 INFO: quant_window   : 3
1:52:22.045339 INFO: ==============================================
1:52:23.413452 INFO: performing precursor FDR with 40 features
1:52:23.413585 INFO: Decoy channel: -1
1:52:23.413617 INFO: competitive: True
1:52:23.565675 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:23.694110 INFO: Estimating optimal hyperparameters - samples: 199,907, batch_size: 818, learning_rate: 4.47e-04
1:52:23.694519 INFO: Using random state 406268 for train-test-split
1:52:31.255827 INFO: Test AUC: 0.590
1:52:31.255977 INFO: Train AUC: 0.614
1:52:31.256015 INFO: AUC difference: 3.84%
1:52:31.695476 INFO: Resetting torch num_threads to 100
1:52:31.764794 PROGRESS: === Extracted 249884 precursors and 1398894 fragments ===
1:52:31.765602 INFO: === FDR correction performed with classifier version -1 ===
1:52:31.766713 PROGRESS: ============================= Precursor FDR =============================
1:52:31.766821 PROGRESS: Total precursors accumulated: 1,319
1:52:31.766891 PROGRESS: Target precursors: 1,306 (99.01%)
1:52:31.766958 PROGRESS: Decoy precursors: 13 (0.99%)
1:52:31.767018 PROGRESS: 
1:52:31.767073 PROGRESS: Precursor Summary:
1:52:31.768863 PROGRESS: Channel   0:	 0.050 FDR: 1,306; 0.010 FDR: 1,306; 0.001 FDR: 1,180
1:52:31.768973 PROGRESS: 
1:52:31.769038 PROGRESS: Protein Summary:
1:52:31.771317 PROGRESS: Channel   0:	 0.050 FDR: 1,098; 0.010 FDR: 1,098; 0.001 FDR:   999
1:52:31.771419 PROGRESS: =========================================================================
1:52:31.778510 INFO: Target number of precursors reached.
1:52:32.020947 INFO: fragments_df: keeping 5000 of 1398894 [sum(precursor_idx_mask)=13867 sum(mass_error_mask)=1398894 stop_rank=5000
1:52:32.533855 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:52:32.874002 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:52:35.347265 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
1:52:35.347859 INFO: Using score_cutoff 11.737319003105164 (fac=0.99, q=1)
1:52:35.348255 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
1:52:35.348346 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
1:52:35.348413 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.737319003105164
1:52:35.348490 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:52:35.510715 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:52:35.870700 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
1:52:35.871002 PROGRESS: Required number of precursors found. Starting search parameter optimization.
1:52:35.871151 INFO: Starting optimization step 7.
1:52:35.871243 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:52:35.871346 INFO: Using rust extraction backend
1:52:35.871432 PROGRESS: Extracting batch of 250442 precursors
1:52:36.318053 INFO: === Search parameters used ===
1:52:36.318347 INFO: rt_error       : 805.6002197265625
1:52:36.318415 INFO: mobility_error : 0.1
1:52:36.318469 INFO: num_candidates : 3
1:52:36.318520 INFO: ms1_error      : 3
1:52:36.318566 INFO: ms2_error      : 10
1:52:36.318611 INFO: fwhm_rt        : 3.0
1:52:36.318653 INFO: quant_window   : 3
1:52:36.318696 INFO: ==============================================
1:52:40.386073 INFO: performing precursor FDR with 40 features
1:52:40.386218 INFO: Decoy channel: -1
1:52:40.386252 INFO: competitive: True
1:52:40.627708 INFO: Setting torch num_threads to 2 for FDR classification task
1:52:41.043224 INFO: Estimating optimal hyperparameters - samples: 599,850, batch_size: 2,456, learning_rate: 7.74e-04
1:52:41.044438 INFO: Using random state 879534 for train-test-split
1:52:55.758621 INFO: Test AUC: 0.601
1:52:55.758775 INFO: Train AUC: 0.607
1:52:55.758823 INFO: AUC difference: 0.97%
1:52:56.382746 INFO: Resetting torch num_threads to 100
1:52:56.417121 PROGRESS: === Extracted 749813 precursors and 4034179 fragments ===
1:52:56.417614 INFO: === FDR correction performed with classifier version 6 ===
1:52:56.418388 PROGRESS: ============================= Precursor FDR =============================
1:52:56.418493 PROGRESS: Total precursors accumulated: 1,333
1:52:56.418558 PROGRESS: Target precursors: 1,320 (99.02%)
1:52:56.418611 PROGRESS: Decoy precursors: 13 (0.98%)
1:52:56.418659 PROGRESS: 
1:52:56.418704 PROGRESS: Precursor Summary:
1:52:56.420026 PROGRESS: Channel   0:	 0.050 FDR: 1,320; 0.010 FDR: 1,320; 0.001 FDR:   152
1:52:56.420121 PROGRESS: 
1:52:56.420178 PROGRESS: Protein Summary:
1:52:56.421814 PROGRESS: Channel   0:	 0.050 FDR: 1,102; 0.010 FDR: 1,102; 0.001 FDR:   146
1:52:56.421906 PROGRESS: =========================================================================
1:52:56.439429 INFO: Target number of precursors reached.
1:52:57.081511 INFO: fragments_df: keeping 5000 of 4034179 [sum(precursor_idx_mask)=31814 sum(mass_error_mask)=4034179 stop_rank=5000
1:52:57.725376 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:52:58.072666 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:52:59.103283 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:52:59.103854 INFO: Using score_cutoff 11.16559529657364 (fac=0.99, q=1)
1:52:59.104242 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:52:59.104333 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:52:59.104398 INFO: Updating optimization_manager: score_cutoff        : 11.737319003105164 -> 11.16559529657364
1:52:59.104467 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:52:59.267103 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:52:59.628143 INFO: === checking if optimization conditions were reached ===
1:52:59.630923 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
1:52:59.631056 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
1:52:59.631152 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:52:59.631231 INFO: ==============================================
1:52:59.631319 INFO: Starting optimization step 8.
1:52:59.631395 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:52:59.631478 INFO: Using rust extraction backend
1:52:59.631553 PROGRESS: Extracting batch of 250442 precursors
1:53:00.087535 INFO: === Search parameters used ===
1:53:00.087859 INFO: rt_error       : 805.6002197265625
1:53:00.087936 INFO: mobility_error : 0.1
1:53:00.088007 INFO: num_candidates : 3
1:53:00.088064 INFO: ms1_error      : 3
1:53:00.088121 INFO: ms2_error      : 10.0
1:53:00.088183 INFO: fwhm_rt        : 3.0
1:53:00.088236 INFO: quant_window   : 3
1:53:00.088286 INFO: ==============================================
1:53:04.247217 INFO: performing precursor FDR with 40 features
1:53:04.247380 INFO: Decoy channel: -1
1:53:04.247416 INFO: competitive: True
1:53:04.491928 INFO: Setting torch num_threads to 2 for FDR classification task
1:53:04.903095 INFO: Estimating optimal hyperparameters - samples: 599,856, batch_size: 2,457, learning_rate: 7.75e-04
1:53:04.904240 INFO: Using random state 666510 for train-test-split
1:53:16.228613 INFO: Test AUC: 0.605
1:53:16.228782 INFO: Train AUC: 0.616
1:53:16.228824 INFO: AUC difference: 1.73%
1:53:16.856725 INFO: Resetting torch num_threads to 100
1:53:16.897274 PROGRESS: === Extracted 749820 precursors and 4034016 fragments ===
1:53:16.897894 INFO: === FDR correction performed with classifier version 7 ===
1:53:16.898992 PROGRESS: ============================= Precursor FDR =============================
1:53:16.899104 PROGRESS: Total precursors accumulated: 1,603
1:53:16.899178 PROGRESS: Target precursors: 1,588 (99.06%)
1:53:16.899245 PROGRESS: Decoy precursors: 15 (0.94%)
1:53:16.899306 PROGRESS: 
1:53:16.899364 PROGRESS: Precursor Summary:
1:53:16.901360 PROGRESS: Channel   0:	 0.050 FDR: 1,588; 0.010 FDR: 1,588; 0.001 FDR:   708
1:53:16.901469 PROGRESS: 
1:53:16.901543 PROGRESS: Protein Summary:
1:53:16.903847 PROGRESS: Channel   0:	 0.050 FDR: 1,315; 0.010 FDR: 1,315; 0.001 FDR:   627
1:53:16.903961 PROGRESS: =========================================================================
1:53:16.929563 INFO: Target number of precursors reached.
1:53:17.585559 INFO: fragments_df: keeping 5000 of 4034016 [sum(precursor_idx_mask)=37640 sum(mass_error_mask)=4034016 stop_rank=5000
1:53:18.137679 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:53:18.648289 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:53:19.720553 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:53:19.721138 INFO: Using score_cutoff 11.095454258823395 (fac=0.99, q=1)
1:53:19.721558 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:53:19.721657 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:53:19.721725 INFO: Updating optimization_manager: score_cutoff        : 11.16559529657364 -> 11.095454258823395
1:53:19.721798 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:53:19.886836 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:53:20.240517 INFO: === checking if optimization conditions were reached ===
1:53:20.243269 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:53:20.243396 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
1:53:20.243480 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:53:20.243555 INFO: ==============================================
1:53:20.243639 INFO: Starting optimization step 9.
1:53:20.243713 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:53:20.243792 INFO: Using rust extraction backend
1:53:20.243930 PROGRESS: Extracting batch of 250442 precursors
1:53:20.718834 INFO: === Search parameters used ===
1:53:20.719158 INFO: rt_error       : 805.6002197265625
1:53:20.719238 INFO: mobility_error : 0.1
1:53:20.719300 INFO: num_candidates : 3
1:53:20.719355 INFO: ms1_error      : 3
1:53:20.719431 INFO: ms2_error      : 10.0
1:53:20.719485 INFO: fwhm_rt        : 3.0
1:53:20.719534 INFO: quant_window   : 3
1:53:20.719597 INFO: ==============================================
1:53:24.765753 INFO: performing precursor FDR with 40 features
1:53:24.765872 INFO: Decoy channel: -1
1:53:24.765899 INFO: competitive: True
1:53:24.975692 INFO: Setting torch num_threads to 2 for FDR classification task
1:53:25.373516 INFO: Estimating optimal hyperparameters - samples: 599,843, batch_size: 2,456, learning_rate: 7.74e-04
1:53:25.374851 INFO: Using random state 246136 for train-test-split
1:53:36.231907 INFO: Test AUC: 0.606
1:53:36.232055 INFO: Train AUC: 0.620
1:53:36.232094 INFO: AUC difference: 2.26%
1:53:36.856586 INFO: Resetting torch num_threads to 100
1:53:36.901863 PROGRESS: === Extracted 749804 precursors and 4034065 fragments ===
1:53:36.902501 INFO: === FDR correction performed with classifier version 8 ===
1:53:36.903707 PROGRESS: ============================= Precursor FDR =============================
1:53:36.903844 PROGRESS: Total precursors accumulated: 1,521
1:53:36.903930 PROGRESS: Target precursors: 1,506 (99.01%)
1:53:36.903993 PROGRESS: Decoy precursors: 15 (0.99%)
1:53:36.904049 PROGRESS: 
1:53:36.904109 PROGRESS: Precursor Summary:
1:53:36.905999 PROGRESS: Channel   0:	 0.050 FDR: 1,506; 0.010 FDR: 1,506; 0.001 FDR:   454
1:53:36.906109 PROGRESS: 
1:53:36.906179 PROGRESS: Protein Summary:
1:53:36.908402 PROGRESS: Channel   0:	 0.050 FDR: 1,248; 0.010 FDR: 1,248; 0.001 FDR:   415
1:53:36.908516 PROGRESS: =========================================================================
1:53:36.935086 INFO: Target number of precursors reached.
1:53:37.536133 INFO: fragments_df: keeping 5000 of 4034065 [sum(precursor_idx_mask)=35871 sum(mass_error_mask)=4034065 stop_rank=5000
1:53:37.973054 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:53:38.413554 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:53:39.465190 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:53:39.465739 INFO: Using score_cutoff 11.553282939434052 (fac=0.99, q=1)
1:53:39.466139 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:53:39.466233 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:53:39.466314 INFO: Updating optimization_manager: score_cutoff        : 11.095454258823395 -> 11.553282939434052
1:53:39.466396 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:53:39.627387 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:53:39.981807 INFO: === checking if optimization conditions were reached ===
1:53:39.984565 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:53:39.984759 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
1:53:39.984862 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:53:39.984935 INFO: ==============================================
1:53:39.985023 INFO: Starting optimization step 10.
1:53:39.985096 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:53:39.985172 INFO: Using rust extraction backend
1:53:39.985246 PROGRESS: Extracting batch of 250442 precursors
1:53:40.435911 INFO: === Search parameters used ===
1:53:40.436243 INFO: rt_error       : 805.6002197265625
1:53:40.436315 INFO: mobility_error : 0.1
1:53:40.436382 INFO: num_candidates : 3
1:53:40.436442 INFO: ms1_error      : 3
1:53:40.436499 INFO: ms2_error      : 10.0
1:53:40.436561 INFO: fwhm_rt        : 3.0
1:53:40.436615 INFO: quant_window   : 3
1:53:40.436670 INFO: ==============================================
1:53:44.557226 INFO: performing precursor FDR with 40 features
1:53:44.557374 INFO: Decoy channel: -1
1:53:44.557405 INFO: competitive: True
1:53:44.807480 INFO: Setting torch num_threads to 2 for FDR classification task
1:53:45.244332 INFO: Estimating optimal hyperparameters - samples: 599,839, batch_size: 2,456, learning_rate: 7.74e-04
1:53:45.245585 INFO: Using random state 261878 for train-test-split
1:53:59.570368 INFO: Test AUC: 0.608
1:53:59.570522 INFO: Train AUC: 0.622
1:53:59.570557 INFO: AUC difference: 2.20%
1:54:00.077256 INFO: Resetting torch num_threads to 100
1:54:00.111066 PROGRESS: === Extracted 749799 precursors and 4033685 fragments ===
1:54:00.111563 INFO: === FDR correction performed with classifier version 9 ===
1:54:00.112419 PROGRESS: ============================= Precursor FDR =============================
1:54:00.112517 PROGRESS: Total precursors accumulated: 1,565
1:54:00.112580 PROGRESS: Target precursors: 1,550 (99.04%)
1:54:00.112632 PROGRESS: Decoy precursors: 15 (0.96%)
1:54:00.112680 PROGRESS: 
1:54:00.112725 PROGRESS: Precursor Summary:
1:54:00.114124 PROGRESS: Channel   0:	 0.050 FDR: 1,550; 0.010 FDR: 1,550; 0.001 FDR:   620
1:54:00.114214 PROGRESS: 
1:54:00.114270 PROGRESS: Protein Summary:
1:54:00.116084 PROGRESS: Channel   0:	 0.050 FDR: 1,293; 0.010 FDR: 1,293; 0.001 FDR:   555
1:54:00.116185 PROGRESS: =========================================================================
1:54:00.133562 INFO: Target number of precursors reached.
1:54:00.781255 INFO: fragments_df: keeping 5000 of 4033685 [sum(precursor_idx_mask)=36304 sum(mass_error_mask)=4033685 stop_rank=5000
1:54:01.329583 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:54:01.710922 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:54:02.732681 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:54:02.733285 INFO: Using score_cutoff 9.71285854511261 (fac=0.99, q=1)
1:54:02.733683 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:54:02.733788 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:54:02.733860 INFO: Updating optimization_manager: score_cutoff        : 11.553282939434052 -> 9.71285854511261
1:54:02.733932 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:54:02.894610 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:54:03.257270 INFO: === checking if optimization conditions were reached ===
1:54:03.260343 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:54:03.260549 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
1:54:03.260637 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
1:54:03.260724 INFO: ==============================================
1:54:03.260814 INFO: Starting optimization step 11.
1:54:03.260890 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:54:03.260972 INFO: Using rust extraction backend
1:54:03.261050 PROGRESS: Extracting batch of 250442 precursors
1:54:03.721252 INFO: === Search parameters used ===
1:54:03.721605 INFO: rt_error       : 805.6002197265625
1:54:03.721677 INFO: mobility_error : 0.1
1:54:03.721740 INFO: num_candidates : 3
1:54:03.721820 INFO: ms1_error      : 3
1:54:03.721873 INFO: ms2_error      : 10.0
1:54:03.721926 INFO: fwhm_rt        : 3.0
1:54:03.721989 INFO: quant_window   : 3
1:54:03.722041 INFO: ==============================================
1:54:07.708580 INFO: performing precursor FDR with 40 features
1:54:07.708723 INFO: Decoy channel: -1
1:54:07.708754 INFO: competitive: True
1:54:07.939142 INFO: Setting torch num_threads to 2 for FDR classification task
1:54:08.273416 INFO: Estimating optimal hyperparameters - samples: 599,852, batch_size: 2,456, learning_rate: 7.74e-04
1:54:08.274407 INFO: Using random state 534127 for train-test-split
1:54:23.149679 INFO: Test AUC: 0.610
1:54:23.149851 INFO: Train AUC: 0.624
1:54:23.149892 INFO: AUC difference: 2.17%
1:54:23.777966 INFO: Resetting torch num_threads to 100
1:54:23.822639 PROGRESS: === Extracted 749816 precursors and 4034406 fragments ===
1:54:23.823312 INFO: === FDR correction performed with classifier version 10 ===
1:54:23.824713 PROGRESS: ============================= Precursor FDR =============================
1:54:23.824873 PROGRESS: Total precursors accumulated: 1,610
1:54:23.824952 PROGRESS: Target precursors: 1,595 (99.07%)
1:54:23.825036 PROGRESS: Decoy precursors: 15 (0.93%)
1:54:23.825096 PROGRESS: 
1:54:23.825151 PROGRESS: Precursor Summary:
1:54:23.827513 PROGRESS: Channel   0:	 0.050 FDR: 1,595; 0.010 FDR: 1,595; 0.001 FDR: 1,002
1:54:23.827646 PROGRESS: 
1:54:23.827729 PROGRESS: Protein Summary:
1:54:23.830324 PROGRESS: Channel   0:	 0.050 FDR: 1,324; 0.010 FDR: 1,324; 0.001 FDR:   853
1:54:23.830462 PROGRESS: =========================================================================
1:54:23.858715 INFO: Target number of precursors reached.
1:54:24.519707 INFO: fragments_df: keeping 5000 of 4034406 [sum(precursor_idx_mask)=37340 sum(mass_error_mask)=4034406 stop_rank=5000
1:54:25.067161 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:54:25.486616 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:54:26.517683 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:54:26.518290 INFO: Using score_cutoff 9.902459950447083 (fac=0.99, q=1)
1:54:26.518760 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:54:26.518879 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:54:26.518948 INFO: Updating optimization_manager: score_cutoff        : 9.71285854511261 -> 9.902459950447083
1:54:26.519015 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:54:26.682674 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:54:27.033083 INFO: === checking if optimization conditions were reached ===
1:54:27.035933 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
1:54:27.036131 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
1:54:27.036216 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
1:54:27.036312 INFO: ==============================================
1:54:27.036396 PROGRESS: Optimization finished for ms2_error.
1:54:27.557250 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:54:27.718934 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:54:28.080996 INFO: Starting optimization step 0.
1:54:28.081279 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:54:28.081382 INFO: Using rust extraction backend
1:54:28.081458 PROGRESS: Extracting batch of 250442 precursors
1:54:28.545846 INFO: === Search parameters used ===
1:54:28.546962 INFO: rt_error       : 805.6002197265625
1:54:28.547064 INFO: mobility_error : 0.1
1:54:28.547122 INFO: num_candidates : 3
1:54:28.547168 INFO: ms1_error      : 3
1:54:28.547213 INFO: ms2_error      : 10.0
1:54:28.547253 INFO: fwhm_rt        : 3.0
1:54:28.547291 INFO: quant_window   : 3
1:54:28.547328 INFO: ==============================================
1:54:32.781860 INFO: performing precursor FDR with 40 features
1:54:32.781998 INFO: Decoy channel: -1
1:54:32.782029 INFO: competitive: True
1:54:33.030322 INFO: Setting torch num_threads to 2 for FDR classification task
1:54:33.432248 INFO: Estimating optimal hyperparameters - samples: 599,846, batch_size: 2,456, learning_rate: 7.74e-04
1:54:33.433465 INFO: Using random state 155933 for train-test-split
1:54:45.503037 INFO: Test AUC: 0.610
1:54:45.503209 INFO: Train AUC: 0.627
1:54:45.503250 INFO: AUC difference: 2.65%
1:54:46.129244 INFO: Resetting torch num_threads to 100
1:54:46.174403 PROGRESS: === Extracted 749808 precursors and 4034490 fragments ===
1:54:46.175005 INFO: === FDR correction performed with classifier version 11 ===
1:54:46.175963 PROGRESS: ============================= Precursor FDR =============================
1:54:46.176070 PROGRESS: Total precursors accumulated: 1,495
1:54:46.176148 PROGRESS: Target precursors: 1,481 (99.06%)
1:54:46.176214 PROGRESS: Decoy precursors: 14 (0.94%)
1:54:46.176271 PROGRESS: 
1:54:46.176332 PROGRESS: Precursor Summary:
1:54:46.178166 PROGRESS: Channel   0:	 0.050 FDR: 1,481; 0.010 FDR: 1,481; 0.001 FDR:     0
1:54:46.178276 PROGRESS: 
1:54:46.178351 PROGRESS: Protein Summary:
1:54:46.180519 PROGRESS: Channel   0:	 0.050 FDR: 1,236; 0.010 FDR: 1,236; 0.001 FDR:     0
1:54:46.180625 PROGRESS: =========================================================================
1:54:46.206197 INFO: Target number of precursors reached.
1:54:46.870032 INFO: fragments_df: keeping 5000 of 4034490 [sum(precursor_idx_mask)=35165 sum(mass_error_mask)=4034490 stop_rank=5000
1:54:47.361938 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:54:47.693006 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:54:48.720385 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:54:48.720914 INFO: Using score_cutoff 10.508556335449217 (fac=0.99, q=1)
1:54:48.721278 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:54:48.721370 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:54:48.721438 INFO: Updating optimization_manager: score_cutoff        : 9.902459950447083 -> 10.508556335449217
1:54:48.721503 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:54:48.895470 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:54:49.253577 INFO: === checking if optimization conditions were reached ===
1:54:49.253877 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
1:54:49.257135 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 719.7099945236018
1:54:49.257262 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 719.7100.
1:54:49.257345 INFO: ==============================================
1:54:49.257434 INFO: Starting optimization step 1.
1:54:49.257504 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:54:49.257581 INFO: Using rust extraction backend
1:54:49.257656 PROGRESS: Extracting batch of 250442 precursors
1:54:49.715041 INFO: === Search parameters used ===
1:54:49.715392 INFO: rt_error       : 719.7099945236018
1:54:49.715463 INFO: mobility_error : 0.1
1:54:49.715520 INFO: num_candidates : 3
1:54:49.715578 INFO: ms1_error      : 3
1:54:49.715627 INFO: ms2_error      : 10.0
1:54:49.715674 INFO: fwhm_rt        : 3.0
1:54:49.715726 INFO: quant_window   : 3
1:54:49.715778 INFO: ==============================================
1:54:53.742673 INFO: performing precursor FDR with 40 features
1:54:53.742803 INFO: Decoy channel: -1
1:54:53.742835 INFO: competitive: True
1:54:53.991170 INFO: Setting torch num_threads to 2 for FDR classification task
1:54:54.430273 INFO: Estimating optimal hyperparameters - samples: 599,813, batch_size: 2,456, learning_rate: 7.74e-04
1:54:54.431956 INFO: Using random state 155933 for train-test-split
1:55:09.232168 INFO: Test AUC: 0.611
1:55:09.232346 INFO: Train AUC: 0.627
1:55:09.232380 INFO: AUC difference: 2.57%
1:55:09.821208 INFO: Resetting torch num_threads to 100
1:55:09.864730 PROGRESS: === Extracted 749767 precursors and 4031878 fragments ===
1:55:09.865342 INFO: === FDR correction performed with classifier version 11 ===
1:55:09.866326 PROGRESS: ============================= Precursor FDR =============================
1:55:09.866432 PROGRESS: Total precursors accumulated: 1,580
1:55:09.866508 PROGRESS: Target precursors: 1,565 (99.05%)
1:55:09.866574 PROGRESS: Decoy precursors: 15 (0.95%)
1:55:09.866632 PROGRESS: 
1:55:09.866691 PROGRESS: Precursor Summary:
1:55:09.868379 PROGRESS: Channel   0:	 0.050 FDR: 1,565; 0.010 FDR: 1,565; 0.001 FDR:     0
1:55:09.868482 PROGRESS: 
1:55:09.868546 PROGRESS: Protein Summary:
1:55:09.870660 PROGRESS: Channel   0:	 0.050 FDR: 1,296; 0.010 FDR: 1,296; 0.001 FDR:     0
1:55:09.870764 PROGRESS: =========================================================================
1:55:09.896455 INFO: Target number of precursors reached.
1:55:10.453447 INFO: fragments_df: keeping 5000 of 4031878 [sum(precursor_idx_mask)=37032 sum(mass_error_mask)=4031878 stop_rank=5000
1:55:11.020409 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:55:11.404727 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:55:12.530674 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:55:12.531144 INFO: Using score_cutoff 10.304949706649781 (fac=0.99, q=1)
1:55:12.531455 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:55:12.531542 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:55:12.531595 INFO: Updating optimization_manager: score_cutoff        : 10.508556335449217 -> 10.304949706649781
1:55:12.531653 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:55:12.690590 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:55:13.036708 INFO: === checking if optimization conditions were reached ===
1:55:13.037044 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
1:55:13.040771 INFO: Updating optimization_manager: rt_error            : 719.7099945236018 -> 669.8315345610132
1:55:13.040961 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 669.8315.
1:55:13.041057 INFO: ==============================================
1:55:13.041160 INFO: Starting optimization step 2.
1:55:13.041248 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:55:13.041356 INFO: Using rust extraction backend
1:55:13.041460 PROGRESS: Extracting batch of 250442 precursors
1:55:13.496597 INFO: === Search parameters used ===
1:55:13.496879 INFO: rt_error       : 669.8315345610132
1:55:13.496943 INFO: mobility_error : 0.1
1:55:13.496996 INFO: num_candidates : 3
1:55:13.497042 INFO: ms1_error      : 3
1:55:13.497087 INFO: ms2_error      : 10.0
1:55:13.497130 INFO: fwhm_rt        : 3.0
1:55:13.497173 INFO: quant_window   : 3
1:55:13.497215 INFO: ==============================================
1:55:17.327307 INFO: performing precursor FDR with 40 features
1:55:17.327448 INFO: Decoy channel: -1
1:55:17.327480 INFO: competitive: True
1:55:17.575701 INFO: Setting torch num_threads to 2 for FDR classification task
1:55:17.994824 INFO: Estimating optimal hyperparameters - samples: 599,800, batch_size: 2,456, learning_rate: 7.74e-04
1:55:17.996138 INFO: Using random state 155933 for train-test-split
1:55:29.700716 INFO: Test AUC: 0.612
1:55:29.700909 INFO: Train AUC: 0.626
1:55:29.700949 INFO: AUC difference: 2.26%
1:55:30.325623 INFO: Resetting torch num_threads to 100
1:55:30.371570 PROGRESS: === Extracted 749751 precursors and 4029352 fragments ===
1:55:30.372252 INFO: === FDR correction performed with classifier version 11 ===
1:55:30.373584 PROGRESS: ============================= Precursor FDR =============================
1:55:30.373729 PROGRESS: Total precursors accumulated: 1,519
1:55:30.373807 PROGRESS: Target precursors: 1,504 (99.01%)
1:55:30.373871 PROGRESS: Decoy precursors: 15 (0.99%)
1:55:30.373935 PROGRESS: 
1:55:30.373995 PROGRESS: Precursor Summary:
1:55:30.375989 PROGRESS: Channel   0:	 0.050 FDR: 1,504; 0.010 FDR: 1,504; 0.001 FDR:     0
1:55:30.376130 PROGRESS: 
1:55:30.376197 PROGRESS: Protein Summary:
1:55:30.378377 PROGRESS: Channel   0:	 0.050 FDR: 1,258; 0.010 FDR: 1,258; 0.001 FDR:     0
1:55:30.378498 PROGRESS: =========================================================================
1:55:30.405591 INFO: Target number of precursors reached.
1:55:31.076294 INFO: fragments_df: keeping 5000 of 4029352 [sum(precursor_idx_mask)=35401 sum(mass_error_mask)=4029352 stop_rank=5000
1:55:31.645857 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:55:32.057361 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:55:33.022986 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:55:33.023456 INFO: Using score_cutoff 9.734666149806976 (fac=0.99, q=1)
1:55:33.023781 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:55:33.023873 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:55:33.023932 INFO: Updating optimization_manager: score_cutoff        : 10.304949706649781 -> 9.734666149806976
1:55:33.023994 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:55:33.183411 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:55:33.529890 INFO: === checking if optimization conditions were reached ===
1:55:33.530172 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
1:55:33.533916 INFO: Updating optimization_manager: rt_error            : 669.8315345610132 -> 689.7427999256417
1:55:33.534046 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 689.7428.
1:55:33.534126 INFO: ==============================================
1:55:33.534207 INFO: Starting optimization step 3.
1:55:33.534291 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:55:33.534368 INFO: Using rust extraction backend
1:55:33.534444 PROGRESS: Extracting batch of 250442 precursors
1:55:33.997778 INFO: === Search parameters used ===
1:55:33.998145 INFO: rt_error       : 689.7427999256417
1:55:33.998224 INFO: mobility_error : 0.1
1:55:33.998291 INFO: num_candidates : 3
1:55:33.998353 INFO: ms1_error      : 3
1:55:33.998413 INFO: ms2_error      : 10.0
1:55:33.998471 INFO: fwhm_rt        : 3.0
1:55:33.998529 INFO: quant_window   : 3
1:55:33.998589 INFO: ==============================================
1:55:38.495887 INFO: performing precursor FDR with 40 features
1:55:38.496034 INFO: Decoy channel: -1
1:55:38.496066 INFO: competitive: True
1:55:38.748370 INFO: Setting torch num_threads to 2 for FDR classification task
1:55:39.183830 INFO: Estimating optimal hyperparameters - samples: 599,844, batch_size: 2,456, learning_rate: 7.74e-04
1:55:39.185053 INFO: Using random state 155933 for train-test-split
1:55:54.263255 INFO: Test AUC: 0.616
1:55:54.263427 INFO: Train AUC: 0.626
1:55:54.263471 INFO: AUC difference: 1.61%
1:55:54.889872 INFO: Resetting torch num_threads to 100
1:55:54.942714 PROGRESS: === Extracted 749805 precursors and 4033525 fragments ===
1:55:54.943347 INFO: === FDR correction performed with classifier version 11 ===
1:55:54.944432 PROGRESS: ============================= Precursor FDR =============================
1:55:54.944541 PROGRESS: Total precursors accumulated: 1,536
1:55:54.944614 PROGRESS: Target precursors: 1,521 (99.02%)
1:55:54.944683 PROGRESS: Decoy precursors: 15 (0.98%)
1:55:54.944745 PROGRESS: 
1:55:54.944800 PROGRESS: Precursor Summary:
1:55:54.946487 PROGRESS: Channel   0:	 0.050 FDR: 1,521; 0.010 FDR: 1,521; 0.001 FDR:     0
1:55:54.946600 PROGRESS: 
1:55:54.946666 PROGRESS: Protein Summary:
1:55:54.948775 PROGRESS: Channel   0:	 0.050 FDR: 1,268; 0.010 FDR: 1,268; 0.001 FDR:     0
1:55:54.948883 PROGRESS: =========================================================================
1:55:54.976241 INFO: Target number of precursors reached.
1:55:55.512535 INFO: fragments_df: keeping 5000 of 4033525 [sum(precursor_idx_mask)=35946 sum(mass_error_mask)=4033525 stop_rank=5000
1:55:56.081128 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:55:56.469228 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:55:57.527109 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:55:57.527645 INFO: Using score_cutoff 10.199722137451172 (fac=0.99, q=1)
1:55:57.528050 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:55:57.528151 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:55:57.528216 INFO: Updating optimization_manager: score_cutoff        : 9.734666149806976 -> 10.199722137451172
1:55:57.528287 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:55:57.698701 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:55:58.049698 INFO: === checking if optimization conditions were reached ===
1:55:58.050027 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
1:55:58.053975 INFO: Updating optimization_manager: rt_error            : 689.7427999256417 -> 693.5851342495707
1:55:58.054179 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 693.5851.
1:55:58.054302 INFO: ==============================================
1:55:58.054405 INFO: Starting optimization step 4.
1:55:58.054492 PROGRESS: === Extracting elution groups 0 to 127000 ===
1:55:58.054591 INFO: Using rust extraction backend
1:55:58.054676 PROGRESS: Extracting batch of 250442 precursors
1:55:58.515756 INFO: === Search parameters used ===
1:55:58.516104 INFO: rt_error       : 693.5851342495707
1:55:58.516180 INFO: mobility_error : 0.1
1:55:58.516251 INFO: num_candidates : 3
1:55:58.516309 INFO: ms1_error      : 3
1:55:58.516367 INFO: ms2_error      : 10.0
1:55:58.516425 INFO: fwhm_rt        : 3.0
1:55:58.516480 INFO: quant_window   : 3
1:55:58.516534 INFO: ==============================================
1:56:02.648831 INFO: performing precursor FDR with 40 features
1:56:02.648975 INFO: Decoy channel: -1
1:56:02.649007 INFO: competitive: True
1:56:02.893198 INFO: Setting torch num_threads to 2 for FDR classification task
1:56:03.290807 INFO: Estimating optimal hyperparameters - samples: 599,826, batch_size: 2,456, learning_rate: 7.74e-04
1:56:03.292020 INFO: Using random state 155933 for train-test-split
1:56:17.790809 INFO: Test AUC: 0.612
1:56:17.790991 INFO: Train AUC: 0.627
1:56:17.791030 INFO: AUC difference: 2.50%
1:56:18.386438 INFO: Resetting torch num_threads to 100
1:56:18.415168 PROGRESS: === Extracted 749783 precursors and 4032163 fragments ===
1:56:18.415669 INFO: === FDR correction performed with classifier version 11 ===
1:56:18.416480 PROGRESS: ============================= Precursor FDR =============================
1:56:18.416583 PROGRESS: Total precursors accumulated: 1,666
1:56:18.416646 PROGRESS: Target precursors: 1,650 (99.04%)
1:56:18.416698 PROGRESS: Decoy precursors: 16 (0.96%)
1:56:18.416745 PROGRESS: 
1:56:18.416790 PROGRESS: Precursor Summary:
1:56:18.418143 PROGRESS: Channel   0:	 0.050 FDR: 1,650; 0.010 FDR: 1,650; 0.001 FDR:     0
1:56:18.418232 PROGRESS: 
1:56:18.418287 PROGRESS: Protein Summary:
1:56:18.419999 PROGRESS: Channel   0:	 0.050 FDR: 1,380; 0.010 FDR: 1,380; 0.001 FDR:     0
1:56:18.420092 PROGRESS: =========================================================================
1:56:18.437421 INFO: Target number of precursors reached.
1:56:18.946527 INFO: fragments_df: keeping 5000 of 4032163 [sum(precursor_idx_mask)=37904 sum(mass_error_mask)=4032163 stop_rank=5000
1:56:19.506131 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
1:56:19.934071 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
1:56:20.848411 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
1:56:20.848975 INFO: Using score_cutoff 8.632081067562103 (fac=0.99, q=1)
1:56:20.849356 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:56:20.849448 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:56:20.849515 INFO: Updating optimization_manager: score_cutoff        : 10.199722137451172 -> 8.632081067562103
1:56:20.849592 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:56:21.010663 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:56:21.368443 INFO: === checking if optimization conditions were reached ===
1:56:21.368755 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
1:56:21.370003 INFO: Updating optimization_manager: rt_error            : 693.5851342495707 -> 693.5851342495707
1:56:21.370224 INFO: Updating optimization_manager: classifier_version  : 11 -> 16
1:56:21.370372 INFO: Updating optimization_manager: score_cutoff        : 8.632081067562103 -> 8.632081067562103
1:56:21.370488 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
1:56:21.370600 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
1:56:21.370718 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 693.5851 found after 5 searches.
1:56:21.370798 INFO: ==============================================
1:56:21.370899 PROGRESS: Optimization finished for rt_error.
1:56:21.807795 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:56:21.970483 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:56:22.361651 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
1:56:22.361938 PROGRESS: ==============================================
1:56:22.362034 PROGRESS: ms2_error      : 10.0000
1:56:22.362126 PROGRESS: rt_error       : 693.5851
1:56:22.362201 PROGRESS: ==============================================
1:56:22.370630 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
1:56:30.233321 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
1:56:48.757176 INFO: Using rust extraction backend
1:56:48.757541 PROGRESS: Extracting batch of 11997144 precursors
1:57:06.001133 INFO: === Search parameters used ===
1:57:06.001480 INFO: rt_error       : 693.5851342495707
1:57:06.001559 INFO: mobility_error : 0.1
1:57:06.001622 INFO: num_candidates : 3
1:57:06.001689 INFO: ms1_error      : 3
1:57:06.001747 INFO: ms2_error      : 10.0
1:57:06.001799 INFO: fwhm_rt        : 3.0
1:57:06.001851 INFO: quant_window   : 3
1:57:06.001909 INFO: ==============================================
1:57:51.866737 INFO: Removed 4195534 precursors with score below cutoff 8.632081067562103
1:58:24.927352 INFO: performing precursor FDR with 40 features
1:58:24.927500 INFO: Decoy channel: -1
1:58:24.927532 INFO: competitive: True
1:58:28.785384 INFO: Setting torch num_threads to 2 for FDR classification task
1:58:49.683902 INFO: Estimating optimal hyperparameters - samples: 25,436,422, batch_size: 4,096, learning_rate: 1.00e-03
1:58:49.767839 INFO: Using random state 12732 for train-test-split
2:08:03.855081 INFO: Test AUC: 0.621
2:08:03.855406 INFO: Train AUC: 0.621
2:08:03.855465 INFO: AUC difference: 0.05%
2:08:11.580724 INFO: Resetting torch num_threads to 100
2:08:14.510777 PROGRESS: ============================= Precursor FDR =============================
2:08:14.511118 PROGRESS: Total precursors accumulated: 95,327
2:08:14.511214 PROGRESS: Target precursors: 94,384 (99.01%)
2:08:14.511281 PROGRESS: Decoy precursors: 943 (0.99%)
2:08:14.511344 PROGRESS: 
2:08:14.511409 PROGRESS: Precursor Summary:
2:08:14.552880 PROGRESS: Channel   0:	 0.050 FDR: 94,384; 0.010 FDR: 94,384; 0.001 FDR: 62,370
2:08:14.553155 PROGRESS: 
2:08:14.553229 PROGRESS: Protein Summary:
2:08:14.611523 PROGRESS: Channel   0:	 0.050 FDR: 13,646; 0.010 FDR: 13,646; 0.001 FDR: 9,353
2:08:14.611794 PROGRESS: =========================================================================
2:08:14.850283 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/psm.parquet
2:08:15.066760 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.parquet
2:08:15.375038 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:08:16.008572 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 
2:08:16.008754 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant
2:08:16.008885 INFO: Initializing TimingManager
2:08:16.009595 INFO: Initializing RawFileManager
2:08:39.036351 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:08:39.053402 INFO: Determining DIA cycle
2:08:39.071699 INFO: Found cycle with start 0.00 min and length 300.
2:08:39.275196 INFO: RT (min)            : 0.0 - 26.9
2:08:39.275313 INFO: RT duration (sec)   : 1611.2
2:08:39.275349 INFO: RT duration (min)   : 26.9
2:08:39.275380 INFO: Cycle len (scans)   : 300
2:08:39.275405 INFO: Cycle len (sec)     : 1.65
2:08:39.275428 INFO: Number of cycles    : 978
2:08:39.275453 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:08:39.275494 INFO: Creating DIA data object took: 23.26577591896057
2:08:40.544274 INFO: Creating DIA data NG object took: 1.2686183452606201
2:08:42.037413 INFO: Initializing CalibrationManager
2:08:42.037757 INFO: Setting up calibration estimators ..
2:08:42.037834 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:08:42.037947 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2:08:42.038065 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:08:42.038136 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:08:42.038207 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2:08:42.038272 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:08:42.038332 INFO: Done setting up calibration estimators.
2:08:42.038574 INFO: Initializing OptimizationManager
2:08:42.038749 INFO: initial parameter: ms1_error = 3
2:08:42.038810 INFO: initial parameter: ms2_error = 10
2:08:42.038872 INFO: initial parameter: rt_error = 805.611083984375
2:08:42.038927 INFO: initial parameter: mobility_error = 0.1
2:08:42.038975 INFO: initial parameter: num_candidates = 1
2:08:42.039022 INFO: initial parameter: fwhm_rt = 5
2:08:42.039078 INFO: initial parameter: fwhm_mobility = 0.01
2:08:42.039137 INFO: initial parameter: score_cutoff = 0
2:08:42.039194 INFO: initial parameter: classifier_version = -1
2:08:42.039279 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:08:42.039619 INFO: FDRManager: loading saved state not requested, will be initialized.
2:08:42.039657 INFO: Initializing FDRManager
2:08:42.039707 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:08:43.984271 PROGRESS: Initializing spectral library: 6,084,242 target precursors potentially observable (7,072 removed)
2:08:45.191067 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
2:08:45.191634 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
2:08:45.191775 PROGRESS: Starting initial search for precursors.
2:08:45.191901 INFO: Starting optimization step 0.
2:08:45.191990 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:08:45.192066 INFO: Using rust extraction backend
2:08:45.192159 PROGRESS: Extracting batch of 1970 precursors
2:08:45.197402 INFO: === Search parameters used ===
2:08:45.197552 INFO: rt_error       : 805.611083984375
2:08:45.197626 INFO: mobility_error : 0.1
2:08:45.197694 INFO: num_candidates : 1
2:08:45.197759 INFO: ms1_error      : 3
2:08:45.197815 INFO: ms2_error      : 10
2:08:45.197868 INFO: fwhm_rt        : 5
2:08:45.197923 INFO: quant_window   : 3
2:08:45.197989 INFO: ==============================================
2:08:45.291649 INFO: performing precursor FDR with 40 features
2:08:45.291771 INFO: Decoy channel: -1
2:08:45.291803 INFO: competitive: True
2:08:45.293660 INFO: Setting torch num_threads to 2 for FDR classification task
2:08:45.296493 INFO: Estimating optimal hyperparameters - samples: 1,571, batch_size: 128, learning_rate: 1.77e-04
2:08:45.297918 INFO: Using random state 367827 for train-test-split
2:08:45.499105 INFO: Test AUC: 0.513
2:08:45.499216 INFO: Train AUC: 0.575
2:08:45.499251 INFO: AUC difference: 10.86%
2:08:45.499278 WARNING: AUC difference > 5%. This may indicate overfitting.
2:08:45.848790 INFO: Resetting torch num_threads to 100
2:08:45.850897 PROGRESS: === Extracted 1964 precursors and 11060 fragments ===
2:08:45.851341 INFO: === FDR correction performed with classifier version -1 ===
2:08:45.852822 PROGRESS: ============================= Precursor FDR =============================
2:08:45.852937 PROGRESS: Total precursors accumulated: 12
2:08:45.853014 PROGRESS: Target precursors: 12 (100.00%)
2:08:45.853076 PROGRESS: Decoy precursors: 0 (0.00%)
2:08:45.853139 PROGRESS: 
2:08:45.853197 PROGRESS: Precursor Summary:
2:08:45.854638 PROGRESS: Channel   0:	 0.050 FDR:    12; 0.010 FDR:    12; 0.001 FDR:    12
2:08:45.854739 PROGRESS: 
2:08:45.854805 PROGRESS: Protein Summary:
2:08:45.856384 PROGRESS: Channel   0:	 0.050 FDR:    12; 0.010 FDR:    12; 0.001 FDR:    12
2:08:45.856482 PROGRESS: =========================================================================
2:08:45.856857 INFO: Target number of precursors not reached yet.
2:08:45.956473 INFO: Starting optimization step 1.
2:08:45.956727 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:08:45.956828 INFO: Using rust extraction backend
2:08:45.956903 PROGRESS: Extracting batch of 3935 precursors
2:08:45.965952 INFO: === Search parameters used ===
2:08:45.966205 INFO: rt_error       : 805.611083984375
2:08:45.966270 INFO: mobility_error : 0.1
2:08:45.966337 INFO: num_candidates : 1
2:08:45.966395 INFO: ms1_error      : 3
2:08:45.966451 INFO: ms2_error      : 10
2:08:45.966511 INFO: fwhm_rt        : 5
2:08:45.966577 INFO: quant_window   : 3
2:08:45.966636 INFO: ==============================================
2:08:46.062540 INFO: performing precursor FDR with 40 features
2:08:46.062659 INFO: Decoy channel: -1
2:08:46.062689 INFO: competitive: True
2:08:46.068577 INFO: Setting torch num_threads to 2 for FDR classification task
2:08:46.071626 INFO: Estimating optimal hyperparameters - samples: 4,715, batch_size: 128, learning_rate: 1.77e-04
2:08:46.071730 INFO: Using random state 388375 for train-test-split
2:08:46.667296 INFO: Test AUC: 0.528
2:08:46.667412 INFO: Train AUC: 0.563
2:08:46.667447 INFO: AUC difference: 6.16%
2:08:46.667474 WARNING: AUC difference > 5%. This may indicate overfitting.
2:08:46.999424 INFO: Resetting torch num_threads to 100
2:08:47.003461 PROGRESS: === Extracted 5894 precursors and 33019 fragments ===
2:08:47.003969 INFO: === FDR correction performed with classifier version -1 ===
2:08:47.004599 PROGRESS: ============================= Precursor FDR =============================
2:08:47.004697 PROGRESS: Total precursors accumulated: 19
2:08:47.004763 PROGRESS: Target precursors: 19 (100.00%)
2:08:47.004819 PROGRESS: Decoy precursors: 0 (0.00%)
2:08:47.004883 PROGRESS: 
2:08:47.004935 PROGRESS: Precursor Summary:
2:08:47.006290 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
2:08:47.006385 PROGRESS: 
2:08:47.006446 PROGRESS: Protein Summary:
2:08:47.008105 PROGRESS: Channel   0:	 0.050 FDR:    19; 0.010 FDR:    19; 0.001 FDR:    19
2:08:47.008223 PROGRESS: =========================================================================
2:08:47.008726 INFO: Target number of precursors not reached yet.
2:08:47.108785 INFO: Starting optimization step 2.
2:08:47.109053 PROGRESS: === Extracting elution groups 3000 to 7000 ===
2:08:47.109157 INFO: Using rust extraction backend
2:08:47.109238 PROGRESS: Extracting batch of 7881 precursors
2:08:47.124925 INFO: === Search parameters used ===
2:08:47.125190 INFO: rt_error       : 805.611083984375
2:08:47.125260 INFO: mobility_error : 0.1
2:08:47.125316 INFO: num_candidates : 1
2:08:47.125369 INFO: ms1_error      : 3
2:08:47.125425 INFO: ms2_error      : 10
2:08:47.125501 INFO: fwhm_rt        : 5
2:08:47.125561 INFO: quant_window   : 3
2:08:47.125612 INFO: ==============================================
2:08:47.299988 INFO: performing precursor FDR with 40 features
2:08:47.300113 INFO: Decoy channel: -1
2:08:47.300158 INFO: competitive: True
2:08:47.308498 INFO: Setting torch num_threads to 2 for FDR classification task
2:08:47.314884 INFO: Estimating optimal hyperparameters - samples: 11,000, batch_size: 128, learning_rate: 1.77e-04
2:08:47.315041 INFO: Using random state 364411 for train-test-split
2:08:48.718990 INFO: Test AUC: 0.536
2:08:48.719118 INFO: Train AUC: 0.574
2:08:48.719155 INFO: AUC difference: 6.68%
2:08:48.719182 WARNING: AUC difference > 5%. This may indicate overfitting.
2:08:49.062626 INFO: Resetting torch num_threads to 100
2:08:49.068470 PROGRESS: === Extracted 13751 precursors and 77257 fragments ===
2:08:49.069021 INFO: === FDR correction performed with classifier version -1 ===
2:08:49.069706 PROGRESS: ============================= Precursor FDR =============================
2:08:49.069813 PROGRESS: Total precursors accumulated: 59
2:08:49.069898 PROGRESS: Target precursors: 59 (100.00%)
2:08:49.069961 PROGRESS: Decoy precursors: 0 (0.00%)
2:08:49.070024 PROGRESS: 
2:08:49.070084 PROGRESS: Precursor Summary:
2:08:49.071496 PROGRESS: Channel   0:	 0.050 FDR:    59; 0.010 FDR:    59; 0.001 FDR:    59
2:08:49.071615 PROGRESS: 
2:08:49.071690 PROGRESS: Protein Summary:
2:08:49.073265 PROGRESS: Channel   0:	 0.050 FDR:    58; 0.010 FDR:    58; 0.001 FDR:    58
2:08:49.073367 PROGRESS: =========================================================================
2:08:49.073857 INFO: Target number of precursors not reached yet.
2:08:49.188661 INFO: Starting optimization step 3.
2:08:49.188928 PROGRESS: === Extracting elution groups 7000 to 15000 ===
2:08:49.189028 INFO: Using rust extraction backend
2:08:49.189103 PROGRESS: Extracting batch of 15776 precursors
2:08:49.218666 INFO: === Search parameters used ===
2:08:49.218951 INFO: rt_error       : 805.611083984375
2:08:49.219021 INFO: mobility_error : 0.1
2:08:49.219078 INFO: num_candidates : 1
2:08:49.219139 INFO: ms1_error      : 3
2:08:49.219193 INFO: ms2_error      : 10
2:08:49.219260 INFO: fwhm_rt        : 5
2:08:49.219314 INFO: quant_window   : 3
2:08:49.219370 INFO: ==============================================
2:08:49.532512 INFO: performing precursor FDR with 40 features
2:08:49.532640 INFO: Decoy channel: -1
2:08:49.532674 INFO: competitive: True
2:08:49.548893 INFO: Setting torch num_threads to 2 for FDR classification task
2:08:49.558910 INFO: Estimating optimal hyperparameters - samples: 23,603, batch_size: 128, learning_rate: 1.77e-04
2:08:49.559143 INFO: Using random state 958738 for train-test-split
2:08:52.035626 INFO: Test AUC: 0.555
2:08:52.035751 INFO: Train AUC: 0.594
2:08:52.035785 INFO: AUC difference: 6.50%
2:08:52.035810 WARNING: AUC difference > 5%. This may indicate overfitting.
2:08:52.321123 INFO: Resetting torch num_threads to 100
2:08:52.329450 PROGRESS: === Extracted 29504 precursors and 165208 fragments ===
2:08:52.330016 INFO: === FDR correction performed with classifier version -1 ===
2:08:52.330552 PROGRESS: ============================= Precursor FDR =============================
2:08:52.330641 PROGRESS: Total precursors accumulated: 117
2:08:52.330699 PROGRESS: Target precursors: 116 (99.15%)
2:08:52.330749 PROGRESS: Decoy precursors: 1 (0.85%)
2:08:52.330796 PROGRESS: 
2:08:52.330840 PROGRESS: Precursor Summary:
2:08:52.331827 PROGRESS: Channel   0:	 0.050 FDR:   116; 0.010 FDR:   116; 0.001 FDR:   116
2:08:52.331923 PROGRESS: 
2:08:52.331978 PROGRESS: Protein Summary:
2:08:52.333109 PROGRESS: Channel   0:	 0.050 FDR:   113; 0.010 FDR:   113; 0.001 FDR:   113
2:08:52.333197 PROGRESS: =========================================================================
2:08:52.333732 INFO: Target number of precursors not reached yet.
2:08:52.458971 INFO: Starting optimization step 4.
2:08:52.459233 PROGRESS: === Extracting elution groups 15000 to 31000 ===
2:08:52.459315 INFO: Using rust extraction backend
2:08:52.459375 PROGRESS: Extracting batch of 31591 precursors
2:08:52.515106 INFO: === Search parameters used ===
2:08:52.515371 INFO: rt_error       : 805.611083984375
2:08:52.515423 INFO: mobility_error : 0.1
2:08:52.515468 INFO: num_candidates : 1
2:08:52.515509 INFO: ms1_error      : 3
2:08:52.515548 INFO: ms2_error      : 10
2:08:52.515588 INFO: fwhm_rt        : 5
2:08:52.515627 INFO: quant_window   : 3
2:08:52.515666 INFO: ==============================================
2:08:52.979766 INFO: performing precursor FDR with 40 features
2:08:52.979914 INFO: Decoy channel: -1
2:08:52.979947 INFO: competitive: True
2:08:53.011601 INFO: Setting torch num_threads to 2 for FDR classification task
2:08:53.031571 INFO: Estimating optimal hyperparameters - samples: 48,809, batch_size: 199, learning_rate: 2.20e-04
2:08:53.031868 INFO: Using random state 319468 for train-test-split
2:08:57.739148 INFO: Test AUC: 0.590
2:08:57.739289 INFO: Train AUC: 0.608
2:08:57.739327 INFO: AUC difference: 2.93%
2:08:58.092680 INFO: Resetting torch num_threads to 100
2:08:58.112295 PROGRESS: === Extracted 61012 precursors and 341385 fragments ===
2:08:58.113052 INFO: === FDR correction performed with classifier version -1 ===
2:08:58.113807 PROGRESS: ============================= Precursor FDR =============================
2:08:58.113912 PROGRESS: Total precursors accumulated: 271
2:08:58.113990 PROGRESS: Target precursors: 269 (99.26%)
2:08:58.114051 PROGRESS: Decoy precursors: 2 (0.74%)
2:08:58.114106 PROGRESS: 
2:08:58.114166 PROGRESS: Precursor Summary:
2:08:58.115515 PROGRESS: Channel   0:	 0.050 FDR:   269; 0.010 FDR:   269; 0.001 FDR:   243
2:08:58.115612 PROGRESS: 
2:08:58.115687 PROGRESS: Protein Summary:
2:08:58.117266 PROGRESS: Channel   0:	 0.050 FDR:   256; 0.010 FDR:   256; 0.001 FDR:   233
2:08:58.117379 PROGRESS: =========================================================================
2:08:58.119448 INFO: Target number of precursors not reached yet.
2:08:58.331919 INFO: Starting optimization step 5.
2:08:58.332205 PROGRESS: === Extracting elution groups 31000 to 63000 ===
2:08:58.332302 INFO: Using rust extraction backend
2:08:58.332375 PROGRESS: Extracting batch of 63056 precursors
2:08:58.446300 INFO: === Search parameters used ===
2:08:58.446617 INFO: rt_error       : 805.611083984375
2:08:58.446684 INFO: mobility_error : 0.1
2:08:58.446746 INFO: num_candidates : 1
2:08:58.446806 INFO: ms1_error      : 3
2:08:58.446858 INFO: ms2_error      : 10
2:08:58.446906 INFO: fwhm_rt        : 5
2:08:58.446961 INFO: quant_window   : 3
2:08:58.447010 INFO: ==============================================
2:08:59.239640 INFO: performing precursor FDR with 40 features
2:08:59.239776 INFO: Decoy channel: -1
2:08:59.239808 INFO: competitive: True
2:08:59.317526 INFO: Setting torch num_threads to 2 for FDR classification task
2:08:59.370272 INFO: Estimating optimal hyperparameters - samples: 99,130, batch_size: 406, learning_rate: 3.15e-04
2:08:59.370665 INFO: Using random state 649770 for train-test-split
2:09:04.698266 INFO: Test AUC: 0.586
2:09:04.698421 INFO: Train AUC: 0.608
2:09:04.698454 INFO: AUC difference: 3.63%
2:09:05.000396 INFO: Resetting torch num_threads to 100
2:09:05.026217 PROGRESS: === Extracted 123913 precursors and 694288 fragments ===
2:09:05.026918 INFO: === FDR correction performed with classifier version -1 ===
2:09:05.027602 PROGRESS: ============================= Precursor FDR =============================
2:09:05.027695 PROGRESS: Total precursors accumulated: 634
2:09:05.027759 PROGRESS: Target precursors: 628 (99.05%)
2:09:05.027812 PROGRESS: Decoy precursors: 6 (0.95%)
2:09:05.027903 PROGRESS: 
2:09:05.027964 PROGRESS: Precursor Summary:
2:09:05.029120 PROGRESS: Channel   0:	 0.050 FDR:   628; 0.010 FDR:   628; 0.001 FDR:   386
2:09:05.029209 PROGRESS: 
2:09:05.029264 PROGRESS: Protein Summary:
2:09:05.030650 PROGRESS: Channel   0:	 0.050 FDR:   575; 0.010 FDR:   575; 0.001 FDR:   363
2:09:05.030740 PROGRESS: =========================================================================
2:09:05.032963 INFO: Target number of precursors not reached yet.
2:09:05.358379 INFO: Starting optimization step 6.
2:09:05.358650 PROGRESS: === Extracting elution groups 63000 to 127000 ===
2:09:05.358746 INFO: Using rust extraction backend
2:09:05.358812 PROGRESS: Extracting batch of 126233 precursors
2:09:05.582389 INFO: === Search parameters used ===
2:09:05.582665 INFO: rt_error       : 805.611083984375
2:09:05.582729 INFO: mobility_error : 0.1
2:09:05.582782 INFO: num_candidates : 1
2:09:05.582828 INFO: ms1_error      : 3
2:09:05.582871 INFO: ms2_error      : 10
2:09:05.582914 INFO: fwhm_rt        : 5
2:09:05.582958 INFO: quant_window   : 3
2:09:05.583000 INFO: ==============================================
2:09:06.799955 INFO: performing precursor FDR with 40 features
2:09:06.800075 INFO: Decoy channel: -1
2:09:06.800103 INFO: competitive: True
2:09:06.905678 INFO: Setting torch num_threads to 2 for FDR classification task
2:09:06.997450 INFO: Estimating optimal hyperparameters - samples: 199,919, batch_size: 818, learning_rate: 4.47e-04
2:09:06.997869 INFO: Using random state 814117 for train-test-split
2:09:12.616454 INFO: Test AUC: 0.596
2:09:12.616617 INFO: Train AUC: 0.609
2:09:12.616657 INFO: AUC difference: 2.23%
2:09:13.044878 INFO: Resetting torch num_threads to 100
2:09:13.112266 PROGRESS: === Extracted 249899 precursors and 1399062 fragments ===
2:09:13.113090 INFO: === FDR correction performed with classifier version -1 ===
2:09:13.114210 PROGRESS: ============================= Precursor FDR =============================
2:09:13.114313 PROGRESS: Total precursors accumulated: 1,354
2:09:13.114393 PROGRESS: Target precursors: 1,341 (99.04%)
2:09:13.114455 PROGRESS: Decoy precursors: 13 (0.96%)
2:09:13.114517 PROGRESS: 
2:09:13.114576 PROGRESS: Precursor Summary:
2:09:13.116357 PROGRESS: Channel   0:	 0.050 FDR: 1,341; 0.010 FDR: 1,341; 0.001 FDR: 1,070
2:09:13.116469 PROGRESS: 
2:09:13.116534 PROGRESS: Protein Summary:
2:09:13.118798 PROGRESS: Channel   0:	 0.050 FDR: 1,130; 0.010 FDR: 1,130; 0.001 FDR:   920
2:09:13.118900 PROGRESS: =========================================================================
2:09:13.126503 INFO: Target number of precursors reached.
2:09:13.366455 INFO: fragments_df: keeping 5000 of 1399062 [sum(precursor_idx_mask)=14308 sum(mass_error_mask)=1399062 stop_rank=5000
2:09:13.878530 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:09:14.297041 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:09:15.273897 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:09:15.274364 INFO: Using score_cutoff 12.532598653793336 (fac=0.99, q=1)
2:09:15.274704 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:09:15.274786 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:09:15.274844 INFO: Updating optimization_manager: score_cutoff        : 0 -> 12.532598653793336
2:09:15.274913 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:09:15.430661 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:09:15.784331 INFO: Updating optimization_manager: classifier_version  : -1 -> 6
2:09:15.784619 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:09:15.784744 INFO: Starting optimization step 7.
2:09:15.784824 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:09:15.784913 INFO: Using rust extraction backend
2:09:15.784992 PROGRESS: Extracting batch of 250442 precursors
2:09:16.231158 INFO: === Search parameters used ===
2:09:16.231464 INFO: rt_error       : 805.611083984375
2:09:16.231542 INFO: mobility_error : 0.1
2:09:16.231604 INFO: num_candidates : 3
2:09:16.231660 INFO: ms1_error      : 3
2:09:16.231714 INFO: ms2_error      : 10
2:09:16.231783 INFO: fwhm_rt        : 3.0
2:09:16.231866 INFO: quant_window   : 3
2:09:16.231922 INFO: ==============================================
2:09:20.183472 INFO: performing precursor FDR with 40 features
2:09:20.183621 INFO: Decoy channel: -1
2:09:20.183651 INFO: competitive: True
2:09:20.432869 INFO: Setting torch num_threads to 2 for FDR classification task
2:09:20.805699 INFO: Estimating optimal hyperparameters - samples: 599,884, batch_size: 2,457, learning_rate: 7.75e-04
2:09:20.806903 INFO: Using random state 636236 for train-test-split
2:09:32.065235 INFO: Test AUC: 0.595
2:09:32.065401 INFO: Train AUC: 0.608
2:09:32.065440 INFO: AUC difference: 2.13%
2:09:32.685933 INFO: Resetting torch num_threads to 100
2:09:32.730013 PROGRESS: === Extracted 749855 precursors and 4032589 fragments ===
2:09:32.730580 INFO: === FDR correction performed with classifier version 6 ===
2:09:32.731513 PROGRESS: ============================= Precursor FDR =============================
2:09:32.731616 PROGRESS: Total precursors accumulated: 1,490
2:09:32.731697 PROGRESS: Target precursors: 1,476 (99.06%)
2:09:32.731765 PROGRESS: Decoy precursors: 14 (0.94%)
2:09:32.731836 PROGRESS: 
2:09:32.731894 PROGRESS: Precursor Summary:
2:09:32.733627 PROGRESS: Channel   0:	 0.050 FDR: 1,476; 0.010 FDR: 1,476; 0.001 FDR: 1,110
2:09:32.733729 PROGRESS: 
2:09:32.733807 PROGRESS: Protein Summary:
2:09:32.736407 PROGRESS: Channel   0:	 0.050 FDR: 1,235; 0.010 FDR: 1,235; 0.001 FDR:   948
2:09:32.736531 PROGRESS: =========================================================================
2:09:32.761794 INFO: Target number of precursors reached.
2:09:33.420690 INFO: fragments_df: keeping 5000 of 4032589 [sum(precursor_idx_mask)=35402 sum(mass_error_mask)=4032589 stop_rank=5000
2:09:34.020314 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:09:34.541854 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:09:35.649273 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:09:35.649820 INFO: Using score_cutoff 12.213719823360442 (fac=0.99, q=1)
2:09:35.650189 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:09:35.650275 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:09:35.650337 INFO: Updating optimization_manager: score_cutoff        : 12.532598653793336 -> 12.213719823360442
2:09:35.650410 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:09:35.810674 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:09:36.158048 INFO: === checking if optimization conditions were reached ===
2:09:36.160756 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
2:09:36.160954 INFO: Updating optimization_manager: classifier_version  : 6 -> 7
2:09:36.161058 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:09:36.161141 INFO: ==============================================
2:09:36.161228 INFO: Starting optimization step 8.
2:09:36.161306 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:09:36.161392 INFO: Using rust extraction backend
2:09:36.161472 PROGRESS: Extracting batch of 250442 precursors
2:09:36.611990 INFO: === Search parameters used ===
2:09:36.612300 INFO: rt_error       : 805.611083984375
2:09:36.612375 INFO: mobility_error : 0.1
2:09:36.612446 INFO: num_candidates : 3
2:09:36.612510 INFO: ms1_error      : 3
2:09:36.612567 INFO: ms2_error      : 10.0
2:09:36.612622 INFO: fwhm_rt        : 3.0
2:09:36.612694 INFO: quant_window   : 3
2:09:36.612750 INFO: ==============================================
2:09:40.666803 INFO: performing precursor FDR with 40 features
2:09:40.667002 INFO: Decoy channel: -1
2:09:40.667038 INFO: competitive: True
2:09:40.886793 INFO: Setting torch num_threads to 2 for FDR classification task
2:09:41.217459 INFO: Estimating optimal hyperparameters - samples: 599,852, batch_size: 2,456, learning_rate: 7.74e-04
2:09:41.218713 INFO: Using random state 405325 for train-test-split
2:09:54.550651 INFO: Test AUC: 0.602
2:09:54.550865 INFO: Train AUC: 0.615
2:09:54.550909 INFO: AUC difference: 2.04%
2:09:55.174749 INFO: Resetting torch num_threads to 100
2:09:55.241956 PROGRESS: === Extracted 749815 precursors and 4033089 fragments ===
2:09:55.242572 INFO: === FDR correction performed with classifier version 7 ===
2:09:55.243520 PROGRESS: ============================= Precursor FDR =============================
2:09:55.243647 PROGRESS: Total precursors accumulated: 1,339
2:09:55.243721 PROGRESS: Target precursors: 1,326 (99.03%)
2:09:55.243791 PROGRESS: Decoy precursors: 13 (0.97%)
2:09:55.243861 PROGRESS: 
2:09:55.243918 PROGRESS: Precursor Summary:
2:09:55.245502 PROGRESS: Channel   0:	 0.050 FDR: 1,326; 0.010 FDR: 1,326; 0.001 FDR:     1
2:09:55.245608 PROGRESS: 
2:09:55.245675 PROGRESS: Protein Summary:
2:09:55.247665 PROGRESS: Channel   0:	 0.050 FDR: 1,121; 0.010 FDR: 1,121; 0.001 FDR:     1
2:09:55.247772 PROGRESS: =========================================================================
2:09:55.274430 INFO: Target number of precursors reached.
2:09:55.946110 INFO: fragments_df: keeping 5000 of 4033089 [sum(precursor_idx_mask)=32034 sum(mass_error_mask)=4033089 stop_rank=5000
2:09:56.625809 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:09:56.923952 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:09:57.942481 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:09:57.943104 INFO: Using score_cutoff 12.11005635023117 (fac=0.99, q=1)
2:09:57.943500 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:09:57.943588 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:09:57.943651 INFO: Updating optimization_manager: score_cutoff        : 12.213719823360442 -> 12.11005635023117
2:09:57.943729 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:09:58.102596 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:09:58.450993 INFO: === checking if optimization conditions were reached ===
2:09:58.453587 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:09:58.453704 INFO: Updating optimization_manager: classifier_version  : 7 -> 8
2:09:58.453784 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:09:58.453860 INFO: ==============================================
2:09:58.453944 INFO: Starting optimization step 9.
2:09:58.454013 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:09:58.454098 INFO: Using rust extraction backend
2:09:58.454169 PROGRESS: Extracting batch of 250442 precursors
2:09:58.908054 INFO: === Search parameters used ===
2:09:58.908365 INFO: rt_error       : 805.611083984375
2:09:58.908437 INFO: mobility_error : 0.1
2:09:58.908513 INFO: num_candidates : 3
2:09:58.908569 INFO: ms1_error      : 3
2:09:58.908618 INFO: ms2_error      : 10.0
2:09:58.908667 INFO: fwhm_rt        : 3.0
2:09:58.908719 INFO: quant_window   : 3
2:09:58.908770 INFO: ==============================================
2:10:03.105293 INFO: performing precursor FDR with 40 features
2:10:03.105423 INFO: Decoy channel: -1
2:10:03.105452 INFO: competitive: True
2:10:03.311300 INFO: Setting torch num_threads to 2 for FDR classification task
2:10:03.658144 INFO: Estimating optimal hyperparameters - samples: 599,854, batch_size: 2,457, learning_rate: 7.75e-04
2:10:03.659281 INFO: Using random state 453190 for train-test-split
2:10:19.479157 INFO: Test AUC: 0.607
2:10:19.479391 INFO: Train AUC: 0.618
2:10:19.479438 INFO: AUC difference: 1.79%
2:10:20.101807 INFO: Resetting torch num_threads to 100
2:10:20.144881 PROGRESS: === Extracted 749818 precursors and 4033588 fragments ===
2:10:20.145417 INFO: === FDR correction performed with classifier version 8 ===
2:10:20.146126 PROGRESS: ============================= Precursor FDR =============================
2:10:20.146217 PROGRESS: Total precursors accumulated: 1,543
2:10:20.146276 PROGRESS: Target precursors: 1,528 (99.03%)
2:10:20.146327 PROGRESS: Decoy precursors: 15 (0.97%)
2:10:20.146380 PROGRESS: 
2:10:20.146426 PROGRESS: Precursor Summary:
2:10:20.147836 PROGRESS: Channel   0:	 0.050 FDR: 1,528; 0.010 FDR: 1,528; 0.001 FDR: 1,242
2:10:20.147931 PROGRESS: 
2:10:20.147988 PROGRESS: Protein Summary:
2:10:20.149808 PROGRESS: Channel   0:	 0.050 FDR: 1,286; 0.010 FDR: 1,286; 0.001 FDR: 1,056
2:10:20.149899 PROGRESS: =========================================================================
2:10:20.166229 INFO: Target number of precursors reached.
2:10:20.706458 INFO: fragments_df: keeping 5000 of 4033588 [sum(precursor_idx_mask)=36509 sum(mass_error_mask)=4033588 stop_rank=5000
2:10:21.185606 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:10:21.546922 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:10:22.587752 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:10:22.588320 INFO: Using score_cutoff 11.84794026031494 (fac=0.99, q=1)
2:10:22.588722 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:10:22.588812 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:10:22.588882 INFO: Updating optimization_manager: score_cutoff        : 12.11005635023117 -> 11.84794026031494
2:10:22.588961 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:10:22.750655 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:10:23.161988 INFO: === checking if optimization conditions were reached ===
2:10:23.165042 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:10:23.165180 INFO: Updating optimization_manager: classifier_version  : 8 -> 9
2:10:23.165264 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:10:23.165336 INFO: ==============================================
2:10:23.165423 INFO: Starting optimization step 10.
2:10:23.165507 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:10:23.165595 INFO: Using rust extraction backend
2:10:23.165690 PROGRESS: Extracting batch of 250442 precursors
2:10:23.649483 INFO: === Search parameters used ===
2:10:23.650403 INFO: rt_error       : 805.611083984375
2:10:23.650466 INFO: mobility_error : 0.1
2:10:23.650513 INFO: num_candidates : 3
2:10:23.650555 INFO: ms1_error      : 3
2:10:23.650594 INFO: ms2_error      : 10.0
2:10:23.650634 INFO: fwhm_rt        : 3.0
2:10:23.650672 INFO: quant_window   : 3
2:10:23.650711 INFO: ==============================================
2:10:27.868538 INFO: performing precursor FDR with 40 features
2:10:27.868698 INFO: Decoy channel: -1
2:10:27.868732 INFO: competitive: True
2:10:28.080142 INFO: Setting torch num_threads to 2 for FDR classification task
2:10:28.421350 INFO: Estimating optimal hyperparameters - samples: 599,857, batch_size: 2,457, learning_rate: 7.75e-04
2:10:28.422344 INFO: Using random state 63576 for train-test-split
2:10:44.104009 INFO: Test AUC: 0.609
2:10:44.104195 INFO: Train AUC: 0.621
2:10:44.104238 INFO: AUC difference: 1.93%
2:10:44.720867 INFO: Resetting torch num_threads to 100
2:10:44.768108 PROGRESS: === Extracted 749822 precursors and 4033443 fragments ===
2:10:44.768729 INFO: === FDR correction performed with classifier version 9 ===
2:10:44.769658 PROGRESS: ============================= Precursor FDR =============================
2:10:44.769768 PROGRESS: Total precursors accumulated: 1,651
2:10:44.769848 PROGRESS: Target precursors: 1,635 (99.03%)
2:10:44.769910 PROGRESS: Decoy precursors: 16 (0.97%)
2:10:44.769975 PROGRESS: 
2:10:44.770033 PROGRESS: Precursor Summary:
2:10:44.771860 PROGRESS: Channel   0:	 0.050 FDR: 1,635; 0.010 FDR: 1,635; 0.001 FDR: 1,090
2:10:44.771964 PROGRESS: 
2:10:44.772038 PROGRESS: Protein Summary:
2:10:44.774776 PROGRESS: Channel   0:	 0.050 FDR: 1,367; 0.010 FDR: 1,367; 0.001 FDR:   936
2:10:44.774898 PROGRESS: =========================================================================
2:10:44.805360 INFO: Target number of precursors reached.
2:10:45.463303 INFO: fragments_df: keeping 5000 of 4033443 [sum(precursor_idx_mask)=38868 sum(mass_error_mask)=4033443 stop_rank=5000
2:10:46.149538 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:10:46.630029 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:10:47.713728 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:10:47.714658 INFO: Using score_cutoff 11.349030624389648 (fac=0.99, q=1)
2:10:47.715057 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:10:47.715160 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:10:47.715226 INFO: Updating optimization_manager: score_cutoff        : 11.84794026031494 -> 11.349030624389648
2:10:47.715320 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:10:47.879115 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:10:48.235118 INFO: === checking if optimization conditions were reached ===
2:10:48.238093 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:10:48.238315 INFO: Updating optimization_manager: classifier_version  : 9 -> 10
2:10:48.238409 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:10:48.238509 INFO: ==============================================
2:10:48.238605 INFO: Starting optimization step 11.
2:10:48.238698 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:10:48.238824 INFO: Using rust extraction backend
2:10:48.238951 PROGRESS: Extracting batch of 250442 precursors
2:10:48.692107 INFO: === Search parameters used ===
2:10:48.692419 INFO: rt_error       : 805.611083984375
2:10:48.692494 INFO: mobility_error : 0.1
2:10:48.692566 INFO: num_candidates : 3
2:10:48.692619 INFO: ms1_error      : 3
2:10:48.692675 INFO: ms2_error      : 10.0
2:10:48.692730 INFO: fwhm_rt        : 3.0
2:10:48.692780 INFO: quant_window   : 3
2:10:48.692835 INFO: ==============================================
2:10:52.943904 INFO: performing precursor FDR with 40 features
2:10:52.944055 INFO: Decoy channel: -1
2:10:52.944091 INFO: competitive: True
2:10:53.189932 INFO: Setting torch num_threads to 2 for FDR classification task
2:10:53.612450 INFO: Estimating optimal hyperparameters - samples: 599,858, batch_size: 2,457, learning_rate: 7.75e-04
2:10:53.613652 INFO: Using random state 262758 for train-test-split
2:11:08.806852 INFO: Test AUC: 0.612
2:11:08.807096 INFO: Train AUC: 0.624
2:11:08.808064 INFO: AUC difference: 1.96%
2:11:09.425730 INFO: Resetting torch num_threads to 100
2:11:09.465430 PROGRESS: === Extracted 749823 precursors and 4033382 fragments ===
2:11:09.466026 INFO: === FDR correction performed with classifier version 10 ===
2:11:09.466918 PROGRESS: ============================= Precursor FDR =============================
2:11:09.467026 PROGRESS: Total precursors accumulated: 1,608
2:11:09.467103 PROGRESS: Target precursors: 1,593 (99.07%)
2:11:09.467165 PROGRESS: Decoy precursors: 15 (0.93%)
2:11:09.467225 PROGRESS: 
2:11:09.467286 PROGRESS: Precursor Summary:
2:11:09.469148 PROGRESS: Channel   0:	 0.050 FDR: 1,593; 0.010 FDR: 1,593; 0.001 FDR: 1,279
2:11:09.469260 PROGRESS: 
2:11:09.469326 PROGRESS: Protein Summary:
2:11:09.471690 PROGRESS: Channel   0:	 0.050 FDR: 1,341; 0.010 FDR: 1,341; 0.001 FDR: 1,087
2:11:09.471794 PROGRESS: =========================================================================
2:11:09.497473 INFO: Target number of precursors reached.
2:11:10.152483 INFO: fragments_df: keeping 5000 of 4033382 [sum(precursor_idx_mask)=37141 sum(mass_error_mask)=4033382 stop_rank=5000
2:11:10.700137 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:11:11.097711 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:11:12.203327 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:11:12.203872 INFO: Using score_cutoff 9.92843632850647 (fac=0.99, q=1)
2:11:12.204266 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:11:12.204361 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:11:12.204436 INFO: Updating optimization_manager: score_cutoff        : 11.349030624389648 -> 9.92843632850647
2:11:12.204501 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:11:12.366645 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:11:12.725270 INFO: === checking if optimization conditions were reached ===
2:11:12.727985 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:11:12.728175 INFO: Updating optimization_manager: classifier_version  : 10 -> 11
2:11:12.728255 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:11:12.728326 INFO: ==============================================
2:11:12.728418 PROGRESS: Optimization finished for ms2_error.
2:11:13.157301 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:11:13.318598 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:11:13.666225 INFO: Starting optimization step 0.
2:11:13.666511 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:11:13.666617 INFO: Using rust extraction backend
2:11:13.666704 PROGRESS: Extracting batch of 250442 precursors
2:11:14.116528 INFO: === Search parameters used ===
2:11:14.116842 INFO: rt_error       : 805.611083984375
2:11:14.116910 INFO: mobility_error : 0.1
2:11:14.116995 INFO: num_candidates : 3
2:11:14.117054 INFO: ms1_error      : 3
2:11:14.117106 INFO: ms2_error      : 10.0
2:11:14.117162 INFO: fwhm_rt        : 3.0
2:11:14.117216 INFO: quant_window   : 3
2:11:14.117266 INFO: ==============================================
2:11:18.234750 INFO: performing precursor FDR with 40 features
2:11:18.234889 INFO: Decoy channel: -1
2:11:18.234925 INFO: competitive: True
2:11:18.481022 INFO: Setting torch num_threads to 2 for FDR classification task
2:11:18.902893 INFO: Estimating optimal hyperparameters - samples: 599,848, batch_size: 2,456, learning_rate: 7.74e-04
2:11:18.904222 INFO: Using random state 285021 for train-test-split
2:11:33.028671 INFO: Test AUC: 0.613
2:11:33.028806 INFO: Train AUC: 0.627
2:11:33.028841 INFO: AUC difference: 2.13%
2:11:35.206760 INFO: Resetting torch num_threads to 100
2:11:35.257230 PROGRESS: === Extracted 749811 precursors and 4033409 fragments ===
2:11:35.257844 INFO: === FDR correction performed with classifier version 11 ===
2:11:35.258868 PROGRESS: ============================= Precursor FDR =============================
2:11:35.258990 PROGRESS: Total precursors accumulated: 1,629
2:11:35.259071 PROGRESS: Target precursors: 1,613 (99.02%)
2:11:35.259135 PROGRESS: Decoy precursors: 16 (0.98%)
2:11:35.259193 PROGRESS: 
2:11:35.259257 PROGRESS: Precursor Summary:
2:11:35.261208 PROGRESS: Channel   0:	 0.050 FDR: 1,613; 0.010 FDR: 1,613; 0.001 FDR: 1,155
2:11:35.261332 PROGRESS: 
2:11:35.261403 PROGRESS: Protein Summary:
2:11:35.263876 PROGRESS: Channel   0:	 0.050 FDR: 1,350; 0.010 FDR: 1,350; 0.001 FDR:   984
2:11:35.263988 PROGRESS: =========================================================================
2:11:35.289723 INFO: Target number of precursors reached.
2:11:35.944768 INFO: fragments_df: keeping 5000 of 4033409 [sum(precursor_idx_mask)=38254 sum(mass_error_mask)=4033409 stop_rank=5000
2:11:36.587455 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:11:37.004323 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:11:38.044412 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:11:38.044960 INFO: Using score_cutoff 11.032579804229735 (fac=0.99, q=1)
2:11:38.045322 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:11:38.045410 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:11:38.045489 INFO: Updating optimization_manager: score_cutoff        : 9.92843632850647 -> 11.032579804229735
2:11:38.045560 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:11:38.212428 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:11:38.582757 INFO: === checking if optimization conditions were reached ===
2:11:38.583091 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:11:38.586596 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 469.19371491891314
2:11:38.586722 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 469.1937.
2:11:38.586802 INFO: ==============================================
2:11:38.586895 INFO: Starting optimization step 1.
2:11:38.586971 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:11:38.587059 INFO: Using rust extraction backend
2:11:38.587132 PROGRESS: Extracting batch of 250442 precursors
2:11:39.030990 INFO: === Search parameters used ===
2:11:39.031323 INFO: rt_error       : 469.19371491891314
2:11:39.031404 INFO: mobility_error : 0.1
2:11:39.031472 INFO: num_candidates : 3
2:11:39.031534 INFO: ms1_error      : 3
2:11:39.031595 INFO: ms2_error      : 10.0
2:11:39.031652 INFO: fwhm_rt        : 3.0
2:11:39.031708 INFO: quant_window   : 3
2:11:39.031767 INFO: ==============================================
2:11:42.941189 INFO: performing precursor FDR with 40 features
2:11:42.941323 INFO: Decoy channel: -1
2:11:42.941355 INFO: competitive: True
2:11:43.188110 INFO: Setting torch num_threads to 2 for FDR classification task
2:11:43.541327 INFO: Estimating optimal hyperparameters - samples: 598,906, batch_size: 2,453, learning_rate: 7.74e-04
2:11:43.542531 INFO: Using random state 285021 for train-test-split
2:11:58.282979 INFO: Test AUC: 0.610
2:11:58.283176 INFO: Train AUC: 0.624
2:11:58.284097 INFO: AUC difference: 2.17%
2:11:58.924821 INFO: Resetting torch num_threads to 100
2:11:59.070248 PROGRESS: === Extracted 748633 precursors and 3948630 fragments ===
2:11:59.070872 INFO: === FDR correction performed with classifier version 11 ===
2:11:59.072246 PROGRESS: ============================= Precursor FDR =============================
2:11:59.072392 PROGRESS: Total precursors accumulated: 1,733
2:11:59.072470 PROGRESS: Target precursors: 1,716 (99.02%)
2:11:59.072529 PROGRESS: Decoy precursors: 17 (0.98%)
2:11:59.072596 PROGRESS: 
2:11:59.072652 PROGRESS: Precursor Summary:
2:11:59.074950 PROGRESS: Channel   0:	 0.050 FDR: 1,716; 0.010 FDR: 1,716; 0.001 FDR: 1,237
2:11:59.075079 PROGRESS: 
2:11:59.075147 PROGRESS: Protein Summary:
2:11:59.077714 PROGRESS: Channel   0:	 0.050 FDR: 1,433; 0.010 FDR: 1,433; 0.001 FDR: 1,046
2:11:59.077833 PROGRESS: =========================================================================
2:11:59.105421 INFO: Target number of precursors reached.
2:11:59.759798 INFO: fragments_df: keeping 5000 of 3948630 [sum(precursor_idx_mask)=40395 sum(mass_error_mask)=3948630 stop_rank=5000
2:12:00.373558 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:12:00.875396 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:12:01.956887 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:12:01.957421 INFO: Using score_cutoff 10.898978087425233 (fac=0.99, q=1)
2:12:01.957817 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:12:01.957906 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:12:01.957970 INFO: Updating optimization_manager: score_cutoff        : 11.032579804229735 -> 10.898978087425233
2:12:01.958040 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:12:02.122359 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:12:02.479653 INFO: === checking if optimization conditions were reached ===
2:12:02.480008 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:12:02.483515 INFO: Updating optimization_manager: rt_error            : 469.19371491891314 -> 475.84518305889094
2:12:02.483634 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 475.8452.
2:12:02.483710 INFO: ==============================================
2:12:02.483802 INFO: Starting optimization step 2.
2:12:02.483917 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:12:02.484007 INFO: Using rust extraction backend
2:12:02.484095 PROGRESS: Extracting batch of 250442 precursors
2:12:02.931232 INFO: === Search parameters used ===
2:12:02.931551 INFO: rt_error       : 475.84518305889094
2:12:02.931635 INFO: mobility_error : 0.1
2:12:02.931706 INFO: num_candidates : 3
2:12:02.931780 INFO: ms1_error      : 3
2:12:02.931860 INFO: ms2_error      : 10.0
2:12:02.931927 INFO: fwhm_rt        : 3.0
2:12:02.931987 INFO: quant_window   : 3
2:12:02.932044 INFO: ==============================================
2:12:06.812981 INFO: performing precursor FDR with 40 features
2:12:06.813128 INFO: Decoy channel: -1
2:12:06.813160 INFO: competitive: True
2:12:07.057947 INFO: Setting torch num_threads to 2 for FDR classification task
2:12:07.477441 INFO: Estimating optimal hyperparameters - samples: 599,026, batch_size: 2,453, learning_rate: 7.74e-04
2:12:07.478753 INFO: Using random state 285021 for train-test-split
2:12:18.348860 INFO: Test AUC: 0.610
2:12:18.349024 INFO: Train AUC: 0.625
2:12:18.349065 INFO: AUC difference: 2.50%
2:12:18.898576 INFO: Resetting torch num_threads to 100
2:12:18.927865 PROGRESS: === Extracted 748783 precursors and 3959717 fragments ===
2:12:18.928365 INFO: === FDR correction performed with classifier version 11 ===
2:12:18.929146 PROGRESS: ============================= Precursor FDR =============================
2:12:18.929241 PROGRESS: Total precursors accumulated: 1,780
2:12:18.929303 PROGRESS: Target precursors: 1,763 (99.04%)
2:12:18.929356 PROGRESS: Decoy precursors: 17 (0.96%)
2:12:18.929403 PROGRESS: 
2:12:18.929449 PROGRESS: Precursor Summary:
2:12:18.930920 PROGRESS: Channel   0:	 0.050 FDR: 1,763; 0.010 FDR: 1,763; 0.001 FDR: 1,325
2:12:18.931014 PROGRESS: 
2:12:18.931073 PROGRESS: Protein Summary:
2:12:18.933084 PROGRESS: Channel   0:	 0.050 FDR: 1,484; 0.010 FDR: 1,484; 0.001 FDR: 1,113
2:12:18.933192 PROGRESS: =========================================================================
2:12:18.958394 INFO: Target number of precursors reached.
2:12:19.562779 INFO: fragments_df: keeping 5000 of 3959717 [sum(precursor_idx_mask)=40554 sum(mass_error_mask)=3959717 stop_rank=5000
2:12:20.129061 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:12:20.642356 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:12:21.777576 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:12:21.778192 INFO: Using score_cutoff 8.449847910118102 (fac=0.99, q=1)
2:12:21.778586 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:12:21.778682 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:12:21.778750 INFO: Updating optimization_manager: score_cutoff        : 10.898978087425233 -> 8.449847910118102
2:12:21.778823 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:12:21.942431 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:12:22.379268 INFO: === checking if optimization conditions were reached ===
2:12:22.380112 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:12:22.385324 INFO: Updating optimization_manager: rt_error            : 475.84518305889094 -> 638.6864756826511
2:12:22.385477 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 638.6865.
2:12:22.385562 INFO: ==============================================
2:12:22.385670 INFO: Starting optimization step 3.
2:12:22.385781 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:12:22.385878 INFO: Using rust extraction backend
2:12:22.385965 PROGRESS: Extracting batch of 250442 precursors
2:12:22.882731 INFO: === Search parameters used ===
2:12:22.883153 INFO: rt_error       : 638.6864756826511
2:12:22.883229 INFO: mobility_error : 0.1
2:12:22.883286 INFO: num_candidates : 3
2:12:22.883349 INFO: ms1_error      : 3
2:12:22.883404 INFO: ms2_error      : 10.0
2:12:22.883457 INFO: fwhm_rt        : 3.0
2:12:22.883511 INFO: quant_window   : 3
2:12:22.883567 INFO: ==============================================
2:12:27.515853 INFO: performing precursor FDR with 40 features
2:12:27.515996 INFO: Decoy channel: -1
2:12:27.516025 INFO: competitive: True
2:12:27.778315 INFO: Setting torch num_threads to 2 for FDR classification task
2:12:28.123095 INFO: Estimating optimal hyperparameters - samples: 599,744, batch_size: 2,456, learning_rate: 7.74e-04
2:12:28.124669 INFO: Using random state 285021 for train-test-split
2:12:44.013412 INFO: Test AUC: 0.612
2:12:44.013685 INFO: Train AUC: 0.626
2:12:44.013731 INFO: AUC difference: 2.32%
2:12:44.603292 INFO: Resetting torch num_threads to 100
2:12:44.773144 PROGRESS: === Extracted 749680 precursors and 4024035 fragments ===
2:12:44.773726 INFO: === FDR correction performed with classifier version 11 ===
2:12:44.774473 PROGRESS: ============================= Precursor FDR =============================
2:12:44.774567 PROGRESS: Total precursors accumulated: 1,544
2:12:44.774630 PROGRESS: Target precursors: 1,529 (99.03%)
2:12:44.774685 PROGRESS: Decoy precursors: 15 (0.97%)
2:12:44.774739 PROGRESS: 
2:12:44.774790 PROGRESS: Precursor Summary:
2:12:44.776216 PROGRESS: Channel   0:	 0.050 FDR: 1,529; 0.010 FDR: 1,529; 0.001 FDR: 1,177
2:12:44.776325 PROGRESS: 
2:12:44.776387 PROGRESS: Protein Summary:
2:12:44.778209 PROGRESS: Channel   0:	 0.050 FDR: 1,279; 0.010 FDR: 1,279; 0.001 FDR: 1,006
2:12:44.778301 PROGRESS: =========================================================================
2:12:44.798267 INFO: Target number of precursors reached.
2:12:45.258954 INFO: fragments_df: keeping 5000 of 4024035 [sum(precursor_idx_mask)=36699 sum(mass_error_mask)=4024035 stop_rank=5000
2:12:45.835553 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:12:46.335140 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:12:47.456174 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:12:47.456845 INFO: Using score_cutoff 11.791435439300537 (fac=0.99, q=1)
2:12:47.457257 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:12:47.457347 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:12:47.457410 INFO: Updating optimization_manager: score_cutoff        : 8.449847910118102 -> 11.791435439300537
2:12:47.457501 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:12:47.618475 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:12:47.988608 INFO: === checking if optimization conditions were reached ===
2:12:47.988960 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:12:47.992763 INFO: Updating optimization_manager: rt_error            : 638.6864756826511 -> 449.28579723718656
2:12:47.992889 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 449.2858.
2:12:47.992989 INFO: ==============================================
2:12:47.993088 INFO: Starting optimization step 4.
2:12:47.993168 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:12:47.993247 INFO: Using rust extraction backend
2:12:47.993324 PROGRESS: Extracting batch of 250442 precursors
2:12:48.457512 INFO: === Search parameters used ===
2:12:48.457827 INFO: rt_error       : 449.28579723718656
2:12:48.457896 INFO: mobility_error : 0.1
2:12:48.457962 INFO: num_candidates : 3
2:12:48.458017 INFO: ms1_error      : 3
2:12:48.458068 INFO: ms2_error      : 10.0
2:12:48.458125 INFO: fwhm_rt        : 3.0
2:12:48.458176 INFO: quant_window   : 3
2:12:48.458226 INFO: ==============================================
2:12:52.106063 INFO: performing precursor FDR with 40 features
2:12:52.106213 INFO: Decoy channel: -1
2:12:52.106248 INFO: competitive: True
2:12:52.340025 INFO: Setting torch num_threads to 2 for FDR classification task
2:12:52.679795 INFO: Estimating optimal hyperparameters - samples: 598,801, batch_size: 2,452, learning_rate: 7.74e-04
2:12:52.681011 INFO: Using random state 285021 for train-test-split
2:13:08.310154 INFO: Test AUC: 0.610
2:13:08.310346 INFO: Train AUC: 0.625
2:13:08.310390 INFO: AUC difference: 2.39%
2:13:08.943729 INFO: Resetting torch num_threads to 100
2:13:08.997505 PROGRESS: === Extracted 748502 precursors and 3935779 fragments ===
2:13:08.998169 INFO: === FDR correction performed with classifier version 11 ===
2:13:08.999157 PROGRESS: ============================= Precursor FDR =============================
2:13:08.999268 PROGRESS: Total precursors accumulated: 1,459
2:13:08.999340 PROGRESS: Target precursors: 1,445 (99.04%)
2:13:08.999407 PROGRESS: Decoy precursors: 14 (0.96%)
2:13:08.999473 PROGRESS: 
2:13:08.999529 PROGRESS: Precursor Summary:
2:13:09.001344 PROGRESS: Channel   0:	 0.050 FDR: 1,445; 0.010 FDR: 1,445; 0.001 FDR: 1,046
2:13:09.001452 PROGRESS: 
2:13:09.001524 PROGRESS: Protein Summary:
2:13:09.003881 PROGRESS: Channel   0:	 0.050 FDR: 1,209; 0.010 FDR: 1,209; 0.001 FDR:   904
2:13:09.003991 PROGRESS: =========================================================================
2:13:09.032007 INFO: Target number of precursors reached.
2:13:09.682797 INFO: fragments_df: keeping 5000 of 3935779 [sum(precursor_idx_mask)=34900 sum(mass_error_mask)=3935779 stop_rank=5000
2:13:10.235465 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:13:10.603585 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:13:11.866763 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:13:11.867536 INFO: Using score_cutoff 11.459193087387085 (fac=0.99, q=1)
2:13:11.868010 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:13:11.868142 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:13:11.868242 INFO: Updating optimization_manager: score_cutoff        : 11.791435439300537 -> 11.459193087387085
2:13:11.868373 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:13:12.043741 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:13:12.448423 INFO: === checking if optimization conditions were reached ===
2:13:12.448838 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:13:12.452810 INFO: Updating optimization_manager: rt_error            : 449.28579723718656 -> 475.1968930388306
2:13:12.452961 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 475.1969.
2:13:12.453051 INFO: ==============================================
2:13:12.453146 INFO: Starting optimization step 5.
2:13:12.453235 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:13:12.453576 INFO: Using rust extraction backend
2:13:12.453676 PROGRESS: Extracting batch of 250442 precursors
2:13:13.003231 INFO: === Search parameters used ===
2:13:13.003532 INFO: rt_error       : 475.1968930388306
2:13:13.003615 INFO: mobility_error : 0.1
2:13:13.003683 INFO: num_candidates : 3
2:13:13.003752 INFO: ms1_error      : 3
2:13:13.003815 INFO: ms2_error      : 10.0
2:13:13.003891 INFO: fwhm_rt        : 3.0
2:13:13.003959 INFO: quant_window   : 3
2:13:13.004016 INFO: ==============================================
2:13:16.998823 INFO: performing precursor FDR with 40 features
2:13:16.998958 INFO: Decoy channel: -1
2:13:16.998993 INFO: competitive: True
2:13:17.249237 INFO: Setting torch num_threads to 2 for FDR classification task
2:13:17.615578 INFO: Estimating optimal hyperparameters - samples: 599,178, batch_size: 2,454, learning_rate: 7.74e-04
2:13:17.616776 INFO: Using random state 285021 for train-test-split
2:13:33.354007 INFO: Test AUC: 0.608
2:13:33.354219 INFO: Train AUC: 0.624
2:13:33.354267 INFO: AUC difference: 2.68%
2:13:33.940666 INFO: Resetting torch num_threads to 100
2:13:33.970251 PROGRESS: === Extracted 748973 precursors and 3967530 fragments ===
2:13:33.970800 INFO: === FDR correction performed with classifier version 11 ===
2:13:33.971744 PROGRESS: ============================= Precursor FDR =============================
2:13:33.971878 PROGRESS: Total precursors accumulated: 1,702
2:13:33.971944 PROGRESS: Target precursors: 1,686 (99.06%)
2:13:33.972004 PROGRESS: Decoy precursors: 16 (0.94%)
2:13:33.972065 PROGRESS: 
2:13:33.972116 PROGRESS: Precursor Summary:
2:13:33.973623 PROGRESS: Channel   0:	 0.050 FDR: 1,686; 0.010 FDR: 1,686; 0.001 FDR: 1,368
2:13:33.973717 PROGRESS: 
2:13:33.973776 PROGRESS: Protein Summary:
2:13:33.975682 PROGRESS: Channel   0:	 0.050 FDR: 1,421; 0.010 FDR: 1,421; 0.001 FDR: 1,153
2:13:33.975777 PROGRESS: =========================================================================
2:13:33.993526 INFO: Target number of precursors reached.
2:13:34.440876 INFO: fragments_df: keeping 5000 of 3967530 [sum(precursor_idx_mask)=39238 sum(mass_error_mask)=3967530 stop_rank=5000
2:13:35.057801 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:13:35.455835 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:13:36.553777 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:13:36.554354 INFO: Using score_cutoff 9.007882802009583 (fac=0.99, q=1)
2:13:36.554754 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:13:36.554848 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:13:36.554913 INFO: Updating optimization_manager: score_cutoff        : 11.459193087387085 -> 9.007882802009583
2:13:36.554991 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:13:36.718507 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:13:37.065447 INFO: === checking if optimization conditions were reached ===
2:13:37.065775 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:13:37.069778 INFO: Updating optimization_manager: rt_error            : 475.1968930388306 -> 648.4133913398216
2:13:37.069938 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 648.4134.
2:13:37.070026 INFO: ==============================================
2:13:37.070134 INFO: Starting optimization step 6.
2:13:37.070212 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:13:37.070311 INFO: Using rust extraction backend
2:13:37.070397 PROGRESS: Extracting batch of 250442 precursors
2:13:37.515730 INFO: === Search parameters used ===
2:13:37.516041 INFO: rt_error       : 648.4133913398216
2:13:37.516115 INFO: mobility_error : 0.1
2:13:37.516176 INFO: num_candidates : 3
2:13:37.516230 INFO: ms1_error      : 3
2:13:37.516295 INFO: ms2_error      : 10.0
2:13:37.516352 INFO: fwhm_rt        : 3.0
2:13:37.516404 INFO: quant_window   : 3
2:13:37.516460 INFO: ==============================================
2:13:41.699427 INFO: performing precursor FDR with 40 features
2:13:41.699582 INFO: Decoy channel: -1
2:13:41.699619 INFO: competitive: True
2:13:41.946737 INFO: Setting torch num_threads to 2 for FDR classification task
2:13:42.319263 INFO: Estimating optimal hyperparameters - samples: 599,744, batch_size: 2,456, learning_rate: 7.74e-04
2:13:42.320600 INFO: Using random state 285021 for train-test-split
2:13:54.531417 INFO: Test AUC: 0.611
2:13:54.531578 INFO: Train AUC: 0.626
2:13:54.531618 INFO: AUC difference: 2.39%
2:13:55.090055 INFO: Resetting torch num_threads to 100
2:13:55.118642 PROGRESS: === Extracted 749680 precursors and 4024820 fragments ===
2:13:55.119128 INFO: === FDR correction performed with classifier version 11 ===
2:13:55.120002 PROGRESS: ============================= Precursor FDR =============================
2:13:55.120098 PROGRESS: Total precursors accumulated: 1,643
2:13:55.120171 PROGRESS: Target precursors: 1,627 (99.03%)
2:13:55.120225 PROGRESS: Decoy precursors: 16 (0.97%)
2:13:55.120273 PROGRESS: 
2:13:55.120322 PROGRESS: Precursor Summary:
2:13:55.121755 PROGRESS: Channel   0:	 0.050 FDR: 1,627; 0.010 FDR: 1,627; 0.001 FDR: 1,161
2:13:55.121847 PROGRESS: 
2:13:55.121907 PROGRESS: Protein Summary:
2:13:55.123855 PROGRESS: Channel   0:	 0.050 FDR: 1,362; 0.010 FDR: 1,362; 0.001 FDR:   992
2:13:55.123952 PROGRESS: =========================================================================
2:13:55.141176 INFO: Target number of precursors reached.
2:13:55.603117 INFO: fragments_df: keeping 5000 of 4024820 [sum(precursor_idx_mask)=38614 sum(mass_error_mask)=4024820 stop_rank=5000
2:13:56.181804 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:13:56.543524 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:13:57.536596 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:13:57.537140 INFO: Using score_cutoff 10.687115202140808 (fac=0.99, q=1)
2:13:57.537527 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:13:57.537618 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:13:57.537682 INFO: Updating optimization_manager: score_cutoff        : 9.007882802009583 -> 10.687115202140808
2:13:57.537755 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:13:57.706664 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:13:58.068074 INFO: === checking if optimization conditions were reached ===
2:13:58.068381 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
2:13:58.072003 INFO: Updating optimization_manager: rt_error            : 648.4133913398216 -> 533.6311687226668
2:13:58.072125 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 533.6312.
2:13:58.072214 INFO: ==============================================
2:13:58.072304 INFO: Starting optimization step 7.
2:13:58.072384 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:13:58.072461 INFO: Using rust extraction backend
2:13:58.072537 PROGRESS: Extracting batch of 250442 precursors
2:13:58.523192 INFO: === Search parameters used ===
2:13:58.523492 INFO: rt_error       : 533.6311687226668
2:13:58.523564 INFO: mobility_error : 0.1
2:13:58.523623 INFO: num_candidates : 3
2:13:58.523682 INFO: ms1_error      : 3
2:13:58.523738 INFO: ms2_error      : 10.0
2:13:58.523805 INFO: fwhm_rt        : 3.0
2:13:58.523868 INFO: quant_window   : 3
2:13:58.523927 INFO: ==============================================
2:14:02.500439 INFO: performing precursor FDR with 40 features
2:14:02.500576 INFO: Decoy channel: -1
2:14:02.500609 INFO: competitive: True
2:14:02.728795 INFO: Setting torch num_threads to 2 for FDR classification task
2:14:03.081217 INFO: Estimating optimal hyperparameters - samples: 599,328, batch_size: 2,454, learning_rate: 7.74e-04
2:14:03.082405 INFO: Using random state 285021 for train-test-split
2:14:19.316627 INFO: Test AUC: 0.612
2:14:19.316778 INFO: Train AUC: 0.625
2:14:19.316818 INFO: AUC difference: 2.01%
2:14:19.869009 INFO: Resetting torch num_threads to 100
2:14:19.901443 PROGRESS: === Extracted 749161 precursors and 3990357 fragments ===
2:14:19.901952 INFO: === FDR correction performed with classifier version 11 ===
2:14:19.902753 PROGRESS: ============================= Precursor FDR =============================
2:14:19.902858 PROGRESS: Total precursors accumulated: 1,541
2:14:19.902923 PROGRESS: Target precursors: 1,526 (99.03%)
2:14:19.902974 PROGRESS: Decoy precursors: 15 (0.97%)
2:14:19.903022 PROGRESS: 
2:14:19.903067 PROGRESS: Precursor Summary:
2:14:19.904460 PROGRESS: Channel   0:	 0.050 FDR: 1,526; 0.010 FDR: 1,526; 0.001 FDR: 1,096
2:14:19.904552 PROGRESS: 
2:14:19.904611 PROGRESS: Protein Summary:
2:14:19.906408 PROGRESS: Channel   0:	 0.050 FDR: 1,288; 0.010 FDR: 1,288; 0.001 FDR:   945
2:14:19.906500 PROGRESS: =========================================================================
2:14:19.925066 INFO: Target number of precursors reached.
2:14:20.524753 INFO: fragments_df: keeping 5000 of 3990357 [sum(precursor_idx_mask)=35847 sum(mass_error_mask)=3990357 stop_rank=5000
2:14:20.976487 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:14:21.415428 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:14:22.465492 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:14:22.465955 INFO: Using score_cutoff 8.858696508407593 (fac=0.99, q=1)
2:14:22.466270 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:14:22.466353 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:14:22.466410 INFO: Updating optimization_manager: score_cutoff        : 10.687115202140808 -> 8.858696508407593
2:14:22.466474 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:14:22.622411 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:14:22.976980 INFO: === checking if optimization conditions were reached ===
2:14:22.977293 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
2:14:22.980726 INFO: Updating optimization_manager: rt_error            : 533.6311687226668 -> 618.1337055143645
2:14:22.980849 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 618.1337.
2:14:22.980927 INFO: ==============================================
2:14:22.981012 INFO: Starting optimization step 8.
2:14:22.981086 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:14:22.981159 INFO: Using rust extraction backend
2:14:22.981235 PROGRESS: Extracting batch of 250442 precursors
2:14:23.427400 INFO: === Search parameters used ===
2:14:23.427711 INFO: rt_error       : 618.1337055143645
2:14:23.427783 INFO: mobility_error : 0.1
2:14:23.427856 INFO: num_candidates : 3
2:14:23.427923 INFO: ms1_error      : 3
2:14:23.427982 INFO: ms2_error      : 10.0
2:14:23.428035 INFO: fwhm_rt        : 3.0
2:14:23.428094 INFO: quant_window   : 3
2:14:23.428169 INFO: ==============================================
2:14:27.396970 INFO: performing precursor FDR with 40 features
2:14:27.397125 INFO: Decoy channel: -1
2:14:27.397161 INFO: competitive: True
2:14:27.633260 INFO: Setting torch num_threads to 2 for FDR classification task
2:14:27.982558 INFO: Estimating optimal hyperparameters - samples: 599,796, batch_size: 2,456, learning_rate: 7.74e-04
2:14:27.983562 INFO: Using random state 285021 for train-test-split
2:14:40.321086 INFO: Test AUC: 0.612
2:14:40.321243 INFO: Train AUC: 0.626
2:14:40.321282 INFO: AUC difference: 2.32%
2:14:40.863522 INFO: Resetting torch num_threads to 100
2:14:40.891849 PROGRESS: === Extracted 749746 precursors and 4025727 fragments ===
2:14:40.892340 INFO: === FDR correction performed with classifier version 11 ===
2:14:40.893056 PROGRESS: ============================= Precursor FDR =============================
2:14:40.893152 PROGRESS: Total precursors accumulated: 1,616
2:14:40.893214 PROGRESS: Target precursors: 1,600 (99.01%)
2:14:40.893266 PROGRESS: Decoy precursors: 16 (0.99%)
2:14:40.893313 PROGRESS: 
2:14:40.893360 PROGRESS: Precursor Summary:
2:14:40.894790 PROGRESS: Channel   0:	 0.050 FDR: 1,600; 0.010 FDR: 1,569; 0.001 FDR: 1,221
2:14:40.894882 PROGRESS: 
2:14:40.894941 PROGRESS: Protein Summary:
2:14:40.896809 PROGRESS: Channel   0:	 0.050 FDR: 1,342; 0.010 FDR: 1,316; 0.001 FDR: 1,034
2:14:40.896908 PROGRESS: =========================================================================
2:14:40.918467 INFO: Target number of precursors reached.
2:14:41.592472 INFO: fragments_df: keeping 5000 of 4025727 [sum(precursor_idx_mask)=37152 sum(mass_error_mask)=4025727 stop_rank=5000
2:14:42.070120 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:14:42.441103 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:14:43.416492 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:14:43.417038 INFO: Using score_cutoff 10.341060967254638 (fac=0.99, q=1)
2:14:43.417408 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:14:43.417496 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:14:43.417586 INFO: Updating optimization_manager: score_cutoff        : 8.858696508407593 -> 10.341060967254638
2:14:43.417654 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:14:43.578693 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:14:43.964851 INFO: === checking if optimization conditions were reached ===
2:14:43.965164 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
2:14:43.968620 INFO: Updating optimization_manager: rt_error            : 618.1337055143645 -> 720.6978069440189
2:14:43.968751 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 720.6978.
2:14:43.968835 INFO: ==============================================
2:14:43.968925 INFO: Starting optimization step 9.
2:14:43.968999 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:14:43.969080 INFO: Using rust extraction backend
2:14:43.969154 PROGRESS: Extracting batch of 250442 precursors
2:14:44.406277 INFO: === Search parameters used ===
2:14:44.406583 INFO: rt_error       : 720.6978069440189
2:14:44.406658 INFO: mobility_error : 0.1
2:14:44.406723 INFO: num_candidates : 3
2:14:44.406779 INFO: ms1_error      : 3
2:14:44.406836 INFO: ms2_error      : 10.0
2:14:44.406886 INFO: fwhm_rt        : 3.0
2:14:44.406941 INFO: quant_window   : 3
2:14:44.406994 INFO: ==============================================
2:14:48.628588 INFO: performing precursor FDR with 40 features
2:14:48.628732 INFO: Decoy channel: -1
2:14:48.628768 INFO: competitive: True
2:14:48.870605 INFO: Setting torch num_threads to 2 for FDR classification task
2:14:49.286107 INFO: Estimating optimal hyperparameters - samples: 599,807, batch_size: 2,456, learning_rate: 7.74e-04
2:14:49.287341 INFO: Using random state 285021 for train-test-split
2:15:03.489366 INFO: Test AUC: 0.611
2:15:03.489523 INFO: Train AUC: 0.626
2:15:03.489563 INFO: AUC difference: 2.42%
2:15:04.101170 INFO: Resetting torch num_threads to 100
2:15:04.141615 PROGRESS: === Extracted 749759 precursors and 4030386 fragments ===
2:15:04.142179 INFO: === FDR correction performed with classifier version 11 ===
2:15:04.143052 PROGRESS: ============================= Precursor FDR =============================
2:15:04.143161 PROGRESS: Total precursors accumulated: 1,631
2:15:04.143233 PROGRESS: Target precursors: 1,615 (99.02%)
2:15:04.143317 PROGRESS: Decoy precursors: 16 (0.98%)
2:15:04.143377 PROGRESS: 
2:15:04.143434 PROGRESS: Precursor Summary:
2:15:04.145128 PROGRESS: Channel   0:	 0.050 FDR: 1,615; 0.010 FDR: 1,615; 0.001 FDR:    43
2:15:04.145237 PROGRESS: 
2:15:04.145301 PROGRESS: Protein Summary:
2:15:04.147376 PROGRESS: Channel   0:	 0.050 FDR: 1,343; 0.010 FDR: 1,343; 0.001 FDR:    42
2:15:04.147476 PROGRESS: =========================================================================
2:15:04.172299 INFO: Target number of precursors reached.
2:15:04.839828 INFO: fragments_df: keeping 5000 of 4030386 [sum(precursor_idx_mask)=38346 sum(mass_error_mask)=4030386 stop_rank=5000
2:15:05.369250 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:15:05.786890 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:15:06.967293 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:15:06.967845 INFO: Using score_cutoff 11.340441521644593 (fac=0.99, q=1)
2:15:06.968243 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:15:06.968333 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:15:06.968396 INFO: Updating optimization_manager: score_cutoff        : 10.341060967254638 -> 11.340441521644593
2:15:06.968468 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:15:07.126281 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:15:07.514542 INFO: === checking if optimization conditions were reached ===
2:15:07.514858 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
2:15:07.518317 INFO: Updating optimization_manager: rt_error            : 720.6978069440189 -> 491.5700824338054
2:15:07.518434 PROGRESS: ❌ rt_error       : optimization incomplete after 10 search(es). Will search with parameter 491.5701.
2:15:07.518529 INFO: ==============================================
2:15:07.518614 INFO: Starting optimization step 10.
2:15:07.518678 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:15:07.518754 INFO: Using rust extraction backend
2:15:07.518824 PROGRESS: Extracting batch of 250442 precursors
2:15:07.964518 INFO: === Search parameters used ===
2:15:07.964820 INFO: rt_error       : 491.5700824338054
2:15:07.964890 INFO: mobility_error : 0.1
2:15:07.964947 INFO: num_candidates : 3
2:15:07.965005 INFO: ms1_error      : 3
2:15:07.965072 INFO: ms2_error      : 10.0
2:15:07.965166 INFO: fwhm_rt        : 3.0
2:15:07.965223 INFO: quant_window   : 3
2:15:07.965274 INFO: ==============================================
2:15:11.536867 INFO: performing precursor FDR with 40 features
2:15:11.537001 INFO: Decoy channel: -1
2:15:11.537029 INFO: competitive: True
2:15:11.770642 INFO: Setting torch num_threads to 2 for FDR classification task
2:15:12.192911 INFO: Estimating optimal hyperparameters - samples: 599,071, batch_size: 2,453, learning_rate: 7.74e-04
2:15:12.194124 INFO: Using random state 285021 for train-test-split
2:15:28.366864 INFO: Test AUC: 0.612
2:15:28.367043 INFO: Train AUC: 0.623
2:15:28.367079 INFO: AUC difference: 1.80%
2:15:29.036096 INFO: Resetting torch num_threads to 100
2:15:29.071427 PROGRESS: === Extracted 748839 precursors and 3966232 fragments ===
2:15:29.071948 INFO: === FDR correction performed with classifier version 11 ===
2:15:29.072775 PROGRESS: ============================= Precursor FDR =============================
2:15:29.072870 PROGRESS: Total precursors accumulated: 1,762
2:15:29.072933 PROGRESS: Target precursors: 1,745 (99.04%)
2:15:29.072986 PROGRESS: Decoy precursors: 17 (0.96%)
2:15:29.073038 PROGRESS: 
2:15:29.073085 PROGRESS: Precursor Summary:
2:15:29.074512 PROGRESS: Channel   0:	 0.050 FDR: 1,745; 0.010 FDR: 1,745; 0.001 FDR: 1,149
2:15:29.074603 PROGRESS: 
2:15:29.074660 PROGRESS: Protein Summary:
2:15:29.076548 PROGRESS: Channel   0:	 0.050 FDR: 1,459; 0.010 FDR: 1,459; 0.001 FDR:   979
2:15:29.076644 PROGRESS: =========================================================================
2:15:29.096894 INFO: Target number of precursors reached.
2:15:29.582453 INFO: fragments_df: keeping 5000 of 3966232 [sum(precursor_idx_mask)=40707 sum(mass_error_mask)=3966232 stop_rank=5000
2:15:30.175976 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:15:30.698140 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:15:31.792592 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:15:31.793226 INFO: Using score_cutoff 8.957830991363526 (fac=0.99, q=1)
2:15:31.793606 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:15:31.793693 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:15:31.793766 INFO: Updating optimization_manager: score_cutoff        : 11.340441521644593 -> 8.957830991363526
2:15:31.793833 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:15:31.954384 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:15:32.300280 INFO: === checking if optimization conditions were reached ===
2:15:32.300623 PROGRESS: === Optimization of rt_error has been performed 11 time(s); minimum number is 5 ===
2:15:32.304292 INFO: Updating optimization_manager: rt_error            : 491.5700824338054 -> 642.505432825371
2:15:32.304413 PROGRESS: ❌ rt_error       : optimization incomplete after 11 search(es). Will search with parameter 642.5054.
2:15:32.304498 INFO: ==============================================
2:15:32.304586 INFO: Starting optimization step 11.
2:15:32.304664 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:15:32.304750 INFO: Using rust extraction backend
2:15:32.304821 PROGRESS: Extracting batch of 250442 precursors
2:15:32.746797 INFO: === Search parameters used ===
2:15:32.747096 INFO: rt_error       : 642.505432825371
2:15:32.747174 INFO: mobility_error : 0.1
2:15:32.747236 INFO: num_candidates : 3
2:15:32.747312 INFO: ms1_error      : 3
2:15:32.747371 INFO: ms2_error      : 10.0
2:15:32.747428 INFO: fwhm_rt        : 3.0
2:15:32.747478 INFO: quant_window   : 3
2:15:32.747526 INFO: ==============================================
2:15:36.821992 INFO: performing precursor FDR with 40 features
2:15:36.822147 INFO: Decoy channel: -1
2:15:36.822180 INFO: competitive: True
2:15:37.065522 INFO: Setting torch num_threads to 2 for FDR classification task
2:15:37.502331 INFO: Estimating optimal hyperparameters - samples: 599,717, batch_size: 2,456, learning_rate: 7.74e-04
2:15:37.503560 INFO: Using random state 285021 for train-test-split
2:15:53.004566 INFO: Test AUC: 0.609
2:15:53.004736 INFO: Train AUC: 0.626
2:15:53.004771 INFO: AUC difference: 2.69%
2:15:53.581520 INFO: Resetting torch num_threads to 100
2:15:53.612447 PROGRESS: === Extracted 749647 precursors and 4021988 fragments ===
2:15:53.612974 INFO: === FDR correction performed with classifier version 11 ===
2:15:53.613816 PROGRESS: ============================= Precursor FDR =============================
2:15:53.613927 PROGRESS: Total precursors accumulated: 1,707
2:15:53.613993 PROGRESS: Target precursors: 1,691 (99.06%)
2:15:53.614047 PROGRESS: Decoy precursors: 16 (0.94%)
2:15:53.614100 PROGRESS: 
2:15:53.614149 PROGRESS: Precursor Summary:
2:15:53.615711 PROGRESS: Channel   0:	 0.050 FDR: 1,691; 0.010 FDR: 1,691; 0.001 FDR: 1,336
2:15:53.615812 PROGRESS: 
2:15:53.615884 PROGRESS: Protein Summary:
2:15:53.617798 PROGRESS: Channel   0:	 0.050 FDR: 1,415; 0.010 FDR: 1,415; 0.001 FDR: 1,127
2:15:53.617900 PROGRESS: =========================================================================
2:15:53.635929 INFO: Target number of precursors reached.
2:15:54.093973 INFO: fragments_df: keeping 5000 of 4021988 [sum(precursor_idx_mask)=39342 sum(mass_error_mask)=4021988 stop_rank=5000
2:15:54.592431 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:15:55.007384 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:15:56.064603 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:15:56.065138 INFO: Using score_cutoff 9.004894323349 (fac=0.99, q=1)
2:15:56.065514 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:15:56.065619 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:15:56.065699 INFO: Updating optimization_manager: score_cutoff        : 8.957830991363526 -> 9.004894323349
2:15:56.065786 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:15:56.230651 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:15:56.584025 INFO: === checking if optimization conditions were reached ===
2:15:56.584319 PROGRESS: === Optimization of rt_error has been performed 12 time(s); minimum number is 5 ===
2:15:56.587929 INFO: Updating optimization_manager: rt_error            : 642.505432825371 -> 713.3872767266256
2:15:56.588051 PROGRESS: ❌ rt_error       : optimization incomplete after 12 search(es). Will search with parameter 713.3873.
2:15:56.588122 INFO: ==============================================
2:15:56.588219 INFO: Starting optimization step 12.
2:15:56.588301 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:15:56.588376 INFO: Using rust extraction backend
2:15:56.588446 PROGRESS: Extracting batch of 250442 precursors
2:15:57.042893 INFO: === Search parameters used ===
2:15:57.043284 INFO: rt_error       : 713.3872767266256
2:15:57.043371 INFO: mobility_error : 0.1
2:15:57.043432 INFO: num_candidates : 3
2:15:57.043486 INFO: ms1_error      : 3
2:15:57.043536 INFO: ms2_error      : 10.0
2:15:57.043596 INFO: fwhm_rt        : 3.0
2:15:57.043647 INFO: quant_window   : 3
2:15:57.043696 INFO: ==============================================
2:16:00.981596 INFO: performing precursor FDR with 40 features
2:16:00.981739 INFO: Decoy channel: -1
2:16:00.981776 INFO: competitive: True
2:16:01.222284 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:01.627171 INFO: Estimating optimal hyperparameters - samples: 599,871, batch_size: 2,457, learning_rate: 7.75e-04
2:16:01.628423 INFO: Using random state 285021 for train-test-split
2:16:17.629311 INFO: Test AUC: 0.615
2:16:17.629519 INFO: Train AUC: 0.627
2:16:17.629562 INFO: AUC difference: 1.99%
2:16:18.243498 INFO: Resetting torch num_threads to 100
2:16:18.284169 PROGRESS: === Extracted 749839 precursors and 4033608 fragments ===
2:16:18.284827 INFO: === FDR correction performed with classifier version 11 ===
2:16:18.285964 PROGRESS: ============================= Precursor FDR =============================
2:16:18.286088 PROGRESS: Total precursors accumulated: 1,638
2:16:18.286173 PROGRESS: Target precursors: 1,622 (99.02%)
2:16:18.286237 PROGRESS: Decoy precursors: 16 (0.98%)
2:16:18.286294 PROGRESS: 
2:16:18.286347 PROGRESS: Precursor Summary:
2:16:18.288286 PROGRESS: Channel   0:	 0.050 FDR: 1,622; 0.010 FDR: 1,622; 0.001 FDR: 1,006
2:16:18.288397 PROGRESS: 
2:16:18.288472 PROGRESS: Protein Summary:
2:16:18.290866 PROGRESS: Channel   0:	 0.050 FDR: 1,352; 0.010 FDR: 1,352; 0.001 FDR:   864
2:16:18.290980 PROGRESS: =========================================================================
2:16:18.316983 INFO: Target number of precursors reached.
2:16:18.969294 INFO: fragments_df: keeping 5000 of 4033608 [sum(precursor_idx_mask)=38685 sum(mass_error_mask)=4033608 stop_rank=5000
2:16:19.561071 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:16:20.026199 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:16:21.157134 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:16:21.157763 INFO: Using score_cutoff 11.78981782951355 (fac=0.99, q=1)
2:16:21.158144 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:16:21.158236 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:16:21.158301 INFO: Updating optimization_manager: score_cutoff        : 9.004894323349 -> 11.78981782951355
2:16:21.158367 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:16:21.318875 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:16:21.664898 INFO: === checking if optimization conditions were reached ===
2:16:21.665223 PROGRESS: === Optimization of rt_error has been performed 13 time(s); minimum number is 5 ===
2:16:21.668839 INFO: Updating optimization_manager: rt_error            : 713.3872767266256 -> 460.47679869447086
2:16:21.668957 PROGRESS: ❌ rt_error       : optimization incomplete after 13 search(es). Will search with parameter 460.4768.
2:16:21.669038 INFO: ==============================================
2:16:21.669125 INFO: Starting optimization step 13.
2:16:21.669210 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:16:21.669288 INFO: Using rust extraction backend
2:16:21.669364 PROGRESS: Extracting batch of 250442 precursors
2:16:22.114113 INFO: === Search parameters used ===
2:16:22.114424 INFO: rt_error       : 460.47679869447086
2:16:22.114493 INFO: mobility_error : 0.1
2:16:22.114556 INFO: num_candidates : 3
2:16:22.114610 INFO: ms1_error      : 3
2:16:22.114663 INFO: ms2_error      : 10.0
2:16:22.114725 INFO: fwhm_rt        : 3.0
2:16:22.114784 INFO: quant_window   : 3
2:16:22.114832 INFO: ==============================================
2:16:25.921267 INFO: performing precursor FDR with 40 features
2:16:25.921392 INFO: Decoy channel: -1
2:16:25.921420 INFO: competitive: True
2:16:26.129103 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:26.449715 INFO: Estimating optimal hyperparameters - samples: 598,929, batch_size: 2,453, learning_rate: 7.74e-04
2:16:26.450960 INFO: Using random state 285021 for train-test-split
2:16:42.533134 INFO: Test AUC: 0.612
2:16:42.533348 INFO: Train AUC: 0.623
2:16:42.533393 INFO: AUC difference: 1.86%
2:16:43.143261 INFO: Resetting torch num_threads to 100
2:16:43.185951 PROGRESS: === Extracted 748662 precursors and 3947197 fragments ===
2:16:43.186575 INFO: === FDR correction performed with classifier version 11 ===
2:16:43.187580 PROGRESS: ============================= Precursor FDR =============================
2:16:43.187708 PROGRESS: Total precursors accumulated: 1,639
2:16:43.187787 PROGRESS: Target precursors: 1,623 (99.02%)
2:16:43.187862 PROGRESS: Decoy precursors: 16 (0.98%)
2:16:43.187922 PROGRESS: 
2:16:43.187976 PROGRESS: Precursor Summary:
2:16:43.189895 PROGRESS: Channel   0:	 0.050 FDR: 1,623; 0.010 FDR: 1,623; 0.001 FDR: 1,081
2:16:43.190008 PROGRESS: 
2:16:43.190086 PROGRESS: Protein Summary:
2:16:43.192444 PROGRESS: Channel   0:	 0.050 FDR: 1,349; 0.010 FDR: 1,349; 0.001 FDR:   926
2:16:43.192559 PROGRESS: =========================================================================
2:16:43.217410 INFO: Target number of precursors reached.
2:16:43.854287 INFO: fragments_df: keeping 5000 of 3947197 [sum(precursor_idx_mask)=38550 sum(mass_error_mask)=3947197 stop_rank=5000
2:16:44.433470 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:16:44.960682 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:16:46.060878 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:16:46.061471 INFO: Using score_cutoff 11.051506401443481 (fac=0.99, q=1)
2:16:46.061878 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:16:46.061968 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:16:46.062051 INFO: Updating optimization_manager: score_cutoff        : 11.78981782951355 -> 11.051506401443481
2:16:46.062135 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:16:46.222268 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:16:46.580800 INFO: === checking if optimization conditions were reached ===
2:16:46.581104 PROGRESS: === Optimization of rt_error has been performed 14 time(s); minimum number is 5 ===
2:16:46.584900 INFO: Updating optimization_manager: rt_error            : 460.47679869447086 -> 462.4808066874418
2:16:46.585056 PROGRESS: ❌ rt_error       : optimization incomplete after 14 search(es). Will search with parameter 462.4808.
2:16:46.585135 INFO: ==============================================
2:16:46.585235 INFO: Starting optimization step 14.
2:16:46.585307 PROGRESS: === Extracting elution groups 0 to 127000 ===
2:16:46.585390 INFO: Using rust extraction backend
2:16:46.585475 PROGRESS: Extracting batch of 250442 precursors
2:16:47.042196 INFO: === Search parameters used ===
2:16:47.042528 INFO: rt_error       : 462.4808066874418
2:16:47.042597 INFO: mobility_error : 0.1
2:16:47.042669 INFO: num_candidates : 3
2:16:47.042726 INFO: ms1_error      : 3
2:16:47.042778 INFO: ms2_error      : 10.0
2:16:47.042837 INFO: fwhm_rt        : 3.0
2:16:47.042907 INFO: quant_window   : 3
2:16:47.042968 INFO: ==============================================
2:16:50.961826 INFO: performing precursor FDR with 40 features
2:16:50.961960 INFO: Decoy channel: -1
2:16:50.961990 INFO: competitive: True
2:16:51.195338 INFO: Setting torch num_threads to 2 for FDR classification task
2:16:51.618794 INFO: Estimating optimal hyperparameters - samples: 598,860, batch_size: 2,452, learning_rate: 7.74e-04
2:16:51.620081 INFO: Using random state 285021 for train-test-split
2:17:02.501033 INFO: Test AUC: 0.607
2:17:02.501238 INFO: Train AUC: 0.622
2:17:02.501276 INFO: AUC difference: 2.47%
2:17:03.036207 INFO: Resetting torch num_threads to 100
2:17:03.078879 PROGRESS: === Extracted 748575 precursors and 3943734 fragments ===
2:17:03.079610 INFO: === FDR correction performed with classifier version 11 ===
2:17:03.080815 PROGRESS: ============================= Precursor FDR =============================
2:17:03.080973 PROGRESS: Total precursors accumulated: 1,730
2:17:03.081055 PROGRESS: Target precursors: 1,713 (99.02%)
2:17:03.081122 PROGRESS: Decoy precursors: 17 (0.98%)
2:17:03.081180 PROGRESS: 
2:17:03.081236 PROGRESS: Precursor Summary:
2:17:03.083227 PROGRESS: Channel   0:	 0.050 FDR: 1,713; 0.010 FDR: 1,713; 0.001 FDR: 1,146
2:17:03.083354 PROGRESS: 
2:17:03.083435 PROGRESS: Protein Summary:
2:17:03.085984 PROGRESS: Channel   0:	 0.050 FDR: 1,432; 0.010 FDR: 1,432; 0.001 FDR:   978
2:17:03.086119 PROGRESS: =========================================================================
2:17:03.110286 INFO: Target number of precursors reached.
2:17:03.751831 INFO: fragments_df: keeping 5000 of 3943734 [sum(precursor_idx_mask)=40005 sum(mass_error_mask)=3943734 stop_rank=5000
2:17:04.298032 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:17:04.703491 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:17:05.813740 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:17:05.814305 INFO: Using score_cutoff 8.679932858276368 (fac=0.99, q=1)
2:17:05.814722 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:17:05.814818 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:17:05.814888 INFO: Updating optimization_manager: score_cutoff        : 11.051506401443481 -> 8.679932858276368
2:17:05.814955 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:17:05.974755 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:17:06.331367 INFO: === checking if optimization conditions were reached ===
2:17:06.331662 PROGRESS: === Optimization of rt_error has been performed 15 time(s); minimum number is 5 ===
2:17:06.332923 INFO: Updating optimization_manager: rt_error            : 462.4808066874418 -> 475.84518305889094
2:17:06.333073 INFO: Updating optimization_manager: classifier_version  : 11 -> 14
2:17:06.333187 INFO: Updating optimization_manager: score_cutoff        : 8.679932858276368 -> 8.449847910118102
2:17:06.333301 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:17:06.333426 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:17:06.333541 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 475.8452 found after 15 searches.
2:17:06.333621 INFO: ==============================================
2:17:06.333708 PROGRESS: Optimization finished for rt_error.
2:17:06.912278 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:17:07.070616 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:17:07.423520 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:17:07.423807 PROGRESS: ==============================================
2:17:07.423961 PROGRESS: ms2_error      : 10.0000
2:17:07.424049 PROGRESS: rt_error       : 475.8452
2:17:07.424114 PROGRESS: ==============================================
2:17:07.431331 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:17:15.363490 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:17:34.169475 INFO: Using rust extraction backend
2:17:34.169970 PROGRESS: Extracting batch of 11997144 precursors
2:17:53.163041 INFO: === Search parameters used ===
2:17:53.163610 INFO: rt_error       : 475.84518305889094
2:17:53.163692 INFO: mobility_error : 0.1
2:17:53.163771 INFO: num_candidates : 3
2:17:53.163847 INFO: ms1_error      : 3
2:17:53.163925 INFO: ms2_error      : 10.0
2:17:53.163996 INFO: fwhm_rt        : 3.0
2:17:53.164054 INFO: quant_window   : 3
2:17:53.164107 INFO: ==============================================
2:18:32.582635 INFO: Removed 4575252 precursors with score below cutoff 8.449847910118102
2:19:09.787755 INFO: performing precursor FDR with 40 features
2:19:09.787989 INFO: Decoy channel: -1
2:19:09.788023 INFO: competitive: True
2:19:13.458384 INFO: Setting torch num_threads to 2 for FDR classification task
2:19:29.519658 INFO: Estimating optimal hyperparameters - samples: 25,130,673, batch_size: 4,096, learning_rate: 1.00e-03
2:19:29.595955 INFO: Using random state 138419 for train-test-split
2:28:07.504742 INFO: Test AUC: 0.619
2:28:07.505086 INFO: Train AUC: 0.619
2:28:07.505147 INFO: AUC difference: 0.08%
2:28:15.570667 INFO: Resetting torch num_threads to 100
2:28:18.331932 PROGRESS: ============================= Precursor FDR =============================
2:28:18.332336 PROGRESS: Total precursors accumulated: 94,772
2:28:18.332428 PROGRESS: Target precursors: 93,834 (99.01%)
2:28:18.332497 PROGRESS: Decoy precursors: 938 (0.99%)
2:28:18.332558 PROGRESS: 
2:28:18.332624 PROGRESS: Precursor Summary:
2:28:18.375501 PROGRESS: Channel   0:	 0.050 FDR: 93,834; 0.010 FDR: 93,834; 0.001 FDR: 60,537
2:28:18.375805 PROGRESS: 
2:28:18.375894 PROGRESS: Protein Summary:
2:28:18.432009 PROGRESS: Channel   0:	 0.050 FDR: 13,664; 0.010 FDR: 13,664; 0.001 FDR: 9,170
2:28:18.432306 PROGRESS: =========================================================================
2:28:18.638357 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/psm.parquet
2:28:18.846759 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.parquet
2:28:19.152623 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:28:52.438153 PROGRESS: Processing search outputs
2:28:52.438446 PROGRESS: === Performing protein grouping and FDR ===
2:28:52.438507 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:28:52.511678 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:28:52.553900 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:28:52.598599 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:28:52.642772 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:28:52.682698 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:28:52.753691 INFO: Performing protein inference
2:28:53.978968 INFO: Inference strategy: heuristic. Using maximum parsimony with grouping for protein inference
2:30:02.054469 INFO: Performing protein FDR
2:30:14.344622 INFO: Normalizing q-values using 19,680 targets and 3,775 decoys
2:30:14.349916 INFO: Test AUC: 0.847
2:30:14.350000 INFO: Train AUC: 0.858
2:30:14.350041 INFO: AUC difference: 1.29%
2:30:15.223078 INFO: ================ Protein FDR =================
2:30:15.223319 INFO: Unique protein groups in output
2:30:15.223362 INFO:   1% protein FDR: 10,153
2:30:15.223389 INFO: 
2:30:15.223416 INFO: Unique precursor in output
2:30:15.223441 INFO:   1% protein FDR: 131,021
2:30:15.223467 INFO: ================================================
2:30:15.309636 PROGRESS: Building search statistics
2:30:15.435009 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
2:30:15.435279 INFO: Initializing OptimizationManager
2:30:15.435658 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
2:30:15.435752 INFO: Initializing CalibrationManager
2:30:15.436064 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
2:30:15.436159 INFO: Initializing RawFileManager
2:30:15.485194 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
2:30:15.485423 INFO: Initializing OptimizationManager
2:30:15.485705 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
2:30:15.485801 INFO: Initializing CalibrationManager
2:30:15.486078 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
2:30:15.486181 INFO: Initializing RawFileManager
2:30:15.535304 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
2:30:15.535532 INFO: Initializing OptimizationManager
2:30:15.535794 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
2:30:15.535902 INFO: Initializing CalibrationManager
2:30:15.536163 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
2:30:15.536258 INFO: Initializing RawFileManager
2:30:15.585294 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
2:30:15.585526 INFO: Initializing OptimizationManager
2:30:15.585793 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
2:30:15.585885 INFO: Initializing CalibrationManager
2:30:15.586134 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
2:30:15.586227 INFO: Initializing RawFileManager
2:30:15.637016 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
2:30:15.637250 INFO: Initializing OptimizationManager
2:30:15.637527 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
2:30:15.637619 INFO: Initializing CalibrationManager
2:30:15.637878 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
2:30:15.637972 INFO: Initializing RawFileManager
2:30:15.688607 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
2:30:15.688851 INFO: Initializing OptimizationManager
2:30:15.689111 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
2:30:15.689202 INFO: Initializing CalibrationManager
2:30:15.689461 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
2:30:15.689564 INFO: Initializing RawFileManager
2:30:15.694182 INFO: Writing stat output to disk
2:30:15.694288 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/stat.tsv to disk
2:30:15.706599 PROGRESS: Building internal statistics
2:30:15.707067 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
2:30:15.707124 INFO: Initializing TimingManager
2:30:15.707628 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
2:30:15.707675 INFO: Initializing TimingManager
2:30:15.707952 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
2:30:15.708000 INFO: Initializing TimingManager
2:30:15.708246 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
2:30:15.708291 INFO: Initializing TimingManager
2:30:15.708532 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
2:30:15.708571 INFO: Initializing TimingManager
2:30:15.708815 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
2:30:15.708858 INFO: Initializing TimingManager
2:30:15.709445 INFO: Writing internal output to disk
2:30:15.709496 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/internal.tsv to disk
2:30:15.791826 INFO: Performing label free quantification
2:30:15.791994 INFO: Accumulating fragment data
2:30:15.792069 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:30:16.079712 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:30:17.676470 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:30:19.210388 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:30:21.100958 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:30:22.738720 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:30:24.733236 INFO: Performing label free quantification on the precursor level
2:30:24.733404 INFO: Filtering fragments by quality
2:30:25.213973 INFO: Performing label-free quantification with directlfq normalization
2:30:25.894019 INFO: Applying directLFQ normalization
2:30:27.190274 INFO: 131021 lfq-groups total
2:31:56.633965 INFO: using 100 processes
2:31:56.926080 INFO: lfq-object 0
2:31:57.054380 INFO: lfq-object 100
2:31:57.095586 INFO: lfq-object 400
2:31:57.163167 INFO: lfq-object 700
2:31:57.163933 INFO: lfq-object 200
2:31:57.210160 INFO: lfq-object 500
2:31:57.239413 INFO: lfq-object 1000
2:31:57.276942 INFO: lfq-object 300
2:31:57.293428 INFO: lfq-object 800
2:31:57.323571 INFO: lfq-object 600
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2:33:37.451911 INFO: Performing label free quantification on the peptide level
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2:36:40.200537 INFO: Performing label free quantification on the pg level
2:36:40.200907 INFO: Filtering fragments by quality
2:36:40.613615 INFO: Performing label-free quantification with directlfq normalization
2:36:40.803520 INFO: Applying directLFQ normalization
2:36:40.995526 INFO: 10153 lfq-groups total
2:38:43.169586 INFO: using 100 processes
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2:38:50.718696 INFO: lfq-object 8000
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2:38:52.217726 INFO: lfq-object 9500
2:38:52.234809 INFO: lfq-object 9300
2:38:52.580574 INFO: lfq-object 9800
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2:38:52.816256 INFO: lfq-object 10000
2:38:52.919338 INFO: lfq-object 9900
2:39:00.109671 INFO: Writing psm output to disk
2:39:00.254967 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/precursors.parquet to disk
2:39:01.486570 INFO: Writing precursor output to disk
2:39:01.502473 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/precursor.matrix.parquet to disk
2:39:01.657531 INFO: Writing peptide output to disk
2:39:01.668208 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/peptide.matrix.parquet to disk
2:39:01.804044 INFO: Writing pg output to disk
2:39:01.809584 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/pg.matrix.parquet to disk
2:39:01.969980 PROGRESS: Building MBR spectral library
2:39:01.970438 INFO: Running MbrLibraryBuilder
2:39:09.255051 INFO: MBR spectral library contains 131,021 precursors, 10,153 proteins
2:39:09.255401 INFO: Writing MBR spectral library to disk
2:39:12.961245 PROGRESS: =================== Search step 'library' finished ===================
2:39:18.784706 INFO: =================== Running step 'mbr' ===================
2:39:18.790300 INFO: Extracted extra_config from previous step: defaultdict(<class 'dict'>, {'search': {'target_ms1_tolerance': 3.0, 'target_ms2_tolerance': 10.0}})
2:39:18.790665 INFO: loading default config from /home/robbe/bin/alphadia/alphadia/constants/default.yaml
2:39:18.807034 INFO: loading additional config provided via CLI
2:39:18.807220 INFO: loading additional config provided via CLI parameters
2:39:18.807790 INFO: Updating config with 'user defined'
2:39:18.807890 INFO: Updating config with 'user defined (cli)'
2:39:18.808129 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/AstralManuscript/HYE_Astral/alphadia_v2.1.1', 'general': {'thread_count': 100, 'mbr_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/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf', 'output_directory': '/home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1'}]
2:39:18.808392 INFO: Updating config with 'user defined'
2:39:18.808442 INFO: Updating config with 'user defined (cli)'
2:39:18.808462 INFO: Updating config with 'multistep search'
2:39:18.808517 INFO: ├──version: None
2:39:18.808540 INFO: ├──workflow_name: None
2:39:18.808564 INFO: [32;20m├──output_directory: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1 [multistep search, default: None][0m
2:39:18.808589 INFO: [32;20m├──library_path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf [multistep search, default: None][0m
2:39:18.808621 INFO: ├──raw_paths:
2:39:18.808643 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw [user defined (cli), default: None][0m
2:39:18.808661 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw [user defined (cli), default: None][0m
2:39:18.808679 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw [user defined (cli), default: None][0m
2:39:18.808696 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw [user defined (cli), default: None][0m
2:39:18.808713 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw [user defined (cli), default: None][0m
2:39:18.808730 INFO: │   [32;20m- /public/local/ProteoBench/HYE_Astral/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw [user defined (cli), default: None][0m
2:39:18.808747 INFO: ├──fasta_paths:
2:39:18.808765 INFO: ├──quant_directory: None
2:39:18.808782 INFO: ├──general
2:39:18.808803 INFO: │   [32;20m├──thread_count: 100 [user defined, default: 10][0m
2:39:18.808822 INFO: │   ├──transfer_step_enabled: False
2:39:18.808841 INFO: │   [32;20m├──mbr_step_enabled: True [user defined, default: False][0m
2:39:18.808859 INFO: │   ├──reuse_calibration: False
2:39:18.808877 INFO: │   ├──reuse_quant: False
2:39:18.808896 INFO: │   ├──log_level: INFO
2:39:18.808915 INFO: │   ├──use_gpu: True
2:39:18.808933 INFO: │   ├──save_figures: True
2:39:18.808951 INFO: │   ├──save_library: True
2:39:18.808969 INFO: │   ├──save_flat_library: False
2:39:18.808987 INFO: │   ├──input_library_type: base
2:39:18.809004 INFO: │   ├──save_mbr_library: True
2:39:18.809021 INFO: │   ├──random_state: None
2:39:18.809040 INFO: │   └──fail_fast: False
2:39:18.809063 INFO: ├──library_loading
2:39:18.809082 INFO: │   └──drop_decoys: False
2:39:18.809099 INFO: ├──library_prediction
2:39:18.809120 INFO: │   ├──enabled: False
2:39:18.809138 INFO: │   [32;20m├──enzyme: trypsin/p [user defined, default: trypsin][0m
2:39:18.809156 INFO: │   ├──fixed_modifications: Carbamidomethyl@C
2:39:18.809174 INFO: │   [32;20m├──variable_modifications: Oxidation@M [user defined, default: Oxidation@M;Acetyl@Protein_N-term][0m
2:39:18.809192 INFO: │   [32;20m├──max_var_mod_num: 1 [user defined, default: 2][0m
2:39:18.809210 INFO: │   ├──missed_cleavages: 1
2:39:18.809227 INFO: │   ├──precursor_len:
2:39:18.809244 INFO: │   │   [32;20m- 6 [user defined, default: 7][0m
2:39:18.809261 INFO: │   │   [32;20m- 30 [user defined, default: 35][0m
2:39:18.809279 INFO: │   ├──precursor_charge:
2:39:18.809297 INFO: │   │   [32;20m- 1 [user defined, default: 2][0m
2:39:18.809314 INFO: │   │   [32;20m- 5 [user defined, default: 4][0m
2:39:18.809332 INFO: │   ├──precursor_mz:
2:39:18.809350 INFO: │   │   [32;20m- 380.0 [user defined, default: 400][0m
2:39:18.809368 INFO: │   │   [32;20m- 980.0 [user defined, default: 1200][0m
2:39:18.809384 INFO: │   ├──fragment_mz:
2:39:18.809401 INFO: │   │   [32;20m- 150.0 [user defined, default: 200][0m
2:39:18.809418 INFO: │   │   - 2000.0
2:39:18.809436 INFO: │   ├──nce: 25.0
2:39:18.809453 INFO: │   ├──fragment_types:
2:39:18.809470 INFO: │   │   - b
2:39:18.809487 INFO: │   │   - y
2:39:18.809504 INFO: │   ├──max_fragment_charge: 2
2:39:18.809522 INFO: │   ├──instrument: Lumos
2:39:18.809539 INFO: │   ├──peptdeep_model_path: None
2:39:18.809557 INFO: │   ├──peptdeep_model_type: generic
2:39:18.809574 INFO: │   ├──predict_charge: False
2:39:18.809592 INFO: │   └──min_charge_probability: 0.1
2:39:18.809609 INFO: ├──custom_modifications:
2:39:18.809627 INFO: │   ├──name: Dimethyl:d12@K
2:39:18.809645 INFO: │   └──composition: H(-2)2H(8)13C(2)
2:39:18.809663 INFO: │   ├──name: Dimethyl:d12@Any_N-term
2:39:18.809680 INFO: │   └──composition: H(-2)2H(8)13C(2)
2:39:18.809697 INFO: │   ├──name: Dimethyl:d12@Protein_N-term
2:39:18.809715 INFO: │   └──composition: H(-2)2H(8)13C(2)
2:39:18.809732 INFO: │   ├──name: mTRAQ:d12@K
2:39:18.809749 INFO: │   └──composition: H(12)C(1)13C(10)15N(2)O(1)
2:39:18.809767 INFO: │   ├──name: mTRAQ:d12@Any_N-term
2:39:18.809784 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
2:39:18.809802 INFO: │   ├──name: mTRAQ:d12@Protein_N-term
2:39:18.809818 INFO: │   └──composition: H(12)C(1)13C(14)15N(2)O(1)
2:39:18.809836 INFO: │   ├──name: Label:13C(12)@K
2:39:18.809854 INFO: │   └──composition: C(12)
2:39:18.809870 INFO: ├──search
2:39:18.809888 INFO: │   ├──extraction_backend: rust
2:39:18.809909 INFO: │   [32;20m├──target_ms1_tolerance: 3.0 [multistep search, default: 5][0m
2:39:18.809927 INFO: │   ├──target_ms2_tolerance: 10.0
2:39:18.809946 INFO: │   ├──target_rt_tolerance: 0.0
2:39:18.809963 INFO: │   ├──target_mobility_tolerance: 0.0
2:39:18.809981 INFO: │   ├──quant_window: 3
2:39:18.809998 INFO: │   ├──target_num_candidates: 3
2:39:18.810016 INFO: │   ├──channel_filter: 
2:39:18.810035 INFO: │   ├──compete_for_fragments: True
2:39:18.810052 INFO: │   ├──top_k_fragments_selection: 12
2:39:18.810070 INFO: │   ├──top_k_fragments_scoring: 12
2:39:18.810088 INFO: │   ├──min_fragment_intensity: 0.01
2:39:18.810105 INFO: │   ├──optimized_peak_group_score: False
2:39:18.810124 INFO: │   ├──exclude_shared_ions: True
2:39:18.810142 INFO: │   ├──quant_all: True
2:39:18.810159 INFO: │   └──experimental_xic: True
2:39:18.810176 INFO: ├──calibration
2:39:18.810193 INFO: │   ├──batch_size: 1000
2:39:18.810215 INFO: │   ├──optimization_lock_target: 1000
2:39:18.810232 INFO: │   ├──max_steps: 20
2:39:18.810252 INFO: │   ├──min_steps: 5
2:39:18.810269 INFO: │   ├──max_skips: 1
2:39:18.810286 INFO: │   ├──max_fragments: 5000
2:39:18.810304 INFO: │   └──min_correlation: 0.7
2:39:18.810321 INFO: ├──search_initial
2:39:18.810338 INFO: │   ├──num_candidates: 1
2:39:18.810356 INFO: │   [32;20m├──ms1_tolerance: 3 [user defined, default: 30][0m
2:39:18.810373 INFO: │   [32;20m├──ms2_tolerance: 10 [user defined, default: 30][0m
2:39:18.810391 INFO: │   ├──mobility_tolerance: 0.1
2:39:18.810408 INFO: │   └──rt_tolerance: 0.5
2:39:18.810425 INFO: ├──library_multiplexing
2:39:18.810443 INFO: │   ├──enabled: False
2:39:18.810461 INFO: │   ├──input_channel: 0
2:39:18.810478 INFO: │   └──multiplex_mapping:
2:39:18.810495 INFO: ├──multiplexing
2:39:18.810512 INFO: │   ├──enabled: False
2:39:18.810529 INFO: │   ├──target_channels: 4,8
2:39:18.810546 INFO: │   ├──decoy_channel: 12
2:39:18.810563 INFO: │   ├──reference_channel: 0
2:39:18.810580 INFO: │   └──competitive_scoring: True
2:39:18.810597 INFO: ├──fdr
2:39:18.810615 INFO: │   ├──fdr: 0.01
2:39:18.810632 INFO: │   ├──group_level: proteins
2:39:18.810649 INFO: │   [32;20m├──inference_strategy: library [multistep search, default: heuristic][0m
2:39:18.810667 INFO: │   ├──competitive_scoring: True
2:39:18.810684 INFO: │   ├──keep_decoys: False
2:39:18.810701 INFO: │   ├──keep_decoys_in_mbr_library: False
2:39:18.810718 INFO: │   ├──channel_wise_fdr: False
2:39:18.810735 INFO: │   └──enable_nn_hyperparameter_tuning: True
2:39:18.810752 INFO: ├──search_output
2:39:18.810770 INFO: │   ├──file_format: parquet
2:39:18.810787 INFO: │   ├──precursor_level_lfq: True
2:39:18.810804 INFO: │   ├──peptide_level_lfq: True
2:39:18.810821 INFO: │   ├──save_fragment_quant_matrix: False
2:39:18.810839 INFO: │   ├──min_k_fragments: 12
2:39:18.810856 INFO: │   ├──min_correlation: 0.9
2:39:18.810874 INFO: │   ├──num_samples_quadratic: 50
2:39:18.810891 INFO: │   ├──min_nonnan: 3
2:39:18.810908 INFO: │   ├──normalization_method: directlfq
2:39:18.810925 INFO: │   └──normalize_directlfq: True
2:39:18.810942 INFO: ├──optimization
2:39:18.810960 INFO: │   ├──order_of_optimization: None
2:39:18.810977 INFO: │   ├──ms2_error
2:39:18.810996 INFO: │   │   ├──targeted_update_percentile_range: 0.95
2:39:18.811014 INFO: │   │   ├──targeted_update_factor: 1.0
2:39:18.811032 INFO: │   │   ├──automatic_update_percentile_range: 0.99
2:39:18.811051 INFO: │   │   ├──automatic_update_factor: 1.1
2:39:18.811069 INFO: │   │   ├──try_narrower_values: True
2:39:18.811087 INFO: │   │   ├──maximal_decrease: 0.5
2:39:18.811105 INFO: │   │   ├──favour_narrower_optimum: False
2:39:18.811123 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
2:39:18.811140 INFO: │   ├──ms1_error
2:39:18.811158 INFO: │   │   ├──targeted_update_percentile_range: 0.95
2:39:18.811175 INFO: │   │   ├──targeted_update_factor: 1.0
2:39:18.811193 INFO: │   │   ├──automatic_update_percentile_range: 0.99
2:39:18.811211 INFO: │   │   ├──automatic_update_factor: 1.1
2:39:18.811229 INFO: │   │   ├──try_narrower_values: False
2:39:18.811247 INFO: │   │   ├──maximal_decrease: 0.2
2:39:18.811265 INFO: │   │   ├──favour_narrower_optimum: False
2:39:18.811282 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
2:39:18.811300 INFO: │   ├──mobility_error
2:39:18.811318 INFO: │   │   ├──targeted_update_percentile_range: 0.95
2:39:18.811337 INFO: │   │   ├──targeted_update_factor: 1.0
2:39:18.811358 INFO: │   │   ├──automatic_update_percentile_range: 0.99
2:39:18.811376 INFO: │   │   ├──automatic_update_factor: 1.1
2:39:18.811397 INFO: │   │   ├──try_narrower_values: False
2:39:18.811416 INFO: │   │   ├──maximal_decrease: 0.2
2:39:18.811434 INFO: │   │   ├──favour_narrower_optimum: False
2:39:18.811452 INFO: │   │   └──maximum_decrease_from_maximum: 0.1
2:39:18.811469 INFO: │   └──rt_error
2:39:18.811486 INFO: │       ├──targeted_update_percentile_range: 0.95
2:39:18.811504 INFO: │       ├──targeted_update_factor: 1.0
2:39:18.811522 INFO: │       ├──automatic_update_percentile_range: 0.999
2:39:18.811540 INFO: │       ├──automatic_update_factor: 1.5
2:39:18.811558 INFO: │       ├──try_narrower_values: True
2:39:18.811576 INFO: │       ├──maximal_decrease: 0.1
2:39:18.811593 INFO: │       ├──favour_narrower_optimum: False
2:39:18.811611 INFO: │       └──maximum_decrease_from_maximum: 0.5
2:39:18.811628 INFO: ├──optimization_manager
2:39:18.811646 INFO: │   ├──fwhm_rt: 5
2:39:18.811664 INFO: │   ├──fwhm_mobility: 0.01
2:39:18.811682 INFO: │   └──score_cutoff: 0
2:39:18.811698 INFO: ├──transfer_library
2:39:18.811715 INFO: │   ├──enabled: False
2:39:18.811732 INFO: │   ├──fragment_types:
2:39:18.811748 INFO: │   │   - b
2:39:18.811765 INFO: │   │   - y
2:39:18.811782 INFO: │   ├──max_charge: 2
2:39:18.811800 INFO: │   ├──top_k_samples: 3
2:39:18.811833 INFO: │   ├──norm_delta_max: True
2:39:18.811865 INFO: │   ├──precursor_correlation_cutoff: 0.5
2:39:18.811883 INFO: │   └──fragment_correlation_ratio: 0.75
2:39:18.811900 INFO: └──transfer_learning
2:39:18.811917 INFO:     ├──enabled: False
2:39:18.811934 INFO:     ├──batch_size: 2000
2:39:18.811953 INFO:     ├──max_lr: 0.0001
2:39:18.811971 INFO:     ├──train_fraction: 0.7
2:39:18.811989 INFO:     ├──validation_fraction: 0.2
2:39:18.812007 INFO:     ├──test_fraction: 0.1
2:39:18.812025 INFO:     ├──test_interval: 1
2:39:18.812042 INFO:     ├──lr_patience: 3
2:39:18.812059 INFO:     ├──epochs: 51
2:39:18.812077 INFO:     ├──warmup_epochs: 5
2:39:18.812094 INFO:     ├──nce: 25
2:39:18.812111 INFO:     └──instrument: Lumos
2:39:18.818272 INFO: Moved existing config file /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/frozen_config.yaml to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/frozen_config.1.bkp.yaml
2:39:18.819211 INFO: Registering 7 custom modifications
2:39:18.846358 INFO: Searching 6 files:
2:39:18.846533 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP1.raw
2:39:18.846557 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP2.raw
2:39:18.846576 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_A_REP3.raw
2:39:18.846593 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP1.raw
2:39:18.846610 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP2.raw
2:39:18.846626 INFO:   LFQ_Astral_DIA_15min_50ng_Condition_B_REP3.raw
2:39:18.846645 INFO: Using 0 fasta files:
2:39:18.846671 INFO: Using library: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf
2:39:18.846691 INFO: Saving output to: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1
2:39:18.846740 PROGRESS: Loading spectral library
2:39:18.846796 PROGRESS: Loading library (type: base) from disk..
2:39:18.846981 INFO: Running DynamicLoader
2:39:18.847089 INFO: Loading .hdf library from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/library/speclib.mbr.hdf
2:39:20.316281 INFO: Running PrecursorInitializer
2:39:20.317868 INFO: Channel column already present, skipping initialization
2:39:20.317968 INFO: Elution group indices already present, skipping initialization
2:39:20.317994 INFO: Precursor indices already present, skipping initialization
2:39:20.318059 INFO: Running AnnotateFasta
2:39:20.377155 INFO: Running IsotopeGenerator
2:39:20.378232 INFO: Isotope information already present, skipping isotope generation
2:39:20.378415 INFO: Running RTNormalization
2:39:20.392322 INFO: Saving library to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/speclib.hdf
2:39:22.551977 INFO: Running DecoyGenerator
2:39:36.224432 INFO: Running FlattenLibrary
2:39:38.991837 INFO: Running InitFlatColumns
2:39:39.018411 INFO: Running LogFlatLibraryStats
2:39:39.018825 INFO: ============ Library Stats ============
2:39:39.018884 INFO: Number of precursors: 262,003
2:39:39.178563 INFO: 	thereof targets:131,021
2:39:39.178973 INFO: 	thereof decoys: 130,982
2:39:39.193456 INFO: Number of elution groups: 131,021
2:39:39.193852 INFO: 	average size: 2.00
2:39:39.293289 INFO: Number of proteins: 10,153
2:39:39.297014 INFO: Number of channels: 1 ([0])
2:39:39.297614 INFO: Isotopes Distribution for 4 isotopes
2:39:39.297660 INFO: =======================================
2:39:39.298150 PROGRESS: =================== Starting Search Workflows for step mbr ===================
2:39:39.298320 PROGRESS: Loading raw file 1/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP1 
2:39:39.298529 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:39:39.298922 INFO: Initializing TimingManager
2:39:39.301684 INFO: Initializing RawFileManager
2:40:05.095550 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:40:05.109646 INFO: Determining DIA cycle
2:40:05.130779 INFO: Found cycle with start 0.00 min and length 300.
2:40:05.566967 INFO: RT (min)            : 0.0 - 26.9
2:40:05.567138 INFO: RT duration (sec)   : 1611.2
2:40:05.567175 INFO: RT duration (min)   : 26.9
2:40:05.567205 INFO: Cycle len (scans)   : 300
2:40:05.567233 INFO: Cycle len (sec)     : 1.65
2:40:05.567257 INFO: Number of cycles    : 977
2:40:05.567284 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:40:05.567331 INFO: Creating DIA data object took: 26.26543951034546
2:40:07.810522 INFO: Creating DIA data NG object took: 2.242976188659668
2:40:07.894255 INFO: Initializing CalibrationManager
2:40:07.894786 INFO: Setting up calibration estimators ..
2:40:07.894862 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:40:07.894986 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2:40:07.895090 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:40:07.895157 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:40:07.895233 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2:40:07.895295 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:40:07.895352 INFO: Done setting up calibration estimators.
2:40:07.895734 INFO: Initializing OptimizationManager
2:40:07.895936 INFO: initial parameter: ms1_error = 3
2:40:07.896006 INFO: initial parameter: ms2_error = 10
2:40:07.896077 INFO: initial parameter: rt_error = 805.5992431640625
2:40:07.896135 INFO: initial parameter: mobility_error = 0.1
2:40:07.896192 INFO: initial parameter: num_candidates = 1
2:40:07.896245 INFO: initial parameter: fwhm_rt = 5
2:40:07.896297 INFO: initial parameter: fwhm_mobility = 0.01
2:40:07.896348 INFO: initial parameter: score_cutoff = 0
2:40:07.896401 INFO: initial parameter: classifier_version = -1
2:40:07.896493 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:40:07.896965 INFO: FDRManager: loading saved state not requested, will be initialized.
2:40:07.897010 INFO: Initializing FDRManager
2:40:07.897075 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:40:08.006842 PROGRESS: Initializing spectral library: 131,021 target precursors potentially observable (0 removed)
2:40:08.140334 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
2:40:08.142344 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 805.5992431640625
2:40:08.143635 PROGRESS: Starting initial search for precursors.
2:40:08.144464 INFO: Starting optimization step 0.
2:40:08.144674 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:40:08.144798 INFO: Using rust extraction backend
2:40:08.144921 PROGRESS: Extracting batch of 1982 precursors
2:40:08.170857 INFO: === Search parameters used ===
2:40:08.171768 INFO: rt_error       : 805.5992431640625
2:40:08.171912 INFO: mobility_error : 0.1
2:40:08.171999 INFO: num_candidates : 1
2:40:08.172060 INFO: ms1_error      : 3
2:40:08.172118 INFO: ms2_error      : 10
2:40:08.172172 INFO: fwhm_rt        : 5
2:40:08.172242 INFO: quant_window   : 3
2:40:08.172295 INFO: ==============================================
2:40:08.433808 INFO: performing precursor FDR with 40 features
2:40:08.434002 INFO: Decoy channel: -1
2:40:08.434032 INFO: competitive: True
2:40:08.439533 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:08.446338 INFO: Estimating optimal hyperparameters - samples: 1,584, batch_size: 128, learning_rate: 1.77e-04
2:40:08.448793 INFO: Using random state 16393 for train-test-split
2:40:08.797044 INFO: Test AUC: 0.869
2:40:08.797312 INFO: Train AUC: 0.865
2:40:08.797359 INFO: AUC difference: 0.45%
2:40:09.277908 INFO: Resetting torch num_threads to 100
2:40:09.282541 PROGRESS: === Extracted 1980 precursors and 15300 fragments ===
2:40:09.283445 INFO: === FDR correction performed with classifier version -1 ===
2:40:09.284815 PROGRESS: ============================= Precursor FDR =============================
2:40:09.285056 PROGRESS: Total precursors accumulated: 571
2:40:09.285175 PROGRESS: Target precursors: 566 (99.12%)
2:40:09.285248 PROGRESS: Decoy precursors: 5 (0.88%)
2:40:09.285309 PROGRESS: 
2:40:09.285367 PROGRESS: Precursor Summary:
2:40:09.287858 PROGRESS: Channel   0:	 0.050 FDR:   566; 0.010 FDR:   566; 0.001 FDR:   444
2:40:09.288003 PROGRESS: 
2:40:09.288103 PROGRESS: Protein Summary:
2:40:09.291004 PROGRESS: Channel   0:	 0.050 FDR:   526; 0.010 FDR:   526; 0.001 FDR:   422
2:40:09.291146 PROGRESS: =========================================================================
2:40:09.291638 INFO: Target number of precursors not reached yet.
2:40:09.307190 INFO: Starting optimization step 1.
2:40:09.307623 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:40:09.307740 INFO: Using rust extraction backend
2:40:09.307851 PROGRESS: Extracting batch of 3958 precursors
2:40:09.327075 INFO: === Search parameters used ===
2:40:09.327719 INFO: rt_error       : 805.5992431640625
2:40:09.327795 INFO: mobility_error : 0.1
2:40:09.327892 INFO: num_candidates : 1
2:40:09.327954 INFO: ms1_error      : 3
2:40:09.328009 INFO: ms2_error      : 10
2:40:09.328063 INFO: fwhm_rt        : 5
2:40:09.328117 INFO: quant_window   : 3
2:40:09.328169 INFO: ==============================================
2:40:09.656171 INFO: performing precursor FDR with 40 features
2:40:09.656428 INFO: Decoy channel: -1
2:40:09.656461 INFO: competitive: True
2:40:09.669177 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:09.676422 INFO: Estimating optimal hyperparameters - samples: 4,750, batch_size: 128, learning_rate: 1.77e-04
2:40:09.676732 INFO: Using random state 53021 for train-test-split
2:40:10.441910 INFO: Test AUC: 0.907
2:40:10.442175 INFO: Train AUC: 0.894
2:40:10.442204 INFO: AUC difference: 1.40%
2:40:10.775041 INFO: Resetting torch num_threads to 100
2:40:10.781952 PROGRESS: === Extracted 5938 precursors and 45962 fragments ===
2:40:10.782984 INFO: === FDR correction performed with classifier version -1 ===
2:40:10.787645 PROGRESS: ============================= Precursor FDR =============================
2:40:10.787944 PROGRESS: Total precursors accumulated: 1,941
2:40:10.788050 PROGRESS: Target precursors: 1,922 (99.02%)
2:40:10.788101 PROGRESS: Decoy precursors: 19 (0.98%)
2:40:10.788155 PROGRESS: 
2:40:10.788198 PROGRESS: Precursor Summary:
2:40:10.790413 PROGRESS: Channel   0:	 0.050 FDR: 1,922; 0.010 FDR: 1,922; 0.001 FDR: 1,235
2:40:10.790576 PROGRESS: 
2:40:10.790661 PROGRESS: Protein Summary:
2:40:10.793162 PROGRESS: Channel   0:	 0.050 FDR: 1,552; 0.010 FDR: 1,552; 0.001 FDR: 1,057
2:40:10.793341 PROGRESS: =========================================================================
2:40:10.794009 INFO: Target number of precursors reached.
2:40:10.810032 INFO: fragments_df: keeping 5000 of 45962 [sum(precursor_idx_mask)=19595 sum(mass_error_mask)=45962 stop_rank=5000
2:40:10.832335 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:11.258762 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:12.112054 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:40:12.112719 INFO: Using score_cutoff 11.45727136144638 (fac=0.99, q=1)
2:40:12.113179 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:40:12.113257 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:40:12.113309 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.45727136144638
2:40:12.113365 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:12.117992 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:12.126799 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:40:12.126997 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:40:12.127092 INFO: Starting optimization step 2.
2:40:12.127172 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:12.127291 INFO: Using rust extraction backend
2:40:12.127354 PROGRESS: Extracting batch of 5940 precursors
2:40:12.144133 INFO: === Search parameters used ===
2:40:12.144476 INFO: rt_error       : 805.5992431640625
2:40:12.144531 INFO: mobility_error : 0.1
2:40:12.144577 INFO: num_candidates : 3
2:40:12.144618 INFO: ms1_error      : 3
2:40:12.144657 INFO: ms2_error      : 10
2:40:12.144695 INFO: fwhm_rt        : 3.0
2:40:12.144733 INFO: quant_window   : 3
2:40:12.144772 INFO: ==============================================
2:40:12.613977 INFO: performing precursor FDR with 40 features
2:40:12.614106 INFO: Decoy channel: -1
2:40:12.614129 INFO: competitive: True
2:40:12.622161 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:12.628581 INFO: Estimating optimal hyperparameters - samples: 14,248, batch_size: 128, learning_rate: 1.77e-04
2:40:12.628840 INFO: Using random state 651651 for train-test-split
2:40:15.228362 INFO: Test AUC: 0.718
2:40:15.228601 INFO: Train AUC: 0.729
2:40:15.228634 INFO: AUC difference: 1.45%
2:40:15.646448 INFO: Resetting torch num_threads to 100
2:40:15.650745 PROGRESS: === Extracted 17811 precursors and 119750 fragments ===
2:40:15.651322 INFO: === FDR correction performed with classifier version 1 ===
2:40:15.652264 PROGRESS: ============================= Precursor FDR =============================
2:40:15.652364 PROGRESS: Total precursors accumulated: 2,266
2:40:15.652429 PROGRESS: Target precursors: 2,244 (99.03%)
2:40:15.652482 PROGRESS: Decoy precursors: 22 (0.97%)
2:40:15.652543 PROGRESS: 
2:40:15.652590 PROGRESS: Precursor Summary:
2:40:15.654836 PROGRESS: Channel   0:	 0.050 FDR: 2,244; 0.010 FDR: 2,244; 0.001 FDR: 1,192
2:40:15.654943 PROGRESS: 
2:40:15.655010 PROGRESS: Protein Summary:
2:40:15.657577 PROGRESS: Channel   0:	 0.050 FDR: 1,798; 0.010 FDR: 1,798; 0.001 FDR: 1,027
2:40:15.657700 PROGRESS: =========================================================================
2:40:15.658511 INFO: Target number of precursors reached.
2:40:15.687560 INFO: fragments_df: keeping 5000 of 119750 [sum(precursor_idx_mask)=51780 sum(mass_error_mask)=119750 stop_rank=5000
2:40:15.703666 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:16.255162 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:17.481302 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:17.482393 INFO: Using score_cutoff 11.261824451065063 (fac=0.99, q=1)
2:40:17.483221 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:17.483309 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:17.483364 INFO: Updating optimization_manager: score_cutoff        : 11.45727136144638 -> 11.261824451065063
2:40:17.483430 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:17.490781 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:17.503341 INFO: === checking if optimization conditions were reached ===
2:40:17.508199 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
2:40:17.508957 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:40:17.509034 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:40:17.509106 INFO: ==============================================
2:40:17.509202 INFO: Starting optimization step 3.
2:40:17.509262 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:17.509389 INFO: Using rust extraction backend
2:40:17.509517 PROGRESS: Extracting batch of 5940 precursors
2:40:17.567895 INFO: === Search parameters used ===
2:40:17.568801 INFO: rt_error       : 805.5992431640625
2:40:17.568861 INFO: mobility_error : 0.1
2:40:17.568910 INFO: num_candidates : 3
2:40:17.568953 INFO: ms1_error      : 3
2:40:17.568994 INFO: ms2_error      : 10.0
2:40:17.569037 INFO: fwhm_rt        : 3.0
2:40:17.569079 INFO: quant_window   : 3
2:40:17.569122 INFO: ==============================================
2:40:17.982136 INFO: performing precursor FDR with 40 features
2:40:17.982401 INFO: Decoy channel: -1
2:40:17.982427 INFO: competitive: True
2:40:17.991515 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:17.998927 INFO: Estimating optimal hyperparameters - samples: 14,248, batch_size: 128, learning_rate: 1.77e-04
2:40:17.999256 INFO: Using random state 56955 for train-test-split
2:40:19.936518 INFO: Test AUC: 0.719
2:40:19.936756 INFO: Train AUC: 0.744
2:40:19.936800 INFO: AUC difference: 3.37%
2:40:20.237389 INFO: Resetting torch num_threads to 100
2:40:20.241131 PROGRESS: === Extracted 17810 precursors and 119802 fragments ===
2:40:20.241610 INFO: === FDR correction performed with classifier version 2 ===
2:40:20.242584 PROGRESS: ============================= Precursor FDR =============================
2:40:20.242684 PROGRESS: Total precursors accumulated: 2,306
2:40:20.242746 PROGRESS: Target precursors: 2,284 (99.05%)
2:40:20.242801 PROGRESS: Decoy precursors: 22 (0.95%)
2:40:20.242849 PROGRESS: 
2:40:20.242897 PROGRESS: Precursor Summary:
2:40:20.244570 PROGRESS: Channel   0:	 0.050 FDR: 2,284; 0.010 FDR: 2,284; 0.001 FDR: 1,268
2:40:20.244676 PROGRESS: 
2:40:20.244735 PROGRESS: Protein Summary:
2:40:20.246989 PROGRESS: Channel   0:	 0.050 FDR: 1,824; 0.010 FDR: 1,824; 0.001 FDR: 1,079
2:40:20.247087 PROGRESS: =========================================================================
2:40:20.247606 INFO: Target number of precursors reached.
2:40:20.275332 INFO: fragments_df: keeping 5000 of 119802 [sum(precursor_idx_mask)=52505 sum(mass_error_mask)=119802 stop_rank=5000
2:40:20.291794 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:20.879255 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:21.872704 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:21.873625 INFO: Using score_cutoff 11.090926165580749 (fac=0.99, q=1)
2:40:21.874088 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:21.874169 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:21.874224 INFO: Updating optimization_manager: score_cutoff        : 11.261824451065063 -> 11.090926165580749
2:40:21.874282 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:21.879923 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:21.890365 INFO: === checking if optimization conditions were reached ===
2:40:21.893656 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:40:21.893936 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:40:21.894008 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:40:21.894094 INFO: ==============================================
2:40:21.894169 INFO: Starting optimization step 4.
2:40:21.894227 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:21.894296 INFO: Using rust extraction backend
2:40:21.894362 PROGRESS: Extracting batch of 5940 precursors
2:40:21.925890 INFO: === Search parameters used ===
2:40:21.926625 INFO: rt_error       : 805.5992431640625
2:40:21.926680 INFO: mobility_error : 0.1
2:40:21.926734 INFO: num_candidates : 3
2:40:21.926777 INFO: ms1_error      : 3
2:40:21.926819 INFO: ms2_error      : 10.0
2:40:21.926863 INFO: fwhm_rt        : 3.0
2:40:21.926907 INFO: quant_window   : 3
2:40:21.926948 INFO: ==============================================
2:40:22.222038 INFO: performing precursor FDR with 40 features
2:40:22.222258 INFO: Decoy channel: -1
2:40:22.222284 INFO: competitive: True
2:40:22.237112 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:22.246901 INFO: Estimating optimal hyperparameters - samples: 14,248, batch_size: 128, learning_rate: 1.77e-04
2:40:22.247242 INFO: Using random state 221716 for train-test-split
2:40:24.268130 INFO: Test AUC: 0.738
2:40:24.268281 INFO: Train AUC: 0.752
2:40:24.268320 INFO: AUC difference: 1.80%
2:40:31.414695 INFO: Resetting torch num_threads to 100
2:40:31.428617 PROGRESS: === Extracted 17811 precursors and 119796 fragments ===
2:40:31.430310 INFO: === FDR correction performed with classifier version 3 ===
2:40:31.435028 PROGRESS: ============================= Precursor FDR =============================
2:40:31.435662 PROGRESS: Total precursors accumulated: 2,364
2:40:31.435807 PROGRESS: Target precursors: 2,341 (99.03%)
2:40:31.435913 PROGRESS: Decoy precursors: 23 (0.97%)
2:40:31.435972 PROGRESS: 
2:40:31.436064 PROGRESS: Precursor Summary:
2:40:31.442770 PROGRESS: Channel   0:	 0.050 FDR: 2,341; 0.010 FDR: 2,341; 0.001 FDR: 1,280
2:40:31.443542 PROGRESS: 
2:40:31.443604 PROGRESS: Protein Summary:
2:40:31.449032 PROGRESS: Channel   0:	 0.050 FDR: 1,860; 0.010 FDR: 1,860; 0.001 FDR: 1,090
2:40:31.449910 PROGRESS: =========================================================================
2:40:31.452151 INFO: Target number of precursors reached.
2:40:31.501690 INFO: fragments_df: keeping 5000 of 119796 [sum(precursor_idx_mask)=53521 sum(mass_error_mask)=119796 stop_rank=5000
2:40:31.548755 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:32.116673 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:32.995698 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:32.996581 INFO: Using score_cutoff 10.841775718688965 (fac=0.99, q=1)
2:40:32.997112 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:32.997193 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:32.997248 INFO: Updating optimization_manager: score_cutoff        : 11.090926165580749 -> 10.841775718688965
2:40:32.997314 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:33.002555 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:33.012604 INFO: === checking if optimization conditions were reached ===
2:40:33.015662 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:40:33.015923 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:40:33.016020 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:40:33.016083 INFO: ==============================================
2:40:33.016158 INFO: Starting optimization step 5.
2:40:33.016223 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:33.016305 INFO: Using rust extraction backend
2:40:33.016374 PROGRESS: Extracting batch of 5940 precursors
2:40:33.042460 INFO: === Search parameters used ===
2:40:33.043054 INFO: rt_error       : 805.5992431640625
2:40:33.043109 INFO: mobility_error : 0.1
2:40:33.043156 INFO: num_candidates : 3
2:40:33.043200 INFO: ms1_error      : 3
2:40:33.043241 INFO: ms2_error      : 10.0
2:40:33.043280 INFO: fwhm_rt        : 3.0
2:40:33.043319 INFO: quant_window   : 3
2:40:33.043357 INFO: ==============================================
2:40:33.338155 INFO: performing precursor FDR with 40 features
2:40:33.338400 INFO: Decoy channel: -1
2:40:33.338425 INFO: competitive: True
2:40:33.358899 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:33.369358 INFO: Estimating optimal hyperparameters - samples: 14,248, batch_size: 128, learning_rate: 1.77e-04
2:40:33.369789 INFO: Using random state 998237 for train-test-split
2:40:35.369918 INFO: Test AUC: 0.748
2:40:35.370136 INFO: Train AUC: 0.758
2:40:35.370167 INFO: AUC difference: 1.28%
2:40:35.724158 INFO: Resetting torch num_threads to 100
2:40:35.729177 PROGRESS: === Extracted 17810 precursors and 119816 fragments ===
2:40:35.730129 INFO: === FDR correction performed with classifier version 4 ===
2:40:35.731378 PROGRESS: ============================= Precursor FDR =============================
2:40:35.731507 PROGRESS: Total precursors accumulated: 2,395
2:40:35.731577 PROGRESS: Target precursors: 2,372 (99.04%)
2:40:35.731630 PROGRESS: Decoy precursors: 23 (0.96%)
2:40:35.731715 PROGRESS: 
2:40:35.731762 PROGRESS: Precursor Summary:
2:40:35.733867 PROGRESS: Channel   0:	 0.050 FDR: 2,372; 0.010 FDR: 2,372; 0.001 FDR: 1,336
2:40:35.733994 PROGRESS: 
2:40:35.734056 PROGRESS: Protein Summary:
2:40:35.736715 PROGRESS: Channel   0:	 0.050 FDR: 1,886; 0.010 FDR: 1,886; 0.001 FDR: 1,123
2:40:35.736841 PROGRESS: =========================================================================
2:40:35.738130 INFO: Target number of precursors reached.
2:40:35.776607 INFO: fragments_df: keeping 5000 of 119816 [sum(precursor_idx_mask)=54185 sum(mass_error_mask)=119816 stop_rank=5000
2:40:35.814150 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:36.473228 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:37.447701 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:37.449031 INFO: Using score_cutoff 10.817754507923127 (fac=0.99, q=1)
2:40:37.449667 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:37.449762 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:37.449832 INFO: Updating optimization_manager: score_cutoff        : 10.841775718688965 -> 10.817754507923127
2:40:37.449956 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:37.457268 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:37.470203 INFO: === checking if optimization conditions were reached ===
2:40:37.474207 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:40:37.474619 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:40:37.474701 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:40:37.474764 INFO: ==============================================
2:40:37.474852 INFO: Starting optimization step 6.
2:40:37.474922 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:37.475011 INFO: Using rust extraction backend
2:40:37.475095 PROGRESS: Extracting batch of 5940 precursors
2:40:37.510454 INFO: === Search parameters used ===
2:40:37.511276 INFO: rt_error       : 805.5992431640625
2:40:37.511351 INFO: mobility_error : 0.1
2:40:37.511401 INFO: num_candidates : 3
2:40:37.511446 INFO: ms1_error      : 3
2:40:37.511491 INFO: ms2_error      : 10.0
2:40:37.511534 INFO: fwhm_rt        : 3.0
2:40:37.511577 INFO: quant_window   : 3
2:40:37.511622 INFO: ==============================================
2:40:37.842680 INFO: performing precursor FDR with 40 features
2:40:37.842977 INFO: Decoy channel: -1
2:40:37.843007 INFO: competitive: True
2:40:37.864178 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:37.879248 INFO: Estimating optimal hyperparameters - samples: 14,248, batch_size: 128, learning_rate: 1.77e-04
2:40:37.879772 INFO: Using random state 570458 for train-test-split
2:40:40.056330 INFO: Test AUC: 0.751
2:40:40.056690 INFO: Train AUC: 0.766
2:40:40.056725 INFO: AUC difference: 1.98%
2:40:40.436535 INFO: Resetting torch num_threads to 100
2:40:40.443496 PROGRESS: === Extracted 17810 precursors and 119815 fragments ===
2:40:40.444801 INFO: === FDR correction performed with classifier version 5 ===
2:40:40.446770 PROGRESS: ============================= Precursor FDR =============================
2:40:40.446942 PROGRESS: Total precursors accumulated: 2,461
2:40:40.447013 PROGRESS: Target precursors: 2,437 (99.02%)
2:40:40.447099 PROGRESS: Decoy precursors: 24 (0.98%)
2:40:40.447150 PROGRESS: 
2:40:40.447200 PROGRESS: Precursor Summary:
2:40:40.449693 PROGRESS: Channel   0:	 0.050 FDR: 2,437; 0.010 FDR: 2,437; 0.001 FDR: 1,358
2:40:40.449868 PROGRESS: 
2:40:40.449927 PROGRESS: Protein Summary:
2:40:40.453004 PROGRESS: Channel   0:	 0.050 FDR: 1,938; 0.010 FDR: 1,938; 0.001 FDR: 1,139
2:40:40.453297 PROGRESS: =========================================================================
2:40:40.454504 INFO: Target number of precursors reached.
2:40:40.491505 INFO: fragments_df: keeping 5000 of 119815 [sum(precursor_idx_mask)=55478 sum(mass_error_mask)=119815 stop_rank=5000
2:40:40.523122 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:41.186851 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:42.464396 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:42.465920 INFO: Using score_cutoff 10.704056787872315 (fac=0.99, q=1)
2:40:42.466545 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:42.466647 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:42.466713 INFO: Updating optimization_manager: score_cutoff        : 10.817754507923127 -> 10.704056787872315
2:40:42.466794 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:42.473272 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:42.486295 INFO: === checking if optimization conditions were reached ===
2:40:42.490802 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:40:42.491249 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:40:42.491327 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:40:42.491400 INFO: ==============================================
2:40:42.491515 PROGRESS: Optimization finished for ms2_error.
2:40:42.522738 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:42.530448 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:42.543459 INFO: Starting optimization step 0.
2:40:42.544173 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:42.544280 INFO: Using rust extraction backend
2:40:42.544363 PROGRESS: Extracting batch of 5940 precursors
2:40:42.581232 INFO: === Search parameters used ===
2:40:42.582243 INFO: rt_error       : 805.5992431640625
2:40:42.582312 INFO: mobility_error : 0.1
2:40:42.582365 INFO: num_candidates : 3
2:40:42.582411 INFO: ms1_error      : 3
2:40:42.582456 INFO: ms2_error      : 10.0
2:40:42.582499 INFO: fwhm_rt        : 3.0
2:40:42.582544 INFO: quant_window   : 3
2:40:42.582586 INFO: ==============================================
2:40:42.936023 INFO: performing precursor FDR with 40 features
2:40:42.936308 INFO: Decoy channel: -1
2:40:42.936335 INFO: competitive: True
2:40:42.957323 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:42.970561 INFO: Estimating optimal hyperparameters - samples: 14,248, batch_size: 128, learning_rate: 1.77e-04
2:40:42.971032 INFO: Using random state 534183 for train-test-split
2:40:44.608432 INFO: Test AUC: 0.748
2:40:44.608773 INFO: Train AUC: 0.774
2:40:44.608818 INFO: AUC difference: 3.47%
2:40:45.057432 INFO: Resetting torch num_threads to 100
2:40:45.064701 PROGRESS: === Extracted 17810 precursors and 119808 fragments ===
2:40:45.065991 INFO: === FDR correction performed with classifier version 6 ===
2:40:45.067692 PROGRESS: ============================= Precursor FDR =============================
2:40:45.067863 PROGRESS: Total precursors accumulated: 2,503
2:40:45.067938 PROGRESS: Target precursors: 2,479 (99.04%)
2:40:45.067991 PROGRESS: Decoy precursors: 24 (0.96%)
2:40:45.068039 PROGRESS: 
2:40:45.068084 PROGRESS: Precursor Summary:
2:40:45.070638 PROGRESS: Channel   0:	 0.050 FDR: 2,479; 0.010 FDR: 2,479; 0.001 FDR: 1,474
2:40:45.070794 PROGRESS: 
2:40:45.070852 PROGRESS: Protein Summary:
2:40:45.073887 PROGRESS: Channel   0:	 0.050 FDR: 1,973; 0.010 FDR: 1,973; 0.001 FDR: 1,230
2:40:45.074188 PROGRESS: =========================================================================
2:40:45.075454 INFO: Target number of precursors reached.
2:40:45.122718 INFO: fragments_df: keeping 5000 of 119808 [sum(precursor_idx_mask)=56229 sum(mass_error_mask)=119808 stop_rank=5000
2:40:45.153951 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:45.895749 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:46.969038 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:46.971204 INFO: Using score_cutoff 10.488097837257385 (fac=0.99, q=1)
2:40:46.972403 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:46.972535 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:46.972631 INFO: Updating optimization_manager: score_cutoff        : 10.704056787872315 -> 10.488097837257385
2:40:46.972719 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:46.980196 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:46.994263 INFO: === checking if optimization conditions were reached ===
2:40:46.995701 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:40:47.003407 INFO: Updating optimization_manager: rt_error            : 805.5992431640625 -> 567.2060764566437
2:40:47.004045 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 567.2061.
2:40:47.004134 INFO: ==============================================
2:40:47.004225 INFO: Starting optimization step 1.
2:40:47.004297 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:47.004400 INFO: Using rust extraction backend
2:40:47.004480 PROGRESS: Extracting batch of 5940 precursors
2:40:47.052231 INFO: === Search parameters used ===
2:40:47.053326 INFO: rt_error       : 567.2060764566437
2:40:47.053396 INFO: mobility_error : 0.1
2:40:47.053446 INFO: num_candidates : 3
2:40:47.053491 INFO: ms1_error      : 3
2:40:47.053536 INFO: ms2_error      : 10.0
2:40:47.053579 INFO: fwhm_rt        : 3.0
2:40:47.053622 INFO: quant_window   : 3
2:40:47.053703 INFO: ==============================================
2:40:47.470836 INFO: performing precursor FDR with 40 features
2:40:47.471231 INFO: Decoy channel: -1
2:40:47.471322 INFO: competitive: True
2:40:47.498947 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:47.523948 INFO: Estimating optimal hyperparameters - samples: 14,250, batch_size: 128, learning_rate: 1.77e-04
2:40:47.524511 INFO: Using random state 534183 for train-test-split
2:40:49.987425 INFO: Test AUC: 0.756
2:40:49.987746 INFO: Train AUC: 0.773
2:40:49.987793 INFO: AUC difference: 2.20%
2:40:50.777512 INFO: Resetting torch num_threads to 100
2:40:50.792701 PROGRESS: === Extracted 17813 precursors and 119734 fragments ===
2:40:50.794902 INFO: === FDR correction performed with classifier version 6 ===
2:40:50.800701 PROGRESS: ============================= Precursor FDR =============================
2:40:50.801634 PROGRESS: Total precursors accumulated: 2,513
2:40:50.801839 PROGRESS: Target precursors: 2,489 (99.04%)
2:40:50.801967 PROGRESS: Decoy precursors: 24 (0.96%)
2:40:50.802035 PROGRESS: 
2:40:50.802108 PROGRESS: Precursor Summary:
2:40:50.813411 PROGRESS: Channel   0:	 0.050 FDR: 2,489; 0.010 FDR: 2,489; 0.001 FDR: 1,427
2:40:50.814588 PROGRESS: 
2:40:50.814971 PROGRESS: Protein Summary:
2:40:50.836102 PROGRESS: Channel   0:	 0.050 FDR: 1,982; 0.010 FDR: 1,982; 0.001 FDR: 1,191
2:40:50.837181 PROGRESS: =========================================================================
2:40:50.841518 INFO: Target number of precursors reached.
2:40:50.915445 INFO: fragments_df: keeping 5000 of 119734 [sum(precursor_idx_mask)=56430 sum(mass_error_mask)=119734 stop_rank=5000
2:40:50.960956 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:51.673760 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:52.826360 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:52.827921 INFO: Using score_cutoff 10.481815602493285 (fac=0.99, q=1)
2:40:52.828577 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:52.828671 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:52.828727 INFO: Updating optimization_manager: score_cutoff        : 10.488097837257385 -> 10.481815602493285
2:40:52.828825 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:52.835675 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:52.849015 INFO: === checking if optimization conditions were reached ===
2:40:52.849660 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:40:52.855577 INFO: Updating optimization_manager: rt_error            : 567.2060764566437 -> 522.2422531193811
2:40:52.856138 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 522.2423.
2:40:52.856220 INFO: ==============================================
2:40:52.856354 INFO: Starting optimization step 2.
2:40:52.856422 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:52.856519 INFO: Using rust extraction backend
2:40:52.856607 PROGRESS: Extracting batch of 5940 precursors
2:40:52.897756 INFO: === Search parameters used ===
2:40:52.899013 INFO: rt_error       : 522.2422531193811
2:40:52.899073 INFO: mobility_error : 0.1
2:40:52.899124 INFO: num_candidates : 3
2:40:52.899230 INFO: ms1_error      : 3
2:40:52.899278 INFO: ms2_error      : 10.0
2:40:52.899337 INFO: fwhm_rt        : 3.0
2:40:52.899377 INFO: quant_window   : 3
2:40:52.899416 INFO: ==============================================
2:40:53.234563 INFO: performing precursor FDR with 40 features
2:40:53.234844 INFO: Decoy channel: -1
2:40:53.234869 INFO: competitive: True
2:40:53.243784 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:53.251851 INFO: Estimating optimal hyperparameters - samples: 14,251, batch_size: 128, learning_rate: 1.77e-04
2:40:53.252170 INFO: Using random state 534183 for train-test-split
2:40:55.459258 INFO: Test AUC: 0.755
2:40:55.459561 INFO: Train AUC: 0.768
2:40:55.459610 INFO: AUC difference: 1.69%
2:40:55.925025 INFO: Resetting torch num_threads to 100
2:40:55.934981 PROGRESS: === Extracted 17814 precursors and 119671 fragments ===
2:40:55.936617 INFO: === FDR correction performed with classifier version 6 ===
2:40:55.940214 PROGRESS: ============================= Precursor FDR =============================
2:40:55.940645 PROGRESS: Total precursors accumulated: 2,533
2:40:55.940778 PROGRESS: Target precursors: 2,508 (99.01%)
2:40:55.940846 PROGRESS: Decoy precursors: 25 (0.99%)
2:40:55.940903 PROGRESS: 
2:40:55.940953 PROGRESS: Precursor Summary:
2:40:55.947309 PROGRESS: Channel   0:	 0.050 FDR: 2,508; 0.010 FDR: 2,508; 0.001 FDR: 1,358
2:40:55.948150 PROGRESS: 
2:40:55.948269 PROGRESS: Protein Summary:
2:40:55.955542 PROGRESS: Channel   0:	 0.050 FDR: 1,998; 0.010 FDR: 1,998; 0.001 FDR: 1,139
2:40:55.956368 PROGRESS: =========================================================================
2:40:55.959172 INFO: Target number of precursors reached.
2:40:56.005249 INFO: fragments_df: keeping 5000 of 119671 [sum(precursor_idx_mask)=56698 sum(mass_error_mask)=119671 stop_rank=5000
2:40:56.030416 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:40:56.660650 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:40:57.583288 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:40:57.584123 INFO: Using score_cutoff 10.43965409116745 (fac=0.99, q=1)
2:40:57.584546 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:40:57.584630 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:40:57.584686 INFO: Updating optimization_manager: score_cutoff        : 10.481815602493285 -> 10.43965409116745
2:40:57.584748 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:40:57.590188 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:40:57.600037 INFO: === checking if optimization conditions were reached ===
2:40:57.600495 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:40:57.605262 INFO: Updating optimization_manager: rt_error            : 522.2422531193811 -> 500.7327745325792
2:40:57.605515 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 500.7328.
2:40:57.605590 INFO: ==============================================
2:40:57.605674 INFO: Starting optimization step 3.
2:40:57.605743 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:40:57.605882 INFO: Using rust extraction backend
2:40:57.605956 PROGRESS: Extracting batch of 5940 precursors
2:40:57.628727 INFO: === Search parameters used ===
2:40:57.629292 INFO: rt_error       : 500.7327745325792
2:40:57.629346 INFO: mobility_error : 0.1
2:40:57.629393 INFO: num_candidates : 3
2:40:57.629436 INFO: ms1_error      : 3
2:40:57.629514 INFO: ms2_error      : 10.0
2:40:57.629556 INFO: fwhm_rt        : 3.0
2:40:57.629595 INFO: quant_window   : 3
2:40:57.629634 INFO: ==============================================
2:40:58.003903 INFO: performing precursor FDR with 40 features
2:40:58.004190 INFO: Decoy channel: -1
2:40:58.004219 INFO: competitive: True
2:40:58.028596 INFO: Setting torch num_threads to 2 for FDR classification task
2:40:58.044942 INFO: Estimating optimal hyperparameters - samples: 14,251, batch_size: 128, learning_rate: 1.77e-04
2:40:58.045362 INFO: Using random state 534183 for train-test-split
2:41:00.317592 INFO: Test AUC: 0.761
2:41:00.317859 INFO: Train AUC: 0.771
2:41:00.317904 INFO: AUC difference: 1.30%
2:41:00.972638 INFO: Resetting torch num_threads to 100
2:41:00.984588 PROGRESS: === Extracted 17814 precursors and 119580 fragments ===
2:41:00.986219 INFO: === FDR correction performed with classifier version 6 ===
2:41:00.989063 PROGRESS: ============================= Precursor FDR =============================
2:41:00.989286 PROGRESS: Total precursors accumulated: 2,500
2:41:00.989379 PROGRESS: Target precursors: 2,476 (99.04%)
2:41:00.989458 PROGRESS: Decoy precursors: 24 (0.96%)
2:41:00.989538 PROGRESS: 
2:41:00.989612 PROGRESS: Precursor Summary:
2:41:00.993394 PROGRESS: Channel   0:	 0.050 FDR: 2,476; 0.010 FDR: 2,476; 0.001 FDR: 1,352
2:41:00.993625 PROGRESS: 
2:41:00.993702 PROGRESS: Protein Summary:
2:41:00.997747 PROGRESS: Channel   0:	 0.050 FDR: 1,967; 0.010 FDR: 1,967; 0.001 FDR: 1,138
2:41:00.998064 PROGRESS: =========================================================================
2:41:00.999727 INFO: Target number of precursors reached.
2:41:01.052923 INFO: fragments_df: keeping 5000 of 119580 [sum(precursor_idx_mask)=56138 sum(mass_error_mask)=119580 stop_rank=5000
2:41:01.095283 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:01.734906 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:02.911082 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:41:02.912090 INFO: Using score_cutoff 10.566408648490906 (fac=0.99, q=1)
2:41:02.912599 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:02.912684 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:02.912742 INFO: Updating optimization_manager: score_cutoff        : 10.43965409116745 -> 10.566408648490906
2:41:02.912798 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:02.918202 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:02.928512 INFO: === checking if optimization conditions were reached ===
2:41:02.928992 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:41:02.933493 INFO: Updating optimization_manager: rt_error            : 500.7327745325792 -> 404.3059753502728
2:41:02.933798 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 404.3060.
2:41:02.933869 INFO: ==============================================
2:41:02.933944 INFO: Starting optimization step 4.
2:41:02.934009 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:41:02.934083 INFO: Using rust extraction backend
2:41:02.934146 PROGRESS: Extracting batch of 5940 precursors
2:41:02.955205 INFO: === Search parameters used ===
2:41:02.955681 INFO: rt_error       : 404.3059753502728
2:41:02.955735 INFO: mobility_error : 0.1
2:41:02.955796 INFO: num_candidates : 3
2:41:02.955930 INFO: ms1_error      : 3
2:41:02.955978 INFO: ms2_error      : 10.0
2:41:02.956018 INFO: fwhm_rt        : 3.0
2:41:02.956057 INFO: quant_window   : 3
2:41:02.956095 INFO: ==============================================
2:41:03.457549 INFO: performing precursor FDR with 40 features
2:41:03.457994 INFO: Decoy channel: -1
2:41:03.458157 INFO: competitive: True
2:41:03.501947 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:03.540160 INFO: Estimating optimal hyperparameters - samples: 14,251, batch_size: 128, learning_rate: 1.77e-04
2:41:03.541141 INFO: Using random state 534183 for train-test-split
2:41:05.876668 INFO: Test AUC: 0.761
2:41:05.877156 INFO: Train AUC: 0.773
2:41:05.877201 INFO: AUC difference: 1.52%
2:41:06.391339 INFO: Resetting torch num_threads to 100
2:41:06.399039 PROGRESS: === Extracted 17814 precursors and 119136 fragments ===
2:41:06.401075 INFO: === FDR correction performed with classifier version 6 ===
2:41:06.403037 PROGRESS: ============================= Precursor FDR =============================
2:41:06.403196 PROGRESS: Total precursors accumulated: 2,584
2:41:06.403265 PROGRESS: Target precursors: 2,559 (99.03%)
2:41:06.403325 PROGRESS: Decoy precursors: 25 (0.97%)
2:41:06.403374 PROGRESS: 
2:41:06.403424 PROGRESS: Precursor Summary:
2:41:06.406273 PROGRESS: Channel   0:	 0.050 FDR: 2,559; 0.010 FDR: 2,559; 0.001 FDR: 1,313
2:41:06.406426 PROGRESS: 
2:41:06.406487 PROGRESS: Protein Summary:
2:41:06.409921 PROGRESS: Channel   0:	 0.050 FDR: 2,030; 0.010 FDR: 2,030; 0.001 FDR: 1,110
2:41:06.410141 PROGRESS: =========================================================================
2:41:06.411610 INFO: Target number of precursors reached.
2:41:06.454604 INFO: fragments_df: keeping 5000 of 119136 [sum(precursor_idx_mask)=57528 sum(mass_error_mask)=119136 stop_rank=5000
2:41:06.495355 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:07.152713 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:08.090710 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:41:08.091814 INFO: Using score_cutoff 10.168279183959962 (fac=0.99, q=1)
2:41:08.092432 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:08.092520 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:08.092575 INFO: Updating optimization_manager: score_cutoff        : 10.566408648490906 -> 10.168279183959962
2:41:08.092638 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:08.099202 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:08.110890 INFO: === checking if optimization conditions were reached ===
2:41:08.111469 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:41:08.116975 INFO: Updating optimization_manager: rt_error            : 404.3059753502728 -> 336.72073130011574
2:41:08.117491 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 336.7207.
2:41:08.117573 INFO: ==============================================
2:41:08.117681 INFO: Starting optimization step 5.
2:41:08.117746 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:41:08.117835 INFO: Using rust extraction backend
2:41:08.117919 PROGRESS: Extracting batch of 5940 precursors
2:41:08.151665 INFO: === Search parameters used ===
2:41:08.152500 INFO: rt_error       : 336.72073130011574
2:41:08.152558 INFO: mobility_error : 0.1
2:41:08.152608 INFO: num_candidates : 3
2:41:08.152651 INFO: ms1_error      : 3
2:41:08.152693 INFO: ms2_error      : 10.0
2:41:08.152732 INFO: fwhm_rt        : 3.0
2:41:08.152772 INFO: quant_window   : 3
2:41:08.152812 INFO: ==============================================
2:41:08.450355 INFO: performing precursor FDR with 40 features
2:41:08.450717 INFO: Decoy channel: -1
2:41:08.450757 INFO: competitive: True
2:41:08.470094 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:08.482593 INFO: Estimating optimal hyperparameters - samples: 14,251, batch_size: 128, learning_rate: 1.77e-04
2:41:08.483016 INFO: Using random state 534183 for train-test-split
2:41:10.852461 INFO: Test AUC: 0.746
2:41:10.852918 INFO: Train AUC: 0.777
2:41:10.852983 INFO: AUC difference: 3.94%
2:41:11.291969 INFO: Resetting torch num_threads to 100
2:41:11.299495 PROGRESS: === Extracted 17814 precursors and 118455 fragments ===
2:41:11.300943 INFO: === FDR correction performed with classifier version 6 ===
2:41:11.303414 PROGRESS: ============================= Precursor FDR =============================
2:41:11.303638 PROGRESS: Total precursors accumulated: 2,573
2:41:11.303714 PROGRESS: Target precursors: 2,548 (99.03%)
2:41:11.303770 PROGRESS: Decoy precursors: 25 (0.97%)
2:41:11.303842 PROGRESS: 
2:41:11.303900 PROGRESS: Precursor Summary:
2:41:11.306769 PROGRESS: Channel   0:	 0.050 FDR: 2,548; 0.010 FDR: 2,548; 0.001 FDR: 1,321
2:41:11.307078 PROGRESS: 
2:41:11.307149 PROGRESS: Protein Summary:
2:41:11.311047 PROGRESS: Channel   0:	 0.050 FDR: 2,025; 0.010 FDR: 2,025; 0.001 FDR: 1,114
2:41:11.311382 PROGRESS: =========================================================================
2:41:11.312928 INFO: Target number of precursors reached.
2:41:11.360339 INFO: fragments_df: keeping 5000 of 118455 [sum(precursor_idx_mask)=57341 sum(mass_error_mask)=118455 stop_rank=5000
2:41:11.400327 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:12.019278 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:12.975606 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:41:12.976764 INFO: Using score_cutoff 10.488083495807647 (fac=0.99, q=1)
2:41:12.977349 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:12.977474 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:12.977562 INFO: Updating optimization_manager: score_cutoff        : 10.168279183959962 -> 10.488083495807647
2:41:12.977633 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:12.983558 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:12.995145 INFO: === checking if optimization conditions were reached ===
2:41:12.995782 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:41:13.001010 INFO: Updating optimization_manager: rt_error            : 336.72073130011574 -> 336.55892953578973
2:41:13.001673 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 336.5589.
2:41:13.001776 INFO: ==============================================
2:41:13.001888 INFO: Starting optimization step 6.
2:41:13.001957 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:41:13.002142 INFO: Using rust extraction backend
2:41:13.002291 PROGRESS: Extracting batch of 5940 precursors
2:41:13.037687 INFO: === Search parameters used ===
2:41:13.038538 INFO: rt_error       : 336.55892953578973
2:41:13.038594 INFO: mobility_error : 0.1
2:41:13.038641 INFO: num_candidates : 3
2:41:13.038686 INFO: ms1_error      : 3
2:41:13.038730 INFO: ms2_error      : 10.0
2:41:13.038772 INFO: fwhm_rt        : 3.0
2:41:13.038813 INFO: quant_window   : 3
2:41:13.038909 INFO: ==============================================
2:41:13.363616 INFO: performing precursor FDR with 40 features
2:41:13.363892 INFO: Decoy channel: -1
2:41:13.363920 INFO: competitive: True
2:41:13.381109 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:13.394771 INFO: Estimating optimal hyperparameters - samples: 14,252, batch_size: 128, learning_rate: 1.77e-04
2:41:13.395168 INFO: Using random state 534183 for train-test-split
2:41:15.612923 INFO: Test AUC: 0.764
2:41:15.613400 INFO: Train AUC: 0.772
2:41:15.613448 INFO: AUC difference: 1.11%
2:41:16.071195 INFO: Resetting torch num_threads to 100
2:41:16.077981 PROGRESS: === Extracted 17815 precursors and 118456 fragments ===
2:41:16.079460 INFO: === FDR correction performed with classifier version 6 ===
2:41:16.080997 PROGRESS: ============================= Precursor FDR =============================
2:41:16.081156 PROGRESS: Total precursors accumulated: 2,553
2:41:16.081230 PROGRESS: Target precursors: 2,528 (99.02%)
2:41:16.081286 PROGRESS: Decoy precursors: 25 (0.98%)
2:41:16.081338 PROGRESS: 
2:41:16.081388 PROGRESS: Precursor Summary:
2:41:16.083782 PROGRESS: Channel   0:	 0.050 FDR: 2,528; 0.010 FDR: 2,528; 0.001 FDR: 1,386
2:41:16.083945 PROGRESS: 
2:41:16.084013 PROGRESS: Protein Summary:
2:41:16.086779 PROGRESS: Channel   0:	 0.050 FDR: 2,009; 0.010 FDR: 2,009; 0.001 FDR: 1,163
2:41:16.086982 PROGRESS: =========================================================================
2:41:16.088348 INFO: Target number of precursors reached.
2:41:16.127071 INFO: fragments_df: keeping 5000 of 118456 [sum(precursor_idx_mask)=56968 sum(mass_error_mask)=118456 stop_rank=5000
2:41:16.157252 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:41:16.751223 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:41:17.908546 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:41:17.909752 INFO: Using score_cutoff 10.620443992710113 (fac=0.99, q=1)
2:41:17.910383 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:17.910464 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:17.910520 INFO: Updating optimization_manager: score_cutoff        : 10.488083495807647 -> 10.620443992710113
2:41:17.910611 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:17.916805 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:17.928729 INFO: === checking if optimization conditions were reached ===
2:41:17.929474 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
2:41:17.931572 INFO: Updating optimization_manager: rt_error            : 336.55892953578973 -> 404.3059753502728
2:41:17.931969 INFO: Updating optimization_manager: classifier_version  : 6 -> 11
2:41:17.932082 INFO: Updating optimization_manager: score_cutoff        : 10.620443992710113 -> 10.168279183959962
2:41:17.932175 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:41:17.932267 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:41:17.932402 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 404.3060 found after 7 searches.
2:41:17.932476 INFO: ==============================================
2:41:17.932555 PROGRESS: Optimization finished for rt_error.
2:41:17.958801 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:17.966001 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:17.978460 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:41:17.979062 PROGRESS: ==============================================
2:41:17.979154 PROGRESS: ms2_error      : 10.0000
2:41:17.979219 PROGRESS: rt_error       : 404.3060
2:41:17.979268 PROGRESS: ==============================================
2:41:17.981892 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:41:18.180708 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:41:18.824626 INFO: Using rust extraction backend
2:41:18.825882 PROGRESS: Extracting batch of 259156 precursors
2:41:19.915591 INFO: === Search parameters used ===
2:41:19.917090 INFO: rt_error       : 404.3059753502728
2:41:19.917160 INFO: mobility_error : 0.1
2:41:19.917216 INFO: num_candidates : 3
2:41:19.917263 INFO: ms1_error      : 3
2:41:19.917304 INFO: ms2_error      : 10.0
2:41:19.917390 INFO: fwhm_rt        : 3.0
2:41:19.917433 INFO: quant_window   : 3
2:41:19.917474 INFO: ==============================================
2:41:21.546168 INFO: Removed 93805 precursors with score below cutoff 10.168279183959962
2:41:22.884505 INFO: performing precursor FDR with 40 features
2:41:22.884760 INFO: Decoy channel: -1
2:41:22.884794 INFO: competitive: True
2:41:23.065374 INFO: Setting torch num_threads to 2 for FDR classification task
2:41:23.173007 WARNING: FDR calculation for 360666 target and 322997 decoy PSMs
2:41:23.173440 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:41:24.060627 INFO: Estimating optimal hyperparameters - samples: 546,930, batch_size: 2,240, learning_rate: 7.40e-04
2:41:24.064788 INFO: Using random state 594070 for train-test-split
2:41:49.222768 INFO: Test AUC: 0.775
2:41:49.223157 INFO: Train AUC: 0.779
2:41:49.223221 INFO: AUC difference: 0.48%
2:41:50.017951 INFO: Resetting torch num_threads to 100
2:41:51.082265 PROGRESS: ============================= Precursor FDR =============================
2:41:51.082995 PROGRESS: Total precursors accumulated: 120,772
2:41:51.083084 PROGRESS: Target precursors: 119,578 (99.01%)
2:41:51.083144 PROGRESS: Decoy precursors: 1,194 (0.99%)
2:41:51.083195 PROGRESS: 
2:41:51.083245 PROGRESS: Precursor Summary:
2:41:51.200884 PROGRESS: Channel   0:	 0.050 FDR: 119,578; 0.010 FDR: 119,578; 0.001 FDR: 105,632
2:41:51.201639 PROGRESS: 
2:41:51.201707 PROGRESS: Protein Summary:
2:41:51.451776 PROGRESS: Channel   0:	 0.050 FDR: 10,129; 0.010 FDR: 10,129; 0.001 FDR: 9,966
2:41:51.452358 PROGRESS: =========================================================================
2:41:51.466202 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/psm.parquet
2:41:52.183639 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/frag.parquet
2:41:53.193135 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:41:54.162525 PROGRESS: Loading raw file 2/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP2 
2:41:54.162983 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:41:54.163239 INFO: Initializing TimingManager
2:41:54.165733 INFO: Initializing RawFileManager
2:42:24.309748 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:42:24.320389 INFO: Determining DIA cycle
2:42:24.338775 INFO: Found cycle with start 0.00 min and length 300.
2:42:24.756888 INFO: RT (min)            : 0.0 - 26.9
2:42:24.757037 INFO: RT duration (sec)   : 1611.2
2:42:24.757067 INFO: RT duration (min)   : 26.9
2:42:24.757091 INFO: Cycle len (scans)   : 300
2:42:24.757111 INFO: Cycle len (sec)     : 1.65
2:42:24.757130 INFO: Number of cycles    : 978
2:42:24.757150 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:42:24.757203 INFO: Creating DIA data object took: 30.591193437576294
2:42:26.643651 INFO: Creating DIA data NG object took: 1.8862473964691162
2:42:26.767337 INFO: Initializing CalibrationManager
2:42:26.768118 INFO: Setting up calibration estimators ..
2:42:26.768191 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:42:26.768327 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2:42:26.768478 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:42:26.768538 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:42:26.768601 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2:42:26.768661 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:42:26.768713 INFO: Done setting up calibration estimators.
2:42:26.769241 INFO: Initializing OptimizationManager
2:42:26.769449 INFO: initial parameter: ms1_error = 3
2:42:26.769508 INFO: initial parameter: ms2_error = 10
2:42:26.769572 INFO: initial parameter: rt_error = 805.6019897460938
2:42:26.769618 INFO: initial parameter: mobility_error = 0.1
2:42:26.769669 INFO: initial parameter: num_candidates = 1
2:42:26.769710 INFO: initial parameter: fwhm_rt = 5
2:42:26.769753 INFO: initial parameter: fwhm_mobility = 0.01
2:42:26.769804 INFO: initial parameter: score_cutoff = 0
2:42:26.769857 INFO: initial parameter: classifier_version = -1
2:42:26.769955 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:42:26.770799 INFO: FDRManager: loading saved state not requested, will be initialized.
2:42:26.770851 INFO: Initializing FDRManager
2:42:26.770907 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:42:26.890357 PROGRESS: Initializing spectral library: 131,021 target precursors potentially observable (0 removed)
2:42:26.980943 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
2:42:26.982353 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 805.6019897460938
2:42:26.982490 PROGRESS: Starting initial search for precursors.
2:42:26.982712 INFO: Starting optimization step 0.
2:42:26.982869 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:42:26.982941 INFO: Using rust extraction backend
2:42:26.983152 PROGRESS: Extracting batch of 1982 precursors
2:42:26.998738 INFO: === Search parameters used ===
2:42:26.999533 INFO: rt_error       : 805.6019897460938
2:42:26.999596 INFO: mobility_error : 0.1
2:42:26.999645 INFO: num_candidates : 1
2:42:26.999699 INFO: ms1_error      : 3
2:42:26.999746 INFO: ms2_error      : 10
2:42:26.999788 INFO: fwhm_rt        : 5
2:42:26.999844 INFO: quant_window   : 3
2:42:26.999891 INFO: ==============================================
2:42:27.137459 INFO: performing precursor FDR with 40 features
2:42:27.137815 INFO: Decoy channel: -1
2:42:27.137876 INFO: competitive: True
2:42:27.142647 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:27.149815 INFO: Estimating optimal hyperparameters - samples: 1,584, batch_size: 128, learning_rate: 1.77e-04
2:42:27.153155 INFO: Using random state 784736 for train-test-split
2:42:27.522821 INFO: Test AUC: 0.840
2:42:27.523111 INFO: Train AUC: 0.876
2:42:27.523142 INFO: AUC difference: 4.16%
2:42:27.953323 INFO: Resetting torch num_threads to 100
2:42:27.958844 PROGRESS: === Extracted 1981 precursors and 15306 fragments ===
2:42:27.960173 INFO: === FDR correction performed with classifier version -1 ===
2:42:27.962114 PROGRESS: ============================= Precursor FDR =============================
2:42:27.962424 PROGRESS: Total precursors accumulated: 551
2:42:27.962523 PROGRESS: Target precursors: 546 (99.09%)
2:42:27.962586 PROGRESS: Decoy precursors: 5 (0.91%)
2:42:27.962644 PROGRESS: 
2:42:27.962688 PROGRESS: Precursor Summary:
2:42:27.966618 PROGRESS: Channel   0:	 0.050 FDR:   546; 0.010 FDR:   546; 0.001 FDR:     6
2:42:27.967198 PROGRESS: 
2:42:27.967328 PROGRESS: Protein Summary:
2:42:27.970497 PROGRESS: Channel   0:	 0.050 FDR:   510; 0.010 FDR:   510; 0.001 FDR:     6
2:42:27.970982 PROGRESS: =========================================================================
2:42:27.971942 INFO: Target number of precursors not reached yet.
2:42:27.992084 INFO: Starting optimization step 1.
2:42:27.992719 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:42:27.992879 INFO: Using rust extraction backend
2:42:27.992980 PROGRESS: Extracting batch of 3958 precursors
2:42:28.011370 INFO: === Search parameters used ===
2:42:28.012133 INFO: rt_error       : 805.6019897460938
2:42:28.012198 INFO: mobility_error : 0.1
2:42:28.012250 INFO: num_candidates : 1
2:42:28.012296 INFO: ms1_error      : 3
2:42:28.012337 INFO: ms2_error      : 10
2:42:28.012380 INFO: fwhm_rt        : 5
2:42:28.012423 INFO: quant_window   : 3
2:42:28.012470 INFO: ==============================================
2:42:28.151361 INFO: performing precursor FDR with 40 features
2:42:28.151766 INFO: Decoy channel: -1
2:42:28.151795 INFO: competitive: True
2:42:28.164371 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:28.173911 INFO: Estimating optimal hyperparameters - samples: 4,749, batch_size: 128, learning_rate: 1.77e-04
2:42:28.174720 INFO: Using random state 617096 for train-test-split
2:42:29.006876 INFO: Test AUC: 0.906
2:42:29.007172 INFO: Train AUC: 0.898
2:42:29.007203 INFO: AUC difference: 0.97%
2:42:29.553203 INFO: Resetting torch num_threads to 100
2:42:29.565692 PROGRESS: === Extracted 5937 precursors and 45865 fragments ===
2:42:29.567153 INFO: === FDR correction performed with classifier version -1 ===
2:42:29.568651 PROGRESS: ============================= Precursor FDR =============================
2:42:29.568827 PROGRESS: Total precursors accumulated: 2,094
2:42:29.568893 PROGRESS: Target precursors: 2,074 (99.04%)
2:42:29.568946 PROGRESS: Decoy precursors: 20 (0.96%)
2:42:29.568996 PROGRESS: 
2:42:29.569041 PROGRESS: Precursor Summary:
2:42:29.571027 PROGRESS: Channel   0:	 0.050 FDR: 2,074; 0.010 FDR: 2,074; 0.001 FDR:     1
2:42:29.571122 PROGRESS: 
2:42:29.571177 PROGRESS: Protein Summary:
2:42:29.573782 PROGRESS: Channel   0:	 0.050 FDR: 1,664; 0.010 FDR: 1,664; 0.001 FDR:     1
2:42:29.573922 PROGRESS: =========================================================================
2:42:29.575077 INFO: Target number of precursors reached.
2:42:29.595520 INFO: fragments_df: keeping 5000 of 45865 [sum(precursor_idx_mask)=20718 sum(mass_error_mask)=45865 stop_rank=5000
2:42:29.634987 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:30.222896 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:31.206767 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:42:31.208263 INFO: Using score_cutoff 11.05522326335907 (fac=0.99, q=1)
2:42:31.209105 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:42:31.209217 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:42:31.209291 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.05522326335907
2:42:31.209369 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:31.216578 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:31.230968 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:42:31.231458 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:42:31.231597 INFO: Starting optimization step 2.
2:42:31.231701 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:31.231841 INFO: Using rust extraction backend
2:42:31.231970 PROGRESS: Extracting batch of 5940 precursors
2:42:31.268362 INFO: === Search parameters used ===
2:42:31.269592 INFO: rt_error       : 805.6019897460938
2:42:31.269696 INFO: mobility_error : 0.1
2:42:31.269768 INFO: num_candidates : 3
2:42:31.269835 INFO: ms1_error      : 3
2:42:31.269911 INFO: ms2_error      : 10
2:42:31.269972 INFO: fwhm_rt        : 3.0
2:42:31.270031 INFO: quant_window   : 3
2:42:31.270092 INFO: ==============================================
2:42:31.507873 INFO: performing precursor FDR with 40 features
2:42:31.508034 INFO: Decoy channel: -1
2:42:31.508061 INFO: competitive: True
2:42:31.514649 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:31.520089 INFO: Estimating optimal hyperparameters - samples: 14,249, batch_size: 128, learning_rate: 1.77e-04
2:42:31.520314 INFO: Using random state 853707 for train-test-split
2:42:33.408662 INFO: Test AUC: 0.724
2:42:33.409042 INFO: Train AUC: 0.739
2:42:33.409081 INFO: AUC difference: 2.00%
2:42:33.781757 INFO: Resetting torch num_threads to 100
2:42:33.788192 PROGRESS: === Extracted 17812 precursors and 119188 fragments ===
2:42:33.789037 INFO: === FDR correction performed with classifier version 1 ===
2:42:33.790189 PROGRESS: ============================= Precursor FDR =============================
2:42:33.790296 PROGRESS: Total precursors accumulated: 2,289
2:42:33.790368 PROGRESS: Target precursors: 2,267 (99.04%)
2:42:33.790426 PROGRESS: Decoy precursors: 22 (0.96%)
2:42:33.790479 PROGRESS: 
2:42:33.790532 PROGRESS: Precursor Summary:
2:42:33.792758 PROGRESS: Channel   0:	 0.050 FDR: 2,267; 0.010 FDR: 2,267; 0.001 FDR: 1,092
2:42:33.792884 PROGRESS: 
2:42:33.792963 PROGRESS: Protein Summary:
2:42:33.796285 PROGRESS: Channel   0:	 0.050 FDR: 1,804; 0.010 FDR: 1,804; 0.001 FDR:   940
2:42:33.796419 PROGRESS: =========================================================================
2:42:33.797899 INFO: Target number of precursors reached.
2:42:33.829559 INFO: fragments_df: keeping 5000 of 119188 [sum(precursor_idx_mask)=52201 sum(mass_error_mask)=119188 stop_rank=5000
2:42:33.851344 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:34.316058 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:35.149722 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:35.150340 INFO: Using score_cutoff 11.193427934074402 (fac=0.99, q=1)
2:42:35.150707 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:35.150780 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:35.150832 INFO: Updating optimization_manager: score_cutoff        : 11.05522326335907 -> 11.193427934074402
2:42:35.150884 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:35.155020 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:35.163181 INFO: === checking if optimization conditions were reached ===
2:42:35.164984 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
2:42:35.165087 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:42:35.165156 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:42:35.165212 INFO: ==============================================
2:42:35.165284 INFO: Starting optimization step 3.
2:42:35.165342 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:35.165403 INFO: Using rust extraction backend
2:42:35.165455 PROGRESS: Extracting batch of 5940 precursors
2:42:35.178401 INFO: === Search parameters used ===
2:42:35.178568 INFO: rt_error       : 805.6019897460938
2:42:35.178621 INFO: mobility_error : 0.1
2:42:35.178666 INFO: num_candidates : 3
2:42:35.178712 INFO: ms1_error      : 3
2:42:35.178753 INFO: ms2_error      : 10.0
2:42:35.178794 INFO: fwhm_rt        : 3.0
2:42:35.178833 INFO: quant_window   : 3
2:42:35.178871 INFO: ==============================================
2:42:35.337722 INFO: performing precursor FDR with 40 features
2:42:35.337891 INFO: Decoy channel: -1
2:42:35.337916 INFO: competitive: True
2:42:35.343804 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:35.349003 INFO: Estimating optimal hyperparameters - samples: 14,248, batch_size: 128, learning_rate: 1.77e-04
2:42:35.349178 INFO: Using random state 801533 for train-test-split
2:42:37.203740 INFO: Test AUC: 0.736
2:42:37.204194 INFO: Train AUC: 0.752
2:42:37.204228 INFO: AUC difference: 2.15%
2:42:37.525716 INFO: Resetting torch num_threads to 100
2:42:37.530532 PROGRESS: === Extracted 17810 precursors and 119168 fragments ===
2:42:37.531612 INFO: === FDR correction performed with classifier version 2 ===
2:42:37.532682 PROGRESS: ============================= Precursor FDR =============================
2:42:37.532862 PROGRESS: Total precursors accumulated: 2,442
2:42:37.532927 PROGRESS: Target precursors: 2,418 (99.02%)
2:42:37.532980 PROGRESS: Decoy precursors: 24 (0.98%)
2:42:37.533028 PROGRESS: 
2:42:37.533073 PROGRESS: Precursor Summary:
2:42:37.534929 PROGRESS: Channel   0:	 0.050 FDR: 2,418; 0.010 FDR: 2,418; 0.001 FDR: 1,182
2:42:37.535061 PROGRESS: 
2:42:37.535125 PROGRESS: Protein Summary:
2:42:37.537553 PROGRESS: Channel   0:	 0.050 FDR: 1,921; 0.010 FDR: 1,921; 0.001 FDR: 1,004
2:42:37.537667 PROGRESS: =========================================================================
2:42:37.538607 INFO: Target number of precursors reached.
2:42:37.570970 INFO: fragments_df: keeping 5000 of 119168 [sum(precursor_idx_mask)=55178 sum(mass_error_mask)=119168 stop_rank=5000
2:42:37.589280 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:38.222077 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:39.141922 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:39.142782 INFO: Using score_cutoff 10.76283191986084 (fac=0.99, q=1)
2:42:39.143325 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:39.143408 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:39.143463 INFO: Updating optimization_manager: score_cutoff        : 11.193427934074402 -> 10.76283191986084
2:42:39.143523 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:39.148856 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:39.159046 INFO: === checking if optimization conditions were reached ===
2:42:39.162370 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:42:39.162649 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:42:39.162725 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:42:39.162828 INFO: ==============================================
2:42:39.162903 INFO: Starting optimization step 4.
2:42:39.162966 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:39.163038 INFO: Using rust extraction backend
2:42:39.163105 PROGRESS: Extracting batch of 5940 precursors
2:42:39.183023 INFO: === Search parameters used ===
2:42:39.183746 INFO: rt_error       : 805.6019897460938
2:42:39.183802 INFO: mobility_error : 0.1
2:42:39.183873 INFO: num_candidates : 3
2:42:39.183921 INFO: ms1_error      : 3
2:42:39.183963 INFO: ms2_error      : 10.0
2:42:39.184002 INFO: fwhm_rt        : 3.0
2:42:39.184041 INFO: quant_window   : 3
2:42:39.184080 INFO: ==============================================
2:42:39.574028 INFO: performing precursor FDR with 40 features
2:42:39.574272 INFO: Decoy channel: -1
2:42:39.574298 INFO: competitive: True
2:42:39.594690 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:39.611181 INFO: Estimating optimal hyperparameters - samples: 14,249, batch_size: 128, learning_rate: 1.77e-04
2:42:39.611706 INFO: Using random state 931146 for train-test-split
2:42:41.564662 INFO: Test AUC: 0.748
2:42:41.564993 INFO: Train AUC: 0.764
2:42:41.565024 INFO: AUC difference: 2.08%
2:42:42.012622 INFO: Resetting torch num_threads to 100
2:42:42.022812 PROGRESS: === Extracted 17812 precursors and 119146 fragments ===
2:42:42.024604 INFO: === FDR correction performed with classifier version 3 ===
2:42:42.027411 PROGRESS: ============================= Precursor FDR =============================
2:42:42.027619 PROGRESS: Total precursors accumulated: 2,554
2:42:42.027687 PROGRESS: Target precursors: 2,529 (99.02%)
2:42:42.027745 PROGRESS: Decoy precursors: 25 (0.98%)
2:42:42.027797 PROGRESS: 
2:42:42.027865 PROGRESS: Precursor Summary:
2:42:42.030595 PROGRESS: Channel   0:	 0.050 FDR: 2,529; 0.010 FDR: 2,529; 0.001 FDR: 2,014
2:42:42.030762 PROGRESS: 
2:42:42.030821 PROGRESS: Protein Summary:
2:42:42.034150 PROGRESS: Channel   0:	 0.050 FDR: 2,004; 0.010 FDR: 2,004; 0.001 FDR: 1,609
2:42:42.034321 PROGRESS: =========================================================================
2:42:42.035810 INFO: Target number of precursors reached.
2:42:42.073520 INFO: fragments_df: keeping 5000 of 119146 [sum(precursor_idx_mask)=57214 sum(mass_error_mask)=119146 stop_rank=5000
2:42:42.108235 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:42.771100 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:43.737029 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:43.739165 INFO: Using score_cutoff 10.218769697570801 (fac=0.99, q=1)
2:42:43.739916 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:43.740035 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:43.740097 INFO: Updating optimization_manager: score_cutoff        : 10.76283191986084 -> 10.218769697570801
2:42:43.740162 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:43.747554 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:43.761690 INFO: === checking if optimization conditions were reached ===
2:42:43.767736 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:42:43.768315 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:42:43.768522 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:42:43.768629 INFO: ==============================================
2:42:43.768741 INFO: Starting optimization step 5.
2:42:43.768854 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:43.769023 INFO: Using rust extraction backend
2:42:43.769172 PROGRESS: Extracting batch of 5940 precursors
2:42:43.807417 INFO: === Search parameters used ===
2:42:43.808403 INFO: rt_error       : 805.6019897460938
2:42:43.808470 INFO: mobility_error : 0.1
2:42:43.808531 INFO: num_candidates : 3
2:42:43.808576 INFO: ms1_error      : 3
2:42:43.808619 INFO: ms2_error      : 10.0
2:42:43.808661 INFO: fwhm_rt        : 3.0
2:42:43.808701 INFO: quant_window   : 3
2:42:43.808741 INFO: ==============================================
2:42:44.125521 INFO: performing precursor FDR with 40 features
2:42:44.125794 INFO: Decoy channel: -1
2:42:44.125819 INFO: competitive: True
2:42:44.142684 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:44.154700 INFO: Estimating optimal hyperparameters - samples: 14,249, batch_size: 128, learning_rate: 1.77e-04
2:42:44.155172 INFO: Using random state 334765 for train-test-split
2:42:46.583521 INFO: Test AUC: 0.744
2:42:46.583943 INFO: Train AUC: 0.774
2:42:46.583992 INFO: AUC difference: 3.89%
2:42:47.059535 INFO: Resetting torch num_threads to 100
2:42:47.065708 PROGRESS: === Extracted 17812 precursors and 119176 fragments ===
2:42:47.066817 INFO: === FDR correction performed with classifier version 4 ===
2:42:47.068798 PROGRESS: ============================= Precursor FDR =============================
2:42:47.068956 PROGRESS: Total precursors accumulated: 2,634
2:42:47.069026 PROGRESS: Target precursors: 2,608 (99.01%)
2:42:47.069082 PROGRESS: Decoy precursors: 26 (0.99%)
2:42:47.069153 PROGRESS: 
2:42:47.069203 PROGRESS: Precursor Summary:
2:42:47.071740 PROGRESS: Channel   0:	 0.050 FDR: 2,608; 0.010 FDR: 2,608; 0.001 FDR: 2,198
2:42:47.071984 PROGRESS: 
2:42:47.072048 PROGRESS: Protein Summary:
2:42:47.075286 PROGRESS: Channel   0:	 0.050 FDR: 2,052; 0.010 FDR: 2,052; 0.001 FDR: 1,745
2:42:47.075668 PROGRESS: =========================================================================
2:42:47.077058 INFO: Target number of precursors reached.
2:42:47.126731 INFO: fragments_df: keeping 5000 of 119176 [sum(precursor_idx_mask)=58681 sum(mass_error_mask)=119176 stop_rank=5000
2:42:47.155075 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:47.832779 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:48.885284 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:48.886429 INFO: Using score_cutoff 10.071718693828583 (fac=0.99, q=1)
2:42:48.887008 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:48.887098 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:48.887155 INFO: Updating optimization_manager: score_cutoff        : 10.218769697570801 -> 10.071718693828583
2:42:48.887240 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:48.892743 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:48.906478 INFO: === checking if optimization conditions were reached ===
2:42:48.912193 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:42:48.913386 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:42:48.913533 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:42:48.913665 INFO: ==============================================
2:42:48.913817 INFO: Starting optimization step 6.
2:42:48.913951 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:48.914106 INFO: Using rust extraction backend
2:42:48.914257 PROGRESS: Extracting batch of 5940 precursors
2:42:48.948549 INFO: === Search parameters used ===
2:42:48.949260 INFO: rt_error       : 805.6019897460938
2:42:48.949329 INFO: mobility_error : 0.1
2:42:48.949384 INFO: num_candidates : 3
2:42:48.949433 INFO: ms1_error      : 3
2:42:48.949480 INFO: ms2_error      : 10.0
2:42:48.949525 INFO: fwhm_rt        : 3.0
2:42:48.949567 INFO: quant_window   : 3
2:42:48.949609 INFO: ==============================================
2:42:49.384609 INFO: performing precursor FDR with 40 features
2:42:49.384874 INFO: Decoy channel: -1
2:42:49.384902 INFO: competitive: True
2:42:49.396244 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:49.405738 INFO: Estimating optimal hyperparameters - samples: 14,249, batch_size: 128, learning_rate: 1.77e-04
2:42:49.406077 INFO: Using random state 556806 for train-test-split
2:42:51.246869 INFO: Test AUC: 0.765
2:42:51.247102 INFO: Train AUC: 0.779
2:42:51.247148 INFO: AUC difference: 1.84%
2:42:51.706808 INFO: Resetting torch num_threads to 100
2:42:51.714706 PROGRESS: === Extracted 17812 precursors and 119193 fragments ===
2:42:51.716018 INFO: === FDR correction performed with classifier version 5 ===
2:42:51.719525 PROGRESS: ============================= Precursor FDR =============================
2:42:51.719954 PROGRESS: Total precursors accumulated: 2,668
2:42:51.720039 PROGRESS: Target precursors: 2,642 (99.03%)
2:42:51.720134 PROGRESS: Decoy precursors: 26 (0.97%)
2:42:51.720204 PROGRESS: 
2:42:51.720264 PROGRESS: Precursor Summary:
2:42:51.723910 PROGRESS: Channel   0:	 0.050 FDR: 2,642; 0.010 FDR: 2,642; 0.001 FDR: 2,141
2:42:51.724190 PROGRESS: 
2:42:51.724250 PROGRESS: Protein Summary:
2:42:51.727519 PROGRESS: Channel   0:	 0.050 FDR: 2,076; 0.010 FDR: 2,076; 0.001 FDR: 1,700
2:42:51.727937 PROGRESS: =========================================================================
2:42:51.729471 INFO: Target number of precursors reached.
2:42:51.766170 INFO: fragments_df: keeping 5000 of 119193 [sum(precursor_idx_mask)=59441 sum(mass_error_mask)=119193 stop_rank=5000
2:42:51.791730 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:52.846797 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:54.185157 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:54.186719 INFO: Using score_cutoff 10.060780151939392 (fac=0.99, q=1)
2:42:54.187658 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:54.187782 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:54.187875 INFO: Updating optimization_manager: score_cutoff        : 10.071718693828583 -> 10.060780151939392
2:42:54.187969 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:54.195209 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:54.209699 INFO: === checking if optimization conditions were reached ===
2:42:54.214522 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:42:54.215085 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:42:54.215191 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:42:54.215279 INFO: ==============================================
2:42:54.215416 PROGRESS: Optimization finished for ms2_error.
2:42:54.255876 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:54.263587 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:54.276892 INFO: Starting optimization step 0.
2:42:54.277583 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:54.277715 INFO: Using rust extraction backend
2:42:54.277818 PROGRESS: Extracting batch of 5940 precursors
2:42:54.307439 INFO: === Search parameters used ===
2:42:54.308117 INFO: rt_error       : 805.6019897460938
2:42:54.308181 INFO: mobility_error : 0.1
2:42:54.308229 INFO: num_candidates : 3
2:42:54.308275 INFO: ms1_error      : 3
2:42:54.308317 INFO: ms2_error      : 10.0
2:42:54.308358 INFO: fwhm_rt        : 3.0
2:42:54.308398 INFO: quant_window   : 3
2:42:54.308460 INFO: ==============================================
2:42:54.707609 INFO: performing precursor FDR with 40 features
2:42:54.707813 INFO: Decoy channel: -1
2:42:54.707866 INFO: competitive: True
2:42:54.723404 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:54.734277 INFO: Estimating optimal hyperparameters - samples: 14,249, batch_size: 128, learning_rate: 1.77e-04
2:42:54.734656 INFO: Using random state 576706 for train-test-split
2:42:56.809719 INFO: Test AUC: 0.762
2:42:56.809983 INFO: Train AUC: 0.789
2:42:56.810018 INFO: AUC difference: 3.40%
2:42:57.156147 INFO: Resetting torch num_threads to 100
2:42:57.161947 PROGRESS: === Extracted 17812 precursors and 119182 fragments ===
2:42:57.162930 INFO: === FDR correction performed with classifier version 6 ===
2:42:57.164724 PROGRESS: ============================= Precursor FDR =============================
2:42:57.164954 PROGRESS: Total precursors accumulated: 2,706
2:42:57.165045 PROGRESS: Target precursors: 2,680 (99.04%)
2:42:57.165116 PROGRESS: Decoy precursors: 26 (0.96%)
2:42:57.165182 PROGRESS: 
2:42:57.165242 PROGRESS: Precursor Summary:
2:42:57.167940 PROGRESS: Channel   0:	 0.050 FDR: 2,680; 0.010 FDR: 2,680; 0.001 FDR: 2,256
2:42:57.168100 PROGRESS: 
2:42:57.168172 PROGRESS: Protein Summary:
2:42:57.171947 PROGRESS: Channel   0:	 0.050 FDR: 2,100; 0.010 FDR: 2,100; 0.001 FDR: 1,793
2:42:57.172121 PROGRESS: =========================================================================
2:42:57.173193 INFO: Target number of precursors reached.
2:42:57.215622 INFO: fragments_df: keeping 5000 of 119182 [sum(precursor_idx_mask)=60079 sum(mass_error_mask)=119182 stop_rank=5000
2:42:57.234269 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:42:58.017093 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:42:59.135876 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:42:59.137012 INFO: Using score_cutoff 10.0679374417305 (fac=0.99, q=1)
2:42:59.137613 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:42:59.137712 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:42:59.137787 INFO: Updating optimization_manager: score_cutoff        : 10.060780151939392 -> 10.0679374417305
2:42:59.137869 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:42:59.143542 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:42:59.154619 INFO: === checking if optimization conditions were reached ===
2:42:59.155225 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:42:59.160388 INFO: Updating optimization_manager: rt_error            : 805.6019897460938 -> 459.895189697374
2:42:59.160684 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 459.8952.
2:42:59.160765 INFO: ==============================================
2:42:59.160855 INFO: Starting optimization step 1.
2:42:59.160932 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:42:59.161091 INFO: Using rust extraction backend
2:42:59.161239 PROGRESS: Extracting batch of 5940 precursors
2:42:59.185428 INFO: === Search parameters used ===
2:42:59.186027 INFO: rt_error       : 459.895189697374
2:42:59.186122 INFO: mobility_error : 0.1
2:42:59.186178 INFO: num_candidates : 3
2:42:59.186224 INFO: ms1_error      : 3
2:42:59.186263 INFO: ms2_error      : 10.0
2:42:59.186302 INFO: fwhm_rt        : 3.0
2:42:59.186342 INFO: quant_window   : 3
2:42:59.186389 INFO: ==============================================
2:42:59.593042 INFO: performing precursor FDR with 40 features
2:42:59.593285 INFO: Decoy channel: -1
2:42:59.593319 INFO: competitive: True
2:42:59.610260 INFO: Setting torch num_threads to 2 for FDR classification task
2:42:59.619015 INFO: Estimating optimal hyperparameters - samples: 14,248, batch_size: 128, learning_rate: 1.77e-04
2:42:59.619289 INFO: Using random state 576706 for train-test-split
2:43:01.726278 INFO: Test AUC: 0.772
2:43:01.726639 INFO: Train AUC: 0.784
2:43:01.726676 INFO: AUC difference: 1.52%
2:43:02.190201 INFO: Resetting torch num_threads to 100
2:43:02.200559 PROGRESS: === Extracted 17811 precursors and 118877 fragments ===
2:43:02.201820 INFO: === FDR correction performed with classifier version 6 ===
2:43:02.203916 PROGRESS: ============================= Precursor FDR =============================
2:43:02.204111 PROGRESS: Total precursors accumulated: 2,687
2:43:02.204176 PROGRESS: Target precursors: 2,661 (99.03%)
2:43:02.204230 PROGRESS: Decoy precursors: 26 (0.97%)
2:43:02.204278 PROGRESS: 
2:43:02.204325 PROGRESS: Precursor Summary:
2:43:02.206383 PROGRESS: Channel   0:	 0.050 FDR: 2,661; 0.010 FDR: 2,661; 0.001 FDR: 2,252
2:43:02.206547 PROGRESS: 
2:43:02.206618 PROGRESS: Protein Summary:
2:43:02.209377 PROGRESS: Channel   0:	 0.050 FDR: 2,094; 0.010 FDR: 2,094; 0.001 FDR: 1,784
2:43:02.209515 PROGRESS: =========================================================================
2:43:02.210541 INFO: Target number of precursors reached.
2:43:02.242386 INFO: fragments_df: keeping 5000 of 118877 [sum(precursor_idx_mask)=59701 sum(mass_error_mask)=118877 stop_rank=5000
2:43:02.266087 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:02.799654 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:03.625772 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:03.626682 INFO: Using score_cutoff 10.092778352737426 (fac=0.99, q=1)
2:43:03.627158 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:03.627257 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:03.627314 INFO: Updating optimization_manager: score_cutoff        : 10.0679374417305 -> 10.092778352737426
2:43:03.627379 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:03.632340 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:03.641785 INFO: === checking if optimization conditions were reached ===
2:43:03.642355 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:43:03.649334 INFO: Updating optimization_manager: rt_error            : 459.895189697374 -> 461.9107699013387
2:43:03.649808 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 461.9108.
2:43:03.649920 INFO: ==============================================
2:43:03.650010 INFO: Starting optimization step 2.
2:43:03.650089 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:43:03.650291 INFO: Using rust extraction backend
2:43:03.650429 PROGRESS: Extracting batch of 5940 precursors
2:43:03.667693 INFO: === Search parameters used ===
2:43:03.668236 INFO: rt_error       : 461.9107699013387
2:43:03.668292 INFO: mobility_error : 0.1
2:43:03.668342 INFO: num_candidates : 3
2:43:03.668390 INFO: ms1_error      : 3
2:43:03.668434 INFO: ms2_error      : 10.0
2:43:03.668477 INFO: fwhm_rt        : 3.0
2:43:03.668552 INFO: quant_window   : 3
2:43:03.668597 INFO: ==============================================
2:43:03.992474 INFO: performing precursor FDR with 40 features
2:43:03.992775 INFO: Decoy channel: -1
2:43:03.992807 INFO: competitive: True
2:43:04.015860 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:04.026048 INFO: Estimating optimal hyperparameters - samples: 14,248, batch_size: 128, learning_rate: 1.77e-04
2:43:04.026473 INFO: Using random state 576706 for train-test-split
2:43:06.070519 INFO: Test AUC: 0.783
2:43:06.070953 INFO: Train AUC: 0.781
2:43:06.070994 INFO: AUC difference: 0.15%
2:43:06.430419 INFO: Resetting torch num_threads to 100
2:43:06.434995 PROGRESS: === Extracted 17811 precursors and 118857 fragments ===
2:43:06.435886 INFO: === FDR correction performed with classifier version 6 ===
2:43:06.436918 PROGRESS: ============================= Precursor FDR =============================
2:43:06.437018 PROGRESS: Total precursors accumulated: 2,717
2:43:06.437076 PROGRESS: Target precursors: 2,691 (99.04%)
2:43:06.437125 PROGRESS: Decoy precursors: 26 (0.96%)
2:43:06.437168 PROGRESS: 
2:43:06.437212 PROGRESS: Precursor Summary:
2:43:06.439131 PROGRESS: Channel   0:	 0.050 FDR: 2,691; 0.010 FDR: 2,691; 0.001 FDR: 2,304
2:43:06.439244 PROGRESS: 
2:43:06.439297 PROGRESS: Protein Summary:
2:43:06.441986 PROGRESS: Channel   0:	 0.050 FDR: 2,111; 0.010 FDR: 2,111; 0.001 FDR: 1,828
2:43:06.442119 PROGRESS: =========================================================================
2:43:06.443264 INFO: Target number of precursors reached.
2:43:06.476869 INFO: fragments_df: keeping 5000 of 118857 [sum(precursor_idx_mask)=60219 sum(mass_error_mask)=118857 stop_rank=5000
2:43:06.501204 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:07.079076 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:08.019709 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:08.020727 INFO: Using score_cutoff 10.064228576660156 (fac=0.99, q=1)
2:43:08.021298 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:08.021395 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:08.021465 INFO: Updating optimization_manager: score_cutoff        : 10.092778352737426 -> 10.064228576660156
2:43:08.021541 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:08.026416 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:08.035969 INFO: === checking if optimization conditions were reached ===
2:43:08.036413 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:43:08.040737 INFO: Updating optimization_manager: rt_error            : 461.9107699013387 -> 472.4558061073531
2:43:08.040968 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 472.4558.
2:43:08.041043 INFO: ==============================================
2:43:08.041121 INFO: Starting optimization step 3.
2:43:08.041183 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:43:08.041251 INFO: Using rust extraction backend
2:43:08.041314 PROGRESS: Extracting batch of 5940 precursors
2:43:08.058389 INFO: === Search parameters used ===
2:43:08.058865 INFO: rt_error       : 472.4558061073531
2:43:08.058918 INFO: mobility_error : 0.1
2:43:08.058963 INFO: num_candidates : 3
2:43:08.059006 INFO: ms1_error      : 3
2:43:08.059059 INFO: ms2_error      : 10.0
2:43:08.059101 INFO: fwhm_rt        : 3.0
2:43:08.059141 INFO: quant_window   : 3
2:43:08.059182 INFO: ==============================================
2:43:08.275806 INFO: performing precursor FDR with 40 features
2:43:08.276002 INFO: Decoy channel: -1
2:43:08.276028 INFO: competitive: True
2:43:08.284686 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:08.292756 INFO: Estimating optimal hyperparameters - samples: 14,248, batch_size: 128, learning_rate: 1.77e-04
2:43:08.293100 INFO: Using random state 576706 for train-test-split
2:43:09.953551 INFO: Test AUC: 0.759
2:43:09.953767 INFO: Train AUC: 0.787
2:43:09.953801 INFO: AUC difference: 3.53%
2:43:10.255474 INFO: Resetting torch num_threads to 100
2:43:10.259264 PROGRESS: === Extracted 17811 precursors and 118907 fragments ===
2:43:10.259870 INFO: === FDR correction performed with classifier version 6 ===
2:43:10.261271 PROGRESS: ============================= Precursor FDR =============================
2:43:10.261439 PROGRESS: Total precursors accumulated: 2,744
2:43:10.261497 PROGRESS: Target precursors: 2,717 (99.02%)
2:43:10.261551 PROGRESS: Decoy precursors: 27 (0.98%)
2:43:10.261597 PROGRESS: 
2:43:10.261640 PROGRESS: Precursor Summary:
2:43:10.263454 PROGRESS: Channel   0:	 0.050 FDR: 2,717; 0.010 FDR: 2,717; 0.001 FDR: 2,301
2:43:10.263543 PROGRESS: 
2:43:10.263595 PROGRESS: Protein Summary:
2:43:10.265967 PROGRESS: Channel   0:	 0.050 FDR: 2,132; 0.010 FDR: 2,132; 0.001 FDR: 1,829
2:43:10.266080 PROGRESS: =========================================================================
2:43:10.266612 INFO: Target number of precursors reached.
2:43:10.294189 INFO: fragments_df: keeping 5000 of 118907 [sum(precursor_idx_mask)=60746 sum(mass_error_mask)=118907 stop_rank=5000
2:43:10.307753 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:10.850420 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:11.753950 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:11.755159 INFO: Using score_cutoff 10.059020751571655 (fac=0.99, q=1)
2:43:11.755856 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:11.755970 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:11.756026 INFO: Updating optimization_manager: score_cutoff        : 10.064228576660156 -> 10.059020751571655
2:43:11.756155 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:11.764289 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:11.777083 INFO: === checking if optimization conditions were reached ===
2:43:11.777710 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:43:11.784031 INFO: Updating optimization_manager: rt_error            : 472.4558061073531 -> 451.57446235148956
2:43:11.784479 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 451.5745.
2:43:11.784559 INFO: ==============================================
2:43:11.784654 INFO: Starting optimization step 4.
2:43:11.784727 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:43:11.784806 INFO: Using rust extraction backend
2:43:11.784871 PROGRESS: Extracting batch of 5940 precursors
2:43:11.820999 INFO: === Search parameters used ===
2:43:11.821682 INFO: rt_error       : 451.57446235148956
2:43:11.821741 INFO: mobility_error : 0.1
2:43:11.821813 INFO: num_candidates : 3
2:43:11.821862 INFO: ms1_error      : 3
2:43:11.821902 INFO: ms2_error      : 10.0
2:43:11.821943 INFO: fwhm_rt        : 3.0
2:43:11.821981 INFO: quant_window   : 3
2:43:11.822018 INFO: ==============================================
2:43:12.143648 INFO: performing precursor FDR with 40 features
2:43:12.144047 INFO: Decoy channel: -1
2:43:12.144076 INFO: competitive: True
2:43:12.165875 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:12.179754 INFO: Estimating optimal hyperparameters - samples: 14,248, batch_size: 128, learning_rate: 1.77e-04
2:43:12.180192 INFO: Using random state 576706 for train-test-split
2:43:13.457083 INFO: Test AUC: 0.760
2:43:13.457312 INFO: Train AUC: 0.787
2:43:13.457343 INFO: AUC difference: 3.44%
2:43:13.817533 INFO: Resetting torch num_threads to 100
2:43:13.824678 PROGRESS: === Extracted 17810 precursors and 118784 fragments ===
2:43:13.825850 INFO: === FDR correction performed with classifier version 6 ===
2:43:13.827567 PROGRESS: ============================= Precursor FDR =============================
2:43:13.827697 PROGRESS: Total precursors accumulated: 2,719
2:43:13.827772 PROGRESS: Target precursors: 2,693 (99.04%)
2:43:13.827842 PROGRESS: Decoy precursors: 26 (0.96%)
2:43:13.827897 PROGRESS: 
2:43:13.827952 PROGRESS: Precursor Summary:
2:43:13.830234 PROGRESS: Channel   0:	 0.050 FDR: 2,693; 0.010 FDR: 2,693; 0.001 FDR: 2,277
2:43:13.830393 PROGRESS: 
2:43:13.830452 PROGRESS: Protein Summary:
2:43:13.833721 PROGRESS: Channel   0:	 0.050 FDR: 2,120; 0.010 FDR: 2,120; 0.001 FDR: 1,811
2:43:13.833887 PROGRESS: =========================================================================
2:43:13.835233 INFO: Target number of precursors reached.
2:43:13.871962 INFO: fragments_df: keeping 5000 of 118784 [sum(precursor_idx_mask)=60111 sum(mass_error_mask)=118784 stop_rank=5000
2:43:13.906060 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:43:14.498870 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:43:15.364135 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:43:15.364668 INFO: Using score_cutoff 9.794691537094115 (fac=0.99, q=1)
2:43:15.365012 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:15.365091 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:15.365151 INFO: Updating optimization_manager: score_cutoff        : 10.059020751571655 -> 9.794691537094115
2:43:15.365205 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:15.369428 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:15.377592 INFO: === checking if optimization conditions were reached ===
2:43:15.377737 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:43:15.378621 INFO: Updating optimization_manager: rt_error            : 451.57446235148956 -> 472.4558061073531
2:43:15.378761 INFO: Updating optimization_manager: classifier_version  : 6 -> 10
2:43:15.378858 INFO: Updating optimization_manager: score_cutoff        : 9.794691537094115 -> 10.059020751571655
2:43:15.378945 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:43:15.379029 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:43:15.379114 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 472.4558 found after 5 searches.
2:43:15.379179 INFO: ==============================================
2:43:15.379245 PROGRESS: Optimization finished for rt_error.
2:43:15.391398 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:15.395563 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:15.403550 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:43:15.403664 PROGRESS: ==============================================
2:43:15.403740 PROGRESS: ms2_error      : 10.0000
2:43:15.403798 PROGRESS: rt_error       : 472.4558
2:43:15.403854 PROGRESS: ==============================================
2:43:15.404840 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:43:15.547045 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:43:15.930323 INFO: Using rust extraction backend
2:43:15.930776 PROGRESS: Extracting batch of 259156 precursors
2:43:16.380622 INFO: === Search parameters used ===
2:43:16.380998 INFO: rt_error       : 472.4558061073531
2:43:16.381058 INFO: mobility_error : 0.1
2:43:16.381107 INFO: num_candidates : 3
2:43:16.381152 INFO: ms1_error      : 3
2:43:16.381194 INFO: ms2_error      : 10.0
2:43:16.381233 INFO: fwhm_rt        : 3.0
2:43:16.381272 INFO: quant_window   : 3
2:43:16.381310 INFO: ==============================================
2:43:17.445679 INFO: Removed 87528 precursors with score below cutoff 10.059020751571655
2:43:18.260166 INFO: performing precursor FDR with 40 features
2:43:18.260334 INFO: Decoy channel: -1
2:43:18.260361 INFO: competitive: True
2:43:18.327009 INFO: Setting torch num_threads to 2 for FDR classification task
2:43:18.368464 WARNING: FDR calculation for 362869 target and 327071 decoy PSMs
2:43:18.368671 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:43:18.591467 INFO: Estimating optimal hyperparameters - samples: 551,952, batch_size: 2,260, learning_rate: 7.43e-04
2:43:18.592403 INFO: Using random state 745246 for train-test-split
2:43:30.348096 INFO: Test AUC: 0.778
2:43:30.348402 INFO: Train AUC: 0.779
2:43:30.348438 INFO: AUC difference: 0.14%
2:43:30.934109 INFO: Resetting torch num_threads to 100
2:43:31.700526 PROGRESS: ============================= Precursor FDR =============================
2:43:31.701032 PROGRESS: Total precursors accumulated: 120,824
2:43:31.701135 PROGRESS: Target precursors: 119,628 (99.01%)
2:43:31.701226 PROGRESS: Decoy precursors: 1,196 (0.99%)
2:43:31.701304 PROGRESS: 
2:43:31.701373 PROGRESS: Precursor Summary:
2:43:31.818538 PROGRESS: Channel   0:	 0.050 FDR: 119,628; 0.010 FDR: 119,628; 0.001 FDR: 107,097
2:43:31.819089 PROGRESS: 
2:43:31.819202 PROGRESS: Protein Summary:
2:43:32.070712 PROGRESS: Channel   0:	 0.050 FDR: 10,128; 0.010 FDR: 10,128; 0.001 FDR: 9,973
2:43:32.071269 PROGRESS: =========================================================================
2:43:32.087188 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/psm.parquet
2:43:32.640235 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/frag.parquet
2:43:33.223929 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:43:33.755658 PROGRESS: Loading raw file 3/6: LFQ_Astral_DIA_15min_50ng_Condition_A_REP3 
2:43:33.755970 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:43:33.756148 INFO: Initializing TimingManager
2:43:33.757403 INFO: Initializing RawFileManager
2:43:59.458117 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:43:59.468436 INFO: Determining DIA cycle
2:43:59.486146 INFO: Found cycle with start 0.00 min and length 300.
2:44:00.070692 INFO: RT (min)            : 0.0 - 26.9
2:44:00.070864 INFO: RT duration (sec)   : 1611.2
2:44:00.070897 INFO: RT duration (min)   : 26.9
2:44:00.070930 INFO: Cycle len (scans)   : 300
2:44:00.070956 INFO: Cycle len (sec)     : 1.65
2:44:00.070982 INFO: Number of cycles    : 977
2:44:00.071004 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:44:00.071112 INFO: Creating DIA data object took: 26.313454627990723
2:44:01.808193 INFO: Creating DIA data NG object took: 1.736600637435913
2:44:01.978765 INFO: Initializing CalibrationManager
2:44:01.979740 INFO: Setting up calibration estimators ..
2:44:01.979948 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:44:01.980105 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2:44:01.980232 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:44:01.980322 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:44:01.980402 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2:44:01.980479 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:44:01.980548 INFO: Done setting up calibration estimators.
2:44:01.981222 INFO: Initializing OptimizationManager
2:44:01.981601 INFO: initial parameter: ms1_error = 3
2:44:01.981682 INFO: initial parameter: ms2_error = 10
2:44:01.981744 INFO: initial parameter: rt_error = 805.6004638671875
2:44:01.981794 INFO: initial parameter: mobility_error = 0.1
2:44:01.981839 INFO: initial parameter: num_candidates = 1
2:44:01.981884 INFO: initial parameter: fwhm_rt = 5
2:44:01.981942 INFO: initial parameter: fwhm_mobility = 0.01
2:44:01.982008 INFO: initial parameter: score_cutoff = 0
2:44:01.982056 INFO: initial parameter: classifier_version = -1
2:44:01.982155 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:44:01.982865 INFO: FDRManager: loading saved state not requested, will be initialized.
2:44:01.982970 INFO: Initializing FDRManager
2:44:01.983023 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:44:02.093334 PROGRESS: Initializing spectral library: 131,021 target precursors potentially observable (0 removed)
2:44:02.171290 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
2:44:02.172619 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 805.6004638671875
2:44:02.172755 PROGRESS: Starting initial search for precursors.
2:44:02.172887 INFO: Starting optimization step 0.
2:44:02.172958 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:44:02.173074 INFO: Using rust extraction backend
2:44:02.173272 PROGRESS: Extracting batch of 1982 precursors
2:44:02.186045 INFO: === Search parameters used ===
2:44:02.186753 INFO: rt_error       : 805.6004638671875
2:44:02.186822 INFO: mobility_error : 0.1
2:44:02.186886 INFO: num_candidates : 1
2:44:02.186940 INFO: ms1_error      : 3
2:44:02.186985 INFO: ms2_error      : 10
2:44:02.187033 INFO: fwhm_rt        : 5
2:44:02.187080 INFO: quant_window   : 3
2:44:02.187125 INFO: ==============================================
2:44:02.256164 INFO: performing precursor FDR with 40 features
2:44:02.256374 INFO: Decoy channel: -1
2:44:02.256399 INFO: competitive: True
2:44:02.258190 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:02.260643 INFO: Estimating optimal hyperparameters - samples: 1,584, batch_size: 128, learning_rate: 1.77e-04
2:44:02.262013 INFO: Using random state 421387 for train-test-split
2:44:02.450975 INFO: Test AUC: 0.849
2:44:02.451152 INFO: Train AUC: 0.874
2:44:02.451180 INFO: AUC difference: 2.91%
2:44:02.760982 INFO: Resetting torch num_threads to 100
2:44:02.763862 PROGRESS: === Extracted 1981 precursors and 15384 fragments ===
2:44:02.764521 INFO: === FDR correction performed with classifier version -1 ===
2:44:02.765105 PROGRESS: ============================= Precursor FDR =============================
2:44:02.765215 PROGRESS: Total precursors accumulated: 474
2:44:02.765274 PROGRESS: Target precursors: 470 (99.16%)
2:44:02.765325 PROGRESS: Decoy precursors: 4 (0.84%)
2:44:02.765368 PROGRESS: 
2:44:02.765409 PROGRESS: Precursor Summary:
2:44:02.766612 PROGRESS: Channel   0:	 0.050 FDR:   470; 0.010 FDR:   470; 0.001 FDR:   112
2:44:02.766711 PROGRESS: 
2:44:02.766773 PROGRESS: Protein Summary:
2:44:02.768166 PROGRESS: Channel   0:	 0.050 FDR:   443; 0.010 FDR:   443; 0.001 FDR:   108
2:44:02.768315 PROGRESS: =========================================================================
2:44:02.768860 INFO: Target number of precursors not reached yet.
2:44:02.780773 INFO: Starting optimization step 1.
2:44:02.781218 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:44:02.781317 INFO: Using rust extraction backend
2:44:02.781385 PROGRESS: Extracting batch of 3958 precursors
2:44:02.793647 INFO: === Search parameters used ===
2:44:02.794261 INFO: rt_error       : 805.6004638671875
2:44:02.794317 INFO: mobility_error : 0.1
2:44:02.794363 INFO: num_candidates : 1
2:44:02.794407 INFO: ms1_error      : 3
2:44:02.794447 INFO: ms2_error      : 10
2:44:02.794488 INFO: fwhm_rt        : 5
2:44:02.794532 INFO: quant_window   : 3
2:44:02.794572 INFO: ==============================================
2:44:02.926124 INFO: performing precursor FDR with 40 features
2:44:02.926462 INFO: Decoy channel: -1
2:44:02.926491 INFO: competitive: True
2:44:02.940274 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:02.952471 INFO: Estimating optimal hyperparameters - samples: 4,751, batch_size: 128, learning_rate: 1.77e-04
2:44:02.953192 INFO: Using random state 505473 for train-test-split
2:44:03.549488 INFO: Test AUC: 0.881
2:44:03.549712 INFO: Train AUC: 0.893
2:44:03.549743 INFO: AUC difference: 1.39%
2:44:03.858277 INFO: Resetting torch num_threads to 100
2:44:03.863793 PROGRESS: === Extracted 5939 precursors and 45818 fragments ===
2:44:03.864447 INFO: === FDR correction performed with classifier version -1 ===
2:44:03.865375 PROGRESS: ============================= Precursor FDR =============================
2:44:03.865476 PROGRESS: Total precursors accumulated: 2,113
2:44:03.865538 PROGRESS: Target precursors: 2,093 (99.05%)
2:44:03.865587 PROGRESS: Decoy precursors: 20 (0.95%)
2:44:03.865631 PROGRESS: 
2:44:03.865674 PROGRESS: Precursor Summary:
2:44:03.867232 PROGRESS: Channel   0:	 0.050 FDR: 2,093; 0.010 FDR: 2,093; 0.001 FDR: 1,142
2:44:03.867325 PROGRESS: 
2:44:03.867378 PROGRESS: Protein Summary:
2:44:03.869435 PROGRESS: Channel   0:	 0.050 FDR: 1,670; 0.010 FDR: 1,670; 0.001 FDR:   998
2:44:03.869560 PROGRESS: =========================================================================
2:44:03.870007 INFO: Target number of precursors reached.
2:44:03.881805 INFO: fragments_df: keeping 5000 of 45818 [sum(precursor_idx_mask)=20991 sum(mass_error_mask)=45818 stop_rank=5000
2:44:03.895402 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:04.306787 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:05.256677 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:44:05.258616 INFO: Using score_cutoff 10.996223218917846 (fac=0.99, q=1)
2:44:05.259150 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:44:05.259238 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:44:05.259297 INFO: Updating optimization_manager: score_cutoff        : 0 -> 10.996223218917846
2:44:05.259372 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:05.265290 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:05.277756 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:44:05.278692 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:44:05.278888 INFO: Starting optimization step 2.
2:44:05.279029 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:05.279497 INFO: Using rust extraction backend
2:44:05.279631 PROGRESS: Extracting batch of 5940 precursors
2:44:05.310025 INFO: === Search parameters used ===
2:44:05.310755 INFO: rt_error       : 805.6004638671875
2:44:05.310817 INFO: mobility_error : 0.1
2:44:05.310868 INFO: num_candidates : 3
2:44:05.310914 INFO: ms1_error      : 3
2:44:05.310958 INFO: ms2_error      : 10
2:44:05.311001 INFO: fwhm_rt        : 3.0
2:44:05.311044 INFO: quant_window   : 3
2:44:05.311086 INFO: ==============================================
2:44:05.522064 INFO: performing precursor FDR with 40 features
2:44:05.522286 INFO: Decoy channel: -1
2:44:05.522314 INFO: competitive: True
2:44:05.531665 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:05.540345 INFO: Estimating optimal hyperparameters - samples: 14,250, batch_size: 128, learning_rate: 1.77e-04
2:44:05.540651 INFO: Using random state 922868 for train-test-split
2:44:07.111046 INFO: Test AUC: 0.685
2:44:07.111239 INFO: Train AUC: 0.687
2:44:07.111274 INFO: AUC difference: 0.26%
2:44:07.384964 INFO: Resetting torch num_threads to 100
2:44:07.387577 PROGRESS: === Extracted 17813 precursors and 119600 fragments ===
2:44:07.388031 INFO: === FDR correction performed with classifier version 1 ===
2:44:07.388765 PROGRESS: ============================= Precursor FDR =============================
2:44:07.388858 PROGRESS: Total precursors accumulated: 2,450
2:44:07.388915 PROGRESS: Target precursors: 2,426 (99.02%)
2:44:07.388973 PROGRESS: Decoy precursors: 24 (0.98%)
2:44:07.389018 PROGRESS: 
2:44:07.389061 PROGRESS: Precursor Summary:
2:44:07.390637 PROGRESS: Channel   0:	 0.050 FDR: 2,426; 0.010 FDR: 2,426; 0.001 FDR: 1,812
2:44:07.390725 PROGRESS: 
2:44:07.390786 PROGRESS: Protein Summary:
2:44:07.392955 PROGRESS: Channel   0:	 0.050 FDR: 1,929; 0.010 FDR: 1,929; 0.001 FDR: 1,476
2:44:07.393079 PROGRESS: =========================================================================
2:44:07.393498 INFO: Target number of precursors reached.
2:44:07.419358 INFO: fragments_df: keeping 5000 of 119600 [sum(precursor_idx_mask)=55517 sum(mass_error_mask)=119600 stop_rank=5000
2:44:07.434273 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:07.893325 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:08.753822 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:08.754706 INFO: Using score_cutoff 10.596766920089722 (fac=0.99, q=1)
2:44:08.755177 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:08.755259 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:08.755313 INFO: Updating optimization_manager: score_cutoff        : 10.996223218917846 -> 10.596766920089722
2:44:08.755376 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:08.760744 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:08.771190 INFO: === checking if optimization conditions were reached ===
2:44:08.774463 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
2:44:08.774787 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:44:08.774857 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:44:08.774919 INFO: ==============================================
2:44:08.775028 INFO: Starting optimization step 3.
2:44:08.775090 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:08.775162 INFO: Using rust extraction backend
2:44:08.775229 PROGRESS: Extracting batch of 5940 precursors
2:44:08.794652 INFO: === Search parameters used ===
2:44:08.795245 INFO: rt_error       : 805.6004638671875
2:44:08.795301 INFO: mobility_error : 0.1
2:44:08.795348 INFO: num_candidates : 3
2:44:08.795433 INFO: ms1_error      : 3
2:44:08.795475 INFO: ms2_error      : 10.0
2:44:08.795516 INFO: fwhm_rt        : 3.0
2:44:08.795555 INFO: quant_window   : 3
2:44:08.795594 INFO: ==============================================
2:44:08.974114 INFO: performing precursor FDR with 40 features
2:44:08.974273 INFO: Decoy channel: -1
2:44:08.974297 INFO: competitive: True
2:44:08.980701 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:08.985918 INFO: Estimating optimal hyperparameters - samples: 14,250, batch_size: 128, learning_rate: 1.77e-04
2:44:08.986143 INFO: Using random state 307572 for train-test-split
2:44:10.640380 INFO: Test AUC: 0.700
2:44:10.640604 INFO: Train AUC: 0.701
2:44:10.640666 INFO: AUC difference: 0.17%
2:44:10.968370 INFO: Resetting torch num_threads to 100
2:44:10.976517 PROGRESS: === Extracted 17813 precursors and 119629 fragments ===
2:44:10.977980 INFO: === FDR correction performed with classifier version 2 ===
2:44:10.980232 PROGRESS: ============================= Precursor FDR =============================
2:44:10.980411 PROGRESS: Total precursors accumulated: 2,543
2:44:10.980483 PROGRESS: Target precursors: 2,518 (99.02%)
2:44:10.980542 PROGRESS: Decoy precursors: 25 (0.98%)
2:44:10.980599 PROGRESS: 
2:44:10.980654 PROGRESS: Precursor Summary:
2:44:10.983063 PROGRESS: Channel   0:	 0.050 FDR: 2,518; 0.010 FDR: 2,518; 0.001 FDR: 2,171
2:44:10.983382 PROGRESS: 
2:44:10.983459 PROGRESS: Protein Summary:
2:44:10.986483 PROGRESS: Channel   0:	 0.050 FDR: 1,992; 0.010 FDR: 1,992; 0.001 FDR: 1,731
2:44:10.986775 PROGRESS: =========================================================================
2:44:10.988787 INFO: Target number of precursors reached.
2:44:11.026362 INFO: fragments_df: keeping 5000 of 119629 [sum(precursor_idx_mask)=57069 sum(mass_error_mask)=119629 stop_rank=5000
2:44:11.060761 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:11.540352 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:21.590633 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:21.592716 INFO: Using score_cutoff 10.26112073507309 (fac=0.99, q=1)
2:44:21.593773 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:21.593946 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:21.594021 INFO: Updating optimization_manager: score_cutoff        : 10.596766920089722 -> 10.26112073507309
2:44:21.594216 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:21.603238 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:21.617676 INFO: === checking if optimization conditions were reached ===
2:44:21.623897 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:44:21.624523 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:44:21.624673 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:44:21.624899 INFO: ==============================================
2:44:21.625052 INFO: Starting optimization step 4.
2:44:21.625181 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:21.625431 INFO: Using rust extraction backend
2:44:21.625646 PROGRESS: Extracting batch of 5940 precursors
2:44:21.663483 INFO: === Search parameters used ===
2:44:21.665069 INFO: rt_error       : 805.6004638671875
2:44:21.665164 INFO: mobility_error : 0.1
2:44:21.665224 INFO: num_candidates : 3
2:44:21.665305 INFO: ms1_error      : 3
2:44:21.665362 INFO: ms2_error      : 10.0
2:44:21.665414 INFO: fwhm_rt        : 3.0
2:44:21.665465 INFO: quant_window   : 3
2:44:21.665515 INFO: ==============================================
2:44:21.894009 INFO: performing precursor FDR with 40 features
2:44:21.894159 INFO: Decoy channel: -1
2:44:21.894184 INFO: competitive: True
2:44:21.901078 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:21.907281 INFO: Estimating optimal hyperparameters - samples: 14,250, batch_size: 128, learning_rate: 1.77e-04
2:44:21.907469 INFO: Using random state 698919 for train-test-split
2:44:23.098633 INFO: Test AUC: 0.708
2:44:23.098814 INFO: Train AUC: 0.708
2:44:23.098846 INFO: AUC difference: 0.01%
2:44:23.439766 INFO: Resetting torch num_threads to 100
2:44:23.445446 PROGRESS: === Extracted 17813 precursors and 119624 fragments ===
2:44:23.446224 INFO: === FDR correction performed with classifier version 3 ===
2:44:23.447881 PROGRESS: ============================= Precursor FDR =============================
2:44:23.448076 PROGRESS: Total precursors accumulated: 2,675
2:44:23.448137 PROGRESS: Target precursors: 2,649 (99.03%)
2:44:23.448187 PROGRESS: Decoy precursors: 26 (0.97%)
2:44:23.448233 PROGRESS: 
2:44:23.448297 PROGRESS: Precursor Summary:
2:44:23.450453 PROGRESS: Channel   0:	 0.050 FDR: 2,649; 0.010 FDR: 2,649; 0.001 FDR: 2,272
2:44:23.450595 PROGRESS: 
2:44:23.450650 PROGRESS: Protein Summary:
2:44:23.453339 PROGRESS: Channel   0:	 0.050 FDR: 2,092; 0.010 FDR: 2,092; 0.001 FDR: 1,804
2:44:23.453510 PROGRESS: =========================================================================
2:44:23.454286 INFO: Target number of precursors reached.
2:44:23.485719 INFO: fragments_df: keeping 5000 of 119624 [sum(precursor_idx_mask)=59683 sum(mass_error_mask)=119624 stop_rank=5000
2:44:23.513709 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:24.136361 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:25.072303 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:25.073787 INFO: Using score_cutoff 10.152203580093385 (fac=0.99, q=1)
2:44:25.074374 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:25.074454 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:25.074507 INFO: Updating optimization_manager: score_cutoff        : 10.26112073507309 -> 10.152203580093385
2:44:25.074573 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:25.082095 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:25.096485 INFO: === checking if optimization conditions were reached ===
2:44:25.101676 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:44:25.102181 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:44:25.102311 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:44:25.102382 INFO: ==============================================
2:44:25.102456 INFO: Starting optimization step 5.
2:44:25.102516 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:25.102933 INFO: Using rust extraction backend
2:44:25.103036 PROGRESS: Extracting batch of 5940 precursors
2:44:25.136523 INFO: === Search parameters used ===
2:44:25.137540 INFO: rt_error       : 805.6004638671875
2:44:25.137609 INFO: mobility_error : 0.1
2:44:25.137664 INFO: num_candidates : 3
2:44:25.137711 INFO: ms1_error      : 3
2:44:25.137758 INFO: ms2_error      : 10.0
2:44:25.137804 INFO: fwhm_rt        : 3.0
2:44:25.137847 INFO: quant_window   : 3
2:44:25.137949 INFO: ==============================================
2:44:25.355549 INFO: performing precursor FDR with 40 features
2:44:25.355739 INFO: Decoy channel: -1
2:44:25.355766 INFO: competitive: True
2:44:25.364661 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:25.372244 INFO: Estimating optimal hyperparameters - samples: 14,250, batch_size: 128, learning_rate: 1.77e-04
2:44:25.372545 INFO: Using random state 454720 for train-test-split
2:44:27.097412 INFO: Test AUC: 0.695
2:44:27.097632 INFO: Train AUC: 0.718
2:44:27.097665 INFO: AUC difference: 3.16%
2:44:27.426025 INFO: Resetting torch num_threads to 100
2:44:27.430877 PROGRESS: === Extracted 17813 precursors and 119607 fragments ===
2:44:27.431667 INFO: === FDR correction performed with classifier version 4 ===
2:44:27.432853 PROGRESS: ============================= Precursor FDR =============================
2:44:27.432976 PROGRESS: Total precursors accumulated: 2,703
2:44:27.433037 PROGRESS: Target precursors: 2,677 (99.04%)
2:44:27.433100 PROGRESS: Decoy precursors: 26 (0.96%)
2:44:27.433173 PROGRESS: 
2:44:27.433220 PROGRESS: Precursor Summary:
2:44:27.435360 PROGRESS: Channel   0:	 0.050 FDR: 2,677; 0.010 FDR: 2,677; 0.001 FDR: 2,356
2:44:27.435506 PROGRESS: 
2:44:27.435565 PROGRESS: Protein Summary:
2:44:27.438360 PROGRESS: Channel   0:	 0.050 FDR: 2,110; 0.010 FDR: 2,110; 0.001 FDR: 1,868
2:44:27.438646 PROGRESS: =========================================================================
2:44:27.439736 INFO: Target number of precursors reached.
2:44:27.471824 INFO: fragments_df: keeping 5000 of 119607 [sum(precursor_idx_mask)=60237 sum(mass_error_mask)=119607 stop_rank=5000
2:44:27.491373 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:28.050868 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:28.929054 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:28.929833 INFO: Using score_cutoff 10.07631100730896 (fac=0.99, q=1)
2:44:28.930276 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:28.930357 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:28.930412 INFO: Updating optimization_manager: score_cutoff        : 10.152203580093385 -> 10.07631100730896
2:44:28.930471 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:28.935264 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:28.944960 INFO: === checking if optimization conditions were reached ===
2:44:28.948004 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:44:28.948341 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:44:28.948416 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:44:28.948478 INFO: ==============================================
2:44:28.948546 INFO: Starting optimization step 6.
2:44:28.948606 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:28.948675 INFO: Using rust extraction backend
2:44:28.948740 PROGRESS: Extracting batch of 5940 precursors
2:44:28.965361 INFO: === Search parameters used ===
2:44:28.965909 INFO: rt_error       : 805.6004638671875
2:44:28.965965 INFO: mobility_error : 0.1
2:44:28.966013 INFO: num_candidates : 3
2:44:28.966058 INFO: ms1_error      : 3
2:44:28.966101 INFO: ms2_error      : 10.0
2:44:28.966146 INFO: fwhm_rt        : 3.0
2:44:28.966189 INFO: quant_window   : 3
2:44:28.966230 INFO: ==============================================
2:44:29.186872 INFO: performing precursor FDR with 40 features
2:44:29.187122 INFO: Decoy channel: -1
2:44:29.187147 INFO: competitive: True
2:44:29.196140 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:29.203962 INFO: Estimating optimal hyperparameters - samples: 14,250, batch_size: 128, learning_rate: 1.77e-04
2:44:29.204289 INFO: Using random state 726080 for train-test-split
2:44:30.802914 INFO: Test AUC: 0.714
2:44:30.803182 INFO: Train AUC: 0.723
2:44:30.803213 INFO: AUC difference: 1.35%
2:44:31.114369 INFO: Resetting torch num_threads to 100
2:44:31.118989 PROGRESS: === Extracted 17813 precursors and 119619 fragments ===
2:44:31.119706 INFO: === FDR correction performed with classifier version 5 ===
2:44:31.120828 PROGRESS: ============================= Precursor FDR =============================
2:44:31.120950 PROGRESS: Total precursors accumulated: 2,788
2:44:31.121015 PROGRESS: Target precursors: 2,761 (99.03%)
2:44:31.121099 PROGRESS: Decoy precursors: 27 (0.97%)
2:44:31.121150 PROGRESS: 
2:44:31.121199 PROGRESS: Precursor Summary:
2:44:31.123262 PROGRESS: Channel   0:	 0.050 FDR: 2,761; 0.010 FDR: 2,761; 0.001 FDR: 2,402
2:44:31.123369 PROGRESS: 
2:44:31.123426 PROGRESS: Protein Summary:
2:44:31.126213 PROGRESS: Channel   0:	 0.050 FDR: 2,173; 0.010 FDR: 2,173; 0.001 FDR: 1,896
2:44:31.126348 PROGRESS: =========================================================================
2:44:31.127108 INFO: Target number of precursors reached.
2:44:31.158683 INFO: fragments_df: keeping 5000 of 119619 [sum(precursor_idx_mask)=61732 sum(mass_error_mask)=119619 stop_rank=5000
2:44:31.176983 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:31.760495 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:32.598911 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:32.599857 INFO: Using score_cutoff 9.963426029205323 (fac=0.99, q=1)
2:44:32.600341 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:32.600424 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:32.600483 INFO: Updating optimization_manager: score_cutoff        : 10.07631100730896 -> 9.963426029205323
2:44:32.600547 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:32.605719 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:32.615460 INFO: === checking if optimization conditions were reached ===
2:44:32.618816 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:44:32.619098 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:44:32.619172 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:44:32.619238 INFO: ==============================================
2:44:32.619330 PROGRESS: Optimization finished for ms2_error.
2:44:32.640175 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:32.645993 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:32.655721 INFO: Starting optimization step 0.
2:44:32.656168 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:32.656263 INFO: Using rust extraction backend
2:44:32.656339 PROGRESS: Extracting batch of 5940 precursors
2:44:32.675695 INFO: === Search parameters used ===
2:44:32.676322 INFO: rt_error       : 805.6004638671875
2:44:32.676379 INFO: mobility_error : 0.1
2:44:32.676430 INFO: num_candidates : 3
2:44:32.676475 INFO: ms1_error      : 3
2:44:32.676519 INFO: ms2_error      : 10.0
2:44:32.676561 INFO: fwhm_rt        : 3.0
2:44:32.676605 INFO: quant_window   : 3
2:44:32.676647 INFO: ==============================================
2:44:32.895486 INFO: performing precursor FDR with 40 features
2:44:32.895773 INFO: Decoy channel: -1
2:44:32.895800 INFO: competitive: True
2:44:32.904855 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:32.912455 INFO: Estimating optimal hyperparameters - samples: 14,250, batch_size: 128, learning_rate: 1.77e-04
2:44:32.912832 INFO: Using random state 678763 for train-test-split
2:44:34.851767 INFO: Test AUC: 0.717
2:44:34.852000 INFO: Train AUC: 0.728
2:44:34.852031 INFO: AUC difference: 1.62%
2:44:35.161531 INFO: Resetting torch num_threads to 100
2:44:35.165700 PROGRESS: === Extracted 17813 precursors and 119624 fragments ===
2:44:35.166581 INFO: === FDR correction performed with classifier version 6 ===
2:44:35.167644 PROGRESS: ============================= Precursor FDR =============================
2:44:35.167739 PROGRESS: Total precursors accumulated: 2,773
2:44:35.167799 PROGRESS: Target precursors: 2,746 (99.03%)
2:44:35.167865 PROGRESS: Decoy precursors: 27 (0.97%)
2:44:35.167913 PROGRESS: 
2:44:35.167956 PROGRESS: Precursor Summary:
2:44:35.169969 PROGRESS: Channel   0:	 0.050 FDR: 2,746; 0.010 FDR: 2,746; 0.001 FDR: 2,394
2:44:35.170064 PROGRESS: 
2:44:35.170117 PROGRESS: Protein Summary:
2:44:35.172878 PROGRESS: Channel   0:	 0.050 FDR: 2,164; 0.010 FDR: 2,164; 0.001 FDR: 1,902
2:44:35.173040 PROGRESS: =========================================================================
2:44:35.173759 INFO: Target number of precursors reached.
2:44:35.206378 INFO: fragments_df: keeping 5000 of 119624 [sum(precursor_idx_mask)=61441 sum(mass_error_mask)=119624 stop_rank=5000
2:44:35.224361 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:35.837484 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:36.867482 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:36.868839 INFO: Using score_cutoff 10.074037741184235 (fac=0.99, q=1)
2:44:36.870047 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:36.870304 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:36.870410 INFO: Updating optimization_manager: score_cutoff        : 9.963426029205323 -> 10.074037741184235
2:44:36.870491 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:36.877068 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:36.888956 INFO: === checking if optimization conditions were reached ===
2:44:36.889732 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:44:36.895272 INFO: Updating optimization_manager: rt_error            : 805.6004638671875 -> 249.8329475003518
2:44:36.895911 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 249.8329.
2:44:36.895995 INFO: ==============================================
2:44:36.896108 INFO: Starting optimization step 1.
2:44:36.896173 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:36.896297 INFO: Using rust extraction backend
2:44:36.896360 PROGRESS: Extracting batch of 5940 precursors
2:44:36.925407 INFO: === Search parameters used ===
2:44:36.926261 INFO: rt_error       : 249.8329475003518
2:44:36.926318 INFO: mobility_error : 0.1
2:44:36.926370 INFO: num_candidates : 3
2:44:36.926451 INFO: ms1_error      : 3
2:44:36.926494 INFO: ms2_error      : 10.0
2:44:36.926536 INFO: fwhm_rt        : 3.0
2:44:36.926577 INFO: quant_window   : 3
2:44:36.926627 INFO: ==============================================
2:44:37.125262 INFO: performing precursor FDR with 40 features
2:44:37.125456 INFO: Decoy channel: -1
2:44:37.125481 INFO: competitive: True
2:44:37.131152 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:37.136073 INFO: Estimating optimal hyperparameters - samples: 14,236, batch_size: 128, learning_rate: 1.77e-04
2:44:37.136303 INFO: Using random state 678763 for train-test-split
2:44:39.022973 INFO: Test AUC: 0.741
2:44:39.023212 INFO: Train AUC: 0.744
2:44:39.023244 INFO: AUC difference: 0.42%
2:44:39.400535 INFO: Resetting torch num_threads to 100
2:44:39.405095 PROGRESS: === Extracted 17796 precursors and 116386 fragments ===
2:44:39.405872 INFO: === FDR correction performed with classifier version 6 ===
2:44:39.407343 PROGRESS: ============================= Precursor FDR =============================
2:44:39.407485 PROGRESS: Total precursors accumulated: 2,835
2:44:39.407580 PROGRESS: Target precursors: 2,807 (99.01%)
2:44:39.407655 PROGRESS: Decoy precursors: 28 (0.99%)
2:44:39.407720 PROGRESS: 
2:44:39.407780 PROGRESS: Precursor Summary:
2:44:39.411227 PROGRESS: Channel   0:	 0.050 FDR: 2,807; 0.010 FDR: 2,807; 0.001 FDR: 2,352
2:44:39.411499 PROGRESS: 
2:44:39.411583 PROGRESS: Protein Summary:
2:44:39.416589 PROGRESS: Channel   0:	 0.050 FDR: 2,201; 0.010 FDR: 2,201; 0.001 FDR: 1,874
2:44:39.416942 PROGRESS: =========================================================================
2:44:39.418247 INFO: Target number of precursors reached.
2:44:39.456643 INFO: fragments_df: keeping 5000 of 116386 [sum(precursor_idx_mask)=61801 sum(mass_error_mask)=116386 stop_rank=5000
2:44:39.477880 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:40.107172 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:41.079558 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:41.080281 INFO: Using score_cutoff 9.860638602447509 (fac=0.99, q=1)
2:44:41.080668 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:41.080751 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:41.080806 INFO: Updating optimization_manager: score_cutoff        : 10.074037741184235 -> 9.860638602447509
2:44:41.080863 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:41.085559 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:41.094954 INFO: === checking if optimization conditions were reached ===
2:44:41.095373 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:44:41.099253 INFO: Updating optimization_manager: rt_error            : 249.8329475003518 -> 183.32050838082145
2:44:41.099659 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 183.3205.
2:44:41.099765 INFO: ==============================================
2:44:41.099884 INFO: Starting optimization step 2.
2:44:41.099975 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:41.100099 INFO: Using rust extraction backend
2:44:41.100165 PROGRESS: Extracting batch of 5940 precursors
2:44:41.114458 INFO: === Search parameters used ===
2:44:41.114960 INFO: rt_error       : 183.32050838082145
2:44:41.115018 INFO: mobility_error : 0.1
2:44:41.115065 INFO: num_candidates : 3
2:44:41.115109 INFO: ms1_error      : 3
2:44:41.115152 INFO: ms2_error      : 10.0
2:44:41.115242 INFO: fwhm_rt        : 3.0
2:44:41.115289 INFO: quant_window   : 3
2:44:41.115330 INFO: ==============================================
2:44:41.374493 INFO: performing precursor FDR with 40 features
2:44:41.374944 INFO: Decoy channel: -1
2:44:41.374985 INFO: competitive: True
2:44:41.398084 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:41.413102 INFO: Estimating optimal hyperparameters - samples: 14,232, batch_size: 128, learning_rate: 1.77e-04
2:44:41.413572 INFO: Using random state 678763 for train-test-split
2:44:43.530705 INFO: Test AUC: 0.734
2:44:43.531133 INFO: Train AUC: 0.747
2:44:43.531181 INFO: AUC difference: 1.81%
2:44:43.981906 INFO: Resetting torch num_threads to 100
2:44:43.991132 PROGRESS: === Extracted 17790 precursors and 113627 fragments ===
2:44:43.992554 INFO: === FDR correction performed with classifier version 6 ===
2:44:43.995790 PROGRESS: ============================= Precursor FDR =============================
2:44:43.996178 PROGRESS: Total precursors accumulated: 2,830
2:44:43.996299 PROGRESS: Target precursors: 2,802 (99.01%)
2:44:43.996360 PROGRESS: Decoy precursors: 28 (0.99%)
2:44:43.996415 PROGRESS: 
2:44:43.996463 PROGRESS: Precursor Summary:
2:44:44.003057 PROGRESS: Channel   0:	 0.050 FDR: 2,802; 0.010 FDR: 2,802; 0.001 FDR: 2,397
2:44:44.003727 PROGRESS: 
2:44:44.003793 PROGRESS: Protein Summary:
2:44:44.010265 PROGRESS: Channel   0:	 0.050 FDR: 2,196; 0.010 FDR: 2,196; 0.001 FDR: 1,908
2:44:44.010822 PROGRESS: =========================================================================
2:44:44.011991 INFO: Target number of precursors reached.
2:44:44.048434 INFO: fragments_df: keeping 5000 of 113627 [sum(precursor_idx_mask)=60931 sum(mass_error_mask)=113627 stop_rank=5000
2:44:44.076086 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:44.700946 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:45.721969 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:45.722661 INFO: Using score_cutoff 9.891710934734345 (fac=0.99, q=1)
2:44:45.723093 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:45.723182 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:45.723247 INFO: Updating optimization_manager: score_cutoff        : 9.860638602447509 -> 9.891710934734345
2:44:45.723313 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:45.728403 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:45.738084 INFO: === checking if optimization conditions were reached ===
2:44:45.738312 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:44:45.742703 INFO: Updating optimization_manager: rt_error            : 183.32050838082145 -> 126.0723988604378
2:44:45.742889 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 126.0724.
2:44:45.742968 INFO: ==============================================
2:44:45.743056 INFO: Starting optimization step 3.
2:44:45.743131 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:45.743210 INFO: Using rust extraction backend
2:44:45.743280 PROGRESS: Extracting batch of 5940 precursors
2:44:45.757299 INFO: === Search parameters used ===
2:44:45.757718 INFO: rt_error       : 126.0723988604378
2:44:45.757818 INFO: mobility_error : 0.1
2:44:45.757905 INFO: num_candidates : 3
2:44:45.757993 INFO: ms1_error      : 3
2:44:45.758070 INFO: ms2_error      : 10.0
2:44:45.758150 INFO: fwhm_rt        : 3.0
2:44:45.758219 INFO: quant_window   : 3
2:44:45.758292 INFO: ==============================================
2:44:46.071650 INFO: performing precursor FDR with 40 features
2:44:46.072037 INFO: Decoy channel: -1
2:44:46.072078 INFO: competitive: True
2:44:46.094002 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:46.114687 INFO: Estimating optimal hyperparameters - samples: 14,230, batch_size: 128, learning_rate: 1.77e-04
2:44:46.115227 INFO: Using random state 678763 for train-test-split
2:44:48.307923 INFO: Test AUC: 0.754
2:44:48.308176 INFO: Train AUC: 0.756
2:44:48.308210 INFO: AUC difference: 0.16%
2:44:48.774465 INFO: Resetting torch num_threads to 100
2:44:48.780864 PROGRESS: === Extracted 17788 precursors and 110160 fragments ===
2:44:48.781956 INFO: === FDR correction performed with classifier version 6 ===
2:44:48.783584 PROGRESS: ============================= Precursor FDR =============================
2:44:48.783701 PROGRESS: Total precursors accumulated: 2,806
2:44:48.783771 PROGRESS: Target precursors: 2,779 (99.04%)
2:44:48.783838 PROGRESS: Decoy precursors: 27 (0.96%)
2:44:48.783895 PROGRESS: 
2:44:48.783941 PROGRESS: Precursor Summary:
2:44:48.786438 PROGRESS: Channel   0:	 0.050 FDR: 2,779; 0.010 FDR: 2,779; 0.001 FDR: 2,273
2:44:48.786596 PROGRESS: 
2:44:48.786667 PROGRESS: Protein Summary:
2:44:48.789851 PROGRESS: Channel   0:	 0.050 FDR: 2,180; 0.010 FDR: 2,180; 0.001 FDR: 1,812
2:44:48.790009 PROGRESS: =========================================================================
2:44:48.791406 INFO: Target number of precursors reached.
2:44:48.830314 INFO: fragments_df: keeping 5000 of 110160 [sum(precursor_idx_mask)=59482 sum(mass_error_mask)=110160 stop_rank=5000
2:44:48.861706 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:49.505915 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:50.420660 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:50.421820 INFO: Using score_cutoff 9.57621713962555 (fac=0.99, q=1)
2:44:50.422972 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:50.423220 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:50.423302 INFO: Updating optimization_manager: score_cutoff        : 9.891710934734345 -> 9.57621713962555
2:44:50.423383 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:50.430391 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:50.442752 INFO: === checking if optimization conditions were reached ===
2:44:50.443363 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:44:50.449378 INFO: Updating optimization_manager: rt_error            : 126.0723988604378 -> 88.25744600408271
2:44:50.450004 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 88.2574.
2:44:50.450090 INFO: ==============================================
2:44:50.450166 INFO: Starting optimization step 4.
2:44:50.450233 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:50.450335 INFO: Using rust extraction backend
2:44:50.450410 PROGRESS: Extracting batch of 5940 precursors
2:44:50.476691 INFO: === Search parameters used ===
2:44:50.477549 INFO: rt_error       : 88.25744600408271
2:44:50.477606 INFO: mobility_error : 0.1
2:44:50.477727 INFO: num_candidates : 3
2:44:50.477771 INFO: ms1_error      : 3
2:44:50.477811 INFO: ms2_error      : 10.0
2:44:50.477854 INFO: fwhm_rt        : 3.0
2:44:50.477892 INFO: quant_window   : 3
2:44:50.477931 INFO: ==============================================
2:44:50.777360 INFO: performing precursor FDR with 40 features
2:44:50.777625 INFO: Decoy channel: -1
2:44:50.777656 INFO: competitive: True
2:44:50.795002 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:50.807790 INFO: Estimating optimal hyperparameters - samples: 14,215, batch_size: 128, learning_rate: 1.77e-04
2:44:50.808363 INFO: Using random state 678763 for train-test-split
2:44:54.174145 INFO: Test AUC: 0.755
2:44:54.174546 INFO: Train AUC: 0.761
2:44:54.174585 INFO: AUC difference: 0.68%
2:44:54.595568 INFO: Resetting torch num_threads to 100
2:44:54.604647 PROGRESS: === Extracted 17769 precursors and 106839 fragments ===
2:44:54.606018 INFO: === FDR correction performed with classifier version 6 ===
2:44:54.608475 PROGRESS: ============================= Precursor FDR =============================
2:44:54.608700 PROGRESS: Total precursors accumulated: 2,793
2:44:54.608768 PROGRESS: Target precursors: 2,766 (99.03%)
2:44:54.608828 PROGRESS: Decoy precursors: 27 (0.97%)
2:44:54.608881 PROGRESS: 
2:44:54.608932 PROGRESS: Precursor Summary:
2:44:54.611713 PROGRESS: Channel   0:	 0.050 FDR: 2,766; 0.010 FDR: 2,766; 0.001 FDR: 2,469
2:44:54.611917 PROGRESS: 
2:44:54.611981 PROGRESS: Protein Summary:
2:44:54.615719 PROGRESS: Channel   0:	 0.050 FDR: 2,173; 0.010 FDR: 2,173; 0.001 FDR: 1,955
2:44:54.616237 PROGRESS: =========================================================================
2:44:54.617444 INFO: Target number of precursors reached.
2:44:54.653711 INFO: fragments_df: keeping 5000 of 106839 [sum(precursor_idx_mask)=58376 sum(mass_error_mask)=106839 stop_rank=5000
2:44:54.688488 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:44:55.419435 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:44:56.540132 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:44:56.541355 INFO: Using score_cutoff 9.719306230545044 (fac=0.99, q=1)
2:44:56.541965 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:44:56.542057 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:44:56.542148 INFO: Updating optimization_manager: score_cutoff        : 9.57621713962555 -> 9.719306230545044
2:44:56.542220 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:44:56.549384 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:44:56.561583 INFO: === checking if optimization conditions were reached ===
2:44:56.562175 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:44:56.568599 INFO: Updating optimization_manager: rt_error            : 88.25744600408271 -> 66.60228853717499
2:44:56.569203 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 66.6023.
2:44:56.569313 INFO: ==============================================
2:44:56.569408 INFO: Starting optimization step 5.
2:44:56.569494 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:44:56.569637 INFO: Using rust extraction backend
2:44:56.569738 PROGRESS: Extracting batch of 5940 precursors
2:44:56.608238 INFO: === Search parameters used ===
2:44:56.609144 INFO: rt_error       : 66.60228853717499
2:44:56.609208 INFO: mobility_error : 0.1
2:44:56.609256 INFO: num_candidates : 3
2:44:56.609300 INFO: ms1_error      : 3
2:44:56.609344 INFO: ms2_error      : 10.0
2:44:56.609384 INFO: fwhm_rt        : 3.0
2:44:56.609424 INFO: quant_window   : 3
2:44:56.609463 INFO: ==============================================
2:44:56.904088 INFO: performing precursor FDR with 40 features
2:44:56.904450 INFO: Decoy channel: -1
2:44:56.904476 INFO: competitive: True
2:44:56.921321 INFO: Setting torch num_threads to 2 for FDR classification task
2:44:56.935326 INFO: Estimating optimal hyperparameters - samples: 14,148, batch_size: 128, learning_rate: 1.77e-04
2:44:56.935839 INFO: Using random state 678763 for train-test-split
2:44:59.189302 INFO: Test AUC: 0.745
2:44:59.189604 INFO: Train AUC: 0.751
2:44:59.189634 INFO: AUC difference: 0.69%
2:44:59.716102 INFO: Resetting torch num_threads to 100
2:44:59.726604 PROGRESS: === Extracted 17685 precursors and 103200 fragments ===
2:44:59.728278 INFO: === FDR correction performed with classifier version 6 ===
2:44:59.730980 PROGRESS: ============================= Precursor FDR =============================
2:44:59.731157 PROGRESS: Total precursors accumulated: 2,777
2:44:59.731227 PROGRESS: Target precursors: 2,750 (99.03%)
2:44:59.731287 PROGRESS: Decoy precursors: 27 (0.97%)
2:44:59.731341 PROGRESS: 
2:44:59.731396 PROGRESS: Precursor Summary:
2:44:59.736384 PROGRESS: Channel   0:	 0.050 FDR: 2,750; 0.010 FDR: 2,750; 0.001 FDR: 2,383
2:44:59.737076 PROGRESS: 
2:44:59.737154 PROGRESS: Protein Summary:
2:44:59.743763 PROGRESS: Channel   0:	 0.050 FDR: 2,161; 0.010 FDR: 2,161; 0.001 FDR: 1,888
2:44:59.744552 PROGRESS: =========================================================================
2:44:59.746441 INFO: Target number of precursors reached.
2:44:59.797212 INFO: fragments_df: keeping 5000 of 103200 [sum(precursor_idx_mask)=56666 sum(mass_error_mask)=103200 stop_rank=5000
2:44:59.838430 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:45:00.479833 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:45:01.367747 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:45:01.368650 INFO: Using score_cutoff 9.576120714855193 (fac=0.99, q=1)
2:45:01.369136 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:45:01.369223 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:45:01.369280 INFO: Updating optimization_manager: score_cutoff        : 9.719306230545044 -> 9.576120714855193
2:45:01.369341 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:45:01.374436 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:45:01.384134 INFO: === checking if optimization conditions were reached ===
2:45:01.384580 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:45:01.388888 INFO: Updating optimization_manager: rt_error            : 66.60228853717499 -> 54.23705248652804
2:45:01.389156 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 54.2371.
2:45:01.389232 INFO: ==============================================
2:45:01.389310 INFO: Starting optimization step 6.
2:45:01.389378 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:45:01.389455 INFO: Using rust extraction backend
2:45:01.389555 PROGRESS: Extracting batch of 5940 precursors
2:45:01.406361 INFO: === Search parameters used ===
2:45:01.406901 INFO: rt_error       : 54.23705248652804
2:45:01.406961 INFO: mobility_error : 0.1
2:45:01.407011 INFO: num_candidates : 3
2:45:01.407058 INFO: ms1_error      : 3
2:45:01.407103 INFO: ms2_error      : 10.0
2:45:01.407180 INFO: fwhm_rt        : 3.0
2:45:01.407222 INFO: quant_window   : 3
2:45:01.407263 INFO: ==============================================
2:45:01.646868 INFO: performing precursor FDR with 40 features
2:45:01.647165 INFO: Decoy channel: -1
2:45:01.647200 INFO: competitive: True
2:45:01.664912 INFO: Setting torch num_threads to 2 for FDR classification task
2:45:01.679465 INFO: Estimating optimal hyperparameters - samples: 13,621, batch_size: 128, learning_rate: 1.77e-04
2:45:01.679944 INFO: Using random state 678763 for train-test-split
2:45:04.036421 INFO: Test AUC: 0.748
2:45:04.036817 INFO: Train AUC: 0.744
2:45:04.036867 INFO: AUC difference: 0.59%
2:45:04.465431 INFO: Resetting torch num_threads to 100
2:45:04.471068 PROGRESS: === Extracted 17027 precursors and 97285 fragments ===
2:45:04.472311 INFO: === FDR correction performed with classifier version 6 ===
2:45:04.473852 PROGRESS: ============================= Precursor FDR =============================
2:45:04.473992 PROGRESS: Total precursors accumulated: 2,716
2:45:04.474061 PROGRESS: Target precursors: 2,690 (99.04%)
2:45:04.474116 PROGRESS: Decoy precursors: 26 (0.96%)
2:45:04.474166 PROGRESS: 
2:45:04.474216 PROGRESS: Precursor Summary:
2:45:04.476650 PROGRESS: Channel   0:	 0.050 FDR: 2,690; 0.010 FDR: 2,690; 0.001 FDR: 2,390
2:45:04.476810 PROGRESS: 
2:45:04.476865 PROGRESS: Protein Summary:
2:45:04.480008 PROGRESS: Channel   0:	 0.050 FDR: 2,121; 0.010 FDR: 2,121; 0.001 FDR: 1,892
2:45:04.480313 PROGRESS: =========================================================================
2:45:04.481374 INFO: Target number of precursors reached.
2:45:04.512658 INFO: fragments_df: keeping 5000 of 97285 [sum(precursor_idx_mask)=52416 sum(mass_error_mask)=97285 stop_rank=5000
2:45:04.538211 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:45:05.148119 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:45:06.125347 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:45:06.127021 INFO: Using score_cutoff 9.804541988754274 (fac=0.99, q=1)
2:45:06.127923 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:45:06.128055 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:45:06.128121 INFO: Updating optimization_manager: score_cutoff        : 9.576120714855193 -> 9.804541988754274
2:45:06.128226 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:45:06.136479 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:45:06.150882 INFO: === checking if optimization conditions were reached ===
2:45:06.152150 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
2:45:06.160366 INFO: Updating optimization_manager: rt_error            : 54.23705248652804 -> 36.30060683556108
2:45:06.161599 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 36.3006.
2:45:06.161698 INFO: ==============================================
2:45:06.161783 INFO: Starting optimization step 7.
2:45:06.161857 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:45:06.162019 INFO: Using rust extraction backend
2:45:06.162105 PROGRESS: Extracting batch of 5940 precursors
2:45:06.194433 INFO: === Search parameters used ===
2:45:06.195849 INFO: rt_error       : 36.30060683556108
2:45:06.195932 INFO: mobility_error : 0.1
2:45:06.195984 INFO: num_candidates : 3
2:45:06.196027 INFO: ms1_error      : 3
2:45:06.196071 INFO: ms2_error      : 10.0
2:45:06.196115 INFO: fwhm_rt        : 3.0
2:45:06.196159 INFO: quant_window   : 3
2:45:06.196200 INFO: ==============================================
2:45:06.538313 INFO: performing precursor FDR with 40 features
2:45:06.538703 INFO: Decoy channel: -1
2:45:06.538731 INFO: competitive: True
2:45:06.552153 INFO: Setting torch num_threads to 2 for FDR classification task
2:45:06.563122 INFO: Estimating optimal hyperparameters - samples: 12,952, batch_size: 128, learning_rate: 1.77e-04
2:45:06.563521 INFO: Using random state 678763 for train-test-split
2:45:08.538740 INFO: Test AUC: 0.761
2:45:08.539137 INFO: Train AUC: 0.763
2:45:08.539173 INFO: AUC difference: 0.26%
2:45:08.967021 INFO: Resetting torch num_threads to 100
2:45:08.974943 PROGRESS: === Extracted 16190 precursors and 92315 fragments ===
2:45:08.976593 INFO: === FDR correction performed with classifier version 6 ===
2:45:08.981265 PROGRESS: ============================= Precursor FDR =============================
2:45:08.981852 PROGRESS: Total precursors accumulated: 2,766
2:45:08.981945 PROGRESS: Target precursors: 2,739 (99.02%)
2:45:08.982016 PROGRESS: Decoy precursors: 27 (0.98%)
2:45:08.982080 PROGRESS: 
2:45:08.982152 PROGRESS: Precursor Summary:
2:45:08.988861 PROGRESS: Channel   0:	 0.050 FDR: 2,739; 0.010 FDR: 2,739; 0.001 FDR: 2,330
2:45:08.989532 PROGRESS: 
2:45:08.989609 PROGRESS: Protein Summary:
2:45:08.996089 PROGRESS: Channel   0:	 0.050 FDR: 2,154; 0.010 FDR: 2,154; 0.001 FDR: 1,851
2:45:08.996746 PROGRESS: =========================================================================
2:45:08.998129 INFO: Target number of precursors reached.
2:45:09.041536 INFO: fragments_df: keeping 5000 of 92315 [sum(precursor_idx_mask)=50312 sum(mass_error_mask)=92315 stop_rank=5000
2:45:09.077116 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:45:09.756156 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:45:10.679745 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:45:10.680619 INFO: Using score_cutoff 9.532627648544311 (fac=0.99, q=1)
2:45:10.681075 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:45:10.681150 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:45:10.681204 INFO: Updating optimization_manager: score_cutoff        : 9.804541988754274 -> 9.532627648544311
2:45:10.681258 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:45:10.686026 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:45:10.695409 INFO: === checking if optimization conditions were reached ===
2:45:10.695988 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
2:45:10.700309 INFO: Updating optimization_manager: rt_error            : 36.30060683556108 -> 32.80961941351418
2:45:10.700547 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 32.8096.
2:45:10.700620 INFO: ==============================================
2:45:10.700729 INFO: Starting optimization step 8.
2:45:10.700795 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:45:10.700883 INFO: Using rust extraction backend
2:45:10.700947 PROGRESS: Extracting batch of 5940 precursors
2:45:10.716761 INFO: === Search parameters used ===
2:45:10.717372 INFO: rt_error       : 32.80961941351418
2:45:10.717425 INFO: mobility_error : 0.1
2:45:10.717476 INFO: num_candidates : 3
2:45:10.717518 INFO: ms1_error      : 3
2:45:10.717557 INFO: ms2_error      : 10.0
2:45:10.717596 INFO: fwhm_rt        : 3.0
2:45:10.717636 INFO: quant_window   : 3
2:45:10.717674 INFO: ==============================================
2:45:10.968858 INFO: performing precursor FDR with 40 features
2:45:10.969207 INFO: Decoy channel: -1
2:45:10.969242 INFO: competitive: True
2:45:10.988192 INFO: Setting torch num_threads to 2 for FDR classification task
2:45:11.000905 INFO: Estimating optimal hyperparameters - samples: 12,951, batch_size: 128, learning_rate: 1.77e-04
2:45:11.001390 INFO: Using random state 678763 for train-test-split
2:45:12.807160 INFO: Test AUC: 0.756
2:45:12.807406 INFO: Train AUC: 0.761
2:45:12.807443 INFO: AUC difference: 0.67%
2:45:13.141373 INFO: Resetting torch num_threads to 100
2:45:13.147570 PROGRESS: === Extracted 16189 precursors and 92284 fragments ===
2:45:13.148622 INFO: === FDR correction performed with classifier version 6 ===
2:45:13.150300 PROGRESS: ============================= Precursor FDR =============================
2:45:13.150446 PROGRESS: Total precursors accumulated: 2,799
2:45:13.150549 PROGRESS: Target precursors: 2,772 (99.04%)
2:45:13.150610 PROGRESS: Decoy precursors: 27 (0.96%)
2:45:13.150659 PROGRESS: 
2:45:13.150706 PROGRESS: Precursor Summary:
2:45:13.153000 PROGRESS: Channel   0:	 0.050 FDR: 2,772; 0.010 FDR: 2,772; 0.001 FDR: 2,322
2:45:13.153173 PROGRESS: 
2:45:13.153229 PROGRESS: Protein Summary:
2:45:13.156597 PROGRESS: Channel   0:	 0.050 FDR: 2,179; 0.010 FDR: 2,179; 0.001 FDR: 1,849
2:45:13.157051 PROGRESS: =========================================================================
2:45:13.157901 INFO: Target number of precursors reached.
2:45:13.184769 INFO: fragments_df: keeping 5000 of 92284 [sum(precursor_idx_mask)=50766 sum(mass_error_mask)=92284 stop_rank=5000
2:45:13.201613 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:45:13.833173 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:45:14.792956 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:45:14.794282 INFO: Using score_cutoff 9.243690092468261 (fac=0.99, q=1)
2:45:14.794903 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:45:14.794986 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:45:14.795047 INFO: Updating optimization_manager: score_cutoff        : 9.532627648544311 -> 9.243690092468261
2:45:14.795130 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:45:14.801500 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:45:14.813529 INFO: === checking if optimization conditions were reached ===
2:45:14.814239 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
2:45:14.820090 INFO: Updating optimization_manager: rt_error            : 32.80961941351418 -> 32.80460704798182
2:45:14.820668 PROGRESS: ❌ rt_error       : optimization incomplete after 9 search(es). Will search with parameter 32.8046.
2:45:14.820796 INFO: ==============================================
2:45:14.820904 INFO: Starting optimization step 9.
2:45:14.820978 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:45:14.821254 INFO: Using rust extraction backend
2:45:14.821342 PROGRESS: Extracting batch of 5940 precursors
2:45:14.849992 INFO: === Search parameters used ===
2:45:14.850809 INFO: rt_error       : 32.80460704798182
2:45:14.850865 INFO: mobility_error : 0.1
2:45:14.850914 INFO: num_candidates : 3
2:45:14.850957 INFO: ms1_error      : 3
2:45:14.850999 INFO: ms2_error      : 10.0
2:45:14.851045 INFO: fwhm_rt        : 3.0
2:45:14.851091 INFO: quant_window   : 3
2:45:14.851133 INFO: ==============================================
2:45:14.979222 INFO: performing precursor FDR with 40 features
2:45:14.979360 INFO: Decoy channel: -1
2:45:14.979384 INFO: competitive: True
2:45:14.984514 INFO: Setting torch num_threads to 2 for FDR classification task
2:45:14.988579 INFO: Estimating optimal hyperparameters - samples: 12,962, batch_size: 128, learning_rate: 1.77e-04
2:45:14.988726 INFO: Using random state 678763 for train-test-split
2:45:16.908247 INFO: Test AUC: 0.756
2:45:16.908711 INFO: Train AUC: 0.760
2:45:16.908769 INFO: AUC difference: 0.59%
2:45:17.460495 INFO: Resetting torch num_threads to 100
2:45:17.471050 PROGRESS: === Extracted 16203 precursors and 92369 fragments ===
2:45:17.472706 INFO: === FDR correction performed with classifier version 6 ===
2:45:17.476015 PROGRESS: ============================= Precursor FDR =============================
2:45:17.476434 PROGRESS: Total precursors accumulated: 2,781
2:45:17.476514 PROGRESS: Target precursors: 2,754 (99.03%)
2:45:17.476572 PROGRESS: Decoy precursors: 27 (0.97%)
2:45:17.476629 PROGRESS: 
2:45:17.476732 PROGRESS: Precursor Summary:
2:45:17.480614 PROGRESS: Channel   0:	 0.050 FDR: 2,754; 0.010 FDR: 2,754; 0.001 FDR: 2,495
2:45:17.480934 PROGRESS: 
2:45:17.480993 PROGRESS: Protein Summary:
2:45:17.484876 PROGRESS: Channel   0:	 0.050 FDR: 2,168; 0.010 FDR: 2,168; 0.001 FDR: 1,974
2:45:17.485461 PROGRESS: =========================================================================
2:45:17.487596 INFO: Target number of precursors reached.
2:45:17.520868 INFO: fragments_df: keeping 5000 of 92369 [sum(precursor_idx_mask)=50517 sum(mass_error_mask)=92369 stop_rank=5000
2:45:17.554595 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:45:18.139966 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:45:19.109688 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:45:19.110815 INFO: Using score_cutoff 9.351643452930452 (fac=0.99, q=1)
2:45:19.111860 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:45:19.112108 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:45:19.112206 INFO: Updating optimization_manager: score_cutoff        : 9.243690092468261 -> 9.351643452930452
2:45:19.112278 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:45:19.118418 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:45:19.130097 INFO: === checking if optimization conditions were reached ===
2:45:19.130679 PROGRESS: === Optimization of rt_error has been performed 10 time(s); minimum number is 5 ===
2:45:19.132360 INFO: Updating optimization_manager: rt_error            : 32.80460704798182 -> 249.8329475003518
2:45:19.132627 INFO: Updating optimization_manager: classifier_version  : 6 -> 8
2:45:19.132727 INFO: Updating optimization_manager: score_cutoff        : 9.351643452930452 -> 9.860638602447509
2:45:19.132813 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:45:19.132898 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:45:19.132999 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 249.8329 found after 10 searches.
2:45:19.133073 INFO: ==============================================
2:45:19.133149 PROGRESS: Optimization finished for rt_error.
2:45:19.154235 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:45:19.160489 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:45:19.171380 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:45:19.171958 PROGRESS: ==============================================
2:45:19.172055 PROGRESS: ms2_error      : 10.0000
2:45:19.172113 PROGRESS: rt_error       : 249.8329
2:45:19.172162 PROGRESS: ==============================================
2:45:19.174190 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:45:19.335033 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:45:19.806867 INFO: Using rust extraction backend
2:45:19.807360 PROGRESS: Extracting batch of 259156 precursors
2:45:20.737385 INFO: === Search parameters used ===
2:45:20.738842 INFO: rt_error       : 249.8329475003518
2:45:20.739028 INFO: mobility_error : 0.1
2:45:20.739091 INFO: num_candidates : 3
2:45:20.739140 INFO: ms1_error      : 3
2:45:20.739184 INFO: ms2_error      : 10.0
2:45:20.739226 INFO: fwhm_rt        : 3.0
2:45:20.739268 INFO: quant_window   : 3
2:45:20.739326 INFO: ==============================================
2:45:21.457911 INFO: Removed 108866 precursors with score below cutoff 9.860638602447509
2:45:22.277395 INFO: performing precursor FDR with 40 features
2:45:22.277665 INFO: Decoy channel: -1
2:45:22.277693 INFO: competitive: True
2:45:22.390735 INFO: Setting torch num_threads to 2 for FDR classification task
2:45:22.471609 WARNING: FDR calculation for 356472 target and 312127 decoy PSMs
2:45:22.471865 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:45:22.950433 INFO: Estimating optimal hyperparameters - samples: 534,879, batch_size: 2,190, learning_rate: 7.31e-04
2:45:22.952375 INFO: Using random state 624679 for train-test-split
2:45:34.230503 INFO: Test AUC: 0.785
2:45:34.231196 INFO: Train AUC: 0.787
2:45:34.231280 INFO: AUC difference: 0.34%
2:45:35.096547 INFO: Resetting torch num_threads to 100
2:45:36.430325 PROGRESS: ============================= Precursor FDR =============================
2:45:36.431177 PROGRESS: Total precursors accumulated: 121,837
2:45:36.431388 PROGRESS: Target precursors: 120,631 (99.01%)
2:45:36.431516 PROGRESS: Decoy precursors: 1,206 (0.99%)
2:45:36.431592 PROGRESS: 
2:45:36.431644 PROGRESS: Precursor Summary:
2:45:36.580968 PROGRESS: Channel   0:	 0.050 FDR: 120,631; 0.010 FDR: 120,631; 0.001 FDR: 107,143
2:45:36.581836 PROGRESS: 
2:45:36.581900 PROGRESS: Protein Summary:
2:45:36.874182 PROGRESS: Channel   0:	 0.050 FDR: 10,137; 0.010 FDR: 10,137; 0.001 FDR: 9,957
2:45:36.875020 PROGRESS: =========================================================================
2:45:36.889310 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/psm.parquet
2:45:37.351712 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/frag.parquet
2:45:37.960788 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:45:38.878942 PROGRESS: Loading raw file 4/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP1 
2:45:38.879348 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:45:38.879621 INFO: Initializing TimingManager
2:45:38.881900 INFO: Initializing RawFileManager
2:46:06.327083 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:46:06.335804 INFO: Determining DIA cycle
2:46:06.353556 INFO: Found cycle with start 0.00 min and length 300.
2:46:06.628655 INFO: RT (min)            : 0.0 - 26.9
2:46:06.628794 INFO: RT duration (sec)   : 1611.2
2:46:06.628838 INFO: RT duration (min)   : 26.9
2:46:06.628872 INFO: Cycle len (scans)   : 300
2:46:06.628900 INFO: Cycle len (sec)     : 1.65
2:46:06.628927 INFO: Number of cycles    : 977
2:46:06.628956 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:46:06.629010 INFO: Creating DIA data object took: 27.746795415878296
2:46:08.232738 INFO: Creating DIA data NG object took: 1.6035161018371582
2:46:08.296754 INFO: Initializing CalibrationManager
2:46:08.297155 INFO: Setting up calibration estimators ..
2:46:08.297221 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:46:08.297322 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2:46:08.297406 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:46:08.297466 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:46:08.297527 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2:46:08.297585 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:46:08.297637 INFO: Done setting up calibration estimators.
2:46:08.297899 INFO: Initializing OptimizationManager
2:46:08.298060 INFO: initial parameter: ms1_error = 3
2:46:08.298115 INFO: initial parameter: ms2_error = 10
2:46:08.298173 INFO: initial parameter: rt_error = 805.5982666015625
2:46:08.298219 INFO: initial parameter: mobility_error = 0.1
2:46:08.298261 INFO: initial parameter: num_candidates = 1
2:46:08.298302 INFO: initial parameter: fwhm_rt = 5
2:46:08.298343 INFO: initial parameter: fwhm_mobility = 0.01
2:46:08.298383 INFO: initial parameter: score_cutoff = 0
2:46:08.298424 INFO: initial parameter: classifier_version = -1
2:46:08.298498 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:46:08.298831 INFO: FDRManager: loading saved state not requested, will be initialized.
2:46:08.298866 INFO: Initializing FDRManager
2:46:08.298900 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:46:08.350283 PROGRESS: Initializing spectral library: 131,021 target precursors potentially observable (0 removed)
2:46:08.379514 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
2:46:08.380088 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 805.5982666015625
2:46:08.380195 PROGRESS: Starting initial search for precursors.
2:46:08.380285 INFO: Starting optimization step 0.
2:46:08.380349 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:46:08.380412 INFO: Using rust extraction backend
2:46:08.380515 PROGRESS: Extracting batch of 1982 precursors
2:46:08.385994 INFO: === Search parameters used ===
2:46:08.386325 INFO: rt_error       : 805.5982666015625
2:46:08.386379 INFO: mobility_error : 0.1
2:46:08.386423 INFO: num_candidates : 1
2:46:08.386464 INFO: ms1_error      : 3
2:46:08.386504 INFO: ms2_error      : 10
2:46:08.386544 INFO: fwhm_rt        : 5
2:46:08.386584 INFO: quant_window   : 3
2:46:08.386622 INFO: ==============================================
2:46:08.426245 INFO: performing precursor FDR with 40 features
2:46:08.426354 INFO: Decoy channel: -1
2:46:08.426377 INFO: competitive: True
2:46:08.427780 INFO: Setting torch num_threads to 2 for FDR classification task
2:46:08.429761 INFO: Estimating optimal hyperparameters - samples: 1,585, batch_size: 128, learning_rate: 1.77e-04
2:46:08.430682 INFO: Using random state 883017 for train-test-split
2:46:08.587068 INFO: Test AUC: 0.871
2:46:08.587242 INFO: Train AUC: 0.888
2:46:08.587271 INFO: AUC difference: 1.93%
2:46:08.864420 INFO: Resetting torch num_threads to 100
2:46:08.866691 PROGRESS: === Extracted 1982 precursors and 15480 fragments ===
2:46:08.867264 INFO: === FDR correction performed with classifier version -1 ===
2:46:08.868166 PROGRESS: ============================= Precursor FDR =============================
2:46:08.868316 PROGRESS: Total precursors accumulated: 546
2:46:08.868382 PROGRESS: Target precursors: 541 (99.08%)
2:46:08.868434 PROGRESS: Decoy precursors: 5 (0.92%)
2:46:08.868477 PROGRESS: 
2:46:08.868520 PROGRESS: Precursor Summary:
2:46:08.870011 PROGRESS: Channel   0:	 0.050 FDR:   541; 0.010 FDR:   541; 0.001 FDR:   234
2:46:08.870128 PROGRESS: 
2:46:08.870183 PROGRESS: Protein Summary:
2:46:08.871865 PROGRESS: Channel   0:	 0.050 FDR:   505; 0.010 FDR:   505; 0.001 FDR:   221
2:46:08.871990 PROGRESS: =========================================================================
2:46:08.872295 INFO: Target number of precursors not reached yet.
2:46:08.881886 INFO: Starting optimization step 1.
2:46:08.882019 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:46:08.882095 INFO: Using rust extraction backend
2:46:08.882155 PROGRESS: Extracting batch of 3958 precursors
2:46:08.890536 INFO: === Search parameters used ===
2:46:08.890676 INFO: rt_error       : 805.5982666015625
2:46:08.890729 INFO: mobility_error : 0.1
2:46:08.890773 INFO: num_candidates : 1
2:46:08.890815 INFO: ms1_error      : 3
2:46:08.890854 INFO: ms2_error      : 10
2:46:08.890892 INFO: fwhm_rt        : 5
2:46:08.890930 INFO: quant_window   : 3
2:46:08.890968 INFO: ==============================================
2:46:08.946794 INFO: performing precursor FDR with 40 features
2:46:08.946914 INFO: Decoy channel: -1
2:46:08.946938 INFO: competitive: True
2:46:08.951224 INFO: Setting torch num_threads to 2 for FDR classification task
2:46:08.953733 INFO: Estimating optimal hyperparameters - samples: 4,751, batch_size: 128, learning_rate: 1.77e-04
2:46:08.953821 INFO: Using random state 385475 for train-test-split
2:46:09.422117 INFO: Test AUC: 0.914
2:46:09.422228 INFO: Train AUC: 0.916
2:46:09.422255 INFO: AUC difference: 0.23%
2:46:09.663835 INFO: Resetting torch num_threads to 100
2:46:09.667080 PROGRESS: === Extracted 5939 precursors and 46246 fragments ===
2:46:09.667516 INFO: === FDR correction performed with classifier version -1 ===
2:46:09.668190 PROGRESS: ============================= Precursor FDR =============================
2:46:09.668283 PROGRESS: Total precursors accumulated: 1,940
2:46:09.668354 PROGRESS: Target precursors: 1,921 (99.02%)
2:46:09.668404 PROGRESS: Decoy precursors: 19 (0.98%)
2:46:09.668447 PROGRESS: 
2:46:09.668489 PROGRESS: Precursor Summary:
2:46:09.669943 PROGRESS: Channel   0:	 0.050 FDR: 1,921; 0.010 FDR: 1,921; 0.001 FDR: 1,209
2:46:09.670029 PROGRESS: 
2:46:09.670082 PROGRESS: Protein Summary:
2:46:09.672011 PROGRESS: Channel   0:	 0.050 FDR: 1,548; 0.010 FDR: 1,548; 0.001 FDR: 1,016
2:46:09.672113 PROGRESS: =========================================================================
2:46:09.672401 INFO: Target number of precursors reached.
2:46:09.682672 INFO: fragments_df: keeping 5000 of 46246 [sum(precursor_idx_mask)=19690 sum(mass_error_mask)=46246 stop_rank=5000
2:46:09.694260 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:46:10.009584 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:46:10.847882 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:46:10.848635 INFO: Using score_cutoff 11.552420516967773 (fac=0.99, q=1)
2:46:10.849330 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:46:10.849501 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:46:10.849589 INFO: Updating optimization_manager: score_cutoff        : 0 -> 11.552420516967773
2:46:10.849684 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:10.854642 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:10.864977 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:46:10.865236 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:46:10.865381 INFO: Starting optimization step 2.
2:46:10.865497 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:46:10.865598 INFO: Using rust extraction backend
2:46:10.865685 PROGRESS: Extracting batch of 5940 precursors
2:46:10.882123 INFO: === Search parameters used ===
2:46:10.882434 INFO: rt_error       : 805.5982666015625
2:46:10.882493 INFO: mobility_error : 0.1
2:46:10.882540 INFO: num_candidates : 3
2:46:10.882588 INFO: ms1_error      : 3
2:46:10.882633 INFO: ms2_error      : 10
2:46:10.882676 INFO: fwhm_rt        : 3.0
2:46:10.882718 INFO: quant_window   : 3
2:46:10.882760 INFO: ==============================================
2:46:11.128978 INFO: performing precursor FDR with 40 features
2:46:11.129164 INFO: Decoy channel: -1
2:46:11.129197 INFO: competitive: True
2:46:11.136493 INFO: Setting torch num_threads to 2 for FDR classification task
2:46:11.143490 INFO: Estimating optimal hyperparameters - samples: 14,248, batch_size: 128, learning_rate: 1.77e-04
2:46:11.143722 INFO: Using random state 421452 for train-test-split
2:46:12.805203 INFO: Test AUC: 0.734
2:46:12.805326 INFO: Train AUC: 0.735
2:46:12.805356 INFO: AUC difference: 0.10%
2:46:13.079171 INFO: Resetting torch num_threads to 100
2:46:13.081878 PROGRESS: === Extracted 17811 precursors and 120235 fragments ===
2:46:13.082367 INFO: === FDR correction performed with classifier version 1 ===
2:46:13.083084 PROGRESS: ============================= Precursor FDR =============================
2:46:13.083169 PROGRESS: Total precursors accumulated: 2,297
2:46:13.083230 PROGRESS: Target precursors: 2,275 (99.04%)
2:46:13.083279 PROGRESS: Decoy precursors: 22 (0.96%)
2:46:13.083324 PROGRESS: 
2:46:13.083369 PROGRESS: Precursor Summary:
2:46:13.084927 PROGRESS: Channel   0:	 0.050 FDR: 2,275; 0.010 FDR: 2,275; 0.001 FDR: 1,401
2:46:13.085029 PROGRESS: 
2:46:13.085092 PROGRESS: Protein Summary:
2:46:13.087192 PROGRESS: Channel   0:	 0.050 FDR: 1,812; 0.010 FDR: 1,812; 0.001 FDR: 1,172
2:46:13.087286 PROGRESS: =========================================================================
2:46:13.087903 INFO: Target number of precursors reached.
2:46:13.114678 INFO: fragments_df: keeping 5000 of 120235 [sum(precursor_idx_mask)=52952 sum(mass_error_mask)=120235 stop_rank=5000
2:46:13.127813 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:46:13.637418 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:46:14.404371 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:46:14.405082 INFO: Using score_cutoff 11.324336215209962 (fac=0.99, q=1)
2:46:14.405475 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:46:14.405548 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:46:14.405600 INFO: Updating optimization_manager: score_cutoff        : 11.552420516967773 -> 11.324336215209962
2:46:14.405654 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:14.410112 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:14.417990 INFO: === checking if optimization conditions were reached ===
2:46:14.419668 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
2:46:14.419769 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:46:14.419844 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:46:14.419909 INFO: ==============================================
2:46:14.419981 INFO: Starting optimization step 3.
2:46:14.420046 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:46:14.420106 INFO: Using rust extraction backend
2:46:14.420161 PROGRESS: Extracting batch of 5940 precursors
2:46:14.431975 INFO: === Search parameters used ===
2:46:14.432094 INFO: rt_error       : 805.5982666015625
2:46:14.432144 INFO: mobility_error : 0.1
2:46:14.432189 INFO: num_candidates : 3
2:46:14.432229 INFO: ms1_error      : 3
2:46:14.432270 INFO: ms2_error      : 10.0
2:46:14.432317 INFO: fwhm_rt        : 3.0
2:46:14.432357 INFO: quant_window   : 3
2:46:14.432395 INFO: ==============================================
2:46:14.580270 INFO: performing precursor FDR with 40 features
2:46:14.580408 INFO: Decoy channel: -1
2:46:14.580432 INFO: competitive: True
2:46:14.585870 INFO: Setting torch num_threads to 2 for FDR classification task
2:46:14.590719 INFO: Estimating optimal hyperparameters - samples: 14,249, batch_size: 128, learning_rate: 1.77e-04
2:46:14.590904 INFO: Using random state 380933 for train-test-split
2:46:16.149672 INFO: Test AUC: 0.739
2:46:16.150010 INFO: Train AUC: 0.751
2:46:16.150041 INFO: AUC difference: 1.59%
2:46:16.472316 INFO: Resetting torch num_threads to 100
2:46:16.477129 PROGRESS: === Extracted 17812 precursors and 120283 fragments ===
2:46:16.478012 INFO: === FDR correction performed with classifier version 2 ===
2:46:16.479070 PROGRESS: ============================= Precursor FDR =============================
2:46:16.479176 PROGRESS: Total precursors accumulated: 2,379
2:46:16.479240 PROGRESS: Target precursors: 2,356 (99.03%)
2:46:16.479294 PROGRESS: Decoy precursors: 23 (0.97%)
2:46:16.479357 PROGRESS: 
2:46:16.479409 PROGRESS: Precursor Summary:
2:46:16.481235 PROGRESS: Channel   0:	 0.050 FDR: 2,356; 0.010 FDR: 2,356; 0.001 FDR: 1,499
2:46:16.481426 PROGRESS: 
2:46:16.481484 PROGRESS: Protein Summary:
2:46:16.483938 PROGRESS: Channel   0:	 0.050 FDR: 1,873; 0.010 FDR: 1,873; 0.001 FDR: 1,256
2:46:16.484054 PROGRESS: =========================================================================
2:46:16.485151 INFO: Target number of precursors reached.
2:46:16.517223 INFO: fragments_df: keeping 5000 of 120283 [sum(precursor_idx_mask)=54540 sum(mass_error_mask)=120283 stop_rank=5000
2:46:16.540379 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:46:17.031107 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:46:17.892248 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:46:17.892864 INFO: Using score_cutoff 11.288792947769165 (fac=0.99, q=1)
2:46:17.893219 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:46:17.893298 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:46:17.893353 INFO: Updating optimization_manager: score_cutoff        : 11.324336215209962 -> 11.288792947769165
2:46:17.893410 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:17.897854 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:17.906751 INFO: === checking if optimization conditions were reached ===
2:46:17.909207 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:46:17.909424 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:46:17.909491 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:46:17.909564 INFO: ==============================================
2:46:17.909636 INFO: Starting optimization step 4.
2:46:17.909698 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:46:17.909765 INFO: Using rust extraction backend
2:46:17.909829 PROGRESS: Extracting batch of 5940 precursors
2:46:17.924189 INFO: === Search parameters used ===
2:46:17.924618 INFO: rt_error       : 805.5982666015625
2:46:17.924670 INFO: mobility_error : 0.1
2:46:17.924715 INFO: num_candidates : 3
2:46:17.924756 INFO: ms1_error      : 3
2:46:17.924796 INFO: ms2_error      : 10.0
2:46:17.924837 INFO: fwhm_rt        : 3.0
2:46:17.924875 INFO: quant_window   : 3
2:46:17.924914 INFO: ==============================================
2:46:18.085943 INFO: performing precursor FDR with 40 features
2:46:18.086091 INFO: Decoy channel: -1
2:46:18.086116 INFO: competitive: True
2:46:18.092618 INFO: Setting torch num_threads to 2 for FDR classification task
2:46:18.097427 INFO: Estimating optimal hyperparameters - samples: 14,249, batch_size: 128, learning_rate: 1.77e-04
2:46:18.097603 INFO: Using random state 521471 for train-test-split
2:46:20.222399 INFO: Test AUC: 0.734
2:46:20.222768 INFO: Train AUC: 0.766
2:46:20.222809 INFO: AUC difference: 4.23%
2:46:20.739032 INFO: Resetting torch num_threads to 100
2:46:20.746392 PROGRESS: === Extracted 17812 precursors and 120262 fragments ===
2:46:20.748177 INFO: === FDR correction performed with classifier version 3 ===
2:46:20.750283 PROGRESS: ============================= Precursor FDR =============================
2:46:20.750537 PROGRESS: Total precursors accumulated: 2,448
2:46:20.750617 PROGRESS: Target precursors: 2,424 (99.02%)
2:46:20.750672 PROGRESS: Decoy precursors: 24 (0.98%)
2:46:20.750722 PROGRESS: 
2:46:20.750823 PROGRESS: Precursor Summary:
2:46:20.755559 PROGRESS: Channel   0:	 0.050 FDR: 2,424; 0.010 FDR: 2,424; 0.001 FDR: 1,613
2:46:20.756214 PROGRESS: 
2:46:20.756304 PROGRESS: Protein Summary:
2:46:20.759668 PROGRESS: Channel   0:	 0.050 FDR: 1,922; 0.010 FDR: 1,922; 0.001 FDR: 1,330
2:46:20.760297 PROGRESS: =========================================================================
2:46:20.762325 INFO: Target number of precursors reached.
2:46:20.802068 INFO: fragments_df: keeping 5000 of 120262 [sum(precursor_idx_mask)=55688 sum(mass_error_mask)=120262 stop_rank=5000
2:46:20.844039 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:46:21.472004 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:46:22.278062 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:46:22.278876 INFO: Using score_cutoff 10.62260730457306 (fac=0.99, q=1)
2:46:22.279333 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:46:22.279424 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:46:22.279483 INFO: Updating optimization_manager: score_cutoff        : 11.288792947769165 -> 10.62260730457306
2:46:22.279539 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:22.284325 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:22.293487 INFO: === checking if optimization conditions were reached ===
2:46:22.296320 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:46:22.296548 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:46:22.296659 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:46:22.296725 INFO: ==============================================
2:46:22.296797 INFO: Starting optimization step 5.
2:46:22.296873 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:46:22.296947 INFO: Using rust extraction backend
2:46:22.297018 PROGRESS: Extracting batch of 5940 precursors
2:46:22.313020 INFO: === Search parameters used ===
2:46:22.313650 INFO: rt_error       : 805.5982666015625
2:46:22.313705 INFO: mobility_error : 0.1
2:46:22.313750 INFO: num_candidates : 3
2:46:22.313792 INFO: ms1_error      : 3
2:46:22.313832 INFO: ms2_error      : 10.0
2:46:22.313872 INFO: fwhm_rt        : 3.0
2:46:22.313912 INFO: quant_window   : 3
2:46:22.313950 INFO: ==============================================
2:46:22.542969 INFO: performing precursor FDR with 40 features
2:46:22.543191 INFO: Decoy channel: -1
2:46:22.543218 INFO: competitive: True
2:46:22.553053 INFO: Setting torch num_threads to 2 for FDR classification task
2:46:22.561033 INFO: Estimating optimal hyperparameters - samples: 14,249, batch_size: 128, learning_rate: 1.77e-04
2:46:22.561302 INFO: Using random state 479824 for train-test-split
2:46:24.395306 INFO: Test AUC: 0.757
2:46:24.395496 INFO: Train AUC: 0.773
2:46:24.395524 INFO: AUC difference: 2.08%
2:46:24.687572 INFO: Resetting torch num_threads to 100
2:46:24.694287 PROGRESS: === Extracted 17812 precursors and 120251 fragments ===
2:46:24.695512 INFO: === FDR correction performed with classifier version 4 ===
2:46:24.697890 PROGRESS: ============================= Precursor FDR =============================
2:46:24.698240 PROGRESS: Total precursors accumulated: 2,493
2:46:24.698345 PROGRESS: Target precursors: 2,469 (99.04%)
2:46:24.698406 PROGRESS: Decoy precursors: 24 (0.96%)
2:46:24.698502 PROGRESS: 
2:46:24.698553 PROGRESS: Precursor Summary:
2:46:24.702248 PROGRESS: Channel   0:	 0.050 FDR: 2,469; 0.010 FDR: 2,469; 0.001 FDR: 1,642
2:46:24.702826 PROGRESS: 
2:46:24.702887 PROGRESS: Protein Summary:
2:46:24.705880 PROGRESS: Channel   0:	 0.050 FDR: 1,951; 0.010 FDR: 1,951; 0.001 FDR: 1,347
2:46:24.706370 PROGRESS: =========================================================================
2:46:24.707591 INFO: Target number of precursors reached.
2:46:24.738845 INFO: fragments_df: keeping 5000 of 120251 [sum(precursor_idx_mask)=56526 sum(mass_error_mask)=120251 stop_rank=5000
2:46:24.760571 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:46:25.322640 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:46:26.343500 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:46:26.345072 INFO: Using score_cutoff 10.589136211395264 (fac=0.99, q=1)
2:46:26.345718 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:46:26.345809 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:46:26.345865 INFO: Updating optimization_manager: score_cutoff        : 10.62260730457306 -> 10.589136211395264
2:46:26.345925 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:26.354209 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:26.366606 INFO: === checking if optimization conditions were reached ===
2:46:26.372237 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:46:26.372756 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:46:26.372851 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:46:26.372926 INFO: ==============================================
2:46:26.373013 INFO: Starting optimization step 6.
2:46:26.373089 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:46:26.373189 INFO: Using rust extraction backend
2:46:26.373250 PROGRESS: Extracting batch of 5940 precursors
2:46:26.412827 INFO: === Search parameters used ===
2:46:26.414129 INFO: rt_error       : 805.5982666015625
2:46:26.414215 INFO: mobility_error : 0.1
2:46:26.414299 INFO: num_candidates : 3
2:46:26.414358 INFO: ms1_error      : 3
2:46:26.414409 INFO: ms2_error      : 10.0
2:46:26.414458 INFO: fwhm_rt        : 3.0
2:46:26.414505 INFO: quant_window   : 3
2:46:26.414558 INFO: ==============================================
2:46:26.829966 INFO: performing precursor FDR with 40 features
2:46:26.830312 INFO: Decoy channel: -1
2:46:26.830340 INFO: competitive: True
2:46:26.851119 INFO: Setting torch num_threads to 2 for FDR classification task
2:46:26.863930 INFO: Estimating optimal hyperparameters - samples: 14,250, batch_size: 128, learning_rate: 1.77e-04
2:46:26.864465 INFO: Using random state 148061 for train-test-split
2:46:29.069747 INFO: Test AUC: 0.765
2:46:29.070034 INFO: Train AUC: 0.780
2:46:29.070066 INFO: AUC difference: 1.91%
2:46:29.537132 INFO: Resetting torch num_threads to 100
2:46:29.545758 PROGRESS: === Extracted 17813 precursors and 120276 fragments ===
2:46:29.547271 INFO: === FDR correction performed with classifier version 5 ===
2:46:29.550750 PROGRESS: ============================= Precursor FDR =============================
2:46:29.551209 PROGRESS: Total precursors accumulated: 2,533
2:46:29.551328 PROGRESS: Target precursors: 2,508 (99.01%)
2:46:29.551447 PROGRESS: Decoy precursors: 25 (0.99%)
2:46:29.551504 PROGRESS: 
2:46:29.551549 PROGRESS: Precursor Summary:
2:46:29.556069 PROGRESS: Channel   0:	 0.050 FDR: 2,508; 0.010 FDR: 2,508; 0.001 FDR: 1,646
2:46:29.556559 PROGRESS: 
2:46:29.556624 PROGRESS: Protein Summary:
2:46:29.560038 PROGRESS: Channel   0:	 0.050 FDR: 1,976; 0.010 FDR: 1,976; 0.001 FDR: 1,354
2:46:29.560415 PROGRESS: =========================================================================
2:46:29.561755 INFO: Target number of precursors reached.
2:46:29.602377 INFO: fragments_df: keeping 5000 of 120276 [sum(precursor_idx_mask)=57166 sum(mass_error_mask)=120276 stop_rank=5000
2:46:29.639523 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:46:30.237401 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:46:31.160183 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:46:31.161450 INFO: Using score_cutoff 10.280588785743713 (fac=0.99, q=1)
2:46:31.162060 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:46:31.162156 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:46:31.162218 INFO: Updating optimization_manager: score_cutoff        : 10.589136211395264 -> 10.280588785743713
2:46:31.162281 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:31.168485 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:31.180158 INFO: === checking if optimization conditions were reached ===
2:46:31.184293 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:46:31.184878 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:46:31.184956 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:46:31.185027 INFO: ==============================================
2:46:31.185133 PROGRESS: Optimization finished for ms2_error.
2:46:31.220753 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:31.228466 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:31.240167 INFO: Starting optimization step 0.
2:46:31.240783 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:46:31.240893 INFO: Using rust extraction backend
2:46:31.240992 PROGRESS: Extracting batch of 5940 precursors
2:46:31.266277 INFO: === Search parameters used ===
2:46:31.266978 INFO: rt_error       : 805.5982666015625
2:46:31.267031 INFO: mobility_error : 0.1
2:46:31.267083 INFO: num_candidates : 3
2:46:31.267129 INFO: ms1_error      : 3
2:46:31.267174 INFO: ms2_error      : 10.0
2:46:31.267218 INFO: fwhm_rt        : 3.0
2:46:31.267259 INFO: quant_window   : 3
2:46:31.267300 INFO: ==============================================
2:46:31.563455 INFO: performing precursor FDR with 40 features
2:46:31.563769 INFO: Decoy channel: -1
2:46:31.563794 INFO: competitive: True
2:46:31.580119 INFO: Setting torch num_threads to 2 for FDR classification task
2:46:31.592091 INFO: Estimating optimal hyperparameters - samples: 14,250, batch_size: 128, learning_rate: 1.77e-04
2:46:31.592533 INFO: Using random state 76602 for train-test-split
2:46:34.038208 INFO: Test AUC: 0.768
2:46:34.038557 INFO: Train AUC: 0.791
2:46:34.038588 INFO: AUC difference: 2.82%
2:46:34.496143 INFO: Resetting torch num_threads to 100
2:46:34.502599 PROGRESS: === Extracted 17813 precursors and 120247 fragments ===
2:46:34.503982 INFO: === FDR correction performed with classifier version 6 ===
2:46:34.505713 PROGRESS: ============================= Precursor FDR =============================
2:46:34.505909 PROGRESS: Total precursors accumulated: 2,596
2:46:34.505976 PROGRESS: Target precursors: 2,571 (99.04%)
2:46:34.506027 PROGRESS: Decoy precursors: 25 (0.96%)
2:46:34.506078 PROGRESS: 
2:46:34.506127 PROGRESS: Precursor Summary:
2:46:34.508452 PROGRESS: Channel   0:	 0.050 FDR: 2,571; 0.010 FDR: 2,571; 0.001 FDR: 1,683
2:46:34.508659 PROGRESS: 
2:46:34.508718 PROGRESS: Protein Summary:
2:46:34.511715 PROGRESS: Channel   0:	 0.050 FDR: 2,022; 0.010 FDR: 2,022; 0.001 FDR: 1,373
2:46:34.511916 PROGRESS: =========================================================================
2:46:34.513484 INFO: Target number of precursors reached.
2:46:34.550859 INFO: fragments_df: keeping 5000 of 120247 [sum(precursor_idx_mask)=58386 sum(mass_error_mask)=120247 stop_rank=5000
2:46:34.580712 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:46:35.197573 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:46:36.156474 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:46:36.158046 INFO: Using score_cutoff 10.186853070259094 (fac=0.99, q=1)
2:46:36.158842 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:46:36.158961 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:46:36.159033 INFO: Updating optimization_manager: score_cutoff        : 10.280588785743713 -> 10.186853070259094
2:46:36.159110 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:36.165179 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:36.176266 INFO: === checking if optimization conditions were reached ===
2:46:36.176839 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:46:36.181453 INFO: Updating optimization_manager: rt_error            : 805.5982666015625 -> 299.8162272899125
2:46:36.181912 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 299.8162.
2:46:36.181993 INFO: ==============================================
2:46:36.182083 INFO: Starting optimization step 1.
2:46:36.182150 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:46:36.182237 INFO: Using rust extraction backend
2:46:36.182307 PROGRESS: Extracting batch of 5940 precursors
2:46:36.207968 INFO: === Search parameters used ===
2:46:36.208772 INFO: rt_error       : 299.8162272899125
2:46:36.208835 INFO: mobility_error : 0.1
2:46:36.208887 INFO: num_candidates : 3
2:46:36.208936 INFO: ms1_error      : 3
2:46:36.208984 INFO: ms2_error      : 10.0
2:46:36.209028 INFO: fwhm_rt        : 3.0
2:46:36.209074 INFO: quant_window   : 3
2:46:36.209180 INFO: ==============================================
2:46:36.535829 INFO: performing precursor FDR with 40 features
2:46:36.536164 INFO: Decoy channel: -1
2:46:36.536191 INFO: competitive: True
2:46:36.550277 INFO: Setting torch num_threads to 2 for FDR classification task
2:46:36.564933 INFO: Estimating optimal hyperparameters - samples: 14,249, batch_size: 128, learning_rate: 1.77e-04
2:46:36.565531 INFO: Using random state 76602 for train-test-split
2:46:38.714580 INFO: Test AUC: 0.773
2:46:38.714970 INFO: Train AUC: 0.787
2:46:38.715009 INFO: AUC difference: 1.77%
2:46:39.118293 INFO: Resetting torch num_threads to 100
2:46:39.124558 PROGRESS: === Extracted 17812 precursors and 118182 fragments ===
2:46:39.125658 INFO: === FDR correction performed with classifier version 6 ===
2:46:39.126996 PROGRESS: ============================= Precursor FDR =============================
2:46:39.127140 PROGRESS: Total precursors accumulated: 2,770
2:46:39.127217 PROGRESS: Target precursors: 2,743 (99.03%)
2:46:39.127271 PROGRESS: Decoy precursors: 27 (0.97%)
2:46:39.127317 PROGRESS: 
2:46:39.127373 PROGRESS: Precursor Summary:
2:46:39.129839 PROGRESS: Channel   0:	 0.050 FDR: 2,743; 0.010 FDR: 2,743; 0.001 FDR: 1,786
2:46:39.130014 PROGRESS: 
2:46:39.130080 PROGRESS: Protein Summary:
2:46:39.133204 PROGRESS: Channel   0:	 0.050 FDR: 2,153; 0.010 FDR: 2,153; 0.001 FDR: 1,450
2:46:39.133427 PROGRESS: =========================================================================
2:46:39.134718 INFO: Target number of precursors reached.
2:46:39.174551 INFO: fragments_df: keeping 5000 of 118182 [sum(precursor_idx_mask)=61300 sum(mass_error_mask)=118182 stop_rank=5000
2:46:39.205721 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:46:39.862210 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:46:40.781328 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:46:40.782675 INFO: Using score_cutoff 9.599674898529052 (fac=0.99, q=1)
2:46:40.783278 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:46:40.783375 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:46:40.783430 INFO: Updating optimization_manager: score_cutoff        : 10.186853070259094 -> 9.599674898529052
2:46:40.783502 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:40.789553 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:40.801290 INFO: === checking if optimization conditions were reached ===
2:46:40.802004 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:46:40.807419 INFO: Updating optimization_manager: rt_error            : 299.8162272899125 -> 287.6629692844954
2:46:40.808098 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 287.6630.
2:46:40.808197 INFO: ==============================================
2:46:40.808285 INFO: Starting optimization step 2.
2:46:40.808355 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:46:40.808447 INFO: Using rust extraction backend
2:46:40.808519 PROGRESS: Extracting batch of 5940 precursors
2:46:40.838366 INFO: === Search parameters used ===
2:46:40.839188 INFO: rt_error       : 287.6629692844954
2:46:40.839248 INFO: mobility_error : 0.1
2:46:40.839296 INFO: num_candidates : 3
2:46:40.839338 INFO: ms1_error      : 3
2:46:40.839380 INFO: ms2_error      : 10.0
2:46:40.839457 INFO: fwhm_rt        : 3.0
2:46:40.839505 INFO: quant_window   : 3
2:46:40.839553 INFO: ==============================================
2:46:41.197078 INFO: performing precursor FDR with 40 features
2:46:41.197445 INFO: Decoy channel: -1
2:46:41.197480 INFO: competitive: True
2:46:41.218353 INFO: Setting torch num_threads to 2 for FDR classification task
2:46:41.233526 INFO: Estimating optimal hyperparameters - samples: 14,248, batch_size: 128, learning_rate: 1.77e-04
2:46:41.233991 INFO: Using random state 76602 for train-test-split
2:46:43.340890 INFO: Test AUC: 0.769
2:46:43.341298 INFO: Train AUC: 0.787
2:46:43.341343 INFO: AUC difference: 2.29%
2:46:43.773925 INFO: Resetting torch num_threads to 100
2:46:43.780567 PROGRESS: === Extracted 17810 precursors and 117984 fragments ===
2:46:43.781969 INFO: === FDR correction performed with classifier version 6 ===
2:46:43.783648 PROGRESS: ============================= Precursor FDR =============================
2:46:43.783782 PROGRESS: Total precursors accumulated: 2,692
2:46:43.783904 PROGRESS: Target precursors: 2,666 (99.03%)
2:46:43.783964 PROGRESS: Decoy precursors: 26 (0.97%)
2:46:43.784024 PROGRESS: 
2:46:43.784074 PROGRESS: Precursor Summary:
2:46:43.786108 PROGRESS: Channel   0:	 0.050 FDR: 2,666; 0.010 FDR: 2,666; 0.001 FDR: 1,632
2:46:43.786234 PROGRESS: 
2:46:43.786295 PROGRESS: Protein Summary:
2:46:43.789043 PROGRESS: Channel   0:	 0.050 FDR: 2,093; 0.010 FDR: 2,093; 0.001 FDR: 1,342
2:46:43.789230 PROGRESS: =========================================================================
2:46:43.790431 INFO: Target number of precursors reached.
2:46:43.826694 INFO: fragments_df: keeping 5000 of 117984 [sum(precursor_idx_mask)=59838 sum(mass_error_mask)=117984 stop_rank=5000
2:46:43.855843 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:46:44.507659 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:46:45.446895 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:46:45.448322 INFO: Using score_cutoff 9.95628556394577 (fac=0.99, q=1)
2:46:45.448988 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:46:45.449069 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:46:45.449121 INFO: Updating optimization_manager: score_cutoff        : 9.599674898529052 -> 9.95628556394577
2:46:45.449228 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:45.458170 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:45.471030 INFO: === checking if optimization conditions were reached ===
2:46:45.471765 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:46:45.478091 INFO: Updating optimization_manager: rt_error            : 287.6629692844954 -> 258.77831383437285
2:46:45.478713 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 258.7783.
2:46:45.478800 INFO: ==============================================
2:46:45.478900 INFO: Starting optimization step 3.
2:46:45.478969 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:46:45.479158 INFO: Using rust extraction backend
2:46:45.479292 PROGRESS: Extracting batch of 5940 precursors
2:46:45.509253 INFO: === Search parameters used ===
2:46:45.510139 INFO: rt_error       : 258.77831383437285
2:46:45.510202 INFO: mobility_error : 0.1
2:46:45.510254 INFO: num_candidates : 3
2:46:45.510356 INFO: ms1_error      : 3
2:46:45.510403 INFO: ms2_error      : 10.0
2:46:45.510447 INFO: fwhm_rt        : 3.0
2:46:45.510491 INFO: quant_window   : 3
2:46:45.510535 INFO: ==============================================
2:46:45.848206 INFO: performing precursor FDR with 40 features
2:46:45.848742 INFO: Decoy channel: -1
2:46:45.848777 INFO: competitive: True
2:46:45.871361 INFO: Setting torch num_threads to 2 for FDR classification task
2:46:45.886506 INFO: Estimating optimal hyperparameters - samples: 14,246, batch_size: 128, learning_rate: 1.77e-04
2:46:45.886979 INFO: Using random state 76602 for train-test-split
2:46:48.069720 INFO: Test AUC: 0.771
2:46:48.070079 INFO: Train AUC: 0.786
2:46:48.070112 INFO: AUC difference: 1.86%
2:46:48.558944 INFO: Resetting torch num_threads to 100
2:46:48.569041 PROGRESS: === Extracted 17808 precursors and 117250 fragments ===
2:46:48.571169 INFO: === FDR correction performed with classifier version 6 ===
2:46:48.575882 PROGRESS: ============================= Precursor FDR =============================
2:46:48.576621 PROGRESS: Total precursors accumulated: 2,750
2:46:48.576773 PROGRESS: Target precursors: 2,723 (99.02%)
2:46:48.576850 PROGRESS: Decoy precursors: 27 (0.98%)
2:46:48.576903 PROGRESS: 
2:46:48.576952 PROGRESS: Precursor Summary:
2:46:48.583919 PROGRESS: Channel   0:	 0.050 FDR: 2,723; 0.010 FDR: 2,723; 0.001 FDR: 1,752
2:46:48.584605 PROGRESS: 
2:46:48.584769 PROGRESS: Protein Summary:
2:46:48.592624 PROGRESS: Channel   0:	 0.050 FDR: 2,135; 0.010 FDR: 2,135; 0.001 FDR: 1,430
2:46:48.593373 PROGRESS: =========================================================================
2:46:48.595068 INFO: Target number of precursors reached.
2:46:48.644532 INFO: fragments_df: keeping 5000 of 117250 [sum(precursor_idx_mask)=60602 sum(mass_error_mask)=117250 stop_rank=5000
2:46:48.678783 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:46:49.266630 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:46:50.199043 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:46:50.200674 INFO: Using score_cutoff 9.589958212280273 (fac=0.99, q=1)
2:46:50.201483 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:46:50.201579 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:46:50.201639 INFO: Updating optimization_manager: score_cutoff        : 9.95628556394577 -> 9.589958212280273
2:46:50.201720 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:50.208479 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:50.221007 INFO: === checking if optimization conditions were reached ===
2:46:50.221738 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:46:50.228319 INFO: Updating optimization_manager: rt_error            : 258.77831383437285 -> 270.45549327932656
2:46:50.229164 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 270.4555.
2:46:50.229248 INFO: ==============================================
2:46:50.229364 INFO: Starting optimization step 4.
2:46:50.229441 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:46:50.229717 INFO: Using rust extraction backend
2:46:50.230005 PROGRESS: Extracting batch of 5940 precursors
2:46:50.262278 INFO: === Search parameters used ===
2:46:50.263113 INFO: rt_error       : 270.45549327932656
2:46:50.263175 INFO: mobility_error : 0.1
2:46:50.263270 INFO: num_candidates : 3
2:46:50.263321 INFO: ms1_error      : 3
2:46:50.263361 INFO: ms2_error      : 10.0
2:46:50.263402 INFO: fwhm_rt        : 3.0
2:46:50.263442 INFO: quant_window   : 3
2:46:50.263481 INFO: ==============================================
2:46:50.373549 INFO: performing precursor FDR with 40 features
2:46:50.373682 INFO: Decoy channel: -1
2:46:50.373706 INFO: competitive: True
2:46:50.379370 INFO: Setting torch num_threads to 2 for FDR classification task
2:46:50.383435 INFO: Estimating optimal hyperparameters - samples: 14,246, batch_size: 128, learning_rate: 1.77e-04
2:46:50.383559 INFO: Using random state 76602 for train-test-split
2:46:51.897423 INFO: Test AUC: 0.767
2:46:51.897709 INFO: Train AUC: 0.788
2:46:51.897743 INFO: AUC difference: 2.63%
2:46:52.188887 INFO: Resetting torch num_threads to 100
2:46:52.191558 PROGRESS: === Extracted 17808 precursors and 117488 fragments ===
2:46:52.192003 INFO: === FDR correction performed with classifier version 6 ===
2:46:52.192739 PROGRESS: ============================= Precursor FDR =============================
2:46:52.192840 PROGRESS: Total precursors accumulated: 2,751
2:46:52.192900 PROGRESS: Target precursors: 2,724 (99.02%)
2:46:52.192951 PROGRESS: Decoy precursors: 27 (0.98%)
2:46:52.193002 PROGRESS: 
2:46:52.193059 PROGRESS: Precursor Summary:
2:46:52.194690 PROGRESS: Channel   0:	 0.050 FDR: 2,724; 0.010 FDR: 2,724; 0.001 FDR: 1,708
2:46:52.194780 PROGRESS: 
2:46:52.194836 PROGRESS: Protein Summary:
2:46:52.197124 PROGRESS: Channel   0:	 0.050 FDR: 2,135; 0.010 FDR: 2,135; 0.001 FDR: 1,392
2:46:52.197231 PROGRESS: =========================================================================
2:46:52.197629 INFO: Target number of precursors reached.
2:46:52.224224 INFO: fragments_df: keeping 5000 of 117488 [sum(precursor_idx_mask)=60703 sum(mass_error_mask)=117488 stop_rank=5000
2:46:52.238829 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:46:52.702183 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:46:53.544505 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:46:53.545624 INFO: Using score_cutoff 9.696678311920166 (fac=0.99, q=1)
2:46:53.546218 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:46:53.546307 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:46:53.546365 INFO: Updating optimization_manager: score_cutoff        : 9.589958212280273 -> 9.696678311920166
2:46:53.546449 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:53.552116 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:53.563061 INFO: === checking if optimization conditions were reached ===
2:46:53.563647 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:46:53.565415 INFO: Updating optimization_manager: rt_error            : 270.45549327932656 -> 299.8162272899125
2:46:53.565678 INFO: Updating optimization_manager: classifier_version  : 6 -> 8
2:46:53.565784 INFO: Updating optimization_manager: score_cutoff        : 9.696678311920166 -> 9.599674898529052
2:46:53.565879 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:46:53.565998 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:46:53.566096 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 299.8162 found after 5 searches.
2:46:53.566159 INFO: ==============================================
2:46:53.566281 PROGRESS: Optimization finished for rt_error.
2:46:53.590045 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:53.596425 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:53.607392 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:46:53.608046 PROGRESS: ==============================================
2:46:53.608152 PROGRESS: ms2_error      : 10.0000
2:46:53.608213 PROGRESS: rt_error       : 299.8162
2:46:53.608257 PROGRESS: ==============================================
2:46:53.610376 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:46:53.782151 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:46:54.332433 INFO: Using rust extraction backend
2:46:54.333207 PROGRESS: Extracting batch of 259156 precursors
2:46:55.264953 INFO: === Search parameters used ===
2:46:55.265784 INFO: rt_error       : 299.8162272899125
2:46:55.265845 INFO: mobility_error : 0.1
2:46:55.265894 INFO: num_candidates : 3
2:46:55.265938 INFO: ms1_error      : 3
2:46:55.265978 INFO: ms2_error      : 10.0
2:46:55.266018 INFO: fwhm_rt        : 3.0
2:46:55.266056 INFO: quant_window   : 3
2:46:55.266093 INFO: ==============================================
2:46:57.208051 INFO: Removed 83444 precursors with score below cutoff 9.599674898529052
2:46:58.322098 INFO: performing precursor FDR with 40 features
2:46:58.322473 INFO: Decoy channel: -1
2:46:58.322499 INFO: competitive: True
2:46:58.478726 INFO: Setting torch num_threads to 2 for FDR classification task
2:46:58.595009 WARNING: FDR calculation for 365859 target and 328165 decoy PSMs
2:46:58.595345 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:46:59.157130 INFO: Estimating optimal hyperparameters - samples: 555,219, batch_size: 2,274, learning_rate: 7.45e-04
2:46:59.159093 INFO: Using random state 680226 for train-test-split
2:47:21.542408 INFO: Test AUC: 0.783
2:47:21.542937 INFO: Train AUC: 0.786
2:47:21.542986 INFO: AUC difference: 0.40%
2:47:22.354306 INFO: Resetting torch num_threads to 100
2:47:23.622212 PROGRESS: ============================= Precursor FDR =============================
2:47:23.623116 PROGRESS: Total precursors accumulated: 124,027
2:47:23.623310 PROGRESS: Target precursors: 122,799 (99.01%)
2:47:23.623406 PROGRESS: Decoy precursors: 1,228 (0.99%)
2:47:23.623475 PROGRESS: 
2:47:23.623535 PROGRESS: Precursor Summary:
2:47:23.774714 PROGRESS: Channel   0:	 0.050 FDR: 122,799; 0.010 FDR: 122,794; 0.001 FDR: 109,823
2:47:23.775574 PROGRESS: 
2:47:23.775831 PROGRESS: Protein Summary:
2:47:24.070112 PROGRESS: Channel   0:	 0.050 FDR: 10,145; 0.010 FDR: 10,145; 0.001 FDR: 10,017
2:47:24.070926 PROGRESS: =========================================================================
2:47:24.085811 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/psm.parquet
2:47:24.623196 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/frag.parquet
2:47:25.414653 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:47:26.160718 PROGRESS: Loading raw file 5/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP2 
2:47:26.161090 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:47:26.161293 INFO: Initializing TimingManager
2:47:26.163078 INFO: Initializing RawFileManager
2:48:00.894311 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:48:00.907292 INFO: Determining DIA cycle
2:48:00.928083 INFO: Found cycle with start 0.00 min and length 300.
2:48:01.309918 INFO: RT (min)            : 0.0 - 26.9
2:48:01.310033 INFO: RT duration (sec)   : 1611.2
2:48:01.310070 INFO: RT duration (min)   : 26.9
2:48:01.310097 INFO: Cycle len (scans)   : 300
2:48:01.310119 INFO: Cycle len (sec)     : 1.65
2:48:01.310139 INFO: Number of cycles    : 977
2:48:01.310158 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:48:01.310196 INFO: Creating DIA data object took: 35.14686417579651
2:48:03.274710 INFO: Creating DIA data NG object took: 1.9643676280975342
2:48:03.318801 INFO: Initializing CalibrationManager
2:48:03.319228 INFO: Setting up calibration estimators ..
2:48:03.319291 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:48:03.319385 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2:48:03.319470 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:48:03.319523 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:48:03.319582 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2:48:03.319637 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:48:03.319685 INFO: Done setting up calibration estimators.
2:48:03.319993 INFO: Initializing OptimizationManager
2:48:03.320162 INFO: initial parameter: ms1_error = 3
2:48:03.320221 INFO: initial parameter: ms2_error = 10
2:48:03.320274 INFO: initial parameter: rt_error = 805.6002197265625
2:48:03.320323 INFO: initial parameter: mobility_error = 0.1
2:48:03.320367 INFO: initial parameter: num_candidates = 1
2:48:03.320410 INFO: initial parameter: fwhm_rt = 5
2:48:03.320464 INFO: initial parameter: fwhm_mobility = 0.01
2:48:03.320506 INFO: initial parameter: score_cutoff = 0
2:48:03.320547 INFO: initial parameter: classifier_version = -1
2:48:03.320621 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:48:03.320975 INFO: FDRManager: loading saved state not requested, will be initialized.
2:48:03.321009 INFO: Initializing FDRManager
2:48:03.321044 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:48:03.396392 PROGRESS: Initializing spectral library: 131,021 target precursors potentially observable (0 removed)
2:48:03.447181 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
2:48:03.447795 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 805.6002197265625
2:48:03.447936 PROGRESS: Starting initial search for precursors.
2:48:03.448049 INFO: Starting optimization step 0.
2:48:03.448133 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:48:03.448215 INFO: Using rust extraction backend
2:48:03.448346 PROGRESS: Extracting batch of 1982 precursors
2:48:03.455183 INFO: === Search parameters used ===
2:48:03.455369 INFO: rt_error       : 805.6002197265625
2:48:03.455441 INFO: mobility_error : 0.1
2:48:03.455504 INFO: num_candidates : 1
2:48:03.455564 INFO: ms1_error      : 3
2:48:03.455621 INFO: ms2_error      : 10
2:48:03.455678 INFO: fwhm_rt        : 5
2:48:03.455733 INFO: quant_window   : 3
2:48:03.455789 INFO: ==============================================
2:48:03.639385 INFO: performing precursor FDR with 40 features
2:48:03.639630 INFO: Decoy channel: -1
2:48:03.639663 INFO: competitive: True
2:48:03.644170 INFO: Setting torch num_threads to 2 for FDR classification task
2:48:03.648975 INFO: Estimating optimal hyperparameters - samples: 1,585, batch_size: 128, learning_rate: 1.77e-04
2:48:03.650905 INFO: Using random state 33775 for train-test-split
2:48:03.884883 INFO: Test AUC: 0.861
2:48:03.885177 INFO: Train AUC: 0.874
2:48:03.885219 INFO: AUC difference: 1.48%
2:48:04.547205 INFO: Resetting torch num_threads to 100
2:48:04.552340 PROGRESS: === Extracted 1982 precursors and 15371 fragments ===
2:48:04.553653 INFO: === FDR correction performed with classifier version -1 ===
2:48:04.555039 PROGRESS: ============================= Precursor FDR =============================
2:48:04.555186 PROGRESS: Total precursors accumulated: 559
2:48:04.555269 PROGRESS: Target precursors: 554 (99.11%)
2:48:04.555335 PROGRESS: Decoy precursors: 5 (0.89%)
2:48:04.555399 PROGRESS: 
2:48:04.555461 PROGRESS: Precursor Summary:
2:48:04.557596 PROGRESS: Channel   0:	 0.050 FDR:   554; 0.010 FDR:   554; 0.001 FDR:   249
2:48:04.557766 PROGRESS: 
2:48:04.557837 PROGRESS: Protein Summary:
2:48:04.560133 PROGRESS: Channel   0:	 0.050 FDR:   522; 0.010 FDR:   522; 0.001 FDR:   238
2:48:04.560277 PROGRESS: =========================================================================
2:48:04.561389 INFO: Target number of precursors not reached yet.
2:48:04.584289 INFO: Starting optimization step 1.
2:48:04.584969 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:48:04.585089 INFO: Using rust extraction backend
2:48:04.585182 PROGRESS: Extracting batch of 3958 precursors
2:48:04.606574 INFO: === Search parameters used ===
2:48:04.607280 INFO: rt_error       : 805.6002197265625
2:48:04.607345 INFO: mobility_error : 0.1
2:48:04.607403 INFO: num_candidates : 1
2:48:04.607457 INFO: ms1_error      : 3
2:48:04.607508 INFO: ms2_error      : 10
2:48:04.607558 INFO: fwhm_rt        : 5
2:48:04.607607 INFO: quant_window   : 3
2:48:04.607663 INFO: ==============================================
2:48:04.897196 INFO: performing precursor FDR with 40 features
2:48:04.897495 INFO: Decoy channel: -1
2:48:04.897536 INFO: competitive: True
2:48:04.908794 INFO: Setting torch num_threads to 2 for FDR classification task
2:48:04.915158 INFO: Estimating optimal hyperparameters - samples: 4,752, batch_size: 128, learning_rate: 1.77e-04
2:48:04.915423 INFO: Using random state 628703 for train-test-split
2:48:05.647861 INFO: Test AUC: 0.908
2:48:05.648062 INFO: Train AUC: 0.912
2:48:05.648095 INFO: AUC difference: 0.44%
2:48:05.952104 INFO: Resetting torch num_threads to 100
2:48:05.958693 PROGRESS: === Extracted 5940 precursors and 46200 fragments ===
2:48:05.959588 INFO: === FDR correction performed with classifier version -1 ===
2:48:05.960497 PROGRESS: ============================= Precursor FDR =============================
2:48:05.960598 PROGRESS: Total precursors accumulated: 2,174
2:48:05.960660 PROGRESS: Target precursors: 2,153 (99.03%)
2:48:05.960709 PROGRESS: Decoy precursors: 21 (0.97%)
2:48:05.960754 PROGRESS: 
2:48:05.960799 PROGRESS: Precursor Summary:
2:48:05.962588 PROGRESS: Channel   0:	 0.050 FDR: 2,153; 0.010 FDR: 2,153; 0.001 FDR: 1,066
2:48:05.962697 PROGRESS: 
2:48:05.962759 PROGRESS: Protein Summary:
2:48:05.965225 PROGRESS: Channel   0:	 0.050 FDR: 1,732; 0.010 FDR: 1,732; 0.001 FDR:   916
2:48:05.965346 PROGRESS: =========================================================================
2:48:05.966159 INFO: Target number of precursors reached.
2:48:05.980436 INFO: fragments_df: keeping 5000 of 46200 [sum(precursor_idx_mask)=21620 sum(mass_error_mask)=46200 stop_rank=5000
2:48:06.001273 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:48:06.548478 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:48:07.519900 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:48:07.522589 INFO: Using score_cutoff 10.72374277381897 (fac=0.99, q=1)
2:48:07.523840 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:48:07.523968 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:48:07.524034 INFO: Updating optimization_manager: score_cutoff        : 0 -> 10.72374277381897
2:48:07.524145 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:48:07.531809 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:48:07.545221 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:48:07.545879 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:48:07.546009 INFO: Starting optimization step 2.
2:48:07.546161 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:48:07.546280 INFO: Using rust extraction backend
2:48:07.546357 PROGRESS: Extracting batch of 5940 precursors
2:48:07.576393 INFO: === Search parameters used ===
2:48:07.577255 INFO: rt_error       : 805.6002197265625
2:48:07.577313 INFO: mobility_error : 0.1
2:48:07.577363 INFO: num_candidates : 3
2:48:07.577412 INFO: ms1_error      : 3
2:48:07.577458 INFO: ms2_error      : 10
2:48:07.577500 INFO: fwhm_rt        : 3.0
2:48:07.577541 INFO: quant_window   : 3
2:48:07.577581 INFO: ==============================================
2:48:07.953800 INFO: performing precursor FDR with 40 features
2:48:07.954178 INFO: Decoy channel: -1
2:48:07.954223 INFO: competitive: True
2:48:07.980202 INFO: Setting torch num_threads to 2 for FDR classification task
2:48:07.998857 INFO: Estimating optimal hyperparameters - samples: 14,250, batch_size: 128, learning_rate: 1.77e-04
2:48:07.999362 INFO: Using random state 168846 for train-test-split
2:48:10.511686 INFO: Test AUC: 0.729
2:48:10.512130 INFO: Train AUC: 0.733
2:48:10.512169 INFO: AUC difference: 0.62%
2:48:10.955357 INFO: Resetting torch num_threads to 100
2:48:10.962535 PROGRESS: === Extracted 17813 precursors and 120041 fragments ===
2:48:10.963594 INFO: === FDR correction performed with classifier version 1 ===
2:48:10.965221 PROGRESS: ============================= Precursor FDR =============================
2:48:10.965404 PROGRESS: Total precursors accumulated: 2,313
2:48:10.965467 PROGRESS: Target precursors: 2,291 (99.05%)
2:48:10.965518 PROGRESS: Decoy precursors: 22 (0.95%)
2:48:10.965564 PROGRESS: 
2:48:10.965610 PROGRESS: Precursor Summary:
2:48:10.967922 PROGRESS: Channel   0:	 0.050 FDR: 2,291; 0.010 FDR: 2,291; 0.001 FDR: 1,130
2:48:10.968168 PROGRESS: 
2:48:10.968256 PROGRESS: Protein Summary:
2:48:10.971015 PROGRESS: Channel   0:	 0.050 FDR: 1,839; 0.010 FDR: 1,839; 0.001 FDR:   968
2:48:10.971241 PROGRESS: =========================================================================
2:48:10.972890 INFO: Target number of precursors reached.
2:48:11.009356 INFO: fragments_df: keeping 5000 of 120041 [sum(precursor_idx_mask)=53137 sum(mass_error_mask)=120041 stop_rank=5000
2:48:11.038709 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:48:11.718138 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:48:12.768718 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:48:12.769913 INFO: Using score_cutoff 11.060063252449035 (fac=0.99, q=1)
2:48:12.770452 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:48:12.770537 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:48:12.770630 INFO: Updating optimization_manager: score_cutoff        : 10.72374277381897 -> 11.060063252449035
2:48:12.770697 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:48:12.776758 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:48:12.788470 INFO: === checking if optimization conditions were reached ===
2:48:12.792657 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
2:48:12.793031 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:48:12.793111 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:48:12.793181 INFO: ==============================================
2:48:12.793304 INFO: Starting optimization step 3.
2:48:12.793373 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:48:12.793462 INFO: Using rust extraction backend
2:48:12.793538 PROGRESS: Extracting batch of 5940 precursors
2:48:12.821557 INFO: === Search parameters used ===
2:48:12.822242 INFO: rt_error       : 805.6002197265625
2:48:12.822313 INFO: mobility_error : 0.1
2:48:12.822376 INFO: num_candidates : 3
2:48:12.822436 INFO: ms1_error      : 3
2:48:12.822537 INFO: ms2_error      : 10.0
2:48:12.822582 INFO: fwhm_rt        : 3.0
2:48:12.822624 INFO: quant_window   : 3
2:48:12.822664 INFO: ==============================================
2:48:13.213748 INFO: performing precursor FDR with 40 features
2:48:13.214015 INFO: Decoy channel: -1
2:48:13.214086 INFO: competitive: True
2:48:13.225010 INFO: Setting torch num_threads to 2 for FDR classification task
2:48:13.236988 INFO: Estimating optimal hyperparameters - samples: 14,252, batch_size: 128, learning_rate: 1.77e-04
2:48:13.237376 INFO: Using random state 9847 for train-test-split
2:48:15.305833 INFO: Test AUC: 0.735
2:48:15.306183 INFO: Train AUC: 0.749
2:48:15.306221 INFO: AUC difference: 1.86%
2:48:15.752087 INFO: Resetting torch num_threads to 100
2:48:15.757445 PROGRESS: === Extracted 17815 precursors and 120053 fragments ===
2:48:15.758486 INFO: === FDR correction performed with classifier version 2 ===
2:48:15.759738 PROGRESS: ============================= Precursor FDR =============================
2:48:15.759890 PROGRESS: Total precursors accumulated: 2,458
2:48:15.759959 PROGRESS: Target precursors: 2,434 (99.02%)
2:48:15.760010 PROGRESS: Decoy precursors: 24 (0.98%)
2:48:15.760056 PROGRESS: 
2:48:15.760104 PROGRESS: Precursor Summary:
2:48:15.762072 PROGRESS: Channel   0:	 0.050 FDR: 2,434; 0.010 FDR: 2,434; 0.001 FDR: 1,207
2:48:15.762238 PROGRESS: 
2:48:15.762306 PROGRESS: Protein Summary:
2:48:15.764953 PROGRESS: Channel   0:	 0.050 FDR: 1,932; 0.010 FDR: 1,932; 0.001 FDR: 1,024
2:48:15.765110 PROGRESS: =========================================================================
2:48:15.766451 INFO: Target number of precursors reached.
2:48:15.800723 INFO: fragments_df: keeping 5000 of 120053 [sum(precursor_idx_mask)=55878 sum(mass_error_mask)=120053 stop_rank=5000
2:48:15.827057 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:48:16.482134 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:48:17.617436 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:48:17.618464 INFO: Using score_cutoff 10.666313509941102 (fac=0.99, q=1)
2:48:17.619051 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:48:17.619147 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:48:17.619214 INFO: Updating optimization_manager: score_cutoff        : 11.060063252449035 -> 10.666313509941102
2:48:17.619286 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:48:17.625086 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:48:17.636966 INFO: === checking if optimization conditions were reached ===
2:48:17.640989 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:48:17.641417 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:48:17.641515 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:48:17.641622 INFO: ==============================================
2:48:17.641722 INFO: Starting optimization step 4.
2:48:17.641803 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:48:17.641892 INFO: Using rust extraction backend
2:48:17.641990 PROGRESS: Extracting batch of 5940 precursors
2:48:17.663895 INFO: === Search parameters used ===
2:48:17.664377 INFO: rt_error       : 805.6002197265625
2:48:17.664451 INFO: mobility_error : 0.1
2:48:17.664513 INFO: num_candidates : 3
2:48:17.664575 INFO: ms1_error      : 3
2:48:17.664635 INFO: ms2_error      : 10.0
2:48:17.664713 INFO: fwhm_rt        : 3.0
2:48:17.664772 INFO: quant_window   : 3
2:48:17.664830 INFO: ==============================================
2:48:17.964697 INFO: performing precursor FDR with 40 features
2:48:17.964847 INFO: Decoy channel: -1
2:48:17.964872 INFO: competitive: True
2:48:17.972004 INFO: Setting torch num_threads to 2 for FDR classification task
2:48:17.977415 INFO: Estimating optimal hyperparameters - samples: 14,251, batch_size: 128, learning_rate: 1.77e-04
2:48:17.977585 INFO: Using random state 459813 for train-test-split
2:48:19.646059 INFO: Test AUC: 0.738
2:48:19.646358 INFO: Train AUC: 0.759
2:48:19.646392 INFO: AUC difference: 2.71%
2:48:19.960841 INFO: Resetting torch num_threads to 100
2:48:19.964915 PROGRESS: === Extracted 17814 precursors and 120074 fragments ===
2:48:19.965662 INFO: === FDR correction performed with classifier version 3 ===
2:48:19.966794 PROGRESS: ============================= Precursor FDR =============================
2:48:19.966913 PROGRESS: Total precursors accumulated: 2,466
2:48:19.966971 PROGRESS: Target precursors: 2,442 (99.03%)
2:48:19.967020 PROGRESS: Decoy precursors: 24 (0.97%)
2:48:19.967065 PROGRESS: 
2:48:19.967109 PROGRESS: Precursor Summary:
2:48:19.968970 PROGRESS: Channel   0:	 0.050 FDR: 2,442; 0.010 FDR: 2,442; 0.001 FDR: 1,319
2:48:19.969127 PROGRESS: 
2:48:19.969181 PROGRESS: Protein Summary:
2:48:19.971673 PROGRESS: Channel   0:	 0.050 FDR: 1,943; 0.010 FDR: 1,943; 0.001 FDR: 1,115
2:48:19.971984 PROGRESS: =========================================================================
2:48:19.972839 INFO: Target number of precursors reached.
2:48:20.005346 INFO: fragments_df: keeping 5000 of 120074 [sum(precursor_idx_mask)=56029 sum(mass_error_mask)=120074 stop_rank=5000
2:48:20.032286 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:48:20.541396 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:48:31.598647 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:48:31.600381 INFO: Using score_cutoff 10.6785963432312 (fac=0.99, q=1)
2:48:31.601169 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:48:31.601268 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:48:31.601327 INFO: Updating optimization_manager: score_cutoff        : 10.666313509941102 -> 10.6785963432312
2:48:31.601432 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:48:31.608305 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:48:31.622299 INFO: === checking if optimization conditions were reached ===
2:48:31.627564 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:48:31.628239 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:48:31.628373 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:48:31.628455 INFO: ==============================================
2:48:31.628558 INFO: Starting optimization step 5.
2:48:31.628645 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:48:31.628774 INFO: Using rust extraction backend
2:48:31.628901 PROGRESS: Extracting batch of 5940 precursors
2:48:31.659932 INFO: === Search parameters used ===
2:48:31.661005 INFO: rt_error       : 805.6002197265625
2:48:31.661072 INFO: mobility_error : 0.1
2:48:31.661130 INFO: num_candidates : 3
2:48:31.661181 INFO: ms1_error      : 3
2:48:31.661224 INFO: ms2_error      : 10.0
2:48:31.661269 INFO: fwhm_rt        : 3.0
2:48:31.661316 INFO: quant_window   : 3
2:48:31.661360 INFO: ==============================================
2:48:32.006657 INFO: performing precursor FDR with 40 features
2:48:32.007014 INFO: Decoy channel: -1
2:48:32.007046 INFO: competitive: True
2:48:32.027723 INFO: Setting torch num_threads to 2 for FDR classification task
2:48:32.042999 INFO: Estimating optimal hyperparameters - samples: 14,251, batch_size: 128, learning_rate: 1.77e-04
2:48:32.043551 INFO: Using random state 270270 for train-test-split
2:48:34.600795 INFO: Test AUC: 0.777
2:48:34.601097 INFO: Train AUC: 0.758
2:48:34.601131 INFO: AUC difference: 2.49%
2:48:35.122452 INFO: Resetting torch num_threads to 100
2:48:35.131911 PROGRESS: === Extracted 17814 precursors and 120071 fragments ===
2:48:35.133649 INFO: === FDR correction performed with classifier version 4 ===
2:48:35.137469 PROGRESS: ============================= Precursor FDR =============================
2:48:35.138017 PROGRESS: Total precursors accumulated: 2,478
2:48:35.138092 PROGRESS: Target precursors: 2,454 (99.03%)
2:48:35.138147 PROGRESS: Decoy precursors: 24 (0.97%)
2:48:35.138240 PROGRESS: 
2:48:35.138290 PROGRESS: Precursor Summary:
2:48:35.142109 PROGRESS: Channel   0:	 0.050 FDR: 2,454; 0.010 FDR: 2,454; 0.001 FDR: 1,296
2:48:35.142445 PROGRESS: 
2:48:35.142506 PROGRESS: Protein Summary:
2:48:35.146015 PROGRESS: Channel   0:	 0.050 FDR: 1,951; 0.010 FDR: 1,951; 0.001 FDR: 1,101
2:48:35.146371 PROGRESS: =========================================================================
2:48:35.147959 INFO: Target number of precursors reached.
2:48:35.186636 INFO: fragments_df: keeping 5000 of 120071 [sum(precursor_idx_mask)=56190 sum(mass_error_mask)=120071 stop_rank=5000
2:48:35.225682 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:48:35.783232 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:48:36.972929 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:48:36.974043 INFO: Using score_cutoff 10.559817491912842 (fac=0.99, q=1)
2:48:36.974658 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:48:36.974750 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:48:36.974808 INFO: Updating optimization_manager: score_cutoff        : 10.6785963432312 -> 10.559817491912842
2:48:36.974873 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:48:36.981019 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:48:36.993720 INFO: === checking if optimization conditions were reached ===
2:48:36.997873 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:48:36.998376 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:48:36.998462 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:48:36.998529 INFO: ==============================================
2:48:36.998611 INFO: Starting optimization step 6.
2:48:36.998677 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:48:36.998801 INFO: Using rust extraction backend
2:48:36.998883 PROGRESS: Extracting batch of 5940 precursors
2:48:37.028888 INFO: === Search parameters used ===
2:48:37.029585 INFO: rt_error       : 805.6002197265625
2:48:37.029643 INFO: mobility_error : 0.1
2:48:37.029691 INFO: num_candidates : 3
2:48:37.029734 INFO: ms1_error      : 3
2:48:37.029775 INFO: ms2_error      : 10.0
2:48:37.029839 INFO: fwhm_rt        : 3.0
2:48:37.029894 INFO: quant_window   : 3
2:48:37.029940 INFO: ==============================================
2:48:37.322899 INFO: performing precursor FDR with 40 features
2:48:37.323202 INFO: Decoy channel: -1
2:48:37.323230 INFO: competitive: True
2:48:37.346697 INFO: Setting torch num_threads to 2 for FDR classification task
2:48:37.362741 INFO: Estimating optimal hyperparameters - samples: 14,251, batch_size: 128, learning_rate: 1.77e-04
2:48:37.363267 INFO: Using random state 172976 for train-test-split
2:48:39.722905 INFO: Test AUC: 0.758
2:48:39.723305 INFO: Train AUC: 0.771
2:48:39.723343 INFO: AUC difference: 1.76%
2:48:40.220045 INFO: Resetting torch num_threads to 100
2:48:40.230407 PROGRESS: === Extracted 17814 precursors and 120120 fragments ===
2:48:40.232522 INFO: === FDR correction performed with classifier version 5 ===
2:48:40.236036 PROGRESS: ============================= Precursor FDR =============================
2:48:40.236480 PROGRESS: Total precursors accumulated: 2,572
2:48:40.236602 PROGRESS: Target precursors: 2,547 (99.03%)
2:48:40.236714 PROGRESS: Decoy precursors: 25 (0.97%)
2:48:40.236770 PROGRESS: 
2:48:40.236821 PROGRESS: Precursor Summary:
2:48:40.242033 PROGRESS: Channel   0:	 0.050 FDR: 2,547; 0.010 FDR: 2,547; 0.001 FDR: 1,497
2:48:40.242380 PROGRESS: 
2:48:40.242450 PROGRESS: Protein Summary:
2:48:40.246114 PROGRESS: Channel   0:	 0.050 FDR: 2,008; 0.010 FDR: 2,008; 0.001 FDR: 1,243
2:48:40.246433 PROGRESS: =========================================================================
2:48:40.247901 INFO: Target number of precursors reached.
2:48:40.287009 INFO: fragments_df: keeping 5000 of 120120 [sum(precursor_idx_mask)=58029 sum(mass_error_mask)=120120 stop_rank=5000
2:48:40.318900 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:48:41.537774 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:48:42.422064 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:48:42.423322 INFO: Using score_cutoff 10.42786618423462 (fac=0.99, q=1)
2:48:42.424288 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:48:42.424566 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:48:42.424659 INFO: Updating optimization_manager: score_cutoff        : 10.559817491912842 -> 10.42786618423462
2:48:42.424745 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:48:42.431975 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:48:42.444548 INFO: === checking if optimization conditions were reached ===
2:48:42.449157 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:48:42.449554 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:48:42.449626 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:48:42.449719 INFO: ==============================================
2:48:42.449804 PROGRESS: Optimization finished for ms2_error.
2:48:42.475816 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:48:42.482680 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:48:42.494223 INFO: Starting optimization step 0.
2:48:42.494830 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:48:42.495003 INFO: Using rust extraction backend
2:48:42.495153 PROGRESS: Extracting batch of 5940 precursors
2:48:42.522410 INFO: === Search parameters used ===
2:48:42.523221 INFO: rt_error       : 805.6002197265625
2:48:42.523281 INFO: mobility_error : 0.1
2:48:42.523330 INFO: num_candidates : 3
2:48:42.523375 INFO: ms1_error      : 3
2:48:42.523417 INFO: ms2_error      : 10.0
2:48:42.523457 INFO: fwhm_rt        : 3.0
2:48:42.523497 INFO: quant_window   : 3
2:48:42.523543 INFO: ==============================================
2:48:42.753450 INFO: performing precursor FDR with 40 features
2:48:42.753736 INFO: Decoy channel: -1
2:48:42.753764 INFO: competitive: True
2:48:42.773149 INFO: Setting torch num_threads to 2 for FDR classification task
2:48:42.787875 INFO: Estimating optimal hyperparameters - samples: 14,251, batch_size: 128, learning_rate: 1.77e-04
2:48:42.788295 INFO: Using random state 848077 for train-test-split
2:48:44.903502 INFO: Test AUC: 0.770
2:48:44.903857 INFO: Train AUC: 0.776
2:48:44.903896 INFO: AUC difference: 0.80%
2:48:45.453934 INFO: Resetting torch num_threads to 100
2:48:45.463634 PROGRESS: === Extracted 17814 precursors and 120138 fragments ===
2:48:45.465710 INFO: === FDR correction performed with classifier version 6 ===
2:48:45.467021 PROGRESS: ============================= Precursor FDR =============================
2:48:45.467134 PROGRESS: Total precursors accumulated: 2,609
2:48:45.467215 PROGRESS: Target precursors: 2,584 (99.04%)
2:48:45.467290 PROGRESS: Decoy precursors: 25 (0.96%)
2:48:45.467354 PROGRESS: 
2:48:45.467408 PROGRESS: Precursor Summary:
2:48:45.470915 PROGRESS: Channel   0:	 0.050 FDR: 2,584; 0.010 FDR: 2,584; 0.001 FDR: 1,432
2:48:45.471084 PROGRESS: 
2:48:45.471149 PROGRESS: Protein Summary:
2:48:45.474759 PROGRESS: Channel   0:	 0.050 FDR: 2,034; 0.010 FDR: 2,034; 0.001 FDR: 1,202
2:48:45.474935 PROGRESS: =========================================================================
2:48:45.476688 INFO: Target number of precursors reached.
2:48:45.520226 INFO: fragments_df: keeping 5000 of 120138 [sum(precursor_idx_mask)=58787 sum(mass_error_mask)=120138 stop_rank=5000
2:48:45.583595 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:48:46.142216 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:48:47.199035 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:48:47.199871 INFO: Using score_cutoff 10.371031094455718 (fac=0.99, q=1)
2:48:47.200322 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:48:47.200408 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:48:47.200472 INFO: Updating optimization_manager: score_cutoff        : 10.42786618423462 -> 10.371031094455718
2:48:47.200557 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:48:47.205259 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:48:47.214393 INFO: === checking if optimization conditions were reached ===
2:48:47.214818 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:48:47.218410 INFO: Updating optimization_manager: rt_error            : 805.6002197265625 -> 345.8699067777564
2:48:47.218584 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 345.8699.
2:48:47.218652 INFO: ==============================================
2:48:47.218737 INFO: Starting optimization step 1.
2:48:47.218801 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:48:47.218936 INFO: Using rust extraction backend
2:48:47.219048 PROGRESS: Extracting batch of 5940 precursors
2:48:47.232193 INFO: === Search parameters used ===
2:48:47.232534 INFO: rt_error       : 345.8699067777564
2:48:47.232586 INFO: mobility_error : 0.1
2:48:47.232640 INFO: num_candidates : 3
2:48:47.232687 INFO: ms1_error      : 3
2:48:47.232733 INFO: ms2_error      : 10.0
2:48:47.232776 INFO: fwhm_rt        : 3.0
2:48:47.232817 INFO: quant_window   : 3
2:48:47.232858 INFO: ==============================================
2:48:47.506794 INFO: performing precursor FDR with 40 features
2:48:47.506999 INFO: Decoy channel: -1
2:48:47.507024 INFO: competitive: True
2:48:47.519959 INFO: Setting torch num_threads to 2 for FDR classification task
2:48:47.529662 INFO: Estimating optimal hyperparameters - samples: 14,252, batch_size: 128, learning_rate: 1.77e-04
2:48:47.530168 INFO: Using random state 848077 for train-test-split
2:48:49.959137 INFO: Test AUC: 0.757
2:48:49.959515 INFO: Train AUC: 0.780
2:48:49.959558 INFO: AUC difference: 2.95%
2:48:50.481254 INFO: Resetting torch num_threads to 100
2:48:50.491631 PROGRESS: === Extracted 17815 precursors and 118895 fragments ===
2:48:50.493400 INFO: === FDR correction performed with classifier version 6 ===
2:48:50.497258 PROGRESS: ============================= Precursor FDR =============================
2:48:50.497759 PROGRESS: Total precursors accumulated: 2,662
2:48:50.497901 PROGRESS: Target precursors: 2,636 (99.02%)
2:48:50.497982 PROGRESS: Decoy precursors: 26 (0.98%)
2:48:50.498055 PROGRESS: 
2:48:50.498105 PROGRESS: Precursor Summary:
2:48:50.505563 PROGRESS: Channel   0:	 0.050 FDR: 2,636; 0.010 FDR: 2,636; 0.001 FDR: 2,120
2:48:50.506308 PROGRESS: 
2:48:50.506461 PROGRESS: Protein Summary:
2:48:50.517706 PROGRESS: Channel   0:	 0.050 FDR: 2,076; 0.010 FDR: 2,076; 0.001 FDR: 1,710
2:48:50.518486 PROGRESS: =========================================================================
2:48:50.521093 INFO: Target number of precursors reached.
2:48:50.567479 INFO: fragments_df: keeping 5000 of 118895 [sum(precursor_idx_mask)=59514 sum(mass_error_mask)=118895 stop_rank=5000
2:48:50.605538 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:48:51.178493 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:48:52.515172 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:48:52.516695 INFO: Using score_cutoff 10.389213428020478 (fac=0.99, q=1)
2:48:52.517447 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:48:52.517568 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:48:52.517639 INFO: Updating optimization_manager: score_cutoff        : 10.371031094455718 -> 10.389213428020478
2:48:52.517734 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:48:52.525763 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:48:52.540950 INFO: === checking if optimization conditions were reached ===
2:48:52.541810 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:48:52.549101 INFO: Updating optimization_manager: rt_error            : 345.8699067777564 -> 303.3041389460001
2:48:52.550032 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 303.3041.
2:48:52.550175 INFO: ==============================================
2:48:52.550262 INFO: Starting optimization step 2.
2:48:52.550325 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:48:52.550422 INFO: Using rust extraction backend
2:48:52.550499 PROGRESS: Extracting batch of 5940 precursors
2:48:52.581023 INFO: === Search parameters used ===
2:48:52.581944 INFO: rt_error       : 303.3041389460001
2:48:52.582018 INFO: mobility_error : 0.1
2:48:52.582076 INFO: num_candidates : 3
2:48:52.582130 INFO: ms1_error      : 3
2:48:52.582185 INFO: ms2_error      : 10.0
2:48:52.582234 INFO: fwhm_rt        : 3.0
2:48:52.582330 INFO: quant_window   : 3
2:48:52.582382 INFO: ==============================================
2:48:53.142599 INFO: performing precursor FDR with 40 features
2:48:53.142938 INFO: Decoy channel: -1
2:48:53.142973 INFO: competitive: True
2:48:53.176183 INFO: Setting torch num_threads to 2 for FDR classification task
2:48:53.205494 INFO: Estimating optimal hyperparameters - samples: 14,249, batch_size: 128, learning_rate: 1.77e-04
2:48:53.206121 INFO: Using random state 848077 for train-test-split
2:48:56.511242 INFO: Test AUC: 0.780
2:48:56.511587 INFO: Train AUC: 0.776
2:48:56.511651 INFO: AUC difference: 0.52%
2:48:57.035590 INFO: Resetting torch num_threads to 100
2:48:57.045941 PROGRESS: === Extracted 17812 precursors and 118129 fragments ===
2:48:57.047618 INFO: === FDR correction performed with classifier version 6 ===
2:48:57.050282 PROGRESS: ============================= Precursor FDR =============================
2:48:57.050665 PROGRESS: Total precursors accumulated: 2,664
2:48:57.050755 PROGRESS: Target precursors: 2,638 (99.02%)
2:48:57.050822 PROGRESS: Decoy precursors: 26 (0.98%)
2:48:57.050877 PROGRESS: 
2:48:57.050931 PROGRESS: Precursor Summary:
2:48:57.054722 PROGRESS: Channel   0:	 0.050 FDR: 2,638; 0.010 FDR: 2,638; 0.001 FDR: 2,121
2:48:57.055501 PROGRESS: 
2:48:57.055582 PROGRESS: Protein Summary:
2:48:57.059854 PROGRESS: Channel   0:	 0.050 FDR: 2,072; 0.010 FDR: 2,072; 0.001 FDR: 1,708
2:48:57.060409 PROGRESS: =========================================================================
2:48:57.062302 INFO: Target number of precursors reached.
2:48:57.106290 INFO: fragments_df: keeping 5000 of 118129 [sum(precursor_idx_mask)=59462 sum(mass_error_mask)=118129 stop_rank=5000
2:48:57.157211 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:48:57.810895 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:48:59.042746 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:48:59.043965 INFO: Using score_cutoff 10.297838585186003 (fac=0.99, q=1)
2:48:59.044560 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:48:59.044643 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:48:59.044704 INFO: Updating optimization_manager: score_cutoff        : 10.389213428020478 -> 10.297838585186003
2:48:59.044789 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:48:59.051047 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:48:59.063521 INFO: === checking if optimization conditions were reached ===
2:48:59.064256 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:48:59.071184 INFO: Updating optimization_manager: rt_error            : 303.3041389460001 -> 260.4820989355015
2:48:59.071805 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 260.4821.
2:48:59.071919 INFO: ==============================================
2:48:59.072028 INFO: Starting optimization step 3.
2:48:59.072115 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:48:59.072304 INFO: Using rust extraction backend
2:48:59.072382 PROGRESS: Extracting batch of 5940 precursors
2:48:59.131013 INFO: === Search parameters used ===
2:48:59.131917 INFO: rt_error       : 260.4820989355015
2:48:59.132002 INFO: mobility_error : 0.1
2:48:59.132070 INFO: num_candidates : 3
2:48:59.132145 INFO: ms1_error      : 3
2:48:59.132233 INFO: ms2_error      : 10.0
2:48:59.132294 INFO: fwhm_rt        : 3.0
2:48:59.132350 INFO: quant_window   : 3
2:48:59.132407 INFO: ==============================================
2:49:00.209666 INFO: performing precursor FDR with 40 features
2:49:00.209846 INFO: Decoy channel: -1
2:49:00.209876 INFO: competitive: True
2:49:00.220593 INFO: Setting torch num_threads to 2 for FDR classification task
2:49:00.227740 INFO: Estimating optimal hyperparameters - samples: 14,247, batch_size: 128, learning_rate: 1.77e-04
2:49:00.228089 INFO: Using random state 848077 for train-test-split
2:49:01.792706 INFO: Test AUC: 0.761
2:49:01.792928 INFO: Train AUC: 0.784
2:49:01.792969 INFO: AUC difference: 2.91%
2:49:02.291389 INFO: Resetting torch num_threads to 100
2:49:02.296821 PROGRESS: === Extracted 17809 precursors and 117170 fragments ===
2:49:02.297536 INFO: === FDR correction performed with classifier version 6 ===
2:49:02.299249 PROGRESS: ============================= Precursor FDR =============================
2:49:02.299424 PROGRESS: Total precursors accumulated: 2,693
2:49:02.299496 PROGRESS: Target precursors: 2,667 (99.03%)
2:49:02.299557 PROGRESS: Decoy precursors: 26 (0.97%)
2:49:02.299618 PROGRESS: 
2:49:02.299673 PROGRESS: Precursor Summary:
2:49:02.302371 PROGRESS: Channel   0:	 0.050 FDR: 2,667; 0.010 FDR: 2,667; 0.001 FDR: 2,242
2:49:02.302527 PROGRESS: 
2:49:02.302597 PROGRESS: Protein Summary:
2:49:02.306184 PROGRESS: Channel   0:	 0.050 FDR: 2,098; 0.010 FDR: 2,098; 0.001 FDR: 1,799
2:49:02.306348 PROGRESS: =========================================================================
2:49:02.307005 INFO: Target number of precursors reached.
2:49:02.349295 INFO: fragments_df: keeping 5000 of 117170 [sum(precursor_idx_mask)=59585 sum(mass_error_mask)=117170 stop_rank=5000
2:49:02.379168 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:49:03.160176 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:49:04.092965 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:49:04.094274 INFO: Using score_cutoff 10.25342290763855 (fac=0.99, q=1)
2:49:04.094955 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:49:04.095052 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:49:04.095110 INFO: Updating optimization_manager: score_cutoff        : 10.297838585186003 -> 10.25342290763855
2:49:04.095219 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:49:04.102828 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:49:04.116630 INFO: === checking if optimization conditions were reached ===
2:49:04.117598 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:49:04.124907 INFO: Updating optimization_manager: rt_error            : 260.4820989355015 -> 177.50393109363833
2:49:04.125592 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 177.5039.
2:49:04.125664 INFO: ==============================================
2:49:04.125754 INFO: Starting optimization step 4.
2:49:04.125844 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:49:04.125929 INFO: Using rust extraction backend
2:49:04.126021 PROGRESS: Extracting batch of 5940 precursors
2:49:04.160317 INFO: === Search parameters used ===
2:49:04.161580 INFO: rt_error       : 177.50393109363833
2:49:04.161645 INFO: mobility_error : 0.1
2:49:04.161747 INFO: num_candidates : 3
2:49:04.161800 INFO: ms1_error      : 3
2:49:04.161852 INFO: ms2_error      : 10.0
2:49:04.161898 INFO: fwhm_rt        : 3.0
2:49:04.161948 INFO: quant_window   : 3
2:49:04.161992 INFO: ==============================================
2:49:04.496253 INFO: performing precursor FDR with 40 features
2:49:04.496509 INFO: Decoy channel: -1
2:49:04.496537 INFO: competitive: True
2:49:04.514477 INFO: Setting torch num_threads to 2 for FDR classification task
2:49:04.527501 INFO: Estimating optimal hyperparameters - samples: 14,239, batch_size: 128, learning_rate: 1.77e-04
2:49:04.527984 INFO: Using random state 848077 for train-test-split
2:49:06.181956 INFO: Test AUC: 0.780
2:49:06.182158 INFO: Train AUC: 0.780
2:49:06.182192 INFO: AUC difference: 0.05%
2:49:06.565182 INFO: Resetting torch num_threads to 100
2:49:06.570405 PROGRESS: === Extracted 17799 precursors and 114143 fragments ===
2:49:06.571359 INFO: === FDR correction performed with classifier version 6 ===
2:49:06.573066 PROGRESS: ============================= Precursor FDR =============================
2:49:06.573219 PROGRESS: Total precursors accumulated: 2,769
2:49:06.573286 PROGRESS: Target precursors: 2,742 (99.02%)
2:49:06.573339 PROGRESS: Decoy precursors: 27 (0.98%)
2:49:06.573402 PROGRESS: 
2:49:06.573447 PROGRESS: Precursor Summary:
2:49:06.575879 PROGRESS: Channel   0:	 0.050 FDR: 2,742; 0.010 FDR: 2,742; 0.001 FDR: 2,150
2:49:06.576032 PROGRESS: 
2:49:06.576099 PROGRESS: Protein Summary:
2:49:06.579065 PROGRESS: Channel   0:	 0.050 FDR: 2,153; 0.010 FDR: 2,153; 0.001 FDR: 1,729
2:49:06.579279 PROGRESS: =========================================================================
2:49:06.580335 INFO: Target number of precursors reached.
2:49:06.615674 INFO: fragments_df: keeping 5000 of 114143 [sum(precursor_idx_mask)=60256 sum(mass_error_mask)=114143 stop_rank=5000
2:49:06.641171 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:49:07.328827 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:49:08.476942 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:49:08.478283 INFO: Using score_cutoff 10.13993422908783 (fac=0.99, q=1)
2:49:08.478950 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:49:08.479036 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:49:08.479092 INFO: Updating optimization_manager: score_cutoff        : 10.25342290763855 -> 10.13993422908783
2:49:08.479154 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:49:08.485643 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:49:08.497678 INFO: === checking if optimization conditions were reached ===
2:49:08.498310 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:49:08.506302 INFO: Updating optimization_manager: rt_error            : 177.50393109363833 -> 165.96076235618506
2:49:08.506832 PROGRESS: ❌ rt_error       : optimization incomplete after 5 search(es). Will search with parameter 165.9608.
2:49:08.506945 INFO: ==============================================
2:49:08.507113 INFO: Starting optimization step 5.
2:49:08.507240 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:49:08.507455 INFO: Using rust extraction backend
2:49:08.507639 PROGRESS: Extracting batch of 5940 precursors
2:49:08.538663 INFO: === Search parameters used ===
2:49:08.539325 INFO: rt_error       : 165.96076235618506
2:49:08.539392 INFO: mobility_error : 0.1
2:49:08.539442 INFO: num_candidates : 3
2:49:08.539492 INFO: ms1_error      : 3
2:49:08.539533 INFO: ms2_error      : 10.0
2:49:08.539576 INFO: fwhm_rt        : 3.0
2:49:08.539618 INFO: quant_window   : 3
2:49:08.539656 INFO: ==============================================
2:49:08.885086 INFO: performing precursor FDR with 40 features
2:49:08.885414 INFO: Decoy channel: -1
2:49:08.885446 INFO: competitive: True
2:49:08.896713 INFO: Setting torch num_threads to 2 for FDR classification task
2:49:08.907688 INFO: Estimating optimal hyperparameters - samples: 14,240, batch_size: 128, learning_rate: 1.77e-04
2:49:08.908205 INFO: Using random state 848077 for train-test-split
2:49:11.108175 INFO: Test AUC: 0.759
2:49:11.108555 INFO: Train AUC: 0.787
2:49:11.108596 INFO: AUC difference: 3.60%
2:49:11.565039 INFO: Resetting torch num_threads to 100
2:49:11.574805 PROGRESS: === Extracted 17801 precursors and 113432 fragments ===
2:49:11.576201 INFO: === FDR correction performed with classifier version 6 ===
2:49:11.579425 PROGRESS: ============================= Precursor FDR =============================
2:49:11.579567 PROGRESS: Total precursors accumulated: 2,783
2:49:11.579647 PROGRESS: Target precursors: 2,756 (99.03%)
2:49:11.579705 PROGRESS: Decoy precursors: 27 (0.97%)
2:49:11.579757 PROGRESS: 
2:49:11.579805 PROGRESS: Precursor Summary:
2:49:11.594228 PROGRESS: Channel   0:	 0.050 FDR: 2,756; 0.010 FDR: 2,756; 0.001 FDR: 2,088
2:49:11.594651 PROGRESS: 
2:49:11.594717 PROGRESS: Protein Summary:
2:49:11.598232 PROGRESS: Channel   0:	 0.050 FDR: 2,164; 0.010 FDR: 2,164; 0.001 FDR: 1,688
2:49:11.598588 PROGRESS: =========================================================================
2:49:11.600384 INFO: Target number of precursors reached.
2:49:11.642681 INFO: fragments_df: keeping 5000 of 113432 [sum(precursor_idx_mask)=60151 sum(mass_error_mask)=113432 stop_rank=5000
2:49:11.678781 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:49:12.449158 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:49:13.378707 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:49:13.379876 INFO: Using score_cutoff 10.043652561664581 (fac=0.99, q=1)
2:49:13.380512 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:49:13.380616 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:49:13.380676 INFO: Updating optimization_manager: score_cutoff        : 10.13993422908783 -> 10.043652561664581
2:49:13.380771 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:49:13.388482 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:49:13.401493 INFO: === checking if optimization conditions were reached ===
2:49:13.403112 PROGRESS: === Optimization of rt_error has been performed 6 time(s); minimum number is 5 ===
2:49:13.411576 INFO: Updating optimization_manager: rt_error            : 165.96076235618506 -> 143.80707767214238
2:49:13.412340 PROGRESS: ❌ rt_error       : optimization incomplete after 6 search(es). Will search with parameter 143.8071.
2:49:13.412436 INFO: ==============================================
2:49:13.412536 INFO: Starting optimization step 6.
2:49:13.412625 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:49:13.412744 INFO: Using rust extraction backend
2:49:13.412874 PROGRESS: Extracting batch of 5940 precursors
2:49:13.445043 INFO: === Search parameters used ===
2:49:13.445958 INFO: rt_error       : 143.80707767214238
2:49:13.446029 INFO: mobility_error : 0.1
2:49:13.446083 INFO: num_candidates : 3
2:49:13.446132 INFO: ms1_error      : 3
2:49:13.446174 INFO: ms2_error      : 10.0
2:49:13.446217 INFO: fwhm_rt        : 3.0
2:49:13.446261 INFO: quant_window   : 3
2:49:13.446303 INFO: ==============================================
2:49:13.855389 INFO: performing precursor FDR with 40 features
2:49:13.855719 INFO: Decoy channel: -1
2:49:13.855745 INFO: competitive: True
2:49:13.873660 INFO: Setting torch num_threads to 2 for FDR classification task
2:49:13.889627 INFO: Estimating optimal hyperparameters - samples: 14,238, batch_size: 128, learning_rate: 1.77e-04
2:49:13.890103 INFO: Using random state 848077 for train-test-split
2:49:16.372126 INFO: Test AUC: 0.780
2:49:16.372634 INFO: Train AUC: 0.782
2:49:16.372667 INFO: AUC difference: 0.22%
2:49:16.909990 INFO: Resetting torch num_threads to 100
2:49:16.920795 PROGRESS: === Extracted 17798 precursors and 112117 fragments ===
2:49:16.922614 INFO: === FDR correction performed with classifier version 6 ===
2:49:16.926989 PROGRESS: ============================= Precursor FDR =============================
2:49:16.927600 PROGRESS: Total precursors accumulated: 2,790
2:49:16.927747 PROGRESS: Target precursors: 2,763 (99.03%)
2:49:16.927834 PROGRESS: Decoy precursors: 27 (0.97%)
2:49:16.927915 PROGRESS: 
2:49:16.927970 PROGRESS: Precursor Summary:
2:49:16.935946 PROGRESS: Channel   0:	 0.050 FDR: 2,763; 0.010 FDR: 2,763; 0.001 FDR: 2,033
2:49:16.936775 PROGRESS: 
2:49:16.936846 PROGRESS: Protein Summary:
2:49:16.944306 PROGRESS: Channel   0:	 0.050 FDR: 2,169; 0.010 FDR: 2,169; 0.001 FDR: 1,653
2:49:16.945136 PROGRESS: =========================================================================
2:49:16.947088 INFO: Target number of precursors reached.
2:49:16.993796 INFO: fragments_df: keeping 5000 of 112117 [sum(precursor_idx_mask)=59878 sum(mass_error_mask)=112117 stop_rank=5000
2:49:17.027505 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:49:17.680265 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:49:18.716642 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:49:18.718917 INFO: Using score_cutoff 10.062241185951232 (fac=0.99, q=1)
2:49:18.720029 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:49:18.720147 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:49:18.720217 INFO: Updating optimization_manager: score_cutoff        : 10.043652561664581 -> 10.062241185951232
2:49:18.720316 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:49:18.726673 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:49:18.740392 INFO: === checking if optimization conditions were reached ===
2:49:18.741247 PROGRESS: === Optimization of rt_error has been performed 7 time(s); minimum number is 5 ===
2:49:18.747133 INFO: Updating optimization_manager: rt_error            : 143.80707767214238 -> 128.26291541583734
2:49:18.748058 PROGRESS: ❌ rt_error       : optimization incomplete after 7 search(es). Will search with parameter 128.2629.
2:49:18.748144 INFO: ==============================================
2:49:18.748259 INFO: Starting optimization step 7.
2:49:18.748332 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:49:18.748506 INFO: Using rust extraction backend
2:49:18.748604 PROGRESS: Extracting batch of 5940 precursors
2:49:18.779757 INFO: === Search parameters used ===
2:49:18.780975 INFO: rt_error       : 128.26291541583734
2:49:18.781064 INFO: mobility_error : 0.1
2:49:18.781129 INFO: num_candidates : 3
2:49:18.781177 INFO: ms1_error      : 3
2:49:18.781226 INFO: ms2_error      : 10.0
2:49:18.781301 INFO: fwhm_rt        : 3.0
2:49:18.781350 INFO: quant_window   : 3
2:49:18.781398 INFO: ==============================================
2:49:19.117503 INFO: performing precursor FDR with 40 features
2:49:19.117826 INFO: Decoy channel: -1
2:49:19.117863 INFO: competitive: True
2:49:19.141573 INFO: Setting torch num_threads to 2 for FDR classification task
2:49:19.157657 INFO: Estimating optimal hyperparameters - samples: 14,234, batch_size: 128, learning_rate: 1.77e-04
2:49:19.158207 INFO: Using random state 848077 for train-test-split
2:49:21.393390 INFO: Test AUC: 0.775
2:49:21.393739 INFO: Train AUC: 0.786
2:49:21.393777 INFO: AUC difference: 1.45%
2:49:21.919157 INFO: Resetting torch num_threads to 100
2:49:21.928062 PROGRESS: === Extracted 17793 precursors and 111095 fragments ===
2:49:21.929460 INFO: === FDR correction performed with classifier version 6 ===
2:49:21.932852 PROGRESS: ============================= Precursor FDR =============================
2:49:21.933298 PROGRESS: Total precursors accumulated: 2,746
2:49:21.933391 PROGRESS: Target precursors: 2,719 (99.02%)
2:49:21.933461 PROGRESS: Decoy precursors: 27 (0.98%)
2:49:21.933526 PROGRESS: 
2:49:21.933587 PROGRESS: Precursor Summary:
2:49:21.937121 PROGRESS: Channel   0:	 0.050 FDR: 2,719; 0.010 FDR: 2,719; 0.001 FDR: 1,707
2:49:21.937457 PROGRESS: 
2:49:21.937561 PROGRESS: Protein Summary:
2:49:21.940769 PROGRESS: Channel   0:	 0.050 FDR: 2,132; 0.010 FDR: 2,132; 0.001 FDR: 1,401
2:49:21.941047 PROGRESS: =========================================================================
2:49:21.942239 INFO: Target number of precursors reached.
2:49:22.022188 INFO: fragments_df: keeping 5000 of 111095 [sum(precursor_idx_mask)=58874 sum(mass_error_mask)=111095 stop_rank=5000
2:49:22.073819 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:49:22.891021 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:49:23.877793 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:49:23.878951 INFO: Using score_cutoff 10.119657326316833 (fac=0.99, q=1)
2:49:23.879546 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:49:23.879650 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:49:23.879703 INFO: Updating optimization_manager: score_cutoff        : 10.062241185951232 -> 10.119657326316833
2:49:23.879765 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:49:23.886355 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:49:23.898691 INFO: === checking if optimization conditions were reached ===
2:49:23.899645 PROGRESS: === Optimization of rt_error has been performed 8 time(s); minimum number is 5 ===
2:49:23.905932 INFO: Updating optimization_manager: rt_error            : 128.26291541583734 -> 126.67080139351015
2:49:23.906599 PROGRESS: ❌ rt_error       : optimization incomplete after 8 search(es). Will search with parameter 126.6708.
2:49:23.906678 INFO: ==============================================
2:49:23.906803 INFO: Starting optimization step 8.
2:49:23.906868 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:49:23.906960 INFO: Using rust extraction backend
2:49:23.907033 PROGRESS: Extracting batch of 5940 precursors
2:49:23.935723 INFO: === Search parameters used ===
2:49:23.936613 INFO: rt_error       : 126.67080139351015
2:49:23.936676 INFO: mobility_error : 0.1
2:49:23.936724 INFO: num_candidates : 3
2:49:23.936767 INFO: ms1_error      : 3
2:49:23.936807 INFO: ms2_error      : 10.0
2:49:23.936849 INFO: fwhm_rt        : 3.0
2:49:23.936888 INFO: quant_window   : 3
2:49:23.936928 INFO: ==============================================
2:49:24.249714 INFO: performing precursor FDR with 40 features
2:49:24.250036 INFO: Decoy channel: -1
2:49:24.250067 INFO: competitive: True
2:49:24.271942 INFO: Setting torch num_threads to 2 for FDR classification task
2:49:24.286448 INFO: Estimating optimal hyperparameters - samples: 14,232, batch_size: 128, learning_rate: 1.77e-04
2:49:24.286872 INFO: Using random state 848077 for train-test-split
2:49:26.334411 INFO: Test AUC: 0.788
2:49:26.334751 INFO: Train AUC: 0.783
2:49:26.334790 INFO: AUC difference: 0.62%
2:49:26.765188 INFO: Resetting torch num_threads to 100
2:49:26.771440 PROGRESS: === Extracted 17791 precursors and 110977 fragments ===
2:49:26.772809 INFO: === FDR correction performed with classifier version 6 ===
2:49:26.775167 PROGRESS: ============================= Precursor FDR =============================
2:49:26.775653 PROGRESS: Total precursors accumulated: 2,803
2:49:26.775722 PROGRESS: Target precursors: 2,776 (99.04%)
2:49:26.775777 PROGRESS: Decoy precursors: 27 (0.96%)
2:49:26.775872 PROGRESS: 
2:49:26.775936 PROGRESS: Precursor Summary:
2:49:26.779928 PROGRESS: Channel   0:	 0.050 FDR: 2,776; 0.010 FDR: 2,776; 0.001 FDR: 1,624
2:49:26.780423 PROGRESS: 
2:49:26.780495 PROGRESS: Protein Summary:
2:49:26.783904 PROGRESS: Channel   0:	 0.050 FDR: 2,173; 0.010 FDR: 2,173; 0.001 FDR: 1,341
2:49:26.784360 PROGRESS: =========================================================================
2:49:26.785473 INFO: Target number of precursors reached.
2:49:26.821235 INFO: fragments_df: keeping 5000 of 110977 [sum(precursor_idx_mask)=59878 sum(mass_error_mask)=110977 stop_rank=5000
2:49:26.848157 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:49:27.900528 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:49:28.999022 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:49:29.000235 INFO: Using score_cutoff 10.135445251464844 (fac=0.99, q=1)
2:49:29.000980 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:49:29.001071 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:49:29.001127 INFO: Updating optimization_manager: score_cutoff        : 10.119657326316833 -> 10.135445251464844
2:49:29.001216 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:49:29.008855 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:49:29.022396 INFO: === checking if optimization conditions were reached ===
2:49:29.023429 PROGRESS: === Optimization of rt_error has been performed 9 time(s); minimum number is 5 ===
2:49:29.026619 INFO: Updating optimization_manager: rt_error            : 126.67080139351015 -> 126.67080139351015
2:49:29.026927 INFO: Updating optimization_manager: classifier_version  : 6 -> 15
2:49:29.027031 INFO: Updating optimization_manager: score_cutoff        : 10.135445251464844 -> 10.135445251464844
2:49:29.027119 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:49:29.027204 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:49:29.027302 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 126.6708 found after 9 searches.
2:49:29.027377 INFO: ==============================================
2:49:29.027477 PROGRESS: Optimization finished for rt_error.
2:49:29.059326 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:49:29.067929 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:49:29.080854 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:49:29.081384 PROGRESS: ==============================================
2:49:29.081503 PROGRESS: ms2_error      : 10.0000
2:49:29.081608 PROGRESS: rt_error       : 126.6708
2:49:29.081657 PROGRESS: ==============================================
2:49:29.085207 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:49:29.344875 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:49:29.999789 INFO: Using rust extraction backend
2:49:30.000900 PROGRESS: Extracting batch of 259156 precursors
2:49:30.855692 INFO: === Search parameters used ===
2:49:30.856126 INFO: rt_error       : 126.67080139351015
2:49:30.856205 INFO: mobility_error : 0.1
2:49:30.856257 INFO: num_candidates : 3
2:49:30.856303 INFO: ms1_error      : 3
2:49:30.856353 INFO: ms2_error      : 10.0
2:49:30.856396 INFO: fwhm_rt        : 3.0
2:49:30.856438 INFO: quant_window   : 3
2:49:30.856479 INFO: ==============================================
2:49:31.578351 INFO: Removed 180715 precursors with score below cutoff 10.135445251464844
2:49:32.492613 INFO: performing precursor FDR with 40 features
2:49:32.492865 INFO: Decoy channel: -1
2:49:32.492893 INFO: competitive: True
2:49:32.646816 INFO: Setting torch num_threads to 2 for FDR classification task
2:49:32.764548 WARNING: FDR calculation for 331834 target and 264842 decoy PSMs
2:49:32.764980 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:49:33.342887 INFO: Estimating optimal hyperparameters - samples: 477,340, batch_size: 1,955, learning_rate: 6.91e-04
2:49:33.345194 INFO: Using random state 605610 for train-test-split
2:49:55.888262 INFO: Test AUC: 0.809
2:49:55.888808 INFO: Train AUC: 0.810
2:49:55.888876 INFO: AUC difference: 0.20%
2:49:56.621060 INFO: Resetting torch num_threads to 100
2:49:57.835610 PROGRESS: ============================= Precursor FDR =============================
2:49:57.836468 PROGRESS: Total precursors accumulated: 123,786
2:49:57.836554 PROGRESS: Target precursors: 122,561 (99.01%)
2:49:57.836617 PROGRESS: Decoy precursors: 1,225 (0.99%)
2:49:57.836669 PROGRESS: 
2:49:57.836719 PROGRESS: Precursor Summary:
2:49:57.978548 PROGRESS: Channel   0:	 0.050 FDR: 122,561; 0.010 FDR: 122,561; 0.001 FDR: 111,546
2:49:57.979317 PROGRESS: 
2:49:57.979387 PROGRESS: Protein Summary:
2:49:58.267373 PROGRESS: Channel   0:	 0.050 FDR: 10,148; 0.010 FDR: 10,148; 0.001 FDR: 10,040
2:49:58.268121 PROGRESS: =========================================================================
2:49:58.281969 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/psm.parquet
2:49:58.996100 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/frag.parquet
2:49:59.792785 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:50:00.294514 PROGRESS: Loading raw file 6/6: LFQ_Astral_DIA_15min_50ng_Condition_B_REP3 
2:50:00.295046 INFO: Quantification results path: /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant
2:50:00.295395 INFO: Initializing TimingManager
2:50:00.298021 INFO: Initializing RawFileManager
2:50:32.360702 WARNING: The MS1 spectra in the raw file do not follow a DIA cycle.
AlphaDIA will therefore not be able to use the MS1 information.
While acquiring data, please make sure to use an integer loop count of 1 or 2 over time based loop count in seconds.
2:50:32.377641 INFO: Determining DIA cycle
2:50:32.396775 INFO: Found cycle with start 0.00 min and length 300.
2:50:33.131875 INFO: RT (min)            : 0.0 - 26.9
2:50:33.132213 INFO: RT duration (sec)   : 1611.2
2:50:33.132247 INFO: RT duration (min)   : 26.9
2:50:33.132282 INFO: Cycle len (scans)   : 300
2:50:33.132307 INFO: Cycle len (sec)     : 1.65
2:50:33.132327 INFO: Number of cycles    : 978
2:50:33.132348 INFO: MS2 range (m/z)     : 380.4 - 980.7
2:50:33.132421 INFO: Creating DIA data object took: 32.83415126800537
2:50:34.957370 INFO: Creating DIA data NG object took: 1.82466459274292
2:50:35.104608 INFO: Initializing CalibrationManager
2:50:35.105254 INFO: Setting up calibration estimators ..
2:50:35.105334 INFO: Found 1 estimator(s) in calibration group 'fragment'
2:50:35.105494 INFO: Initializing estimator 'mz' in group 'fragment' with '{'input_columns': ['mz_library'], 'target_columns': ['mz_observed'], 'output_columns': ['mz_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 2}, 'transform_deviation': '1e6'}' ..
2:50:35.105626 INFO: Found 3 estimator(s) in calibration group 'precursor'
2:50:35.105687 INFO: Skipping estimator 'mz' in group 'precursor' as it is not available in the raw data
2:50:35.105771 INFO: Initializing estimator 'rt' in group 'precursor' with '{'input_columns': ['rt_library'], 'target_columns': ['rt_observed'], 'output_columns': ['rt_calibrated'], 'model': 'LOESSRegression', 'model_args': {'n_kernels': 6}}' ..
2:50:35.105845 INFO: Skipping estimator 'mobility' in group 'precursor' as it is not available in the raw data
2:50:35.105898 INFO: Done setting up calibration estimators.
2:50:35.106514 INFO: Initializing OptimizationManager
2:50:35.106710 INFO: initial parameter: ms1_error = 3
2:50:35.106765 INFO: initial parameter: ms2_error = 10
2:50:35.106822 INFO: initial parameter: rt_error = 805.611083984375
2:50:35.106869 INFO: initial parameter: mobility_error = 0.1
2:50:35.106910 INFO: initial parameter: num_candidates = 1
2:50:35.106950 INFO: initial parameter: fwhm_rt = 5
2:50:35.107003 INFO: initial parameter: fwhm_mobility = 0.01
2:50:35.107046 INFO: initial parameter: score_cutoff = 0
2:50:35.107086 INFO: initial parameter: classifier_version = -1
2:50:35.107172 PROGRESS: Initializing workflow LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:50:35.107991 INFO: FDRManager: loading saved state not requested, will be initialized.
2:50:35.108055 INFO: Initializing FDRManager
2:50:35.108120 INFO: Loading classifier store from /home/robbe/bin/alphadia/alphadia/constants/classifier
2:50:35.252046 PROGRESS: Initializing spectral library: 131,021 target precursors potentially observable (0 removed)
2:50:35.357806 INFO: Updating optimization_manager: ms2_error           : 10 -> 10
2:50:35.359286 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 805.611083984375
2:50:35.359522 PROGRESS: Starting initial search for precursors.
2:50:35.359785 INFO: Starting optimization step 0.
2:50:35.359891 PROGRESS: === Extracting elution groups 0 to 1000 ===
2:50:35.359979 INFO: Using rust extraction backend
2:50:35.360145 PROGRESS: Extracting batch of 1982 precursors
2:50:35.378276 INFO: === Search parameters used ===
2:50:35.379584 INFO: rt_error       : 805.611083984375
2:50:35.379671 INFO: mobility_error : 0.1
2:50:35.379739 INFO: num_candidates : 1
2:50:35.379807 INFO: ms1_error      : 3
2:50:35.379891 INFO: ms2_error      : 10
2:50:35.379945 INFO: fwhm_rt        : 5
2:50:35.379989 INFO: quant_window   : 3
2:50:35.380047 INFO: ==============================================
2:50:35.489545 INFO: performing precursor FDR with 40 features
2:50:35.490088 INFO: Decoy channel: -1
2:50:35.490136 INFO: competitive: True
2:50:35.495373 INFO: Setting torch num_threads to 2 for FDR classification task
2:50:35.500593 INFO: Estimating optimal hyperparameters - samples: 1,585, batch_size: 128, learning_rate: 1.77e-04
2:50:35.503865 INFO: Using random state 526724 for train-test-split
2:50:35.742626 INFO: Test AUC: 0.880
2:50:35.742841 INFO: Train AUC: 0.880
2:50:35.742872 INFO: AUC difference: 0.02%
2:50:36.065494 INFO: Resetting torch num_threads to 100
2:50:36.068260 PROGRESS: === Extracted 1982 precursors and 15417 fragments ===
2:50:36.068907 INFO: === FDR correction performed with classifier version -1 ===
2:50:36.069695 PROGRESS: ============================= Precursor FDR =============================
2:50:36.069793 PROGRESS: Total precursors accumulated: 661
2:50:36.069855 PROGRESS: Target precursors: 655 (99.09%)
2:50:36.069911 PROGRESS: Decoy precursors: 6 (0.91%)
2:50:36.069969 PROGRESS: 
2:50:36.070021 PROGRESS: Precursor Summary:
2:50:36.071369 PROGRESS: Channel   0:	 0.050 FDR:   655; 0.010 FDR:   655; 0.001 FDR:   655
2:50:36.071471 PROGRESS: 
2:50:36.071529 PROGRESS: Protein Summary:
2:50:36.073254 PROGRESS: Channel   0:	 0.050 FDR:   604; 0.010 FDR:   604; 0.001 FDR:   604
2:50:36.073394 PROGRESS: =========================================================================
2:50:36.073889 INFO: Target number of precursors not reached yet.
2:50:36.086325 INFO: Starting optimization step 1.
2:50:36.086774 PROGRESS: === Extracting elution groups 1000 to 3000 ===
2:50:36.086869 INFO: Using rust extraction backend
2:50:36.086938 PROGRESS: Extracting batch of 3958 precursors
2:50:36.099094 INFO: === Search parameters used ===
2:50:36.099613 INFO: rt_error       : 805.611083984375
2:50:36.099669 INFO: mobility_error : 0.1
2:50:36.099719 INFO: num_candidates : 1
2:50:36.099765 INFO: ms1_error      : 3
2:50:36.099807 INFO: ms2_error      : 10
2:50:36.099874 INFO: fwhm_rt        : 5
2:50:36.099918 INFO: quant_window   : 3
2:50:36.099962 INFO: ==============================================
2:50:36.194513 INFO: performing precursor FDR with 40 features
2:50:36.194674 INFO: Decoy channel: -1
2:50:36.194700 INFO: competitive: True
2:50:36.201427 INFO: Setting torch num_threads to 2 for FDR classification task
2:50:36.205072 INFO: Estimating optimal hyperparameters - samples: 4,752, batch_size: 128, learning_rate: 1.77e-04
2:50:36.205272 INFO: Using random state 215387 for train-test-split
2:50:36.893075 INFO: Test AUC: 0.867
2:50:36.893346 INFO: Train AUC: 0.895
2:50:36.893389 INFO: AUC difference: 3.11%
2:50:37.297073 INFO: Resetting torch num_threads to 100
2:50:37.309261 PROGRESS: === Extracted 5940 precursors and 46145 fragments ===
2:50:37.310552 INFO: === FDR correction performed with classifier version -1 ===
2:50:37.312210 PROGRESS: ============================= Precursor FDR =============================
2:50:37.312356 PROGRESS: Total precursors accumulated: 2,336
2:50:37.312424 PROGRESS: Target precursors: 2,313 (99.02%)
2:50:37.312476 PROGRESS: Decoy precursors: 23 (0.98%)
2:50:37.312524 PROGRESS: 
2:50:37.312574 PROGRESS: Precursor Summary:
2:50:37.314868 PROGRESS: Channel   0:	 0.050 FDR: 2,313; 0.010 FDR: 2,313; 0.001 FDR: 2,313
2:50:37.315022 PROGRESS: 
2:50:37.315080 PROGRESS: Protein Summary:
2:50:37.317840 PROGRESS: Channel   0:	 0.050 FDR: 1,829; 0.010 FDR: 1,829; 0.001 FDR: 1,829
2:50:37.318001 PROGRESS: =========================================================================
2:50:37.318850 INFO: Target number of precursors reached.
2:50:37.335419 INFO: fragments_df: keeping 5000 of 46145 [sum(precursor_idx_mask)=22901 sum(mass_error_mask)=46145 stop_rank=5000
2:50:37.361128 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:50:37.964881 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:50:38.893000 INFO: Updating optimization_manager: num_candidates      : 1 -> 3
2:50:38.894127 INFO: Using score_cutoff 10.344606392669679 (fac=0.99, q=1)
2:50:38.894778 INFO: Updating optimization_manager: fwhm_rt             : 5 -> 3.0
2:50:38.894881 INFO: Updating optimization_manager: fwhm_mobility       : 0.01 -> -1.0
2:50:38.894939 INFO: Updating optimization_manager: score_cutoff        : 0 -> 10.344606392669679
2:50:38.895013 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:50:38.901302 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:50:38.914583 INFO: Updating optimization_manager: classifier_version  : -1 -> 1
2:50:38.915721 PROGRESS: Required number of precursors found. Starting search parameter optimization.
2:50:38.915888 INFO: Starting optimization step 2.
2:50:38.915971 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:50:38.916055 INFO: Using rust extraction backend
2:50:38.916124 PROGRESS: Extracting batch of 5940 precursors
2:50:38.946099 INFO: === Search parameters used ===
2:50:38.946741 INFO: rt_error       : 805.611083984375
2:50:38.946796 INFO: mobility_error : 0.1
2:50:38.946842 INFO: num_candidates : 3
2:50:38.946884 INFO: ms1_error      : 3
2:50:38.946924 INFO: ms2_error      : 10
2:50:38.946965 INFO: fwhm_rt        : 3.0
2:50:38.947006 INFO: quant_window   : 3
2:50:38.947048 INFO: ==============================================
2:50:39.107402 INFO: performing precursor FDR with 40 features
2:50:39.107522 INFO: Decoy channel: -1
2:50:39.107545 INFO: competitive: True
2:50:39.112624 INFO: Setting torch num_threads to 2 for FDR classification task
2:50:39.117721 INFO: Estimating optimal hyperparameters - samples: 14,249, batch_size: 128, learning_rate: 1.77e-04
2:50:39.117880 INFO: Using random state 632797 for train-test-split
2:50:41.001623 INFO: Test AUC: 0.645
2:50:41.001897 INFO: Train AUC: 0.664
2:50:41.001931 INFO: AUC difference: 2.88%
2:50:41.511338 INFO: Resetting torch num_threads to 100
2:50:41.519885 PROGRESS: === Extracted 17812 precursors and 120179 fragments ===
2:50:41.521614 INFO: === FDR correction performed with classifier version 1 ===
2:50:41.524658 PROGRESS: ============================= Precursor FDR =============================
2:50:41.524829 PROGRESS: Total precursors accumulated: 3,000
2:50:41.524899 PROGRESS: Target precursors: 2,975 (99.17%)
2:50:41.524966 PROGRESS: Decoy precursors: 25 (0.83%)
2:50:41.525034 PROGRESS: 
2:50:41.525088 PROGRESS: Precursor Summary:
2:50:41.527961 PROGRESS: Channel   0:	 0.050 FDR: 2,975; 0.010 FDR: 2,975; 0.001 FDR: 2,956
2:50:41.528163 PROGRESS: 
2:50:41.528265 PROGRESS: Protein Summary:
2:50:41.531707 PROGRESS: Channel   0:	 0.050 FDR: 2,324; 0.010 FDR: 2,324; 0.001 FDR: 2,311
2:50:41.532039 PROGRESS: =========================================================================
2:50:41.533375 INFO: Target number of precursors reached.
2:50:41.573480 INFO: fragments_df: keeping 5000 of 120179 [sum(precursor_idx_mask)=66243 sum(mass_error_mask)=120179 stop_rank=5000
2:50:41.608544 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:50:42.207814 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:50:43.150720 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:50:43.152626 INFO: Using score_cutoff 9.656464037132263 (fac=0.99, q=1)
2:50:43.153340 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:50:43.153425 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:50:43.153482 INFO: Updating optimization_manager: score_cutoff        : 10.344606392669679 -> 9.656464037132263
2:50:43.153571 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:50:43.160180 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:50:43.173011 INFO: === checking if optimization conditions were reached ===
2:50:43.177439 INFO: Updating optimization_manager: ms2_error           : 10 -> 10.0
2:50:43.177929 INFO: Updating optimization_manager: classifier_version  : 1 -> 2
2:50:43.178014 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:50:43.178087 INFO: ==============================================
2:50:43.178190 INFO: Starting optimization step 3.
2:50:43.178290 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:50:43.178560 INFO: Using rust extraction backend
2:50:43.178737 PROGRESS: Extracting batch of 5940 precursors
2:50:43.208205 INFO: === Search parameters used ===
2:50:43.208930 INFO: rt_error       : 805.611083984375
2:50:43.208986 INFO: mobility_error : 0.1
2:50:43.209036 INFO: num_candidates : 3
2:50:43.209081 INFO: ms1_error      : 3
2:50:43.209123 INFO: ms2_error      : 10.0
2:50:43.209164 INFO: fwhm_rt        : 3.0
2:50:43.209208 INFO: quant_window   : 3
2:50:43.209268 INFO: ==============================================
2:50:43.509843 INFO: performing precursor FDR with 40 features
2:50:43.510266 INFO: Decoy channel: -1
2:50:43.510300 INFO: competitive: True
2:50:43.529248 INFO: Setting torch num_threads to 2 for FDR classification task
2:50:43.543037 INFO: Estimating optimal hyperparameters - samples: 14,250, batch_size: 128, learning_rate: 1.77e-04
2:50:43.543461 INFO: Using random state 110667 for train-test-split
2:50:45.753927 INFO: Test AUC: 0.735
2:50:45.754484 INFO: Train AUC: 0.750
2:50:45.754524 INFO: AUC difference: 1.91%
2:50:46.284774 INFO: Resetting torch num_threads to 100
2:50:46.305723 PROGRESS: === Extracted 17813 precursors and 120249 fragments ===
2:50:46.307420 INFO: === FDR correction performed with classifier version 2 ===
2:50:46.311558 PROGRESS: ============================= Precursor FDR =============================
2:50:46.312018 PROGRESS: Total precursors accumulated: 2,384
2:50:46.312177 PROGRESS: Target precursors: 2,361 (99.04%)
2:50:46.312263 PROGRESS: Decoy precursors: 23 (0.96%)
2:50:46.312342 PROGRESS: 
2:50:46.312414 PROGRESS: Precursor Summary:
2:50:46.319840 PROGRESS: Channel   0:	 0.050 FDR: 2,361; 0.010 FDR: 2,361; 0.001 FDR: 1,227
2:50:46.320423 PROGRESS: 
2:50:46.320493 PROGRESS: Protein Summary:
2:50:46.324711 PROGRESS: Channel   0:	 0.050 FDR: 1,868; 0.010 FDR: 1,868; 0.001 FDR: 1,047
2:50:46.325052 PROGRESS: =========================================================================
2:50:46.327521 INFO: Target number of precursors reached.
2:50:46.381850 INFO: fragments_df: keeping 5000 of 120249 [sum(precursor_idx_mask)=54598 sum(mass_error_mask)=120249 stop_rank=5000
2:50:46.437438 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:50:46.971547 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:50:48.016815 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:50:48.017894 INFO: Using score_cutoff 10.691726955413818 (fac=0.99, q=1)
2:50:48.018543 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:50:48.018633 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:50:48.018694 INFO: Updating optimization_manager: score_cutoff        : 9.656464037132263 -> 10.691726955413818
2:50:48.018802 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:50:48.025303 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:50:48.037625 INFO: === checking if optimization conditions were reached ===
2:50:48.042412 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:50:48.042838 INFO: Updating optimization_manager: classifier_version  : 2 -> 3
2:50:48.042929 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:50:48.043029 INFO: ==============================================
2:50:48.043117 INFO: Starting optimization step 4.
2:50:48.043192 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:50:48.043284 INFO: Using rust extraction backend
2:50:48.043376 PROGRESS: Extracting batch of 5940 precursors
2:50:48.075511 INFO: === Search parameters used ===
2:50:48.076264 INFO: rt_error       : 805.611083984375
2:50:48.076335 INFO: mobility_error : 0.1
2:50:48.076390 INFO: num_candidates : 3
2:50:48.076438 INFO: ms1_error      : 3
2:50:48.076483 INFO: ms2_error      : 10.0
2:50:48.076528 INFO: fwhm_rt        : 3.0
2:50:48.076574 INFO: quant_window   : 3
2:50:48.076617 INFO: ==============================================
2:50:48.447618 INFO: performing precursor FDR with 40 features
2:50:48.447842 INFO: Decoy channel: -1
2:50:48.447873 INFO: competitive: True
2:50:48.459390 INFO: Setting torch num_threads to 2 for FDR classification task
2:50:48.468933 INFO: Estimating optimal hyperparameters - samples: 14,250, batch_size: 128, learning_rate: 1.77e-04
2:50:48.469241 INFO: Using random state 250920 for train-test-split
2:50:50.760441 INFO: Test AUC: 0.749
2:50:50.760740 INFO: Train AUC: 0.763
2:50:50.760782 INFO: AUC difference: 1.84%
2:50:51.299317 INFO: Resetting torch num_threads to 100
2:50:51.310809 PROGRESS: === Extracted 17813 precursors and 120265 fragments ===
2:50:51.312679 INFO: === FDR correction performed with classifier version 3 ===
2:50:51.316730 PROGRESS: ============================= Precursor FDR =============================
2:50:51.317156 PROGRESS: Total precursors accumulated: 2,502
2:50:51.317390 PROGRESS: Target precursors: 2,478 (99.04%)
2:50:51.317566 PROGRESS: Decoy precursors: 24 (0.96%)
2:50:51.317674 PROGRESS: 
2:50:51.317737 PROGRESS: Precursor Summary:
2:50:51.325799 PROGRESS: Channel   0:	 0.050 FDR: 2,478; 0.010 FDR: 2,478; 0.001 FDR: 1,574
2:50:51.326585 PROGRESS: 
2:50:51.326929 PROGRESS: Protein Summary:
2:50:51.340331 PROGRESS: Channel   0:	 0.050 FDR: 1,955; 0.010 FDR: 1,955; 0.001 FDR: 1,312
2:50:51.341169 PROGRESS: =========================================================================
2:50:51.344557 INFO: Target number of precursors reached.
2:50:51.393377 INFO: fragments_df: keeping 5000 of 120265 [sum(precursor_idx_mask)=56878 sum(mass_error_mask)=120265 stop_rank=5000
2:50:51.416589 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:50:52.123671 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:50:53.273630 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:50:53.274797 INFO: Using score_cutoff 10.592010128402709 (fac=0.99, q=1)
2:50:53.275626 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:50:53.275753 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:50:53.276044 INFO: Updating optimization_manager: score_cutoff        : 10.691726955413818 -> 10.592010128402709
2:50:53.276154 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:50:53.282274 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:50:53.293708 INFO: === checking if optimization conditions were reached ===
2:50:53.297618 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:50:53.297918 INFO: Updating optimization_manager: classifier_version  : 3 -> 4
2:50:53.298042 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:50:53.298119 INFO: ==============================================
2:50:53.298209 INFO: Starting optimization step 5.
2:50:53.298286 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:50:53.298373 INFO: Using rust extraction backend
2:50:53.298455 PROGRESS: Extracting batch of 5940 precursors
2:50:53.320284 INFO: === Search parameters used ===
2:50:53.320811 INFO: rt_error       : 805.611083984375
2:50:53.320876 INFO: mobility_error : 0.1
2:50:53.320934 INFO: num_candidates : 3
2:50:53.320990 INFO: ms1_error      : 3
2:50:53.321042 INFO: ms2_error      : 10.0
2:50:53.321093 INFO: fwhm_rt        : 3.0
2:50:53.321145 INFO: quant_window   : 3
2:50:53.321194 INFO: ==============================================
2:50:53.975251 INFO: performing precursor FDR with 40 features
2:50:53.975525 INFO: Decoy channel: -1
2:50:53.975564 INFO: competitive: True
2:50:53.991797 INFO: Setting torch num_threads to 2 for FDR classification task
2:50:54.005353 INFO: Estimating optimal hyperparameters - samples: 14,250, batch_size: 128, learning_rate: 1.77e-04
2:50:54.005813 INFO: Using random state 820486 for train-test-split
2:50:56.287935 INFO: Test AUC: 0.744
2:50:56.288237 INFO: Train AUC: 0.775
2:50:56.288296 INFO: AUC difference: 3.92%
2:50:57.456754 INFO: Resetting torch num_threads to 100
2:50:57.465824 PROGRESS: === Extracted 17813 precursors and 120241 fragments ===
2:50:57.466935 INFO: === FDR correction performed with classifier version 4 ===
2:50:57.469079 PROGRESS: ============================= Precursor FDR =============================
2:50:57.469232 PROGRESS: Total precursors accumulated: 2,537
2:50:57.469300 PROGRESS: Target precursors: 2,512 (99.01%)
2:50:57.469355 PROGRESS: Decoy precursors: 25 (0.99%)
2:50:57.469421 PROGRESS: 
2:50:57.469469 PROGRESS: Precursor Summary:
2:50:57.472198 PROGRESS: Channel   0:	 0.050 FDR: 2,512; 0.010 FDR: 2,512; 0.001 FDR: 1,617
2:50:57.472352 PROGRESS: 
2:50:57.472410 PROGRESS: Protein Summary:
2:50:57.475331 PROGRESS: Channel   0:	 0.050 FDR: 1,978; 0.010 FDR: 1,978; 0.001 FDR: 1,342
2:50:57.475508 PROGRESS: =========================================================================
2:50:57.476983 INFO: Target number of precursors reached.
2:50:57.517260 INFO: fragments_df: keeping 5000 of 120241 [sum(precursor_idx_mask)=57461 sum(mass_error_mask)=120241 stop_rank=5000
2:50:57.547069 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:50:58.300116 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:51:01.252504 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:51:01.254863 INFO: Using score_cutoff 10.527428389835357 (fac=0.99, q=1)
2:51:01.256628 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:51:01.257044 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:51:01.257275 INFO: Updating optimization_manager: score_cutoff        : 10.592010128402709 -> 10.527428389835357
2:51:01.257546 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:51:01.268900 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:51:01.291054 INFO: === checking if optimization conditions were reached ===
2:51:01.300614 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:51:01.301404 INFO: Updating optimization_manager: classifier_version  : 4 -> 5
2:51:01.301635 PROGRESS: ❌ ms2_error      : 10.0000 > 10.0000 or insufficient steps taken.
2:51:01.301879 INFO: ==============================================
2:51:01.302277 INFO: Starting optimization step 6.
2:51:01.302526 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:51:01.302811 INFO: Using rust extraction backend
2:51:01.303131 PROGRESS: Extracting batch of 5940 precursors
2:51:01.374587 INFO: === Search parameters used ===
2:51:01.375613 INFO: rt_error       : 805.611083984375
2:51:01.375886 INFO: mobility_error : 0.1
2:51:01.376122 INFO: num_candidates : 3
2:51:01.376347 INFO: ms1_error      : 3
2:51:01.376539 INFO: ms2_error      : 10.0
2:51:01.376746 INFO: fwhm_rt        : 3.0
2:51:01.376957 INFO: quant_window   : 3
2:51:01.377081 INFO: ==============================================
2:51:02.533088 INFO: performing precursor FDR with 40 features
2:51:02.533508 INFO: Decoy channel: -1
2:51:02.533653 INFO: competitive: True
2:51:02.579260 INFO: Setting torch num_threads to 2 for FDR classification task
2:51:02.614304 INFO: Estimating optimal hyperparameters - samples: 14,250, batch_size: 128, learning_rate: 1.77e-04
2:51:02.615150 INFO: Using random state 180237 for train-test-split
2:51:07.377311 INFO: Test AUC: 0.767
2:51:07.377793 INFO: Train AUC: 0.779
2:51:07.377838 INFO: AUC difference: 1.46%
2:51:08.146134 INFO: Resetting torch num_threads to 100
2:51:08.158623 PROGRESS: === Extracted 17813 precursors and 120249 fragments ===
2:51:08.160156 INFO: === FDR correction performed with classifier version 5 ===
2:51:08.163539 PROGRESS: ============================= Precursor FDR =============================
2:51:08.163799 PROGRESS: Total precursors accumulated: 2,636
2:51:08.163903 PROGRESS: Target precursors: 2,610 (99.01%)
2:51:08.163998 PROGRESS: Decoy precursors: 26 (0.99%)
2:51:08.164059 PROGRESS: 
2:51:08.164127 PROGRESS: Precursor Summary:
2:51:08.168584 PROGRESS: Channel   0:	 0.050 FDR: 2,610; 0.010 FDR: 2,610; 0.001 FDR: 1,512
2:51:08.169032 PROGRESS: 
2:51:08.169104 PROGRESS: Protein Summary:
2:51:08.174346 PROGRESS: Channel   0:	 0.050 FDR: 2,055; 0.010 FDR: 2,055; 0.001 FDR: 1,270
2:51:08.174952 PROGRESS: =========================================================================
2:51:08.177444 INFO: Target number of precursors reached.
2:51:08.242678 INFO: fragments_df: keeping 5000 of 120249 [sum(precursor_idx_mask)=59470 sum(mass_error_mask)=120249 stop_rank=5000
2:51:08.327493 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:51:09.248928 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:51:10.350712 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:51:10.352233 INFO: Using score_cutoff 10.493186502742768 (fac=0.99, q=1)
2:51:10.353636 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:51:10.353920 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:51:10.354023 INFO: Updating optimization_manager: score_cutoff        : 10.527428389835357 -> 10.493186502742768
2:51:10.354110 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:51:10.362218 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:51:10.376848 INFO: === checking if optimization conditions were reached ===
2:51:10.381544 INFO: Updating optimization_manager: ms2_error           : 10.0 -> 10.0
2:51:10.382044 INFO: Updating optimization_manager: classifier_version  : 5 -> 6
2:51:10.382136 PROGRESS: ✅ ms2_error      : 10.0000 <= 10.0000
2:51:10.382220 INFO: ==============================================
2:51:10.382390 PROGRESS: Optimization finished for ms2_error.
2:51:10.421911 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:51:10.429621 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:51:10.443754 INFO: Starting optimization step 0.
2:51:10.444319 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:51:10.444445 INFO: Using rust extraction backend
2:51:10.444547 PROGRESS: Extracting batch of 5940 precursors
2:51:10.482216 INFO: === Search parameters used ===
2:51:10.482875 INFO: rt_error       : 805.611083984375
2:51:10.482955 INFO: mobility_error : 0.1
2:51:10.483025 INFO: num_candidates : 3
2:51:10.483086 INFO: ms1_error      : 3
2:51:10.483143 INFO: ms2_error      : 10.0
2:51:10.483256 INFO: fwhm_rt        : 3.0
2:51:10.483315 INFO: quant_window   : 3
2:51:10.483372 INFO: ==============================================
2:51:11.197188 INFO: performing precursor FDR with 40 features
2:51:11.197502 INFO: Decoy channel: -1
2:51:11.197550 INFO: competitive: True
2:51:11.235259 INFO: Setting torch num_threads to 2 for FDR classification task
2:51:11.265847 INFO: Estimating optimal hyperparameters - samples: 14,250, batch_size: 128, learning_rate: 1.77e-04
2:51:11.266324 INFO: Using random state 657903 for train-test-split
2:51:13.878618 INFO: Test AUC: 0.771
2:51:13.878917 INFO: Train AUC: 0.788
2:51:13.878953 INFO: AUC difference: 2.17%
2:51:14.319111 INFO: Resetting torch num_threads to 100
2:51:14.327976 PROGRESS: === Extracted 17813 precursors and 120290 fragments ===
2:51:14.329321 INFO: === FDR correction performed with classifier version 6 ===
2:51:14.332661 PROGRESS: ============================= Precursor FDR =============================
2:51:14.333011 PROGRESS: Total precursors accumulated: 2,605
2:51:14.333115 PROGRESS: Target precursors: 2,580 (99.04%)
2:51:14.333182 PROGRESS: Decoy precursors: 25 (0.96%)
2:51:14.333232 PROGRESS: 
2:51:14.333277 PROGRESS: Precursor Summary:
2:51:14.339051 PROGRESS: Channel   0:	 0.050 FDR: 2,580; 0.010 FDR: 2,580; 0.001 FDR: 1,468
2:51:14.339544 PROGRESS: 
2:51:14.339609 PROGRESS: Protein Summary:
2:51:14.343570 PROGRESS: Channel   0:	 0.050 FDR: 2,032; 0.010 FDR: 2,032; 0.001 FDR: 1,236
2:51:14.343946 PROGRESS: =========================================================================
2:51:14.345251 INFO: Target number of precursors reached.
2:51:14.386976 INFO: fragments_df: keeping 5000 of 120290 [sum(precursor_idx_mask)=58743 sum(mass_error_mask)=120290 stop_rank=5000
2:51:14.416913 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:51:15.853530 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:51:18.319918 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:51:18.321729 INFO: Using score_cutoff 10.310233298778533 (fac=0.99, q=1)
2:51:18.322879 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:51:18.323071 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:51:18.323252 INFO: Updating optimization_manager: score_cutoff        : 10.493186502742768 -> 10.310233298778533
2:51:18.323425 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:51:18.332235 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:51:18.348561 INFO: === checking if optimization conditions were reached ===
2:51:18.349376 PROGRESS: === Optimization of rt_error has been performed 1 time(s); minimum number is 5 ===
2:51:18.358570 INFO: Updating optimization_manager: rt_error            : 805.611083984375 -> 490.46314786721365
2:51:18.359379 PROGRESS: ❌ rt_error       : optimization incomplete after 1 search(es). Will search with parameter 490.4631.
2:51:18.359589 INFO: ==============================================
2:51:18.359810 INFO: Starting optimization step 1.
2:51:18.360022 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:51:18.360183 INFO: Using rust extraction backend
2:51:18.360328 PROGRESS: Extracting batch of 5940 precursors
2:51:18.408353 INFO: === Search parameters used ===
2:51:18.409251 INFO: rt_error       : 490.46314786721365
2:51:18.409404 INFO: mobility_error : 0.1
2:51:18.409565 INFO: num_candidates : 3
2:51:18.409699 INFO: ms1_error      : 3
2:51:18.409828 INFO: ms2_error      : 10.0
2:51:18.409971 INFO: fwhm_rt        : 3.0
2:51:18.410130 INFO: quant_window   : 3
2:51:18.410311 INFO: ==============================================
2:51:18.714660 INFO: performing precursor FDR with 40 features
2:51:18.714937 INFO: Decoy channel: -1
2:51:18.714970 INFO: competitive: True
2:51:18.738229 INFO: Setting torch num_threads to 2 for FDR classification task
2:51:18.757006 INFO: Estimating optimal hyperparameters - samples: 14,252, batch_size: 128, learning_rate: 1.77e-04
2:51:18.757404 INFO: Using random state 657903 for train-test-split
2:51:20.986011 INFO: Test AUC: 0.753
2:51:20.986259 INFO: Train AUC: 0.789
2:51:20.986300 INFO: AUC difference: 4.58%
2:51:21.377561 INFO: Resetting torch num_threads to 100
2:51:21.384168 PROGRESS: === Extracted 17816 precursors and 120146 fragments ===
2:51:21.385182 INFO: === FDR correction performed with classifier version 6 ===
2:51:21.386971 PROGRESS: ============================= Precursor FDR =============================
2:51:21.387120 PROGRESS: Total precursors accumulated: 2,633
2:51:21.387220 PROGRESS: Target precursors: 2,607 (99.01%)
2:51:21.387272 PROGRESS: Decoy precursors: 26 (0.99%)
2:51:21.387321 PROGRESS: 
2:51:21.387367 PROGRESS: Precursor Summary:
2:51:21.389694 PROGRESS: Channel   0:	 0.050 FDR: 2,607; 0.010 FDR: 2,607; 0.001 FDR: 1,574
2:51:21.389844 PROGRESS: 
2:51:21.389904 PROGRESS: Protein Summary:
2:51:21.392783 PROGRESS: Channel   0:	 0.050 FDR: 2,056; 0.010 FDR: 2,056; 0.001 FDR: 1,318
2:51:21.392977 PROGRESS: =========================================================================
2:51:21.394244 INFO: Target number of precursors reached.
2:51:21.433804 INFO: fragments_df: keeping 5000 of 120146 [sum(precursor_idx_mask)=59242 sum(mass_error_mask)=120146 stop_rank=5000
2:51:21.463439 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:51:22.629627 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:51:23.840668 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:51:23.841858 INFO: Using score_cutoff 10.18156837348938 (fac=0.99, q=1)
2:51:23.842490 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:51:23.842609 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:51:23.842669 INFO: Updating optimization_manager: score_cutoff        : 10.310233298778533 -> 10.18156837348938
2:51:23.842752 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:51:23.849013 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:51:23.862125 INFO: === checking if optimization conditions were reached ===
2:51:23.862880 PROGRESS: === Optimization of rt_error has been performed 2 time(s); minimum number is 5 ===
2:51:23.868393 INFO: Updating optimization_manager: rt_error            : 490.46314786721365 -> 470.9328058884592
2:51:23.868814 PROGRESS: ❌ rt_error       : optimization incomplete after 2 search(es). Will search with parameter 470.9328.
2:51:23.868904 INFO: ==============================================
2:51:23.869001 INFO: Starting optimization step 2.
2:51:23.869081 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:51:23.869204 INFO: Using rust extraction backend
2:51:23.869318 PROGRESS: Extracting batch of 5940 precursors
2:51:23.897232 INFO: === Search parameters used ===
2:51:23.898054 INFO: rt_error       : 470.9328058884592
2:51:23.898112 INFO: mobility_error : 0.1
2:51:23.898162 INFO: num_candidates : 3
2:51:23.898211 INFO: ms1_error      : 3
2:51:23.898256 INFO: ms2_error      : 10.0
2:51:23.898300 INFO: fwhm_rt        : 3.0
2:51:23.898403 INFO: quant_window   : 3
2:51:23.898448 INFO: ==============================================
2:51:24.302041 INFO: performing precursor FDR with 40 features
2:51:24.302423 INFO: Decoy channel: -1
2:51:24.302456 INFO: competitive: True
2:51:24.336417 INFO: Setting torch num_threads to 2 for FDR classification task
2:51:24.364773 INFO: Estimating optimal hyperparameters - samples: 14,253, batch_size: 128, learning_rate: 1.77e-04
2:51:24.365414 INFO: Using random state 657903 for train-test-split
2:51:26.821973 INFO: Test AUC: 0.762
2:51:26.822589 INFO: Train AUC: 0.788
2:51:26.822631 INFO: AUC difference: 3.33%
2:51:27.308563 INFO: Resetting torch num_threads to 100
2:51:27.315953 PROGRESS: === Extracted 17817 precursors and 119955 fragments ===
2:51:27.317249 INFO: === FDR correction performed with classifier version 6 ===
2:51:27.319890 PROGRESS: ============================= Precursor FDR =============================
2:51:27.320270 PROGRESS: Total precursors accumulated: 2,618
2:51:27.320335 PROGRESS: Target precursors: 2,593 (99.05%)
2:51:27.320385 PROGRESS: Decoy precursors: 25 (0.95%)
2:51:27.320431 PROGRESS: 
2:51:27.320477 PROGRESS: Precursor Summary:
2:51:27.323296 PROGRESS: Channel   0:	 0.050 FDR: 2,593; 0.010 FDR: 2,593; 0.001 FDR: 1,572
2:51:27.323530 PROGRESS: 
2:51:27.323588 PROGRESS: Protein Summary:
2:51:27.326952 PROGRESS: Channel   0:	 0.050 FDR: 2,042; 0.010 FDR: 2,042; 0.001 FDR: 1,315
2:51:27.327361 PROGRESS: =========================================================================
2:51:27.329350 INFO: Target number of precursors reached.
2:51:27.368053 INFO: fragments_df: keeping 5000 of 119955 [sum(precursor_idx_mask)=58933 sum(mass_error_mask)=119955 stop_rank=5000
2:51:27.403335 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:51:27.964210 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:51:29.033203 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:51:29.034409 INFO: Using score_cutoff 10.323994056701661 (fac=0.99, q=1)
2:51:29.035177 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:51:29.035281 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:51:29.035348 INFO: Updating optimization_manager: score_cutoff        : 10.18156837348938 -> 10.323994056701661
2:51:29.035448 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:51:29.041829 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:51:29.054993 INFO: === checking if optimization conditions were reached ===
2:51:29.055670 PROGRESS: === Optimization of rt_error has been performed 3 time(s); minimum number is 5 ===
2:51:29.063362 INFO: Updating optimization_manager: rt_error            : 470.9328058884592 -> 523.3990898008246
2:51:29.064044 PROGRESS: ❌ rt_error       : optimization incomplete after 3 search(es). Will search with parameter 523.3991.
2:51:29.064139 INFO: ==============================================
2:51:29.064262 INFO: Starting optimization step 3.
2:51:29.064334 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:51:29.064433 INFO: Using rust extraction backend
2:51:29.064510 PROGRESS: Extracting batch of 5940 precursors
2:51:29.094826 INFO: === Search parameters used ===
2:51:29.096315 INFO: rt_error       : 523.3990898008246
2:51:29.096385 INFO: mobility_error : 0.1
2:51:29.096435 INFO: num_candidates : 3
2:51:29.096480 INFO: ms1_error      : 3
2:51:29.096568 INFO: ms2_error      : 10.0
2:51:29.096615 INFO: fwhm_rt        : 3.0
2:51:29.096656 INFO: quant_window   : 3
2:51:29.096697 INFO: ==============================================
2:51:29.467272 INFO: performing precursor FDR with 40 features
2:51:29.467557 INFO: Decoy channel: -1
2:51:29.467589 INFO: competitive: True
2:51:29.494129 INFO: Setting torch num_threads to 2 for FDR classification task
2:51:29.509822 INFO: Estimating optimal hyperparameters - samples: 14,253, batch_size: 128, learning_rate: 1.77e-04
2:51:29.510331 INFO: Using random state 657903 for train-test-split
2:51:31.639130 INFO: Test AUC: 0.763
2:51:31.639552 INFO: Train AUC: 0.786
2:51:31.639588 INFO: AUC difference: 2.92%
2:51:32.495361 INFO: Resetting torch num_threads to 100
2:51:32.503259 PROGRESS: === Extracted 17817 precursors and 120144 fragments ===
2:51:32.504532 INFO: === FDR correction performed with classifier version 6 ===
2:51:32.506712 PROGRESS: ============================= Precursor FDR =============================
2:51:32.506870 PROGRESS: Total precursors accumulated: 2,623
2:51:32.506933 PROGRESS: Target precursors: 2,598 (99.05%)
2:51:32.506981 PROGRESS: Decoy precursors: 25 (0.95%)
2:51:32.507026 PROGRESS: 
2:51:32.507073 PROGRESS: Precursor Summary:
2:51:32.509501 PROGRESS: Channel   0:	 0.050 FDR: 2,598; 0.010 FDR: 2,598; 0.001 FDR: 1,609
2:51:32.509712 PROGRESS: 
2:51:32.509768 PROGRESS: Protein Summary:
2:51:32.513191 PROGRESS: Channel   0:	 0.050 FDR: 2,049; 0.010 FDR: 2,049; 0.001 FDR: 1,337
2:51:32.513390 PROGRESS: =========================================================================
2:51:32.516055 INFO: Target number of precursors reached.
2:51:32.557959 INFO: fragments_df: keeping 5000 of 120144 [sum(precursor_idx_mask)=59103 sum(mass_error_mask)=120144 stop_rank=5000
2:51:32.594568 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:51:33.250997 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:51:34.280108 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:51:34.281889 INFO: Using score_cutoff 10.22517272529602 (fac=0.99, q=1)
2:51:34.282988 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:51:34.283103 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:51:34.283162 INFO: Updating optimization_manager: score_cutoff        : 10.323994056701661 -> 10.22517272529602
2:51:34.283246 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:51:34.289840 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:51:34.302625 INFO: === checking if optimization conditions were reached ===
2:51:34.303416 PROGRESS: === Optimization of rt_error has been performed 4 time(s); minimum number is 5 ===
2:51:34.309170 INFO: Updating optimization_manager: rt_error            : 523.3990898008246 -> 532.9865772574454
2:51:34.309881 PROGRESS: ❌ rt_error       : optimization incomplete after 4 search(es). Will search with parameter 532.9866.
2:51:34.309991 INFO: ==============================================
2:51:34.310084 INFO: Starting optimization step 4.
2:51:34.310171 PROGRESS: === Extracting elution groups 0 to 3000 ===
2:51:34.310292 INFO: Using rust extraction backend
2:51:34.310371 PROGRESS: Extracting batch of 5940 precursors
2:51:34.338421 INFO: === Search parameters used ===
2:51:34.339217 INFO: rt_error       : 532.9865772574454
2:51:34.339288 INFO: mobility_error : 0.1
2:51:34.339443 INFO: num_candidates : 3
2:51:34.339499 INFO: ms1_error      : 3
2:51:34.339575 INFO: ms2_error      : 10.0
2:51:34.339623 INFO: fwhm_rt        : 3.0
2:51:34.339685 INFO: quant_window   : 3
2:51:34.339745 INFO: ==============================================
2:51:34.866601 INFO: performing precursor FDR with 40 features
2:51:34.866970 INFO: Decoy channel: -1
2:51:34.866999 INFO: competitive: True
2:51:34.892832 INFO: Setting torch num_threads to 2 for FDR classification task
2:51:34.908032 INFO: Estimating optimal hyperparameters - samples: 14,253, batch_size: 128, learning_rate: 1.77e-04
2:51:34.908706 INFO: Using random state 657903 for train-test-split
2:51:40.045613 INFO: Test AUC: 0.758
2:51:40.046480 INFO: Train AUC: 0.788
2:51:40.046728 INFO: AUC difference: 3.85%
2:51:40.519671 INFO: Resetting torch num_threads to 100
2:51:40.527665 PROGRESS: === Extracted 17817 precursors and 120132 fragments ===
2:51:40.528925 INFO: === FDR correction performed with classifier version 6 ===
2:51:40.530922 PROGRESS: ============================= Precursor FDR =============================
2:51:40.531093 PROGRESS: Total precursors accumulated: 2,605
2:51:40.531162 PROGRESS: Target precursors: 2,580 (99.04%)
2:51:40.531216 PROGRESS: Decoy precursors: 25 (0.96%)
2:51:40.531265 PROGRESS: 
2:51:40.531314 PROGRESS: Precursor Summary:
2:51:40.533878 PROGRESS: Channel   0:	 0.050 FDR: 2,580; 0.010 FDR: 2,580; 0.001 FDR: 1,582
2:51:40.534024 PROGRESS: 
2:51:40.534086 PROGRESS: Protein Summary:
2:51:40.537218 PROGRESS: Channel   0:	 0.050 FDR: 2,036; 0.010 FDR: 2,036; 0.001 FDR: 1,317
2:51:40.537435 PROGRESS: =========================================================================
2:51:40.539566 INFO: Target number of precursors reached.
2:51:40.577661 INFO: fragments_df: keeping 5000 of 120132 [sum(precursor_idx_mask)=58681 sum(mass_error_mask)=120132 stop_rank=5000
2:51:40.612792 INFO: Fitting estimator 'rt' in calibration group 'precursor' ..
2:51:41.411166 INFO: Fitting estimator 'mz' in calibration group 'fragment' ..
2:51:42.604132 INFO: Updating optimization_manager: num_candidates      : 3 -> 3
2:51:42.605786 INFO: Using score_cutoff 10.437623742198943 (fac=0.99, q=1)
2:51:42.606468 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:51:42.606557 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:51:42.606617 INFO: Updating optimization_manager: score_cutoff        : 10.22517272529602 -> 10.437623742198943
2:51:42.606711 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:51:42.614550 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:51:42.626725 INFO: === checking if optimization conditions were reached ===
2:51:42.627377 PROGRESS: === Optimization of rt_error has been performed 5 time(s); minimum number is 5 ===
2:51:42.629588 INFO: Updating optimization_manager: rt_error            : 532.9865772574454 -> 490.46314786721365
2:51:42.629886 INFO: Updating optimization_manager: classifier_version  : 6 -> 8
2:51:42.629990 INFO: Updating optimization_manager: score_cutoff        : 10.437623742198943 -> 10.18156837348938
2:51:42.630093 INFO: Updating optimization_manager: fwhm_rt             : 3.0 -> 3.0
2:51:42.630193 INFO: Updating optimization_manager: fwhm_mobility       : -1.0 -> -1.0
2:51:42.630295 PROGRESS: ✅ rt_error       : optimization just completed. Optimal parameter 490.4631 found after 5 searches.
2:51:42.630376 INFO: ==============================================
2:51:42.630520 PROGRESS: Optimization finished for rt_error.
2:51:42.695796 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:51:42.702802 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:51:42.714943 PROGRESS: Search parameter optimization finished. Values taken forward for search are:
2:51:42.715669 PROGRESS: ==============================================
2:51:42.715793 PROGRESS: ms2_error      : 10.0000
2:51:42.715883 PROGRESS: rt_error       : 490.4631
2:51:42.715935 PROGRESS: ==============================================
2:51:42.719687 INFO: Predicting estimator 'rt' in calibration group 'precursor' ..
2:51:42.916534 INFO: Predicting estimator 'mz' in calibration group 'fragment' ..
2:51:43.634231 INFO: Using rust extraction backend
2:51:43.635117 PROGRESS: Extracting batch of 259156 precursors
2:51:44.882374 INFO: === Search parameters used ===
2:51:44.883556 INFO: rt_error       : 490.46314786721365
2:51:44.883712 INFO: mobility_error : 0.1
2:51:44.883777 INFO: num_candidates : 3
2:51:44.883894 INFO: ms1_error      : 3
2:51:44.883960 INFO: ms2_error      : 10.0
2:51:44.884008 INFO: fwhm_rt        : 3.0
2:51:44.884055 INFO: quant_window   : 3
2:51:44.884097 INFO: ==============================================
2:51:45.846764 INFO: Removed 88378 precursors with score below cutoff 10.18156837348938
2:51:46.634005 INFO: performing precursor FDR with 40 features
2:51:46.634194 INFO: Decoy channel: -1
2:51:46.634221 INFO: competitive: True
2:51:46.762000 INFO: Setting torch num_threads to 2 for FDR classification task
2:51:46.840343 WARNING: FDR calculation for 362091 target and 326999 decoy PSMs
2:51:46.840572 WARNING: FDR calculation may be inaccurate as there is more than 10% difference in the number of target and decoy PSMs
2:51:47.366560 INFO: Estimating optimal hyperparameters - samples: 551,272, batch_size: 2,258, learning_rate: 7.42e-04
2:51:47.370513 INFO: Using random state 266418 for train-test-split
2:52:02.125614 INFO: Test AUC: 0.776
2:52:02.126008 INFO: Train AUC: 0.783
2:52:02.126057 INFO: AUC difference: 0.89%
2:52:02.911741 INFO: Resetting torch num_threads to 100
2:52:03.658953 PROGRESS: ============================= Precursor FDR =============================
2:52:03.659305 PROGRESS: Total precursors accumulated: 121,830
2:52:03.659383 PROGRESS: Target precursors: 120,625 (99.01%)
2:52:03.659438 PROGRESS: Decoy precursors: 1,205 (0.99%)
2:52:03.659486 PROGRESS: 
2:52:03.659539 PROGRESS: Precursor Summary:
2:52:03.722803 PROGRESS: Channel   0:	 0.050 FDR: 120,625; 0.010 FDR: 120,625; 0.001 FDR: 107,986
2:52:03.723156 PROGRESS: 
2:52:03.723225 PROGRESS: Protein Summary:
2:52:03.830619 PROGRESS: Channel   0:	 0.050 FDR: 10,148; 0.010 FDR: 10,148; 0.001 FDR: 10,002
2:52:03.830959 PROGRESS: =========================================================================
2:52:03.838385 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/psm.parquet
2:52:04.295783 INFO: Saving results to /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/frag.parquet
2:52:05.008217 INFO: Finished workflow for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:52:06.490916 PROGRESS: Processing search outputs
2:52:06.491416 PROGRESS: === Performing protein grouping and FDR ===
2:52:06.491510 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:52:06.651721 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:52:06.883497 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:52:07.116579 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:52:07.341968 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:52:07.555225 INFO: Building output for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:52:08.049877 INFO: Performing protein inference
2:52:10.109869 INFO: Inference strategy: library. Using library grouping for protein inference
2:52:10.132937 INFO: Performing protein FDR
2:52:29.488921 INFO: Normalizing q-values using 10,153 targets and 3,612 decoys
2:52:29.497582 INFO: Test AUC: 1.000
2:52:29.497929 INFO: Train AUC: 1.000
2:52:29.497996 INFO: AUC difference: 0.00%
2:52:32.184805 INFO: ================ Protein FDR =================
2:52:32.185165 INFO: Unique protein groups in output
2:52:32.185205 INFO:   1% protein FDR: 10,150
2:52:32.185226 INFO: 
2:52:32.185246 INFO: Unique precursor in output
2:52:32.185267 INFO:   1% protein FDR: 130,708
2:52:32.185285 INFO: ================================================
2:52:32.497727 PROGRESS: Building search statistics
2:52:32.954056 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/optimization_manager.pkl
2:52:32.954712 INFO: Initializing OptimizationManager
2:52:32.955199 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/calibration_manager.pkl
2:52:32.955296 INFO: Initializing CalibrationManager
2:52:32.955758 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/raw_file_manager.pkl
2:52:32.955890 INFO: Initializing RawFileManager
2:52:33.055083 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/optimization_manager.pkl
2:52:33.055556 INFO: Initializing OptimizationManager
2:52:33.055933 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/calibration_manager.pkl
2:52:33.056107 INFO: Initializing CalibrationManager
2:52:33.056469 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/raw_file_manager.pkl
2:52:33.056559 INFO: Initializing RawFileManager
2:52:33.155015 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/optimization_manager.pkl
2:52:33.155450 INFO: Initializing OptimizationManager
2:52:33.155796 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/calibration_manager.pkl
2:52:33.155905 INFO: Initializing CalibrationManager
2:52:33.156298 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/raw_file_manager.pkl
2:52:33.156384 INFO: Initializing RawFileManager
2:52:33.258117 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/optimization_manager.pkl
2:52:33.258546 INFO: Initializing OptimizationManager
2:52:33.258900 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/calibration_manager.pkl
2:52:33.259027 INFO: Initializing CalibrationManager
2:52:33.259367 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/raw_file_manager.pkl
2:52:33.259458 INFO: Initializing RawFileManager
2:52:33.352525 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/optimization_manager.pkl
2:52:33.353020 INFO: Initializing OptimizationManager
2:52:33.353509 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/calibration_manager.pkl
2:52:33.353726 INFO: Initializing CalibrationManager
2:52:33.354194 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/raw_file_manager.pkl
2:52:33.354350 INFO: Initializing RawFileManager
2:52:33.440393 INFO: Loaded OptimizationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/optimization_manager.pkl
2:52:33.440728 INFO: Initializing OptimizationManager
2:52:33.441058 INFO: Loaded CalibrationManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/calibration_manager.pkl
2:52:33.441174 INFO: Initializing CalibrationManager
2:52:33.441527 INFO: Loaded RawFileManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/raw_file_manager.pkl
2:52:33.441607 INFO: Initializing RawFileManager
2:52:33.454714 INFO: Writing stat output to disk
2:52:33.454996 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/stat.tsv to disk
2:52:33.489595 PROGRESS: Building internal statistics
2:52:33.490405 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP1/timing_manager.pkl
2:52:33.490530 INFO: Initializing TimingManager
2:52:33.491464 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP2/timing_manager.pkl
2:52:33.491580 INFO: Initializing TimingManager
2:52:33.492184 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_A_REP3/timing_manager.pkl
2:52:33.492288 INFO: Initializing TimingManager
2:52:33.492793 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP1/timing_manager.pkl
2:52:33.492858 INFO: Initializing TimingManager
2:52:33.493311 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP2/timing_manager.pkl
2:52:33.493376 INFO: Initializing TimingManager
2:52:33.493782 INFO: Loaded TimingManager from /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/quant/LFQ_Astral_DIA_15min_50ng_Condition_B_REP3/timing_manager.pkl
2:52:33.493833 INFO: Initializing TimingManager
2:52:33.494973 INFO: Writing internal output to disk
2:52:33.495079 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/internal.tsv to disk
2:52:33.804402 INFO: Performing label free quantification
2:52:33.804781 INFO: Accumulating fragment data
2:52:33.804895 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP1
2:52:34.155683 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP2
2:52:39.084801 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_A_REP3
2:52:43.680005 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP1
2:52:48.676255 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP2
2:52:53.940797 INFO: reading frag file for LFQ_Astral_DIA_15min_50ng_Condition_B_REP3
2:53:00.040015 INFO: Performing label free quantification on the precursor level
2:53:00.040429 INFO: Filtering fragments by quality
2:53:00.986293 INFO: Performing label-free quantification with directlfq normalization
2:53:02.434639 INFO: Applying directLFQ normalization
2:53:03.475668 INFO: 130708 lfq-groups total
2:56:06.346502 INFO: using 100 processes
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2:56:07.139017 INFO: lfq-object 100
2:56:07.300819 INFO: lfq-object 400
2:56:07.339370 INFO: lfq-object 200
2:56:07.499156 INFO: lfq-object 700
2:56:07.519431 INFO: lfq-object 300
2:56:07.563715 INFO: lfq-object 500
2:56:07.687856 INFO: lfq-object 1000
2:56:07.729382 INFO: lfq-object 800
2:56:07.756893 INFO: lfq-object 600
2:56:07.881952 INFO: lfq-object 1100
2:56:07.933149 INFO: lfq-object 900
2:56:08.020154 INFO: lfq-object 1400
2:56:08.088934 INFO: lfq-object 1200
2:56:08.210505 INFO: lfq-object 1700
2:56:08.217447 INFO: lfq-object 1500
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2:56:08.357569 INFO: lfq-object 2000
2:56:08.406657 INFO: lfq-object 1600
2:56:08.433394 INFO: lfq-object 1800
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2:56:11.115388 INFO: lfq-object 4800
2:56:11.167976 INFO: lfq-object 5000
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3:00:35.032391 INFO: lfq-object 112900
3:00:35.097084 INFO: lfq-object 113400
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3:00:35.420509 INFO: lfq-object 113600
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3:00:35.940036 INFO: lfq-object 114900
3:00:35.970704 INFO: lfq-object 114500
3:00:36.046437 INFO: lfq-object 115200
3:00:36.067183 INFO: lfq-object 114800
3:00:36.099477 INFO: lfq-object 115000
3:00:36.178778 INFO: lfq-object 115300
3:00:36.222003 INFO: lfq-object 115500
3:00:36.293651 INFO: lfq-object 115100
3:00:36.354169 INFO: lfq-object 115800
3:00:36.371608 INFO: lfq-object 115400
3:00:36.377513 INFO: lfq-object 115600
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3:00:36.513440 INFO: lfq-object 115700
3:00:36.532442 INFO: lfq-object 115900
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3:00:36.618684 INFO: lfq-object 116400
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3:00:36.731046 INFO: lfq-object 116000
3:00:36.738465 INFO: lfq-object 116700
3:00:36.816667 INFO: lfq-object 116500
3:00:36.849621 INFO: lfq-object 117000
3:00:36.874969 INFO: lfq-object 116800
3:00:36.949756 INFO: lfq-object 116600
3:00:36.968566 INFO: lfq-object 117300
3:00:36.982426 INFO: lfq-object 117100
3:00:37.012448 INFO: lfq-object 116900
3:00:37.094486 INFO: lfq-object 117400
3:00:37.098767 INFO: lfq-object 117600
3:00:37.112812 INFO: lfq-object 117200
3:00:37.228405 INFO: lfq-object 117500
3:00:37.232051 INFO: lfq-object 117700
3:00:37.286876 INFO: lfq-object 117900
3:00:37.368879 INFO: lfq-object 117800
3:00:37.422765 INFO: lfq-object 118000
3:00:37.429242 INFO: lfq-object 118200
3:00:37.559301 INFO: lfq-object 118100
3:00:37.575068 INFO: lfq-object 118300
3:00:37.580172 INFO: lfq-object 118500
3:00:37.720649 INFO: lfq-object 118600
3:00:37.736501 INFO: lfq-object 118400
3:00:37.771434 INFO: lfq-object 118800
3:00:37.853868 INFO: lfq-object 118700
3:00:37.902934 INFO: lfq-object 119100
3:00:37.942045 INFO: lfq-object 118900
3:00:38.007063 INFO: lfq-object 119400
3:00:38.035807 INFO: lfq-object 119200
3:00:38.076263 INFO: lfq-object 119700
3:00:38.089292 INFO: lfq-object 119000
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3:00:38.171758 INFO: lfq-object 119300
3:00:38.290686 INFO: lfq-object 119600
3:00:44.658342 INFO: Performing label free quantification on the pg level
3:00:44.658762 INFO: Filtering fragments by quality
3:00:45.099308 INFO: Performing label-free quantification with directlfq normalization
3:00:45.297160 INFO: Applying directLFQ normalization
3:00:45.529766 INFO: 10150 lfq-groups total
3:01:24.264873 INFO: using 100 processes
3:01:24.482523 INFO: lfq-object 0
3:01:24.816340 INFO: lfq-object 400
3:01:24.821624 INFO: lfq-object 100
3:01:24.887035 INFO: lfq-object 500
3:01:24.931035 INFO: lfq-object 600
3:01:24.948927 INFO: lfq-object 200
3:01:24.972020 INFO: lfq-object 300
3:01:25.262820 INFO: lfq-object 700
3:01:25.287091 INFO: lfq-object 1000
3:01:25.359211 INFO: lfq-object 900
3:01:25.381255 INFO: lfq-object 1100
3:01:25.386533 INFO: lfq-object 800
3:01:25.435569 INFO: lfq-object 1200
3:01:25.543397 INFO: lfq-object 1300
3:01:25.824047 INFO: lfq-object 1400
3:01:25.905499 INFO: lfq-object 1800
3:01:25.919445 INFO: lfq-object 1900
3:01:25.979612 INFO: lfq-object 1700
3:01:26.012275 INFO: lfq-object 1600
3:01:26.123296 INFO: lfq-object 1500
3:01:26.131364 INFO: lfq-object 2000
3:01:26.205742 INFO: lfq-object 2300
3:01:26.255467 INFO: lfq-object 2100
3:01:26.396499 INFO: lfq-object 2200
3:01:26.417530 INFO: lfq-object 2600
3:01:26.470219 INFO: lfq-object 2400
3:01:26.531083 INFO: lfq-object 2700
3:01:26.552829 INFO: lfq-object 2500
3:01:26.608445 INFO: lfq-object 2900
3:01:26.652588 INFO: lfq-object 3000
3:01:26.736564 INFO: lfq-object 2800
3:01:26.772762 INFO: lfq-object 3100
3:01:26.780892 INFO: lfq-object 3200
3:01:26.935334 INFO: lfq-object 3500
3:01:26.952502 INFO: lfq-object 3600
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3:01:27.020847 INFO: lfq-object 3700
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3:01:27.269412 INFO: lfq-object 4000
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3:01:27.926539 INFO: lfq-object 5000
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3:01:28.224370 INFO: lfq-object 5700
3:01:28.261137 INFO: lfq-object 5800
3:01:28.406153 INFO: lfq-object 6100
3:01:28.414589 INFO: lfq-object 5900
3:01:28.432479 INFO: lfq-object 6000
3:01:28.446956 INFO: lfq-object 6200
3:01:28.489032 INFO: lfq-object 6300
3:01:28.522981 INFO: lfq-object 6400
3:01:28.558975 INFO: lfq-object 6500
3:01:28.760121 INFO: lfq-object 6800
3:01:28.762245 INFO: lfq-object 7000
3:01:28.770022 INFO: lfq-object 6600
3:01:28.786728 INFO: lfq-object 6900
3:01:28.798429 INFO: lfq-object 7100
3:01:28.845691 INFO: lfq-object 6700
3:01:28.958763 INFO: lfq-object 7200
3:01:29.067795 INFO: lfq-object 7300
3:01:29.121993 INFO: lfq-object 7500
3:01:29.166063 INFO: lfq-object 7600
3:01:29.197253 INFO: lfq-object 7700
3:01:29.239224 INFO: lfq-object 7800
3:01:29.251512 INFO: lfq-object 7400
3:01:29.408038 INFO: lfq-object 7900
3:01:29.475048 INFO: lfq-object 8000
3:01:29.532726 INFO: lfq-object 8200
3:01:29.545586 INFO: lfq-object 8100
3:01:29.546852 INFO: lfq-object 8300
3:01:29.568229 INFO: lfq-object 8400
3:01:29.782122 INFO: lfq-object 8500
3:01:29.793904 INFO: lfq-object 8700
3:01:29.896663 INFO: lfq-object 8800
3:01:29.907717 INFO: lfq-object 8900
3:01:29.924475 INFO: lfq-object 8600
3:01:29.951498 INFO: lfq-object 9000
3:01:30.000324 INFO: lfq-object 9100
3:01:37.150945 INFO: lfq-object 9200
3:01:37.208517 INFO: lfq-object 9300
3:01:37.246467 INFO: lfq-object 9400
3:01:37.285155 INFO: lfq-object 9500
3:01:37.311073 INFO: lfq-object 9600
3:01:37.448739 INFO: lfq-object 9700
3:01:37.527129 INFO: lfq-object 9800
3:01:37.636804 INFO: lfq-object 10000
3:01:37.705690 INFO: lfq-object 9900
3:01:37.759527 INFO: lfq-object 10100
3:01:40.948328 INFO: Writing psm output to disk
3:01:41.078232 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/precursors.parquet to disk
3:01:42.261476 INFO: Writing precursor output to disk
3:01:42.268723 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/precursor.matrix.parquet to disk
3:01:42.406029 INFO: Writing peptide output to disk
3:01:42.411870 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/peptide.matrix.parquet to disk
3:01:42.509614 INFO: Writing pg output to disk
3:01:42.513146 INFO: Saving /home/robbe/PB_output/results/AstralManuscript/HYE_Astral/alphadia_v2.1.1/pg.matrix.parquet to disk
3:01:42.618577 PROGRESS: Building MBR spectral library
3:01:42.618793 INFO: Running MbrLibraryBuilder
3:01:43.081111 INFO: MBR spectral library contains 130,708 precursors, 10,150 proteins
3:01:43.081255 INFO: Writing MBR spectral library to disk
3:01:43.928976 PROGRESS: =================== Search step 'mbr' finished ===================
3:01:43.997666 INFO: =================== Search Finished ===================
